Sample records for amphipathic dna polymers

  1. Inhibition of Cellular Entry of Lymphocytic Choriomeningitis Virus by Amphipathic DNA Polymers (United States)

    Lee, Andrew M.; Rojek, Jillian M.; Gundersen, Anette; Ströher, Ute; Juteau, Jean-Marc; Vaillant, Andrew; Kunz, Stefan


    The prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) represents a powerful experimental model for the study of the basic virology and pathogenesis of arenaviruses. In the present study, we used the LCMV model to evaluate the anti-viral potential of phosphorothioate oligonucleotides against arenaviruses. Our findings indicate that amphipathic DNA polymers (APs) are potent inhibitors of infection with a series of LCMV isolates with IC50 in the low nanomolar range. APs target the surface glycoprotein (GP) of LCMV and block viral entry and cell-cell propagation of the virus, without affecting later steps in replication or release of progeny virus from infected cells. The anti-viral action of APs is sequence-independent but is critically dependent on their size and hydrophobicity. Mechanistically, we provide evidence that APs disrupt the interaction between LCMVGP and its cellular receptor, α-dystroglycan. Exposure of LCMV to APs does not affect the stability of the GP virion spike and has no effect on the conformation of a neutralizing antibody epitope, suggesting rather subtle changes in the conformation and/or conformational dynamics of the viral GP. PMID:18022208

  2. Amphipathic DNA polymers exhibit antiviral activity against systemic Murine Cytomegalovirus infection

    Directory of Open Access Journals (Sweden)

    Juteau Jean-Marc


    Full Text Available Abstract Background Phosphorothioated oligonucleotides (PS-ONs have a sequence-independent, broad spectrum antiviral activity as amphipathic polymers (APs and exhibit potent in vitro antiviral activity against a broad spectrum of herpesviruses: HSV-1, HSV-2, HCMV, VZV, EBV, and HHV-6A/B, and in vivo activity in a murine microbiocide model of genital HSV-2 infection. The activity of these agents against animal cytomegalovirus (CMV infections in vitro and in vivo was therefore investigated. Results In vitro, a 40 mer degenerate AP (REP 9 inhibited both murine CMV (MCMV and guinea pig CMV (GPCMV with an IC50 of 0.045 μM and 0.16 μM, respectively, and a 40 mer poly C AP (REP 9C inhibited MCMV with an IC50 of 0.05 μM. Addition of REP 9 to plaque assays during the first two hours of infection inhibited 78% of plaque formation whereas addition of REP 9 after 10 hours of infection did not significantly reduce the number of plaques, indicating that REP 9 antiviral activity against MCMV occurs at early times after infection. In a murine model of CMV infection, systemic treatment for 5 days significantly reduced virus replication in the spleens and livers of infected mice compared to saline-treated control mice. REP 9 and REP 9C were administered intraperitoneally for 5 consecutive days at 10 mg/kg, starting 2 days prior to MCMV infection. Splenomegaly was observed in infected mice treated with REP 9 but not in control mice or in REP 9 treated, uninfected mice, consistent with mild CpG-like activity. When REP 9C (which lacks CpG motifs was compared to REP 9, it exhibited comparable antiviral activity as REP 9 but was not associated with splenomegaly. This suggests that the direct antiviral activity of APs is the predominant therapeutic mechanism in vivo. Moreover, REP 9C, which is acid stable, was effective when administered orally in combination with known permeation enhancers. Conclusion These studies indicate that APs exhibit potent, well tolerated

  3. Amphipathic polymers: tools to fold integral membrane proteins to their active form. (United States)

    Pocanschi, Cosmin L; Dahmane, Tassadite; Gohon, Yann; Rappaport, Fabrice; Apell, Hans-Jürgen; Kleinschmidt, Jörg H; Popot, Jean-Luc


    Among the major obstacles to pharmacological and structural studies of integral membrane proteins (MPs) are their natural scarcity and the difficulty in overproducing them in their native form. MPs can be overexpressed in the non-native state as inclusion bodies, but inducing them to achieve their functional three-dimensional structure has proven to be a major challenge. We describe here the use of an amphipathic polymer, amphipol A8-35, as a novel environment that allows both beta-barrel and alpha-helical MPs to fold to their native state, in the absence of detergents or lipids. Amphipols, which are extremely mild surfactants, appear to favor the formation of native intramolecular protein-protein interactions over intermolecular or protein-surfactant ones. The feasibility of the approach is demonstrated using as models OmpA and FomA, two outer membrane proteins from the eubacteria Escherichia coli and Fusobacterium nucleatum, respectively, and bacteriorhodopsin, a light-driven proton pump from the plasma membrane of the archaebacterium Halobacterium salinarium.

  4. An amphipathic trans-acting phosphorothioate DNA element delivers uncharged PNA and PMO nucleic acid sequences in mammalian cells. (United States)

    Jain, Harsh V; Beaucage, Serge L

    An innovative approach to the delivery of uncharged peptide nucleic acids (PNA) and phosphorodiamidate morpholino (PMO) oligomers in mammalian cells is described and consists of extending the sequence of those oligomers with a short PNA-polyA or PMO-polyA tail. Recognition of the polyA-tailed PNA or PMO oligomers by an amphipathic trans-acting polythymidylic thiophosphate triester element (dTtaPS) results in efficient internalization of those oligomers in several cell lines. Our findings indicate that cellular uptake of the oligomers occurs through an energy-dependent mechanism and macropinocytosis appears to be the predo-minant endocytic pathway used for internalization. The functionality of the internalized oligomers is demonstrated by alternate splicing of the pre-mRNA encoding luciferase in HeLa pLuc 705 cells. Amphipathic phosphorothioate DNA elements may represent a unique class of cellular transporters for robust delivery of uncharged nucleic acid sequences in live mammalian cells.

  5. Plasminogen activator inhibitor-1 polymers, induced by inactivating amphipathic organochemical ligands

    DEFF Research Database (Denmark)

    Pedersen, Katrine E; Einholm, Anja P; Christensen, Anni;


    -induced polymerization was observed only with PAI-1 and heparin cofactor II, which were also able to copolymerize. On the basis of these results, we suggest that the binding of ligands in a specific region of PAI-1 leads to so-called loop-sheet polymerization, in which the reactive centre loop of one molecule binds....... As compared with native PAI-1, the polymers exhibited an increased resistance to temperature-induced unfolding. Polymerization was associated with specific changes in patterns of digestion with non-target proteases. During incubation with urokinase-type plasminogen activator, the polymers were slowly...

  6. DNA: Polymer and molecular code (United States)

    Shivashankar, G. V.


    The thesis work focusses upon two aspects of DNA, the polymer and the molecular code. Our approach was to bring single molecule micromanipulation methods to the study of DNA. It included a home built optical microscope combined with an atomic force microscope and an optical tweezer. This combined approach led to a novel method to graft a single DNA molecule onto a force cantilever using the optical tweezer and local heating. With this method, a force versus extension assay of double stranded DNA was realized. The resolution was about 10 picoN. To improve on this force measurement resolution, a simple light backscattering technique was developed and used to probe the DNA polymer flexibility and its fluctuations. It combined the optical tweezer to trap a DNA tethered bead and the laser backscattering to detect the beads Brownian fluctuations. With this technique the resolution was about 0.1 picoN with a millisecond access time, and the whole entropic part of the DNA force-extension was measured. With this experimental strategy, we measured the polymerization of the protein RecA on an isolated double stranded DNA. We observed the progressive decoration of RecA on the l DNA molecule, which results in the extension of l , due to unwinding of the double helix. The dynamics of polymerization, the resulting change in the DNA entropic elasticity and the role of ATP hydrolysis were the main parts of the study. A simple model for RecA assembly on DNA was proposed. This work presents a first step in the study of genetic recombination. Recently we have started a study of equilibrium binding which utilizes fluorescence polarization methods to probe the polymerization of RecA on single stranded DNA. In addition to the study of material properties of DNA and DNA-RecA, we have developed experiments for which the code of the DNA is central. We studied one aspect of DNA as a molecular code, using different techniques. In particular the programmatic use of template specificity makes

  7. Conducting polymers for electrochemical DNA sensing. (United States)

    Peng, Hui; Zhang, Lijuan; Soeller, Christian; Travas-Sejdic, Jadranka


    Conducting polymers (CPs) are a class of polymeric materials that have attracted considerable interest because of their unique electronic, chemical and biochemical properties, making them suitable for numerous applications such as energy storage, memory devices, chemical sensors, and in electrocatalysis. Conducting polymer-based electrochemical DNA sensors have shown applicability in a number of areas related to human health such as diagnosis of infectious diseases, genetic mutations, drug discovery, forensics and food technology due to their simplicity and high sensitivity. This review paper summarizes the advances in electrochemical DNA sensing based on conducting polymers as active substrates. The various conducting polymers used for DNA detection, along with different DNA immobilization and detection methodologies are presented. Current trends in this field and newly developed applications due to advances in nanotechnology are also discussed.

  8. Programmed Switching of Single Polymer Conformation on DNA Origami

    DEFF Research Database (Denmark)

    Krissanaprasit, Abhichart; Madsen, Mikael; Knudsen, Jakob Bach;


    -molecule conjugated polymer. The polymer is functionalized with short single-stranded (ss) DNA strands that extend from the backbone of the polymer and serve as handles. The DNA polymer conjugate can be aligned on DNA origami in three well-defined geometries (straight line, left-turned, and right-turned pattern......) by DNA hybridization directed by single-stranded guiding strands and ssDNA tracks extending from the origami surface and polymer handle. We demonstrate switching of a conjugated organic polymer conformation between left- and right-turned conformations of the polymer on DNA origami based on toehold...

  9. Applications of Conjugated Polymers to DNA Sensing

    Institute of Scientific and Technical Information of China (English)

    Jadranka; Travas-Sejdic; Christian; Soeller


    1 Results Detection of biomolecules relies on a highly specific recognition event between an analyte biomolecule and a probe that is often closely connected or integrated within a sensor transducer element to provide a suitable signal. More widespread application of gene detection on a routine basis demands the development of a new generation of gene sensors that are fast, reliable and cost-effective.Conjugated polymers (CPs) have been shown to be a versatile substrate for DNA sensor construction, where...

  10. Hyaluronic acid functional amphipathic and redox-responsive polymer particles for the co-delivery of doxorubicin and cyclopamine to eradicate breast cancer cells and cancer stem cells (United States)

    Hu, Kelei; Zhou, Huige; Liu, Ying; Liu, Zhu; Liu, Jing; Tang, Jinglong; Li, Jiayang; Zhang, Jiakun; Sheng, Wang; Zhao, Yuliang; Wu, Yan; Chen, Chunying


    Cancer stem cells (CSCs) have the ability to transform into bulk cancer cells, to promote tumor growth and establish tumor metastasis. To effectively inhibit tumor growth and prevent metastasis, treatments with conventional chemotherapy drugs should be combined with CSC targeted drugs. In this study, we describe the synthesis and characterization of a new amphiphilic polymer, hyaluronic acid-cystamine-polylactic-co-glycolic acid (HA-SS-PLGA), composed of a hydrophobic PLGA head and a hydrophilic HA segment linked by a bioreducible disulfide bond. With a double emulsion method, a nano delivery system was constructed to deliver doxorubicin (DOX) and cyclopamine (CYC, a primary inhibitor of the hedgehog signaling pathway of CSCs) to both a CD44-overexpressing breast CSC subpopulation and bulk breast cancer cells and allow an on-demand release. The resulting drug-loaded NPs exhibited a redox-responsive drug release profile. Dual drug-loaded particles potently diminished the number and size of tumorspheres and HA showed a targeting effect towards breast CSCs. In vivo combination therapy further demonstrated a remarkable synergistic anti-tumor effect and prolonged survival compared to mono-therapy using the orthotopic mammary fat pad tumor growth model. The co-delivery of drug and the CSC specific inhibitor towards targeted cancer chemotherapeutics provides an insight into anticancer strategy with facile control and high efficacy.Cancer stem cells (CSCs) have the ability to transform into bulk cancer cells, to promote tumor growth and establish tumor metastasis. To effectively inhibit tumor growth and prevent metastasis, treatments with conventional chemotherapy drugs should be combined with CSC targeted drugs. In this study, we describe the synthesis and characterization of a new amphiphilic polymer, hyaluronic acid-cystamine-polylactic-co-glycolic acid (HA-SS-PLGA), composed of a hydrophobic PLGA head and a hydrophilic HA segment linked by a bioreducible disulfide bond

  11. Polymer multilayer tattooing for enhanced DNA vaccination (United States)

    Demuth, Peter C.; Min, Younjin; Huang, Bonnie; Kramer, Joshua A.; Miller, Andrew D.; Barouch, Dan H.; Hammond, Paula T.; Irvine, Darrell J.


    DNA vaccines have many potential benefits but have failed to generate robust immune responses in humans. Recently, methods such as in vivo electroporation have demonstrated improved performance, but an optimal strategy for safe, reproducible, and pain-free DNA vaccination remains elusive. Here we report an approach for rapid implantation of vaccine-loaded polymer films carrying DNA, immune-stimulatory RNA, and biodegradable polycations into the immune-cell-rich epidermis, using microneedles coated with releasable polyelectrolyte multilayers. Films transferred into the skin following brief microneedle application promoted local transfection and controlled the persistence of DNA and adjuvants in the skin from days to weeks, with kinetics determined by the film composition. These ‘multilayer tattoo’ DNA vaccines induced immune responses against a model HIV antigen comparable to electroporation in mice, enhanced memory T-cell generation, and elicited 140-fold higher gene expression in non-human primate skin than intradermal DNA injection, indicating the potential of this strategy for enhancing DNA vaccination.

  12. Programmed Switching of Single Polymer Conformation on DNA Origami. (United States)

    Krissanaprasit, Abhichart; Madsen, Mikael; Knudsen, Jakob Bach; Gudnason, Daniel; Surareungchai, Werasak; Birkedal, Victoria; Gothelf, Kurt Vesterager


    DNA nanotechnology offers precise geometrical control of the positioning of materials, and it is increasingly also being used in the development of nanomechanical devices. Here we describe the development of a nanomechanical device that allows switching of the position of a single-molecule conjugated polymer. The polymer is functionalized with short single-stranded (ss) DNA strands that extend from the backbone of the polymer and serve as handles. The DNA polymer conjugate can be aligned on DNA origami in three well-defined geometries (straight line, left-turned, and right-turned pattern) by DNA hybridization directed by single-stranded guiding strands and ssDNA tracks extending from the origami surface and polymer handle. We demonstrate switching of a conjugated organic polymer conformation between left- and right-turned conformations of the polymer on DNA origami based on toehold-mediated strand displacement. The switching is observed by atomic force microscopy and by Förster resonance energy transfer between the polymer and two different organic dyes positioned in close proximity to the respective patterns. Using this method, the polymer conformation can be switched six times successively. This controlled nanomechanical switching of conjugated organic polymer conformation demonstrates unique control of the shape of a single polymer molecule, and it may constitute a new component for the development of reconfigurable nanophotonic and nanoelectronic devices.

  13. DNA Polymer Brush Patterning through Photocontrollable Surface-Initiated DNA Hybridization Chain Reaction. (United States)

    Huang, Fujian; Zhou, Xiang; Yao, Dongbao; Xiao, Shiyan; Liang, Haojun


    The fabrication of DNA polymer brushes with spatial resolution onto a solid surface is a crucial step for biochip research and related applications, cell-free gene expression study, and even artificial cell fabrication. Here, for the first time, a DNA polymer brush patterning method is reported based on the photoactivation of an ortho-nitrobenzyl linker-embedded DNA hairpin structure and a subsequent surface-initiated DNA hybridization chain reaction (HCR). Inert DNA hairpins are exposed to ultraviolet light irradiation to generate DNA duplexes with two active sticky ends (toeholds) in a programmable manner. These activated DNA duplexes can initiate DNA HCR to generate multifunctional patterned DNA polymer brushes with complex geometrical shapes. Different multifunctional DNA polymer brush patterns can be fabricated on certain areas of the same solid surface using this method. Moreover, the patterned DNA brush surface can be used to capture target molecules in a desired manner.

  14. Electronic polymers and DNA self-assembled in nanowire transistors. (United States)

    Hamedi, Mahiar; Elfwing, Anders; Gabrielsson, Roger; Inganäs, Olle


    Aqueous self-assembly of DNA and molecular electronic materials can lead to the creation of innumerable copies of identical devices, and inherently programmed complex nanocircuits. Here self-assembly of a water soluble and highly conducting polymer PEDOT-S with DNA in aqueous conditions is shown. Orientation and assembly of the conducting DNA/PEDOT-S complex into electrochemical DNA nanowire transistors is demonstrated.

  15. Polymer induced condensation of dna supercoils

    NARCIS (Netherlands)

    Bessa Ramos Jr., J.E.; Ruggiero Neto, J.; Vries, de R.J.


    Macromolecular crowding is thought to be a significant factor driving DNA condensation in prokaryotic cells. Whereas DNA in prokaryotes is supercoiled, studies on crowding-induced DNA condensation have so far focused on linear DNA. Here we compare DNA condensation by poly(ethylene oxide) for superco

  16. Conjugated Polymers/DNA Hybrid Materials for Protein Inactivation. (United States)

    Zhao, Likun; Zhang, Jiangyan; Xu, Huiming; Geng, Hao; Cheng, Yongqiang


    Chromophore-assisted light inactivation (CALI) is a powerful tool for analyzing protein functions due to the high degree of spatial and temporal resolution. In this work, we demonstrate a CALI approach based on conjugated polymers (CPs)/DNA hybrid material for protein inactivation. The target protein is conjugated with single-stranded DNA in advance. Single-stranded DNA can form CPs/DNA hybrid material with cationic CPs via electrostatic and hydrophobic interactions. Through the formation of CPs/DNA hybrid material, the target protein that is conjugated with DNA is brought into close proximity to CPs. Under irradiation, CPs harvest light and generate reactive oxygen species (ROS), resulting in the inactivation of the adjacent target protein. This approach can efficiently inactivate any target protein which is conjugated with DNA and has good specificity and universality, providing a new strategy for studies of protein function and adjustment of protein activity.

  17. DNA as a Model for Probing Polymer Entanglements: Circular Polymers and Non-Classical Dynamics

    Directory of Open Access Journals (Sweden)

    Kathryn Regan


    Full Text Available Double-stranded DNA offers a robust platform for investigating fundamental questions regarding the dynamics of entangled polymer solutions. The exceptional monodispersity and multiple naturally occurring topologies of DNA, as well as a wide range of tunable lengths and concentrations that encompass the entanglement regime, enable direct testing of molecular-level entanglement theories and corresponding scaling laws. DNA is also amenable to a wide range of techniques from passive to nonlinear measurements and from single-molecule to bulk macroscopic experiments. Over the past two decades, researchers have developed methods to directly visualize and manipulate single entangled DNA molecules in steady-state and stressed conditions using fluorescence microscopy, particle tracking and optical tweezers. Developments in microfluidics, microrheology and bulk rheology have also enabled characterization of the viscoelastic response of entangled DNA from molecular levels to macroscopic scales and over timescales that span from linear to nonlinear regimes. Experiments using DNA have uniquely elucidated the debated entanglement properties of circular polymers and blends of linear and circular polymers. Experiments have also revealed important lengthscale and timescale dependent entanglement dynamics not predicted by classical tube models, both validating and refuting new proposed extensions and alternatives to tube theory and motivating further theoretical work to describe the rich dynamics exhibited in entangled polymer systems.

  18. Dual-Colored DNA Comb Polymers for Single Molecule Rheology (United States)

    Mai, Danielle; Marciel, Amanda; Schroeder, Charles


    We report the synthesis and characterization of branched biopolymers for single molecule rheology. In our work, we utilize a hybrid enzymatic-synthetic approach to graft ``short'' DNA branches to ``long'' DNA backbones, thereby producing macromolecular DNA comb polymers. The branches and backbones are synthesized via polymerase chain reaction with chemically modified deoxyribonucleotides (dNTPs): ``short'' branches consist of Cy5-labeled dNTPs and a terminal azide group, and ``long'' backbones contain dibenzylcyclooctyne-modified (DBCO) dNTPs. In this way, we utilize strain-promoted, copper-free cycloaddition ``click'' reactions for facile grafting of azide-terminated branches at DBCO sites along backbones. Copper-free click reactions are bio-orthogonal and nearly quantitative when carried out under mild conditions. Moreover, comb polymers can be labeled with an intercalating dye (e.g., YOYO) for dual-color fluorescence imaging. We characterized these materials using gel electrophoresis, HPLC, and optical microscopy, with atomic force microscopy in progress. Overall, DNA combs are suitable for single molecule dynamics, and in this way, our work holds the potential to improve our understanding of topologically complex polymer melts and solutions.

  19. The inhibition of anti-DNA binding to DNA by nucleic acid binding polymers.

    Directory of Open Access Journals (Sweden)

    Nancy A Stearns

    Full Text Available Antibodies to DNA (anti-DNA are the serological hallmark of systemic lupus erythematosus (SLE and can mediate disease pathogenesis by the formation of immune complexes. Since blocking immune complex formation can attenuate disease manifestations, the effects of nucleic acid binding polymers (NABPs on anti-DNA binding in vitro were investigated. The compounds tested included polyamidoamine dendrimer, 1,4-diaminobutane core, generation 3.0 (PAMAM-G3, hexadimethrine bromide, and a β-cylodextrin-containing polycation. As shown with plasma from patients with SLE, NABPs can inhibit anti-DNA antibody binding in ELISA assays. The inhibition was specific since the NABPs did not affect binding to tetanus toxoid or the Sm protein, another lupus autoantigen. Furthermore, the polymers could displace antibody from preformed complexes. Together, these results indicate that NABPs can inhibit the formation of immune complexes and may represent a new approach to treatment.

  20. Waves of DNA: Propagating Excitations in Extended Nanoconfined Polymers

    CERN Document Server

    Klotz, Alexander R; Reisner, Walter W


    We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain occupies multiple cavities. Fluorescent video-microscopy data shows that waves of excess fluorescence propagate across the cavity-straddling molecule, corresponding to propagating fluctuations of contour overdensity in the cavities. The waves are quantified by examining the correlation in intensity fluctuations between neighbouring cavities. Correlations grow from an anti-correlated minimum to a correlated maximum before decaying, corresponding to a transfer of contour between neighbouring cavities at a fixed transfer time-scale. The observed dynamics can be modelled using Langevin dynamics simulations and a minimal lattice model of coupled diffusion. This study shows how confinement-based sculpting of the polymer ...

  1. Electrochemical DNA Hybridization Sensors Based on Conducting Polymers

    Directory of Open Access Journals (Sweden)

    Md. Mahbubur Rahman


    Full Text Available Conducting polymers (CPs are a group of polymeric materials that have attracted considerable attention because of their unique electronic, chemical, and biochemical properties. This is reflected in their use in a wide range of potential applications, including light-emitting diodes, anti-static coating, electrochromic materials, solar cells, chemical sensors, biosensors, and drug-release systems. Electrochemical DNA sensors based on CPs can be used in numerous areas related to human health. This review summarizes the recent progress made in the development and use of CP-based electrochemical DNA hybridization sensors. We discuss the distinct properties of CPs with respect to their use in the immobilization of probe DNA on electrode surfaces, and we describe the immobilization techniques used for developing DNA hybridization sensors together with the various transduction methods employed. In the concluding part of this review, we present some of the challenges faced in the use of CP-based DNA hybridization sensors, as well as a future perspective.

  2. Amphipathic Alpha-Helical Peptide Compositions as Antiviral Agents (United States)

    Glenn, Jeffrey (Inventor); Cho, Nam-Joon (Inventor); Frank, Curtis W. (Inventor); Cheong, Kwang Ho (Inventor)


    The invention features methods and compositions that exploit the ability of amphipathic alpha-helical (AH) peptides to cause disruption of lipid-containing vesicles, such as enveloped viruses, in a size-dependent manner.

  3. Like-charge attraction and opposite-charge decomplexation between polymers and DNA molecules (United States)

    Buyukdagli, Sahin


    We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test-charge theory [S. Buyukdagli et al., Phys. Rev. E 94, 042502 (2016), 10.1103/PhysRevE.94.042502] to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loop level electrostatic correlation effects such as the ionic cloud deformation around the strongly charged DNA molecule as well as image-charge forces induced by the low DNA permittivity. Our model can reproduce and explain various characteristics of the experimental phase diagrams for polymer solutions. First, the addition of polyvalent cations to the electrolyte solution results in the attraction of the negatively charged polymer by the DNA molecule. The glue of the like-charge attraction is the enhanced shielding of the polymer charges by the dense counterion layer at the DNA surface. Second, through the shielding of the DNA-induced electrostatic potential, mono- and polyvalent cations of large concentration both suppress the like-charge attraction. Within the same formalism, we also predict a new opposite-charge repulsion effect between the DNA molecule and a positively charged polymer. In the presence of polyvalent anions such as sulfate or phosphate, their repulsion by the DNA charges leads to the charge screening deficiency of the region around the DNA molecule. This translates into a repulsive force that results in the decomplexation of the polymer from DNA. This opposite-charge repulsion phenomenon can be verified by current experiments and the underlying mechanism can be beneficial to gene therapeutic applications where the control over polymer-DNA interactions is the key factor.

  4. Isolation and characterization of a new class of amphipathic biopolymers capable of self-assembly from aqueous media

    Energy Technology Data Exchange (ETDEWEB)

    Martin, G.G.; Cannon, G.C.; McCormick, C.L. [Univ. of Southern Mississippi, Hattiesburg, MS (United States)


    Extensive research is being done in many laboratories to investigate the role of synthetic hydrophobically-modified polymers and amphipathic proteins for their potential in phase-transfer, sequestration, and elimination of polluting hydrocarbons and surfactants. Our laboratory has begun a research program which is aimed at the development of a new class of environmentally benign biomaterials using the amphipathic proteins termed {open_quotes}hydrophobins{close_quotes} and an associated polysaccharide, schizophyllan. These biopolymers can stabilize oil dispersions, attach strongly to polyethylene and polytetrafluoroethylene surfaces rendering them hydrophilic, and can self-assemble into a stable, flexible membrane. Preliminary experiments in our laboratory and others have demonstrated the immense technological potential of this class of biomaterials for surface modification of membranes and coatings, fouling resistance, controlled delivery, protective encapsulation, and drag reduction.

  5. Polymers modified with double-tailed fluorous compounds for efficient DNA and siRNA delivery. (United States)

    He, Bingwei; Wang, Yitong; Shao, Naimin; Chang, Hong; Cheng, Yiyun


    Cationic polymers are widely used as gene carriers, however, these polymers are usually associated with low transfection efficacy and non-negligible toxicity. Fluorination on polymers significantly improves their performances in gene delivery, but a high density of fluorous chains must be conjugated on a single polymer. Here we present a new strategy to construct fluorinated polymers with minimal fluorous chains for efficient DNA and siRNA delivery. A double-tailed fluorous compound 2-chloro-4,6-bis[(perfluorohexyl)propyloxy]-1,3,5-triazine (CBT) was conjugated on dendrimers of different generations and low molecular weight polyethylenimine via a facile synthesis. The yielding products with average numbers of 1-2 conjugated CBT moieties showed much improved EGFP and luciferase transfection efficacy compared to unmodified polymers. In addition, these polymers show high siRNA delivery efficacy on different cell lines. Among the synthesized polymers, generation 1 (G1) dendrimer modified with an average number of 1.9 CBT moieties (G1-CBT1.9) shows the highest efficacy when delivering both DNA and siRNA and its efficacy approaches that of Lipofectamine 2000. G1-CBT1.9 also shows efficient gene silencing in vivo. All of the CBT-modified polymers exhibit minimal toxicity on the cells at their optimal transfection conditions. This study provides a new strategy to design efficient fluorous polymers for DNA and siRNA delivery.

  6. How curved membranes recruit amphipathic helices and protein anchoring motifs

    DEFF Research Database (Denmark)

    Hatzakis, Nikos; Bhatia, Vikram Kjøller; Larsen, Jannik;


    Lipids and several specialized proteins are thought to be able to sense the curvature of membranes (MC). Here we used quantitative fluorescence microscopy to measure curvature-selective binding of amphipathic motifs on single liposomes 50-700 nm in diameter. Our results revealed that sensing...

  7. DNA-SMART: Biopatterned Polymer Film Microchannels for Selective Immobilization of Proteins and Cells. (United States)

    Schneider, Ann-Kathrin; Nikolov, Pavel M; Giselbrecht, Stefan; Niemeyer, Christof M


    A novel SMART module, dubbed "DNA-SMART" (DNA substrate modification and replication by thermoforming) is reported, where polymer films are premodified with single-stranded DNA capture strands, microthermoformed into 3D structures, and postmodified with complementary DNA-protein conjugates to realize complex biologically active surfaces within microfluidic devices. As a proof of feasibility, it is demonstrated that microchannels presenting three different proteins on their inner curvilinear surface can be used for selective capture of cells under flow conditions.

  8. Cationic polymers for DNA origami coating - examining their binding efficiency and tuning the enzymatic reaction rates (United States)

    Kiviaho, Jenny K.; Linko, Veikko; Ora, Ari; Tiainen, Tony; Järvihaavisto, Erika; Mikkilä, Joona; Tenhu, Heikki; Nonappa, Affc; Kostiainen, Mauri A.


    DNA origamis are fully tailored, programmable, biocompatible and readily functionalizable nanostructures that provide an excellent foundation for the development of sophisticated drug-delivery systems. However, the DNA origami objects suffer from certain drawbacks such as low cell-transfection rates and low stability. A great deal of studies on polymer-based transfection agents, mainly focusing on polyplex formation and toxicity, exists. In this study, the electrostatic binding between a brick-like DNA origami and cationic block-copolymers was explored. The effect of the polymer structure on the binding was investigated and the toxicity of the polymer-origami complexes evaluated. The study shows that all of the analyzed polymers had a suitable binding efficiency irrespective of the block structure. It was also observed that the toxicity of polymer-origami complexes was insignificant at the biologically relevant concentration levels. Besides brick-like DNA origamis, tubular origami carriers equipped with enzymes were also coated with the polymers. By adjusting the amount of cationic polymers that cover the DNA structures, we showed that it is possible to control the enzyme kinetics of the complexes. This work gives a starting point for further development of biocompatible and effective polycation-based block copolymers that can be used in coating different DNA origami nanostructures for various bioapplications.DNA origamis are fully tailored, programmable, biocompatible and readily functionalizable nanostructures that provide an excellent foundation for the development of sophisticated drug-delivery systems. However, the DNA origami objects suffer from certain drawbacks such as low cell-transfection rates and low stability. A great deal of studies on polymer-based transfection agents, mainly focusing on polyplex formation and toxicity, exists. In this study, the electrostatic binding between a brick-like DNA origami and cationic block-copolymers was explored. The

  9. DNA detection using water-soluble conjugated polymers and peptide nucleic acid probes (United States)

    Gaylord, Brent S.; Heeger, Alan J.; Bazan, Guillermo C.


    The light-harvesting properties of cationic conjugated polymers are used to sensitize the emission of a dye on a specific peptide nucleic acid (PNA) sequence for the purpose of homogeneous, "real-time" DNA detection. Signal transduction is controlled by hybridization of the neutral PNA probe and the negative DNA target. Electrostatic interactions bring the hybrid complex and cationic polymer within distances required for Förster energy transfer. Conjugated polymer excitation provides fluorescein emission >25 times higher than that obtained by exciting the dye, allowing detection of target DNA at concentrations of 10 pM with a standard fluorometer. A simple and highly sensitive assay with optical amplification that uses the improved hybridization behavior of PNA/DNA complexes is thus demonstrated.

  10. Hierarchical-Multiplex DNA Patterns Mediated by Polymer Brush Nanocone Arrays That Possess Potential Application for Specific DNA Sensing. (United States)

    Liu, Wendong; Liu, Xueyao; Ge, Peng; Fang, Liping; Xiang, Siyuan; Zhao, Xiaohuan; Shen, Huaizhong; Yang, Bai


    This paper provides a facile and cost-efficient method to prepare single-strand DNA (ssDNA) nanocone arrays and hierarchical DNA patterns that were mediated by poly(2-hydroxyethyl methacrylate) (PHEMA) brush. The PHEMA brush nanocone arrays with different morphology and period were fabricated via colloidal lithography. The hierarchical structure was prepared through the combination of colloidal lithography and traditional photolithography. The DNA patterns were easily achieved via grafting the amino group modified ssDNA onto the side chain of polymer brush, and the anchored DNA maintained their reactivity. The as-prepared ssDNA nanocone arrays can be applied for target DNA sensing with the detection limit reaching 1.65 nM. Besides, with the help of introducing microfluidic ideology, the hierarchical-multiplex DNA patterns on the same substrate could be easily achieved with each kind of pattern possessing one kind of ssDNA, which are promising surfaces for the preparation of rapid, visible, and multiplex DNA sensors.

  11. New conjugated polymers for photoinduced unwinding of DNA supercoiling and gene regulation. (United States)

    Yang, Gaomai; Yuan, Huanxiang; Zhu, Chunlei; Liu, Libing; Yang, Qiong; Lv, Fengting; Wang, Shu


    Three cationic polythiophene derivatives (P1, P2, P3) were synthesized and characterized. Under white light irradiation (400-800 nm), they sensitize oxygen molecule in the surrounding to generate reactive oxygen species (ROS) that can efficiently unwind the supercoiled DNA in vitro. Further study shows that this relaxation of the DNA supercoiling results in the decrease of gene (pCX-EGFP plasmid) expression level. The ability of these conjugated polymers for regulating gene expression will add a new dimension to the function of conjugated polymers.

  12. Equilibrium properties of DNA and other semiflexible polymers confined in nanochannels (United States)

    Muralidhar, Abhiram

    Recent developments in next-generation sequencing (NGS) techniques have opened the door for low-cost, high-throughput sequencing of genomes. However, these developments have also exposed the inability of NGS to track large scale genomic information, which are extremely important to understand the relationship between genotype and phenotype. Genome mapping offers a reliable way to obtain information about large-scale structural variations in a given genome. A promising variant of genome mapping involves confining single DNA molecules in nanochannels whose cross-sectional dimensions are approximately 50 nm. Despite the development and commercialization of nanochannel-based genome mapping technology, the polymer physics of DNA in confinement is only beginning to be understood. Apart from its biological relevance, DNA is also used as a model polymer in experiments by polymer physicists. Indeed, the seminal experiments by Reisner et al. (2005) of DNA confined in nanochannels of different widths revealed discrepancies with the classical theories of Odijk and de Gennes for polymer confinement. Picking up from the conclusions of the dissertation of Tree (2014), this dissertation addresses a number of key outstanding problems in the area of nanoconfined DNA. Adopting a Monte Carlo chain growth technique known as the pruned-enriched Rosenbluth method, we examine the equilibrium and near-equilibrium properties of DNA and other semiflexible polymers in nanochannel confinement. We begin by analyzing the dependence of molecular weight on various thermodynamic properties of confined semiflexible polymers. This allows us to point out the finite size effects that can occur when using low molecular weight DNA in experiments. We then analyze the statistics of backfolding and hairpin formation in the context of existing theories and discuss how our results can be used to engineer better conditions for genome mapping. Finally, we elucidate the diffusion behavior of confined

  13. Self-assembly of DNA-polymer complexes using template polymerization. (United States)

    Trubetskoy, V S; Budker, V G; Hanson, L J; Slattum, P M; Wolff, J A; Hagstrom, J E


    The self-assembly of supramolecular complexes of nucleic acids and polymers is of relevance to several biological processes including viral and chromatin formation as well as gene therapy vector design. We now show that template polymerization facilitates condensation of DNA into particles that are <150 nm in diameter. Inclusion of a poly(ethylene glycol)-containing monomer prevents aggregation of these particles. The DNA within the particles remains biologically active and can express foreign genes in cells. The formation or breakage of covalent bonds has until now not been employed to compact DNA into artificial particles.

  14. DNA-inspired hierarchical polymer design: electrostatics and hydrogen bonding in concert. (United States)

    Hemp, Sean T; Long, Timothy E


    Nucleic acids and proteins, two of nature's biopolymers, assemble into complex structures to achieve desired biological functions and inspire the design of synthetic macromolecules containing a wide variety of noncovalent interactions including electrostatics and hydrogen bonding. Researchers have incorporated DNA nucleobases into a wide variety of synthetic monomers/polymers achieving stimuli-responsive materials, supramolecular assemblies, and well-controlled macromolecules. Recently, scientists utilized both electrostatics and complementary hydrogen bonding to orthogonally functionalize a polymer backbone through supramolecular assembly. Diverse macromolecules with noncovalent interactions will create materials with properties necessary for biomedical applications.

  15. Synthesis of biodegradable polymer-mesoporous silica composite microspheres for DNA prime-protein boost vaccination. (United States)

    Ho, Jenny; Huang, Yi; Danquah, Michael K; Wang, Huanting; Forde, Gareth M


    DNA vaccines or proteins are capable of inducing specific immunity; however, the translation to the clinic has generally been problematic, primarily due to the reduced magnitude of immune response and poor pharmacokinetics. Herein we demonstrate a composite microsphere formulation, composed of mesoporous silica spheres (MPS) and poly(D,L-lactide-co-glycolide) (PLGA), enables the controlled delivery of a prime-boost vaccine via the encapsulation of plasmid DNA (pDNA) and protein in different compartments. Method with modified dual-concentric-feeding needles attached to a 40 kHz ultrasonic atomizer was studied. These needles focus the flow of two different solutions, which passed through the ultrasonic atomizer. The process synthesis parameters, which are important to the scale-up of composite microspheres, were also studied. These parameters include polymer concentration, feed flowrate, and volumetric ratio of polymer and pDNA-PEI/MPS-BSA. This fabrication technique produced composite microspheres with mean D[4,3] ranging from 6 to 34 microm, depending upon the microsphere preparation. The resultant physical morphology of composite microspheres was largely influenced by the volumetric ratio of pDNA-PEI/MPS-BSA to polymer, and this was due to the precipitation of MPS at the surface of the microspheres. The encapsulation efficiencies were predominantly in the range of 93-98% for pDNA and 46-68% for MPS. In the in vitro studies, the pDNA and protein showed different release kinetics in a 40 day time frame. The dual-concentric-feeding in ultrasonic atomization was shown to have excellent reproducibility. It was concluded that this fabrication technique is an effective method to prepare formulations containing a heterologous prime-boost vaccine in a single delivery system.

  16. Structuring polymers for delivery of DNA-based therapeutics: updated insights. (United States)

    Gupta, Madhu; Tiwari, Shailja; Vyas, Suresh


    Gene therapy offers greater opportunities for treating numerous incurable diseases from genetic disorders, infections, and cancer. However, development of appropriate delivery systems could be one of the most important factors to overcome numerous biological barriers for delivery of various therapeutic molecules. A number of nonviral polymer-mediated vectors have been developed for DNA delivery and offer the potential to surmount the associated problems of their viral counterpart. To address the concerns associated with safety issues, a wide range of polymeric vectors are available and have been utilized successfully to deliver their therapeutics in vivo. Today's research is mainly focused on the various natural or synthetic polymer-based delivery carriers that protect the DNA molecule from degradation, which offer specific targeting to the desired cells after systemic administration, have transfection efficiencies equivalent to virus-mediated gene delivery, and have long-term gene expression through sustained-release mechanisms. This review explores an updated overview of different nonviral polymeric delivery system for delivery of DNA-based therapeutics. These polymeric carriers have been evaluated in vitro and in vivo and are being utilized in various stages of clinical evaluation. Continued research and understanding of the principles of polymer-based gene delivery systems will enable us to develop new and efficient delivery systems for the delivery of DNA-based therapeutics to achieve the goal of efficacious and specific gene therapy for a vast array of clinical disorders as the therapeutic solutions of tomorrow.

  17. Tuning backbones and side-chains of cationic conjugated polymers for optical signal amplification of fluorescent DNA detection. (United States)

    Huang, Yan-Qin; Liu, Xing-Fen; Fan, Qu-Li; Wang, Lihua; Song, Shiping; Wang, Lian-Hui; Fan, Chunhai; Huang, Wei


    Three cationic conjugated polymers (CCPs) exhibiting different backbone geometries and charge densities were used to investigate how their conjugated backbone and side chain properties, together with the transitions of DNA amphiphilic properties, interplay in the CCP/DNA-C* (DNA-C*: fluorophore-labeled DNA) complexes to influence the optical signal amplification of fluorescent DNA detection based on Förster resonance energy transfer (FRET). By examining the FRET efficiencies to dsDNA-C* (dsDNA: double-stranded DNA) and ssDNA-C* (ssDNA: single-stranded DNA) for each CCP, twisted conjugated backbones and higher charge densities were proved to facilitate electrostatic attraction in CCP/dsDNA-C* complexes, and induced improved sensitivity to DNA hybridization. Especially, by using the CCP with twisted conjugated backbone and the highest charge density, a more than 7-fold higher efficiency of FRET to dsDNA-C* was found than to ssDNA-C*, indicating a high signal amplification for discriminating between dsDNA and ssDNA. By contrast, linear conjugated backbones and lower charge density were demonstrated to favor hydrophobic interactions in CCP/ssDNA-C* complexes. These findings provided guidelines for the design of novel sensitive CCP, which can be useful to recognize many other important DNA activities involving transitions of DNA amphiphilic properties like DNA hybridization, such as specific DNA binding with ions, some secondary or tertiary structural changes of DNA, and so forth.

  18. Neutron diffraction studies of amphipathic helices in phospholipid bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Bradshaw, J.P.; Gilchrist, P.J. [Univ. of Edinburgh (United Kingdom); Duff, K.C. [Univ. of Edinburgh Medical School (United Kingdom); Saxena, A.M. [Brookhaven National Laboratory, Upton, NY (United States)


    The structural feature which is thought to facilitate the interaction of many peptides with phospholipid bilayers is the ability to fold into an amphipathic helix. In most cases the exact location and orientation of this helix with respect to the membrane is not known, and may vary with factors such as pH and phospholipid content of the bilayer. The growing interest in this area is stimulated by indications that similar interactions can contribute to the binding of certain hormones to their cell-surface receptors. We have been using the techniques of neutron diffraction from stacked phospholipid bilayers in an attempt to investigate this phenomenon with a number of membrane-active peptides. Here we report some of our findings with three of these: the bee venom melittin; the hormone calcitonin; and a synthetic peptide representing the ion channel fragment of influenza A M2 protein.

  19. Amphipathic α-Helices in Apolipoproteins Are Crucial to the Formation of Infectious Hepatitis C Virus Particles (United States)

    Nakamura, Shota; Ono, Chikako; Shiokawa, Mai; Yamamoto, Satomi; Motomura, Takashi; Okamoto, Toru; Okuzaki, Daisuke; Yamamoto, Masahiro; Saito, Izumu; Wakita, Takaji; Koike, Kazuhiko; Matsuura, Yoshiharu


    Apolipoprotein B (ApoB) and ApoE have been shown to participate in the particle formation and the tissue tropism of hepatitis C virus (HCV), but their precise roles remain uncertain. Here we show that amphipathic α-helices in the apolipoproteins participate in the HCV particle formation by using zinc finger nucleases-mediated apolipoprotein B (ApoB) and/or ApoE gene knockout Huh7 cells. Although Huh7 cells deficient in either ApoB or ApoE gene exhibited slight reduction of particles formation, knockout of both ApoB and ApoE genes in Huh7 (DKO) cells severely impaired the formation of infectious HCV particles, suggesting that ApoB and ApoE have redundant roles in the formation of infectious HCV particles. cDNA microarray analyses revealed that ApoB and ApoE are dominantly expressed in Huh7 cells, in contrast to the high level expression of all of the exchangeable apolipoproteins, including ApoA1, ApoA2, ApoC1, ApoC2 and ApoC3 in human liver tissues. The exogenous expression of not only ApoE, but also other exchangeable apolipoproteins rescued the infectious particle formation of HCV in DKO cells. In addition, expression of these apolipoproteins facilitated the formation of infectious particles of genotype 1b and 3a chimeric viruses. Furthermore, expression of amphipathic α-helices in the exchangeable apolipoproteins facilitated the particle formation in DKO cells through an interaction with viral particles. These results suggest that amphipathic α-helices in the exchangeable apolipoproteins play crucial roles in the infectious particle formation of HCV and provide clues to the understanding of life cycle of HCV and the development of novel anti-HCV therapeutics targeting for viral assembly. PMID:25502789

  20. Amphipathic α-helices in apolipoproteins are crucial to the formation of infectious hepatitis C virus particles.

    Directory of Open Access Journals (Sweden)

    Takasuke Fukuhara


    Full Text Available Apolipoprotein B (ApoB and ApoE have been shown to participate in the particle formation and the tissue tropism of hepatitis C virus (HCV, but their precise roles remain uncertain. Here we show that amphipathic α-helices in the apolipoproteins participate in the HCV particle formation by using zinc finger nucleases-mediated apolipoprotein B (ApoB and/or ApoE gene knockout Huh7 cells. Although Huh7 cells deficient in either ApoB or ApoE gene exhibited slight reduction of particles formation, knockout of both ApoB and ApoE genes in Huh7 (DKO cells severely impaired the formation of infectious HCV particles, suggesting that ApoB and ApoE have redundant roles in the formation of infectious HCV particles. cDNA microarray analyses revealed that ApoB and ApoE are dominantly expressed in Huh7 cells, in contrast to the high level expression of all of the exchangeable apolipoproteins, including ApoA1, ApoA2, ApoC1, ApoC2 and ApoC3 in human liver tissues. The exogenous expression of not only ApoE, but also other exchangeable apolipoproteins rescued the infectious particle formation of HCV in DKO cells. In addition, expression of these apolipoproteins facilitated the formation of infectious particles of genotype 1b and 3a chimeric viruses. Furthermore, expression of amphipathic α-helices in the exchangeable apolipoproteins facilitated the particle formation in DKO cells through an interaction with viral particles. These results suggest that amphipathic α-helices in the exchangeable apolipoproteins play crucial roles in the infectious particle formation of HCV and provide clues to the understanding of life cycle of HCV and the development of novel anti-HCV therapeutics targeting for viral assembly.

  1. Highly sensitive polymer-based cantilever-sensors for DNA detection

    Energy Technology Data Exchange (ETDEWEB)

    Calleja, M. [Biosensors Group, Nacional Center of Microelectronics (CNM-CSIC), Isaac Newton 8, Tres Cantos, E-28760 Madrid (Spain) and Mikroelektronics Centret, Technical University of Denmark, 345E, DK-2800, Lyngby (Denmark)]. E-mail:; Nordstroem, M. [Mikroelektronics Centret, Technical University of Denmark, 345E, DK-2800, Lyngby (Denmark); Alvarez, M. [Biosensors Group, Nacional Center of Microelectronics (CNM-CSIC), Isaac Newton 8, Tres Cantos, E-28760 Madrid (Spain); Tamayo, J. [Biosensors Group, Nacional Center of Microelectronics (CNM-CSIC), Isaac Newton 8, Tres Cantos, E-28760 Madrid (Spain); Lechuga, L.M. [Biosensors Group, Nacional Center of Microelectronics (CNM-CSIC), Isaac Newton 8, Tres Cantos, E-28760 Madrid (Spain); Boisen, A. [Mikroelektronics Centret, Technical University of Denmark, 345E, DK-2800, Lyngby (Denmark)


    We present a technology for the fabrication of cantilever arrays aimed to develop an integrated biosensor microsystem. The fabrication process is based on spin coating of the photosensitive polymer and near-ultraviolet exposure. Arrays of up to 33 microcantilevers are fabricated in the novel polymer material SU-8. The low Young's modulus of the polymer, 40 times lower than that of silicon, enables to improve the sensitivity of the sensor device for target detection. The mechanical properties of SU-8 cantilevers, such as spring constant, resonant frequency and quality factor are characterized as a function of the dimensions and the medium. The devices have been tested for measurement of the adsorption of single stranded DNA and subsequent interstitial adsorption of lateral spacer molecules. We demonstrate that sensitivity is enhanced by a factor of six compared to that of commercial silicon nitride cantilevers.

  2. Stretching DNA in polymer nanochannels fabricated by thermal imprint in PMMA

    DEFF Research Database (Denmark)

    Thamdrup, Lasse Højlund; Klukowska, A.; Kristensen, Anders


    We present results regarding the fast and inexpensive fabrication of polymer biochips for investigating the statics and dynamics of DNA confined in nanochannels. The biochips have been fabricated by means of nanoimprint lithography ( NIL) in low molecular weight polymethyl methacrylate ( PMMA) us...... investigated using epi-fluorescence microscopy. The measured average extension length amounts to 20% of the full contour length with a standard deviation of 4%. These results are in good agreement with results obtained by stretching DNA in conventional fused silica nanochannels....

  3. Degradable polymer-coated gold nanoparticles for co-delivery of DNA and siRNA. (United States)

    Bishop, Corey J; Tzeng, Stephany Y; Green, Jordan J


    Gold nanoparticles have utility for in vitro, ex vivo and in vivo imaging applications as well as for serving as a scaffold for therapeutic delivery and theranostic applications. Starting with gold nanoparticles as a core, layer-by-layer degradable polymer coatings enable the simultaneous co-delivery of DNA and short interfering RNA (siRNA). To engineer release kinetics, polymers which degrade through two different mechanisms can be utilized to construct hybrid inorganic/polymeric particles. During fabrication of the nanoparticles, the zeta potential reverses upon the addition of each oppositely charged polyelectrolyte layer and the final nanoparticle size reaches approximately 200nm in diameter. When the hybrid gold/polymer/nucleic acid nanoparticles are added to human primary brain cancer cells in vitro, they are internalizable by cells and reach the cytoplasm and nucleus as visualized by transmission electron microscopy and observed through exogenous gene expression. This nanoparticle delivery leads to both exogenous DNA expression and siRNA-mediated knockdown, with the knockdown efficacy superior to that of Lipofectamine® 2000, a commercially available transfection reagent. These gold/polymer/nucleic acid hybrid nanoparticles are an enabling theranostic platform technology capable of delivering combinations of genetic therapies to human cells.

  4. The enzyme-amplified amperometric DNA sensor using an electrodeposited polymer redox mediator

    Institute of Scientific and Technical Information of China (English)


    A highly sensitive method for the detection of a breast cancer-associated BRCA-1 gene is reported. The detection is based on a classical sandwich-type assay using horseradish peroxidase (HRP) as a catalytic label and electrodeposited Os2+/3+ conducting polymer (PAA-PVI-Os) as a redox mediator. Target DNA could be detected by the HRP-catalyzed reduction of H2O2, leading to a limit of detection as low as 10 fM.

  5. DNA Separation by Capillary Electrophoresis with Ultraviolet Detection using Mixed Synthetic Polymers

    Institute of Scientific and Technical Information of China (English)

    Qian WANG; Xu XU


    The mixtures of two polymers, poly (N,N-dimethylacrylamide) (PDMA) and polyvinylpyrrolidone (PVP) were synthesized and used as the separation medium for double-stranded and single-stranded DNA fragments by capillary electrophoresis with UV detector. On optimal conditions, 2%w/v PDMA ( 2%w/v PVP can be used to separate the doublet 123/124bp in pBR322/Hae III Markers.

  6. Theory of DNA electrophoresis in physical gels and entangled polymer solutions (United States)

    Duke, Thomas; Viovy, Jean Louis


    A scaling theory is presented for the electrophoretic mobility of DNA in sieving media that form dynamically evolving meshworks, such as physical gels and solutions of entangled polymers. In such media, the topological constraints on the DNA's motion are perpetually changing as cross links break and rejoin or as the polymers diffuse. It is shown that if the rate of constraint release falls within a certain range (which depends on the field strength), fractionation can be extended to higher molecular weights than would be feasible using a permanent gel of equivalent pore size. This improvement is a consequence of the disruptive effect that constraint release has on the mechanism of molecular orientation. Numerical simulations support the predictions of the theory. The possibility of realizing such a system in practice, with the aim of improving on current electrophoresis methods, is commented upon. It is suggested that semidilute polymer solutions may be a versatile medium for the rapid separation of long single-stranded DNA molecules, and the particular quality of solution required is identified.

  7. Comparative DNA isolation behaviours of silica and polymer based sorbents in batch fashion: monodisperse silica microspheres with bimodal pore size distribution as a new sorbent for DNA isolation. (United States)

    Günal, Gülçin; Kip, Çiğdem; Eda Öğüt, S; İlhan, Hasan; Kibar, Güneş; Tuncel, Ali


    Monodisperse silica microspheres with bimodal pore-size distribution were proposed as a high performance sorbent for DNA isolation in batch fashion under equilibrium conditions. The proposed sorbent including both macroporous and mesoporous compartments was synthesized 5.1 μm in-size, by a "staged shape templated hydrolysis and condensation method". Hydrophilic polymer based sorbents were also obtained in the form of monodisperse-macroporous microspheres ca 5.5 μm in size, with different functionalities, by a developed "multi-stage microsuspension copolymerization" technique. The batch DNA isolation performance of proposed material was comparatively investigated using polymer based sorbents with similar morphologies. Among all sorbents tried, the best DNA isolation performance was achieved with the monodisperse silica microspheres with bimodal pore size distribution. The collocation of interconnected mesoporous and macroporous compartments within the monodisperse silica microspheres provided a high surface area and reduced the intraparticular mass transfer resistance and made easier both the adsorption and desorption of DNA. Among the polymer based sorbents, higher DNA isolation yields were achieved with the monodisperse-macroporous polymer microspheres carrying trimethoxysilyl and quaternary ammonium functionalities. However, batch DNA isolation performances of polymer based sorbents were significantly lower with respect to the silica microspheres.

  8. A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

    Directory of Open Access Journals (Sweden)

    Glass John I


    Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

  9. Direct suppression of phagocytosis by amphipathic polymeric surfactants. (United States)

    Watrous-Peltier, N; Uhl, J; Steel, V; Brophy, L; Merisko-Liversidge, E


    Recent studies have demonstrated that phagocytosis of colloidal particles by the mononuclear phagocytes of the liver and spleen can be controlled by either coating or stabilizing particulate carriers with the amphipathic polymeric surfactants, F108 and T908. These surfactants consist of copolymers of polypropylene oxide (PPO) and polyethylene oxide (PEO) and, when adsorbed to particulate surfaces, significantly decrease sequestration of particulates by the mononuclear phagocytes (MPS) of the liver. To evaluate these observations further, murine peritoneal macrophages were incubated for varying periods with surfactant-coated and noncoated polystyrene particles (PSPs). Phagocytosis was monitored using gamma counting and quantitative fluorescence microscopy. The data show that phagocytosis is decreased when PSPs are coated with F108 and T908. In addition, suppression of phagocytic activity was observed when cells were pretreated with the surfactant and then challenged with noncoated particles. The data confirm previous observations that polymeric surfactants consisting of PEO and PPO protect particulate carriers from rapid uptake by the MPS of the liver. Further, F108 and T908 suppress phagocytosis directly without affecting the integrity, viability, or functional state of the cell.

  10. Bottom-Up Fabrication of Nanopatterned Polymers on DNA Origami by In Situ Atom-Transfer Radical Polymerization. (United States)

    Tokura, Yu; Jiang, Yanyan; Welle, Alexander; Stenzel, Martina H; Krzemien, Katarzyna M; Michaelis, Jens; Berger, Rüdiger; Barner-Kowollik, Christopher; Wu, Yuzhou; Weil, Tanja


    Bottom-up strategies to fabricate patterned polymers at the nanoscale represent an emerging field in the development of advanced nanodevices, such as biosensors, nanofluidics, and nanophotonics. DNA origami techniques provide access to distinct architectures of various sizes and shapes and present manifold opportunities for functionalization at the nanoscale with the highest precision. Herein, we conduct in situ atom-transfer radical polymerization (ATRP) on DNA origami, yielding differently nanopatterned polymers of various heights. After cross-linking, the grafted polymeric nanostructures can even stably exist in solution without the DNA origami template. This straightforward approach allows for the fabrication of patterned polymers with low nanometer resolution, which provides access to unique DNA-based functional hybrid materials.

  11. Modulation of Gene Expression by Polymer Nanocapsule Delivery of DNA Cassettes Encoding Small RNAs.

    Directory of Open Access Journals (Sweden)

    Ming Yan

    Full Text Available Small RNAs, including siRNAs, gRNAs and miRNAs, modulate gene expression and serve as potential therapies for human diseases. Delivery to target cells remains the fundamental limitation for use of these RNAs in humans. To address this challenge, we have developed a nanocapsule delivery technology that encapsulates small DNA molecules encoding RNAs into a small (30 nm polymer nanocapsule. For proof of concept, we transduced DNA expression cassettes for three small RNAs. In one application, the DNA cassette encodes an shRNA transcriptional unit that downregulates CCR5 and protects from HIV-1 infection. The DNA cassette nanocapsules were further engineered for timed release of the DNA cargo for prolonged knockdown of CCR5. Secondly, the nanocapsules provide an efficient means for delivery of gRNAs in the CRISPR/Cas9 system to mutate integrated HIV-1. Finally, delivery of microRNA-125b to mobilized human CD34+ cells enhances survival and expansion of the CD34+ cells in culture.

  12. The enzyme-amplified amperometric DNA sensor using an electrodeposited polymer redox mediator

    Institute of Scientific and Technical Information of China (English)

    ZHANG LanYong; WAN Ying; ZHANG Jiong; LI Di; WANG LiHua; SONG ShiPing; FAN ChunHai


    A highly sensitive method for the detection of a breast cancer-associated BRCA-1 gene is reported. The detection is based on a classical sandwich-type assay using horseradish peroxidase (HRP) as a cata-lytic label and electrodeposited Os2+/3+ conducting polymer (PAA-PVi-Os) as a redox mediator. Target DNA could be detected by the HRP-catalyzed reduction of H2O2, leading to a limit of detection as low as 10 fM.

  13. DNA binding and biological studies of some novel water-soluble polymer-copper(II)-phenanthroline complexes. (United States)

    Kumar, Rajendran Senthil; Arunachalam, Sankaralingam; Periasamy, Vaiyapuri Subbarayan; Preethy, Christo Paul; Riyasdeen, Anvarbatcha; Akbarsha, Mohammad Abdulkader


    Some novel water-soluble polymer-copper(II)-phenanthroline complex samples, [Cu(phen)2(BPEI)]Cl(2).4H2O (phen=1,10-phenanthroline, BPEI=branched polyethyleneimine), with different degrees of copper complex content in the polymer chain have been prepared by ligand substitution method in water-ethanol medium and characterized by infrared, UV-visible, EPR spectral and elemental analysis methods. The binding of these complex samples with DNA has been investigated by electronic absorption spectroscopy, emission spectroscopy and gel retardation assay. Electrostatic interactions between DNA molecule and polymer-copper(II) complex molecule containing many high positive charges have been observed. Besides these ionic interactions, van der Waals interactions, hydrogen bonding and other partial intercalation binding modes may also exist in this system. The polymer-copper(II) complex with higher degree of copper complex content was screened for its antimicrobial activity and antitumor activity.

  14. A highly parallel method for synthesizing DNA repeats enables the discovery of 'smart' protein polymers. (United States)

    Amiram, Miriam; Quiroz, Felipe Garcia; Callahan, Daniel J; Chilkoti, Ashutosh


    Robust high-throughput synthesis methods are needed to expand the repertoire of repetitive protein-polymers for different applications. To address this need, we developed a new method, overlap extension rolling circle amplification (OERCA), for the highly parallel synthesis of genes encoding repetitive protein-polymers. OERCA involves a single PCR-type reaction for the rolling circle amplification of a circular DNA template and simultaneous overlap extension by thermal cycling. We characterized the variables that control OERCA and demonstrated its superiority over existing methods, its robustness, high-throughput and versatility by synthesizing variants of elastin-like polypeptides (ELPs) and protease-responsive polymers of glucagon-like peptide-1 analogues. Despite the GC-rich, highly repetitive sequences of ELPs, we synthesized remarkably large genes without recursive ligation. OERCA also enabled us to discover 'smart' biopolymers that exhibit fully reversible thermally responsive behaviour. This powerful strategy generates libraries of repetitive genes over a wide and tunable range of molecular weights in a 'one-pot' parallel format.

  15. Polymer-cobalt(III) complexes: structural analysis of metal chelates on DNA interaction and comparative cytotoxic activity. (United States)

    Nehru, Selvan; Arunachalam, Sankaralingam; Arun, Renganathan; Premkumar, Kumpati


    A new series of pendant-type polymer-cobalt(III) complexes, [Co(LL)2(BPEI)Cl](2+), (where BPEI = branched polyethyleneimine, LL = dipyrido[3,2-a:2',3'-c](6,7,8,9-tetrahydro)phenazine (dpqc), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq) and imidazo[4,5-f]1,10-phenanthroline (ip)) each with three different degrees of coordination have been synthesized and characterized. Studies to know the mode and strength of interaction between these polymer-metal complexes and calf thymus DNA have been performed by UV-Visible absorption and emission techniques. Among these series, each polymer metal complex having higher binding strength with DNA has been selected to test against human cancer/normal cell lines. On the basis of these spectral studies, it is proposed that our polymer-metal complexes bind with DNA mainly through intercalation along with some electrostatic binding. The order of binding strength for the complexes with ligand, dpqc > dpq > ip. The analysis of the results suggests that polymer-cobalt(III) complexes with higher degree of coordination effectively binds with DNA due to the presence of large number of positively charged cobalt(III) chelates in the polymer chain which cooperatively act to increase the overall binding strength. These polymer-cobalt(III) complexes with hydrophobic ligands around the cobalt(III) metal centre favour the base stacking interactions via intercalation. All the complexes show very good anticancer activities and increasing of binding strength results in higher inhibition value. The polymer-cobalt(III) complex with dpqc ligand possess two fold increased anticancer activity when compared to complexes with other ligands against MCF-7 cells. Besides, the complexes were insensitive towards the growth of normal cells (HEK-293) at the IC50 concentration.

  16. Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array. (United States)

    Fuller, Carl W; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Bibillo, Arek; Stranges, P Benjamin; Dorwart, Michael; Tao, Chuanjuan; Li, Zengmin; Guo, Wenjing; Shi, Shundi; Korenblum, Daniel; Trans, Andrew; Aguirre, Anne; Liu, Edward; Harada, Eric T; Pollard, James; Bhat, Ashwini; Cech, Cynthia; Yang, Alexander; Arnold, Cleoma; Palla, Mirkó; Hovis, Jennifer; Chen, Roger; Morozova, Irina; Kalachikov, Sergey; Russo, James J; Kasianowicz, John J; Davis, Randy; Roever, Stefan; Church, George M; Ju, Jingyue


    DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5'-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods.

  17. Conducting polymer based DNA biosensor for the detection of the Bacillus cereus group species (United States)

    Velusamy, Vijayalakshmi; Arshak, Khalil; Korostynska, Olga; Oliwa, Kamila; Adley, Catherine


    Biosensor designs are emerging at a significant rate and play an increasingly important role in foodborne pathogen detection. Conducting polymers are excellent tools for the fabrication of biosensors and polypyrrole has been used in the detection of biomolecules due to its unique properties. The prime intention of this paper was to pioneer the design and fabrication of a single-strand (ss) DNA biosensor for the detection of the Bacillus cereus (B.cereus) group species. Growth of B. cereus, results in production of several highly active toxins. Therefore, consumption of food containing >106 bacteria/gm may results in emetic and diarrhoeal syndromes. The most common source of this bacterium is found in liquid food products, milk powder, mixed food products and is of particular concern in the baby formula industry. The electrochemical deposition technique, such as cyclic voltammetry, was used to develop and test a model DNA-based biosensor on a gold electrode electropolymerized with polypyrrole. The electrically conducting polymer, polypyrrole is used as a platform for immobilizing DNA (1μg) on the gold electrode surface, since it can be more easily deposited from neutral pH aqueous solutions of pyrrolemonomers. The average current peak during the electrodeposition event is 288μA. There is a clear change in the current after hybridization of the complementary oligonucleotide (6.35μA) and for the noncomplementary oligonucleotide (5.77μA). The drop in current after each event was clearly noticeable and it proved to be effective.

  18. Stretching and imaging of single DNA chains on a hydrophobic polymer surface made of amphiphilic alternating comb-copolymer. (United States)

    Liu, Rongrong; Wong, Sheau Tyug; Lau, Peggy Pei Zhi; Tomczak, Nikodem


    Functionalization of amine derivatized glass slides with a poly(maleic anhydride)-based comb-copolymer to facilitate stretching, aligning, and imaging of individual dsDNA chains is presented. The polymer-coated surface is hydrophobic due to the presence of the long alkyl side chains along the polymer backbone. The surface is also characterized by low roughness and a globular morphology. Stretched and aligned bacteriophage λ-DNA chains were obtained using a robust method based on stretching by a receding water meniscus at pH 7.8 without the need for small droplet volumes or precoating the surface with additional layers of (bio)molecules. Although the dye to DNA base pairs ratio did not influence substantially the stretching length distributions, a clear peak at stretching lengths close to the contour length of the dsDNA is visible at larger staining ratios.

  19. Anti-plasmodial action of de novo-designed, cationic, lysine-branched, amphipathic, helical peptides

    Directory of Open Access Journals (Sweden)

    Kaushik Naveen K


    Full Text Available Abstract Background A lack of vaccine and rampant drug resistance demands new anti-malarials. Methods In vitro blood stage anti-plasmodial properties of several de novo-designed, chemically synthesized, cationic, amphipathic, helical, antibiotic peptides were examined against Plasmodium falciparum using SYBR Green assay. Mechanistic details of anti-plasmodial action were examined by optical/fluorescence microscopy and FACS analysis. Results Unlike the monomeric decapeptides {(Ac-GXRKXHKXWA-NH2 (X = F,ΔF (Fm, ΔFm IC50 >100 μM}, the lysine-branched,dimeric versions showed far greater potency {IC50 (μM Fd 1.5 , ΔFd 1.39}. The more helical and proteolytically stable ΔFd was studied for mechanistic details. ΔFq, a K-K2 dendrimer of ΔFm and (ΔFm2 a linear dimer of ΔFm showed IC50 (μM of 0.25 and 2.4 respectively. The healthy/infected red cell selectivity indices were >35 (ΔFd, >20 (ΔFm2 and 10 (ΔFq. FITC-ΔFd showed rapid and selective accumulation in parasitized red cells. Overlaying DAPI and FITC florescence suggested that ΔFd binds DNA. Trophozoites and schizonts incubated with ΔFd (2.5 μM egressed anomalously and Band-3 immunostaining revealed them not to be associated with RBC membrane. Prematurely egressed merozoites from peptide-treated cultures were found to be invasion incompetent. Conclusion Good selectivity (>35, good resistance index (1.1 and low cytotoxicity indicate the promise of ΔFd against malaria.

  20. Mannitol influence on the separation of DNA fragments by capillary electrophoresis in entangled polymer solutions. (United States)

    Han, F; Xue, J; Lin, B


    A new kind of sieving matrix is presented in this paper to allow satisfactory separation of DNA fragments in a relatively low viscous solution. When a certain amount of mannitol was added to cellulose solution not concentrated enough to separate PGEM-3Zf(+)/HaeIII standards well, a polymer solution with low viscosity but with very good separation effects was obtained. The separation result of this sieving buffer was comparable with those using highly concentrated cellulose solutions. The sieving ability of solutions with different cellulose concentrations and different amounts of mannitol has been investigated. It was proved that 0.5% was the minimum hydroxypropylmethylcellulose (HPMC) concentration that could be used to separate DNA fragments satisfactorily. HPMC solutions with a concentration of less than 0.5% could not separate the standard DNA fragments even in the presence of mannitol. It was found that 6% was the optimized mannitol concentration because either more or less mannitol will lead a decrease of resolution. The principle of the positive influence of mannitol has also been discussed.

  1. Well-defined star polymers for co-delivery of plasmid DNA and imiquimod to dendritic cells. (United States)

    Lin, Wenjing; Hanson, Samuel; Han, Wenqing; Zhang, Xiaofang; Yao, Na; Li, Hongru; Zhang, Lijuan; Wang, Chun


    Co-delivery of antigen-encoding plasmid DNA (pDNA) and immune-modulatory molecules has importance in advancing gene-based immunotherapy and vaccines. Here novel star polymer nanocarriers were synthesized for co-delivery of pDNA and imiquimod (IMQ), a poorly soluble small-molecule adjuvant, to dendritic cells. Computational modeling and experimental results revealed that the polymers formed either multimolecular or unimolecular core-shell-type micelles in water, depending on the nature of the outer hydrophilic shell. Micelles loaded with both IMQ and pDNA were able to release IMQ in response to intracellular pH of the endo-lysosome and transfect mouse dendritic cells (DC2.4 line) in vitro. Importantly, IMQ-loaded micelle/pDNA complexes displayed much enhanced transfection efficiency than IMQ-free complexes. These results demonstrate the feasibility of co-delivery of pDNA and IMQ to antigen-presenting cells by multifunctional polymer nanocarriers with potential use in gene-based vaccine approaches.

  2. Biogenesis and the growth of DNA-like polymer chains: A computer simulation (United States)

    Herrmann, Hans J.; Tsallis, Constantino


    We study, through computer simulation, a crucial step of biogenesis, namely the growth of self-replicating codified DNA-like polymers starting from a mixture of oligomers. We have adopted the growth scheme that has been recently proposed by Ferreira and Tsallis which incorporates usual ideas of autocatalysis through complementary pairs and within which a central role is played by the hydrogen-like links (characterized by the probabilities pAT and PCG of chemical bonding of the A-T and C-G pairs respectively) between the two chains of the growing polymer. We find that the average equilibrium polymeric length ξ diverges, for any fixed ratio (1 - pAT)/(1 - pCG), as ξ ∝ 1/√1 - pAT. Selection of patterns may happen at all stages and in particular at chemical equilibrium. Selection occurs via two different mechanisms: (i) away from the critical point pAT = pCG = 1 if PAT ≠ PCG; (ii) both on and away from the critical point if the initial concentrations of nucleotides (A, T, C and G or their precursors) are different.

  3. Multi-colored fibers by self-assembly of DNA, histone proteins, and cationic conjugated polymers. (United States)

    Wang, Fengyan; Liu, Zhang; Wang, Bing; Feng, Liheng; Liu, Libing; Lv, Fengting; Wang, Yilin; Wang, Shu


    The development of biomolecular fiber materials with imaging ability has become more and more useful for biological applications. In this work, cationic conjugated polymers (CCPs) were used to construct inherent fluorescent microfibers with natural biological macromolecules (DNA and histone proteins) through the interfacial polyelectrolyte complexation (IPC) procedure. Isothermal titration microcalorimetry results show that the driving forces for fiber formation are electrostatic and hydrophobic interactions, as well as the release of counterions and bound water molecules. Color-encoded IPC fibers were also obtained based on the co-assembly of DNA, histone proteins, and blue-, green-, or red- (RGB-) emissive CCPs by tuning the fluorescence resonance energy-transfer among the CCPs at a single excitation wavelength. The fibers could encapsulate GFP-coded Escherichia coli BL21, and the expression of GFP proteins was successfully regulated by the external environment of the fibers. These multi-colored fibers show a great potential in biomedical applications, such as biosensor, delivery, and release of biological molecules and tissue engineering.

  4. A systematic study of electron or hole transfer along DNA dimers, trimers and polymers

    CERN Document Server

    Simserides, Constantinos


    A systematic study of electron or hole transfer along DNA dimers, trimers and polymers is presented with a tight-binding approach at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters between successive base-pairs. A system of $N$ coupled differential equations is solved numerically with the eigenvalue method, allowing the temporal and spatial evolution of electrons or holes along a $N$ base-pair DNA segment to be determined. Useful physical quantities are defined and calculated including the maximum transfer percentage $p$ and the pure maximum transfer rate $\\frac{p}{T}$ for cases where a period $T$ can be defined, as well as the pure mean carrier transfer rate $k$ and the speed of charge transfer $u=kd$, where $d = N \\times$ 3.4 {\\AA} is the charge transfer distance. The inverse decay length $\\beta$ used for the exponential fit $k = k_0 \\exp(-\\beta d)$ and the exponent $\\eta$ used for the power law fit $k = k_0' N^{-\\eta}$ are computed. The electron and hol...

  5. DNA damage induced by bare and loaded microporous coordination polymers from their ground and electronic excited states. (United States)

    Yañuk, Juan G; Alomar, María L; Gonzalez, M Micaela; Simon, Francisco; Erra-Balsells, Rosa; Rafti, Matías; Cabrerizo, Franco M


    We report on interactions of cell free double-stranded DNA (dsDNA) with a selected subgroup of Microporous Coordination Polymers (MCPs). In particular, we have studied the influence of different metal ion constituents and chemically modified linkers using a set of five benzene carboxylate-based MCPs. Our results suggest that the DNA moiety can be structurally modified in two different ways: by direct MCPs-dsDNA interaction and/or through photosensitized processes. The extent of the observed damage was found to be strongly dependent on the charge density of the material. The potential use of the MCPs tested as inert carriers of photosensitizers was demonstrated by analyzing the interaction between dsDNA and harmine-loaded Cr-based materials, both in the absence of light and upon UVA irradiation.

  6. Poly(ethylenimine)-grafted-poly[(aspartic acid)-co-lysine]:A Non-viral Polymer with Potential for DNA Delivery

    Institute of Scientific and Technical Information of China (English)

    Zhi YANG; Gu Ping TANG


    A biodegradable gene transfer vector, poly(ethylenimine)-grafted-poly[(aspartic acid)-co-lysine] has been developed by thermal polycondensation of aspartic acid and lysine, and branch poly(ethylenimine) (Mw less than 600) was grafted to the backbone. The polymer was characterized by 1H NMR. It appeared lower cytotoxity compared to poly(ethylenimine) (25KDa), which was quantified by MTT assay. Electrophoresis indicated that the polymer could retardate DNA at N/P ratio 1.2-1.8 (w/w). Transfection efficiency of the complexes was studied in NT2 cell lines. It was 1.5 fold higher than molecular weight PEI (Mw = 25KDa).

  7. Label-free DNA electrochemical sensor based on a PNA-functionalized conductive polymer

    DEFF Research Database (Denmark)

    Reisberg, S; Dang, L A; Nguyen, Q A;


    An electrochemical hybridization biosensor based on peptide nucleic acid (PNA) probe is presented. PNA were attached covalently onto a quinone-based electroactive polymer. Changes in flexibility of the PNA probe strand upon hybridization generates electrochemical changes at the polymer...

  8. Zwitterionic peptide anchored to conducting polymer PEDOT for the development of antifouling and ultrasensitive electrochemical DNA sensor. (United States)

    Wang, Guixiang; Han, Rui; Su, Xiaoli; Li, Yinan; Xu, Guiyun; Luo, Xiliang


    Zwitterionic peptides were anchored to a conducting polymer of citrate doped poly(3,4-ethylenedioxythiophene) (PEDOT) via the nickel cation coordination, and the obtained peptide modified PEDOT, with excellent antifouling ability and good conductivity, was further used for the immobilization of a DNA probe to construct an electrochemical biosensor for the breast cancer marker BRCA1. The DNA biosensor was highly sensitive (with detection limit of 0.03fM) and selective, and it was able to detect BRCA1 in 5% (v/v) human plasma with satisfying accuracy and low fouling. The marriage of antifouling and biocompatible peptides with conducting polymers opened a new avenue to construct electrochemical biosensors capable of assaying targets in complex biological media with high sensitivity and without biofouling.

  9. One-step polymer surface modification for minimizing drug, protein, and DNA adsorption in microanalytical systems

    DEFF Research Database (Denmark)

    Larsen, Esben Kjær Unmack; Larsen, Niels Bent


    The non-specific adsorption of dissolved analytes strongly reduces the sensitivity and reliability in polymer microanalytical systems. Here, a one-step aqueous phase procedure modifies polymer material surfaces to strongly reduce their non-specific adsorption of a broad range of organic analytes ...... systems, including polystyrene (PS), cyclic olefin copolymer (COC), liquid crystalline polymer (LCP), and polyimide (PI)....

  10. Precise Coating of a Wide Range of DNA Templates by a Protein Polymer with a DNA Binding Domain

    NARCIS (Netherlands)

    Hernandez-Garcia, Armando; Estrich, Nicole A.; Werten, Marc W.T.; Maarel, van der Johan R.C.; Labean, Thomas H.; Wolf, de Frits A.; Cohen Stuart, Martien A.; Vries, de Renko


    Emerging DNA-based nanotechnologies would benefit from the ability to modulate the properties (e.g., solubility, melting temperature, chemical stability) of diverse DNA templates (single molecules or origami nanostructures) through controlled, self-assembling coatings. We here introduce a DNA coatin

  11. Glycosaminoglycans are required for translocation of amphipathic cell-penetrating peptides across membranes. (United States)

    Pae, Janely; Liivamägi, Laura; Lubenets, Dmitri; Arukuusk, Piret; Langel, Ülo; Pooga, Margus


    Cell-penetrating peptides (CPPs) are considered as one of the most promising tools to mediate the cellular delivery of various biologically active compounds that are otherwise cell impermeable. CPPs can internalize into cells via two different pathways - endocytosis and direct translocation across the plasma membrane. In both cases, the initial step of internalization requires interactions between CPPs and different plasma membrane components. Despite the extensive research, it is not yet fully understood, which of these cell surface molecules mediate the direct translocation of CPPs across the plasma- and endosomal membrane. In the present study we used giant plasma membrane vesicles (GPMVs) as a model membrane system to elucidate the specific molecular mechanisms behind the internalization and the role of cell surface glycosaminoglycans (GAGs) in the translocation of four well-known CPPs, classified as cationic (nona-arginine, Tat peptide) and amphipathic (transportan and TP10). We demonstrate here that GAGs facilitate the translocation of amphipathic CPPs, but not the internalization of cationic CPPs; and that the uptake is not mediated by a specific GAG class, but rather the overall amount of these polysaccharides is crucial for the internalization of amphipathic peptides.

  12. Packing of coat protein amphipathic and transmembrane helices in filamentous bacteriophage M13: role of small residues in protein oligomerization. (United States)

    Williams, K A; Glibowicka, M; Li, Z; Li, H; Khan, A R; Chen, Y M; Wang, J; Marvin, D A; Deber, C M


    Filamentous bacteriophage M13, an important cloning and phage display vector, is encapsulated by ca 2700 copies of its 50-residue major coat protein (gene 8). This protein occurs as a membrane protein while stably inserted into its E. coli host inner membrane, and as a coat protein upon assembly and packing onto phage DNA in the lipid-free virion. To examine the specific protein-protein interactions underlying these processes, we used a combination of randomized and saturation mutagenesis of the entire gene 8 to assess the susceptibility of each position to mutation. In the resulting library of ca 100 viable M13 mutants, "small" residues (Ala,Gly,Ser), which constitute the non-polar face of the N-terminal amphipathic helical segment, and a face of the hydrophobic (effective transmembrane) helical segment, were found to be highly conserved. These results support a model in which coat protein packing is stabilized by the presence within each protein subunit of two "oligomerization segments", i.e. specific helical regions with faces rich in small residues which function to promote the close approach of alpha-helices.

  13. DNA translocation across protein channels: How does a polymer worm through a hole? (United States)

    Muthukumar, M.


    Free energy barriers control the translocation of polymers through narrow channels. Based on an analogy with the classical nucleation and growth process, we have calculated the translocation time and its dependencies on the length, stiffness, and sequence of the polymer, solution conditions, and the strength of the driving electrochemical potential gradient. Our predictions will be compared with experimental results and prospects of reading polymer sequences.

  14. Nucleic acid chemistry in the organic phase: from functionalized oligonucleotides to DNA side chain polymers. (United States)

    Liu, Kai; Zheng, Lifei; Liu, Qing; de Vries, Jan Willem; Gerasimov, Jennifer Y; Herrmann, Andreas


    DNA-incorporating hydrophobic moieties can be synthesized by either solid-phase or solution-phase coupling. On a solid support the DNA is protected, and hydrophobic units are usually attached employing phosphoramidite chemistry involving a DNA synthesizer. On the other hand, solution coupling in aqueous medium results in low yields due to the solvent incompatibility of DNA and hydrophobic compounds. Hence, the development of a general coupling method for producing amphiphilic DNA conjugates with high yield in solution remains a major challenge. Here, we report an organic-phase coupling strategy for nucleic acid modification and polymerization by introducing a hydrophobic DNA-surfactant complex as a reactive scaffold. A remarkable range of amphiphile-DNA structures (DNA-pyrene, DNA-triphenylphosphine, DNA-hydrocarbon, and DNA block copolymers) and a series of new brush-type DNA side-chain homopolymers with high DNA grafting density are produced efficiently. We believe that this method is an important breakthrough in developing a generalized approach to synthesizing functional DNA molecules for self-assembly and related technological applications.

  15. A sandwich-hybridization assay for simultaneous determination of HIV and tuberculosis DNA targets based on signal amplification by quantum dots-PowerVision™ polymer coding nanotracers. (United States)

    Yan, Zhongdan; Gan, Ning; Zhang, Huairong; Wang, De; Qiao, Li; Cao, Yuting; Li, Tianhua; Hu, Futao


    A novel sandwich-hybridization assay for simultaneous electrochemical detection of multiple DNA targets related to human immune deficiency virus (HIV) and tuberculosis (TB) was developed based on the different quantum dots-PowerVision(TM) polymer nanotracers. The polymer nanotracers were respectively fabricated by immobilizing SH-labeled oligonucleotides (s-HIV or s-TB), which can partially hybrid with virus DNA (HIV or TB), on gold nanoparticles (Au NPs) and then modified with PowerVision(TM) (PV) polymer-encapsulated quantum dots (CdS or PbS) as signal tags. PV is a dendrimer enzyme linked polymer, which can immobilize abundant QDs to amplify the stripping voltammetry signals from the metal ions (Pb or Cd). The capture probes were prepared through the immobilization of SH-labeled oligonucleotides, which can complementary with HIV and TB DNA, on the magnetic Fe3O4@Au (GMPs) beads. After sandwich-hybridization, the polymer nanotracers together with HIV and TB DNA targets were simultaneously introduced onto the surface of GMPs. Then the two encoding metal ions (Cd(2+) and Pb(2+)) were used to differentiate two viruses DNA due to the different subsequent anodic stripping voltammetric peaks at -0.84 V (Cd) and -0.61 V (Pb). Because of the excellent signal amplification of the polymer nanotracers and the great specificity of DNA targets, this assay could detect targets DNA as low as 0.2 femtomolar and exhibited excellent selectivity with the dynamitic range from 0.5 fM to 500 pM. Those results demonstrated that this electrochemical coding assay has great potential in applications for screening more viruses DNA while changing the probes.

  16. Transfer-matrix calculations of DNA polymer micromechanics under tension and torque constraints (United States)

    Efremov, Artem K.; Winardhi, Ricksen S.; Yan, Jie


    Recent development of single-molecule manipulation technologies has made it possible to exert constant force and torque on individual DNA biopolymers to probe their elastic characteristics and structural stability. It has been previously shown that depending on the nature of applied mechanical constraints, DNA can exist in several forms including B-, L-, and P-DNA. However, there is still a lack of understanding of how structural heterogeneity of DNA, which may naturally arise due to sequence-dependent DNA properties, protein binding, or DNA damage, influences local stability of the above DNA states. To provide a more complete and detailed description of the DNA mechanics, we developed a theoretical framework based on transfer-matrix calculations and demonstrated how it can be used to predict the DNA behavior upon application of a wide range of force and torque constraints. The resulting phase diagram shows DNA structural transitions that are in good agreement with previous experimental and theoretical studies. We further discuss how the constructed formalism can be extended to include local inhomogeneities in the DNA physical properties, thus making it possible to investigate the effect of DNA sequence as well as protein binding on DNA structural stability.

  17. Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of wire model vs. extended ladder model

    CERN Document Server

    Lambropoulos, K; Morphis, A; Kaklamanis, K; Lopp, R; Theodorakou, M; Tassi, M; Simserides, C


    We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of $N$ monomers (base pairs): (I) at the base-pair level, using the on-site energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the on-site energies of the bases and the hopping integrals between neighboring bases, i.e., an \\textit{extended} ladder model since we also include diagonal hoppings. We solve a system of $MD$ ("matrix dimension") coupled equations [(I) $MD$ = $N$, (II) $MD$ = $2N$] for the time-independent problem, and a system of $MD$ coupled $1^\\text{st}$ order differential equations for the time-dependent problem. We study the HOMO and the LUMO eigenspectra, the occupation probabilities, the Density of States (DOS) and the HOMO-LUMO gap as well as the mean over time probabilities to find the carrier at each site [(I) base pair or (II) base)], the Four...

  18. Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling. (United States)

    Cui, Haosheng; Mim, Carsten; Vázquez, Francisco X; Lyman, Edward; Unger, Vinzenz M; Voth, Gregory A


    Endophilin N-BAR (N-terminal helix and Bin/amphiphysin/Rvs) domain tubulates and vesiculates lipid membranes in vitro via its crescent-shaped dimer and four amphipathic helices that penetrate into membranes as wedges. Like F-BAR domains, endophilin N-BAR also forms a scaffold on membrane tubes. Unlike F-BARs, endophilin N-BARs have N-terminal H0 amphipathic helices that are proposed to interact with other N-BARs in oligomer lattices. Recent cryo-electron microscopy reconstructions shed light on the organization of the N-BAR lattice coats on a nanometer scale. However, because of the resolution of the reconstructions, the precise positioning of the amphipathic helices is still ambiguous. In this work, we applied a coarse-grained model to study various membrane remodeling scenarios induced by endophilin N-BARs. We found that H0 helices of N-BARs prefer to align in an antiparallel manner at two ends of the protein to form a stable lattice. The deletion of H0 helices causes disruption of the lattice. In addition, we analyzed the persistence lengths of the protein-coated tubes and found that the stiffness of endophilin N-BAR-coated tubules qualitatively agrees with previous experimental work studying N-BAR-coated tubules. Large-scale simulations on membrane liposomes revealed a systematic relation between H0 helix density and local membrane curvature fluctuations. The data also suggest that the H0 helix is required for BARs to form organized structures on the liposome, further illustrating its important function.

  19. Electrophoretic mobility of semi-flexible double-stranded DNA in defect-controlled polymer networks: Mechanism investigation and role of structural parameters. (United States)

    Khairulina, Kateryna; Li, Xiang; Nishi, Kengo; Shibayama, Mitsuhiro; Chung, Ung-il; Sakai, Takamasa


    Our previous studies have reported an empirical model, which explains the electrophoretic mobility (μ) of double-stranded DNA (dsDNA) as a combination of a basic migration term (Rouse-like or reptation) and entropy loss term in polymer gels with ideal network structure. However, this case is of exception, considering a large amount of heterogeneity in the conventional polymer gels. In this study, we systematically tune the heterogeneity in the polymer gels and study the migration of dsDNA in these gels. Our experimental data well agree with the model found for ideal networks. The basic migration mechanism (Rouse-like or reptation) persists perfectly in the conventional heterogeneous polymer gel system, while the entropy loss term continuously changes with increase in the heterogeneity. Furthermore, we found that in the limit where dsDNA is shorter than dsDNA persistence length, the entropy loss term may be related to the collisional motions between DNA fragments and the cross-links.

  20. A highly parallel method for synthesizing DNA repeats enables the discovery of ‘smart’ protein polymers (United States)

    Amiram, Miriam; Quiroz, Felipe Garcia; Callahan, Daniel J.; Chilkoti, Ashutosh


    Robust high-throughput synthesis methods are needed to expand the repertoire of repetitive protein-polymers for different applications. To address this need, we developed a new method, overlap extension rolling circle amplification (OERCA), for the highly parallel synthesis of genes encoding repetitive protein-polymers. OERCA involves a single PCR-type reaction for the rolling circle amplification of a circular DNA template and simultaneous overlap extension by thermal cycling. We characterized the variables that control OERCA and demonstrated its superiority over existing methods, its robustness, high-throughput and versatility by synthesizing variants of elastin-like polypeptides (ELPs) and protease-responsive polymers of glucagon-like peptide-1 analogues. Despite the GC-rich, highly repetitive sequences of ELPs, we synthesized remarkably large genes without recursive ligation. OERCA also enabled us to discover ‘smart’ biopolymers that exhibit fully reversible thermally responsive behaviour. This powerful strategy generates libraries of repetitive genes over a wide and tunable range of molecular weights in a ‘one-pot’ parallel format.

  1. "Giant surfactants" created by the fast and efficient functionalization of a DNA tetrahedron with a temperature-responsive polymer. (United States)

    Wilks, Thomas R; Bath, Jonathan; de Vries, Jan Willem; Raymond, Jeffery E; Herrmann, Andreas; Turberfield, Andrew J; O'Reilly, Rachel K


    Copper catalyzed azide-alkyne cycloaddition (CuAAC) was employed to synthesize DNA block copolymers (DBCs) with a range of polymer blocks including temperature-responsive poly(N-isoproylacrylamide) (poly(NIPAM)) and highly hydrophobic poly(styrene). Exceptionally high yields were achieved at low DNA concentrations, in organic solvents, and in the absence of any solid support. The DNA segment of the DBC remained capable of sequence-specific hybridization: it was used to assemble a precisely defined nanostructure, a DNA tetrahedron, with pendant poly(NIPAM) segments. In the presence of an excess of poly(NIPAM) homopolymer, the tetrahedron-poly(NIPAM) conjugate nucleated the formation of large, well-defined nanoparticles at 40 °C, a temperature at which the homopolymer precipitated from solution. These composite nanoparticles were observed by dynamic light scattering and cryoTEM, and their hybrid nature was confirmed by AFM imaging. As a result of the large effective surface area of the tetrahedron, only very low concentrations of the conjugate were required in order for this surfactant-like behavior to be observed.

  2. Interaction of 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes

    Indian Academy of Sciences (India)

    Chandrasekaran Sivakamasundari; Ramakrishnan Nagaraj


    We investigated the interaction of six 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes. The net charge of the peptides at neutral pH varies from –1 to +6. Circular dichroism spectra indicate that peptides with a high net positive charge tend to fold into a helical conformation in the presence of negatively charged lipid vesicles. In helical conformation, their average hydrophobic moment and hydrophobicity would render them surface-active. The composition of amino acids on the polar face of the helix in the peptides is considerably different. The peptides show variations in their ability to permeabilise zwitterionic and anionic lipid vesicles. Whereas increased net positive charge favours greater permeabilisation, the distribution of charged residues in the polar face also plays a role in determining membrane activity. The distribution of amino acids in the polar face of the helix in the peptides that were investigated do not fall into the canonical classes described. Amphipathic helices, which are part of proteins, with a pattern of amino acid distribution different from those observed in class L, A and others, could help in providing newer insights into peptide–membrane interactions.

  3. Helix stabilization of amphipathic peptides by hydrocarbon stapling increases cholesterol efflux by the ABCA1 transporter. (United States)

    Sviridov, D O; Ikpot, I Z; Stonik, J; Drake, S K; Amar, M; Osei-Hwedieh, D O; Piszczek, G; Turner, S; Remaley, A T


    Apolipoprotein mimetic peptides are short amphipathic peptides that efflux cholesterol from cells by the ABCA1 transporter and are being investigated as therapeutic agents for cardiovascular disease. We examined the role of helix stabilization of these peptides in cholesterol efflux. A 23-amino acid long peptide (Ac-VLEDSFKVSFLSALEEYTKKLNTQ-NH2) based on the last helix of apoA-I (A10) was synthesized, as well as two variants, S1A10 and S2A10, in which the third and fourth and third and fifth turn of each peptide, respectively, were covalently joined by hydrocarbon staples. By CD spectroscopy, the stapled variants at 24 °C were more helical in aqueous buffer than A10 (A10 17%, S1A10 62%, S2A10 97%). S1A10 and S2A10 unlike A10 were resistant to proteolysis by pepsin and chymotrypsin. S1A10 and S2A10 showed more than a 10-fold increase in cholesterol efflux by the ABCA1 transporter compared to A10. In summary, hydrocarbon stapling of amphipathic peptides increases their helicity, makes them resistant to proteolysis and enhances their ability to promote cholesterol efflux by the ABCA1 transporter, indicating that this peptide modification may be useful in the development of apolipoprotein mimetic peptides.

  4. Luminescence quenching of Ru(phen)$^{2+}_{3}$ by some polymer-cobalt(III) complexes - Effect of micelles and DNA

    Indian Academy of Sciences (India)

    R Senthil Kumar; K Sasikala; S Arunachalam


    Studies on the luminescence quenching of Ru(phen)$^{2+}_{3}$ (phen = 1,10-phenanthroline) by the polymer-cobalt(III) complex ions, cis-[Co(phen)2(BPEI)Cl]2+ and cis-[Co(bpy)2(BPEI)Cl]2+ (bpy = 2,2'-bipyridine, BPEI = branched polyethyleneimine) in DNA as well as in various micellar media by steadystate emission spectroscopic technique have been reported. The quenching rate constants were arrived through Stern-Volmer equation. The results have been analysed based on hydrophobic as well as electrostatic binding between polymer-cobalt(III) complexes and DNA/micelles.

  5. Novel cyclen-based linear polymer as a high-affinity binding material for DNA condensation

    Institute of Scientific and Technical Information of China (English)


    A novel cyclen-based linear polyamine (POGEC) was designed and synthesized from the reaction between 1,3-propanediol diglycidyl ether and 1,7-bis(diethoxyphosphory)-1,4,7,10-tetraazacyclod-odecane. High-affinity binding between POGEC and DNA was demonstrated by agarose gel electrophoresis and scanning electron microscopy (SEM). Moreover,the formed POGEC/DNA complex (termed polyplex) could be disassociated to release the free DNA through addition of the physiological concentration of NaCl solution. Fluorescence spectrum was used to measure the high-affinity binding and DNA condensation capability of POGEC. Circular dichroism (CD) spectrum indicates that the DNA conformation did not change after binding to POEGC.

  6. Novel cyclen-based linear polymer as a high-affinity binding material for DNA condensation

    Institute of Scientific and Technical Information of China (English)

    XIANG YongZhe; WANG Na; ZHANG Ji; LI Kun; ZHANG ZhongWei; LIN HongHui; YU XiaoQi


    A novel cyclen-based linear polyamine (POGEC) was designed and synthesized from the reaction be-tween 1,3-propanediol diglycidyl ether and 1,7-bis(diethoxyphosphory)-1,4,7,10-tetraazacyclod- odecane.High-affinity binding between POGEC and DNA was demonstrated by agarose gel electrophoresis and scanning electron microscopy (SEM). Moreover, the formed POGEC/DNA complex (termed polyplex) could be disassociated to release the free DNA through addition of the physiological concentration of NaCl solution. Fluorescence spectrum was used to measure the high-affinity binding and DNA con-densation capability of POGEC. Circular dichroism (CD) spectrum indicates that the DNA conformation did not change after binding to POEGC.

  7. Light-Induced Local Heating for Thermophoretic Manipulation of DNA in Polymer Micro- and Nanochannels

    DEFF Research Database (Denmark)

    Thamdrup, Lasse Højlund; Larsen, Niels Bent; Kristensen, Anders


    We present a method for making polymer chips with a narrow-band near-infrared absorber layer that enables light-induced local heating of liquids inside fluidic micro- and nanochannels fabricated by thermal imprint in polymethyl methacrylate. We have characterized the resulting liquid temperature...

  8. Highly Sensitive Polymer-based Cantilever-sensors for DNA Detection

    DEFF Research Database (Denmark)

    Gomez, Montserrat; Nordström, Maria; Alvarez, M.


    We present a technology for the fabrication of cantilever arrays aimed to develop an integrated biosensor microsystem. The fabrication process is based on spin coating of the photosensitive polymer and near-ultraviolet exposure. Arrays of up to 33 microcantilevers are fabricated in the novel poly...

  9. Polymers & People (United States)

    Lentz, Linda; Robinson, Thomas; Martin, Elizabeth; Miller, Mary; Ashburn, Norma


    Each Tuesday during the fall of 2002, teams of high school students from three South Carolina counties conducted a four-hour polymer institute for their peers. In less than two months, over 300 students visited the Charleston County Public Library in Charleston, South Carolina, to explore DNA, nylon, rubber, gluep, and other polymers. Teams of…

  10. Amphipathic motifs in BAR domains are essential for membrane curvature sensing

    DEFF Research Database (Denmark)

    Bhatia, Vikram K; Madsen, Kenneth L; Bolinger, Pierre-Yves;


    nanosized liposomes of different diameters and therefore membrane curvature. Characterization of members of the three BAR domain families showed surprisingly that the crescent-shaped BAR dimer with its positively charged concave face is not able to sense membrane curvature. Mutagenesis on BAR domains showed...... that membrane curvature sensing critically depends on the N-terminal AH and furthermore that BAR domains sense membrane curvature through hydrophobic insertion in lipid packing defects and not through electrostatics. Consequently, amphipathic motifs, such as AHs, that are often associated with BAR domains...... emerge as an important means for a protein to sense membrane curvature. Measurements on single liposomes allowed us to document heterogeneous binding behaviour within the ensemble and quantify the influence of liposome polydispersity on bulk membrane curvature sensing experiments. The latter results...


    DEFF Research Database (Denmark)

    Zeng, Guanghong; Ogaki, Ryosuke; Regina, Viduthalai R.;

    Polymer brush coatings of poly(ethylene glycol) are considered the gold standard for nonfouling surfaces, but nevertheless, a few bacteria manage to attach and initiate biofilm formation on these coatings. To achieve robust resistance against bacterial adhesion and biofilm formation, grafting...... density plays a critical role and we therefore investigated the antifouling properties of the poly(L-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG) coating produced by the recently developed temperature-induced polyelectrolyte (TIP) grafting technique. The PLL-g-PEG coatings with higher density resulted...

  12. A New FRET-Based Sensitive DNA Sensor for Medical Diagnostics using PNA Probe and Water-Soluble Blue Light Emitting Polymer

    Directory of Open Access Journals (Sweden)

    Nidhi Mathur


    Full Text Available A reliable, fast, and low-cost biosensor for medical diagnostics using DNA sequence detection has been developed and tested for the detection of the bacterium “Bacillus anthracis.” In this sensor, Poly [9,9-di (6,6′- N, N′ trimethylammonium hexylfluorenyl-2, 7-diyl-alt-co- (1,4-phenylene] dibromide salt (PFP has been taken as cationic conjugated polymer (CCP and PNA attached with fluorescein dye (PNAC∗ as a probe. The basic principle of this sensor is that when a PNAC∗ probe is hybridized with a single strand DNA (ssDNA having complementary sequence, Forster resonance energy transfer (FRET may take place from PFP to the PNAC∗/DNA complex. If the FRET is efficient, the photoluminescence from the PFP will be highly quenched and that from PNAC∗ will be enhanced. On the other hand, if the DNA sequence is noncomplementary to PNA, FRET will not occur.

  13. Synthesis, characterisation and electrical properties of supramolecular DNA-templated polymer nanowires of 2,5-(bis-2-thienyl)-pyrrole. (United States)

    Watson, Scott M D; Hedley, Joseph H; Galindo, Miguel A; Al-Said, Said A F; Wright, Nick G; Connolly, Bernard A; Horrocks, Benjamin R; Houlton, Andrew


    Supramolecular polymer nanowires have been prepared by using DNA-templating of 2,5-(bis-2-thienyl)-pyrrole (TPT) by oxidation with FeCl(3) in a mixed aqueous/organic solvent system. Despite the reduced capacity for strong hydrogen bonding in polyTPT compared to other systems, such as polypyrrole, the templating proceeds well. FTIR spectroscopic studies confirm that the resulting material is not a simple mixture and that the two types of polymer interact. This is indicated by shifts in bands associated with both the phosphodiester backbone and the nucleobases. XPS studies further confirm the presence of DNA and TPT, as well as dopant Cl(-) ions. Molecular dynamics simulations on a [{dA(24):dT(24)}/{TPT}(4)] model support these findings and indicate a non-coplanar conformation for oligoTPT over much of the trajectory. AFM studies show that the resulting nanowires typically lie in the 7-8 nm diameter range and exhibit a smooth, continuous, morphology. Studies on the electrical properties of the prepared nanowires by using a combination of scanned conductance microscopy, conductive AFM and variable temperature two-terminal I-V measurements show, that in contrast to similar DNA/polymer systems, the conductivity is markedly reduced compared to bulk material. The temperature dependence of the conductivity shows a simple Arrhenius behaviour consistent with the hopping models developed for redox polymers.

  14. Using Temperature-Sensitive Smart Polymers to Regulate DNA-mediated Nanoassembly (United States)

    Hamner, Kristen L.

    Nanoparticle (NP) self-assembly has been proven as an effective route to organize nanoscale building blocks into ordered structures for potential technological applications. In order to successfully exploit the self-assembly processes a high level of direction and control is required. In my dissertation research, I synthesized a temperature responsive copolymer (p) to modify gold nanoparticles (AuNP) for controlling self-assembly. The copolymers' ability to regulate DNA-mediated NP self-assembly is a particular focus. In Chapter 2, the results show that by the addition of the p to create thermally responsive NP interfaces allows for controlled aggregation behavior and interparticle distances defined by the transition temperature (TC) of the p, to aid in NP assembly and help to regulate DNA-mediated interactions between NP. The work in Chapter 3 revealed that the reconfigurable conformation of the p sterically regulates the assembly: at T TC, assembly was observed, due the hydrophobic collapse of the p and the subsequent exposure of the complementary DNA bases. In Chapter 4, to gain insight into the mechanism, the rate of assembly was monitored, with DNA lengths that had hydrodynamic diameters more comparable to that of the p, and found the p was capable of slowing the kinetics. I further investigated to find that the addition of p extended the interparticle distances while disrupting the long range ordering. Finally, how the temperature responsive behavior of the p acted on the interparticle distances was probed, and it was found that without p, the interparticle distances expanded, while the addition of p compressed the interparticle distances.

  15. Free-solution electrophoretic separations of DNA-drag-tag conjugates on glass microchips with no polymer network and no loss of resolution at increased electric field strength. (United States)

    Albrecht, Jennifer Coyne; Kerby, Matthew B; Niedringhaus, Thomas P; Lin, Jennifer S; Wang, Xiaoxiao; Barron, Annelise E


    Here, we demonstrate the potential for high-resolution electrophoretic separations of ssDNA-protein conjugates in borosilicate glass microfluidic chips, with no sieving media and excellent repeatability. Using polynucleotides of two different lengths conjugated to moderately cationic protein polymer drag-tags, we measured separation efficiency as a function of applied electric field. In excellent agreement with prior theoretical predictions of Slater et al., resolution is found to remain constant as applied field is increased up to 700 V/cm, the highest field we were able to apply. This remarkable result illustrates the fundamentally different physical limitations of free-solution conjugate electrophoresis (FSCE)-based DNA separations relative to matrix-based DNA electrophoresis. ssDNA separations in "gels" have always shown rapidly declining resolution as the field strength is increased; this is especially true for ssDNA > 400 bases in length. FSCE's ability to decouple DNA peak resolution from applied electric field suggests the future possibility of ultra-rapid FSCE sequencing on chips. We investigated sources of peak broadening for FSCE separations on borosilicate glass microchips, using six different protein polymer drag-tags. For drag-tags with four or more positive charges, electrostatic and adsorptive interactions with poly(N-hydroxyethylacrylamide)-coated microchannel walls led to appreciable band-broadening, while much sharper peaks were seen for bioconjugates with nearly charge-neutral protein drag-tags.

  16. Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of a wire model versus an extended ladder model (United States)

    Lambropoulos, K.; Chatzieleftheriou, M.; Morphis, A.; Kaklamanis, K.; Lopp, R.; Theodorakou, M.; Tassi, M.; Simserides, C.


    We employ two tight-binding (TB) approaches to systematically study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of N monomers (base pairs): (I) at the base-pair level, using the onsite energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the onsite energies of the bases and the hopping integrals between neighboring bases, i.e., an extended ladder model since we also include diagonal hoppings. We solve a system of M (matrix dimension) coupled equations [(I) M =N , (II) M =2 N ] for the time-independent problem, and a system of M coupled first order differential equations for the time-dependent problem. We perform a comparative study of stationary and time-dependent aspects of the two TB variants, using realistic sets of parameters. The studied properties include HOMO and LUMO eigenspectra, occupation probabilities, density of states and HOMO-LUMO gaps as well as mean over time probabilities to find the carrier at each site [(I) base pair or (II) base], Fourier spectra, which reflect the frequency content of charge transfer, and pure mean transfer rates from a certain site to another. The two TB approaches give coherent, complementary aspects of electronic properties and charge transfer in B-DNA monomer polymers and dimer polymers.

  17. The high resolution structure of tyrocidine A reveals an amphipathic dimer. (United States)

    Loll, Patrick J; Upton, Elizabeth C; Nahoum, Virginie; Economou, Nicoleta J; Cocklin, Simon


    Tyrocidine A, one of the first antibiotics ever to be discovered, is a cyclic decapeptide that binds to membranes of target bacteria, disrupting their integrity. It is active against a broad spectrum of Gram-positive organisms, and has recently engendered interest as a potential scaffold for the development of new drugs to combat antibiotic-resistant pathogens. We present here the X-ray crystal structure of tyrocidine A at a resolution of 0.95Å. The structure reveals that tyrocidine forms an intimate and highly amphipathic homodimer made up of four beta strands that associate into a single, highly curved antiparallel beta sheet. We used surface plasmon resonance and potassium efflux assays to demonstrate that tyrocidine binds tightly to mimetics of bacterial membranes with an apparent dissociation constant (K(D)) of 10 μM, and efficiently permeabilizes bacterial cells at concentrations equal to and below the K(D). Using variant forms of tyrocidine in which the fluorescent probe p-cyano-phenylalanine had been inserted on either the polar or apolar face of the molecule, we performed fluorescence quenching experiments, using both water-soluble and membrane-embedded quenchers. The quenching results, together with the structure, strongly support a membrane association model in which the convex, apolar face of tyrocidine's beta sheet is oriented toward the membrane interior, while the concave, polar face is presented to the aqueous phase.

  18. Amphipathic antenna of an inward rectifier K+ channel responds to changes in the inner membrane leaflet. (United States)

    Iwamoto, Masayuki; Oiki, Shigetoshi


    Membrane lipids modulate the function of membrane proteins. In the case of ion channels, they bias the gating equilibrium, although the underlying mechanism has remained elusive. Here we demonstrate that the N-terminal segment (M0) of the KcsA potassium channel mediates the effect of changes in the lipid milieu on channel gating. The M0 segment is a membrane-anchored amphipathic helix, bearing positively charged residues. In asymmetric membranes, the M0 helix senses the presence of negatively charged phospholipids on the inner leaflet. Upon gating, the M0 helix revolves around the axis of the helix on the membrane surface, inducing the positively charged residues to interact with the negative head groups of the lipids so as to stabilize the open conformation (i.e., the "roll-and-stabilize model"). The M0 helix is thus a charge-sensitive "antenna," capturing temporary changes in lipid composition in the fluidic membrane. This unique type of sensory device may be shared by various types of membrane proteins.

  19. Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds. (United States)

    Navarri, Marion; Jégou, Camille; Meslet-Cladière, Laurence; Brillet, Benjamin; Barbier, Georges; Burgaud, Gaëtan; Fleury, Yannick


    The evolving global threat of antimicrobial resistance requires a deep renewal of the antibiotic arsenal including the isolation and characterization of new drugs. Underexplored marine ecosystems may represent an untapped reservoir of novel bioactive molecules. Deep-sea fungi isolated from a record-depth sediment core of almost 2000 m below the seafloor were investigated for antimicrobial activities. This antimicrobial screening, using 16 microbial targets, revealed 33% of filamentous fungi synthesizing bioactive compounds with activities against pathogenic bacteria and fungi. Interestingly, occurrence of antimicrobial producing isolates was well correlated with the complexity of the habitat (in term of microbial richness), as higher antimicrobial activities were obtained at specific layers of the sediment core. It clearly highlights complex deep-sea habitats as chemical battlefields where synthesis of numerous bioactive compounds appears critical for microbial competition. The six most promising deep subseafloor fungal isolates were selected for the production and extraction of bioactive compounds. Depending on the fungal isolates, antimicrobial compounds were only biosynthesized in semi-liquid or solid-state conditions as no antimicrobial activities were ever detected using liquid fermentation. An exception was made for one fungal isolate, and the extraction procedure designed to extract amphipathic compounds was successful and highlighted the amphiphilic profile of the bioactive metabolites.

  20. Optimization of simultaneous saccharification and fermentation conditions with amphipathic lignin derivatives for concentrated bioethanol production. (United States)

    Cheng, Ningning; Koda, Keiichi; Tamai, Yutaka; Yamamoto, Yoko; Takasuka, Taichi E; Uraki, Yasumitsu


    Amphipathic lignin derivatives (A-LDs) prepared from the black liquor of soda pulping of Japanese cedar are strong accelerators for bioethanol production under a fed-batch simultaneous enzymatic saccharification and fermentation (SSF) process. To improve the bioethanol production concentration, conditions such as reaction temperature, stirring program, and A-LDs loadings were optimized in both small scale and large scale fed-batch SSF. The fed-batch SSF in the presence of 3.0g/L A-LDs at 38°C gave the maximum ethanol production and a high enzyme recovery rate. Furthermore, a jar-fermenter equipped with a powerful mechanical stirrer was designed for 1.5L-scale fed-batch SSF to achieve rigorous mixing during high substrate loading. Finally, the 1.5L fed-batch SSF with a substrate loading of 30% (w/v) produced a high ethanol concentration of 87.9g/L in the presence of A-LDs under optimized conditions.

  1. Does DNA Exert an Active Role in Generating Cell-Sized Spheres in an Aqueous Solution with a Crowding Binary Polymer?

    Directory of Open Access Journals (Sweden)

    Kanta Tsumoto


    Full Text Available We report the spontaneous generation of a cell-like morphology in an environment crowded with the polymers dextran and polyethylene glycol (PEG in the presence of DNA. DNA molecules were selectively located in the interior of dextran-rich micro-droplets, when the composition of an aqueous two-phase system (ATPS was near the critical condition of phase-segregation. The resulting micro-droplets could be controlled by the use of optical tweezers. As an example of laser manipulation, the dynamic fusion of two droplets is reported, which resembles the process of cell division in time-reverse. A hypothetical scenario for the emergence of a primitive cell with DNA is briefly discussed.

  2. Does DNA exert an active role in generating cell-sized spheres in an aqueous solution with a crowding binary polymer? (United States)

    Tsumoto, Kanta; Arai, Masafumi; Nakatani, Naoki; Watanabe, Shun N; Yoshikawa, Kenichi


    We report the spontaneous generation of a cell-like morphology in an environment crowded with the polymers dextran and polyethylene glycol (PEG) in the presence of DNA. DNA molecules were selectively located in the interior of dextran-rich micro-droplets, when the composition of an aqueous two-phase system (ATPS) was near the critical condition of phase-segregation. The resulting micro-droplets could be controlled by the use of optical tweezers. As an example of laser manipulation, the dynamic fusion of two droplets is reported, which resembles the process of cell division in time-reverse. A hypothetical scenario for the emergence of a primitive cell with DNA is briefly discussed.

  3. Intranasal administration of HIV-DNA vaccine formulated with a polymer, carboxymethylcellulose, augments mucosal antibody production and cell-mediated immune response. (United States)

    Hamajima, K; Sasaki, S; Fukushima, J; Kaneko, T; Xin, K Q; Kudoh, I; Okuda, K


    We previously reported that intramuscular (i.m.) immunization of DNA vaccine encoding human immunodeficiency virus type 1 (HIV-1)IIIB env and rev genes alone or in combination with appropriate adjuvant induces substantial and enhanced immune response against HIV-1. In the present study, we examined whether a polymer, low-viscosity carboxymethylcellulose sodium salt (CMCS-L), has an adjuvant effect on immune response induced by DNA vaccination. BALB/c mice were immunized with HIV-DNA vaccine formulated with CMCS-L via the intranasal (i.n.) and i.m. routes. The combination with the polymer elicited higher levels of antigen-specific serum IgG and fecal IgA antibodies than DNA vaccine alone. For cell-mediated immunity, HIV-specific delayed-type hypersensitivity response and cytotoxic T lymphocyte activity were measured by the footpad-swelling test and the 51Cr-release assay, respectively. Both were enhanced by the combination with CMCS-L via i.n. and i.m. inoculation. Cytokine analysis in culture media of bulk splenocytes harvested from immunized animals showed higher levels of IL-4 production in i.n. -immunized mice compared with i.m.-immunized mice. Nevertheless, the increased IFN-gamma production resulting from the combination with CMCS-L was observed only in i.n.-immunized mice. These data indicate that i.n. immunization of HIV-DNA vaccine formulated with CMCS-L enhances HIV-specific mucosal antibody (Ab) and systemic Ab and cell-mediated immune response.

  4. Co-Delivery of Imiquimod and Plasmid DNA via an Amphiphilic pH-Responsive Star Polymer that Forms Unimolecular Micelles in Water

    Directory of Open Access Journals (Sweden)

    Wenjing Lin


    Full Text Available Dual functional unimolecular micelles based on a pH-responsive amphiphilic star polymer β-CD-(PLA-b-PDMAEMA-b-PEtOxMA21 have been developed for the co-delivery of imiquimod and plasmid DNA to dendritic cells. The star polymer with well-defined triblock arms was synthesized by combining activator regenerated by electron-transfer atom-transfer radical polymerization with ring-opening polymerization. Dissipative particle dynamics simulation showed that core-mesophere-shell-type unimolecular micelles could be formed. Imiquimod-loaded micelles had a drug loading of 1.6 wt % and a larger average size (28 nm than blank micelles (19 nm. The release of imiquimod in vitro was accelerated at the mildly acidic endolysosomal pH (5.0 in comparison to physiologic pH (7.4. Compared with blank micelles, a higher N:P ratio was required for imiquimod-loaded micelles to fully condense DNA into micelleplexes averaging 200–400 nm in size. In comparison to blank micelleplexes, imiquimod-loaded micelleplexes of the same N:P ratio displayed similar or slightly higher efficiency of gene transfection in a mouse dendritic cell line (DC2.4 without cytotoxicity. These results suggest that such pH-responsive unimolecular micelles formed by the well-defined amphiphilic star polymer may serve as promising nano-scale carriers for combined delivery of hydrophobic immunostimulatory drugs (such as imiquimod and plasmid DNA with potential application in gene-based immunotherapy.

  5. The application of polymer-mediated plasmid DNA transit systems in bone tissue engineering%聚合物介导质粒DNA转运系统在骨组织工程中的应用

    Institute of Scientific and Technical Information of China (English)

    夏伦果; 蒋欣泉; 张志愿


    Gene therapy can further promote osteogenesis in bone tissue engineering. By protecting DNA from degradation and maintaining the concentration of DNA effectively, polymer-mediated plasmid DNA transit systems could extend its endocytosis opportunities and enhance the efficiency of gene transfer. At present, polymer-mediated plasmid DNA transit systems used for bone tissue engineering mainly include plasmid DNA and collagen protein composite transit system, plasmid DNA and polyethylene glycol hyaluronic acid hydroge composite transit system, plasmid DNA and liposome composite transit system, plasmid DNA and cationic polymer composite transit systems. This review focuses on the present status of application of polymer-mediated plasmid DNA transit systems.%基因治疗技术应用于骨组织工程,可以进一步促进成骨.聚合物介导的质粒DNA转运系统通过保护DNA免受降解并维持DNA在效应浓度,延长其内吞的机会,从而提高基因转染效率.目前用于骨组织工程研究的聚合物介导的质粒DNA转运系统主要有质粒DNA与胶原蛋白复合转运系统、质粒DNA与聚乙二醇-透明质酸水凝胶复合转运系统、质粒DNA与脂质体复合转运系统、质粒DNA与阳离子聚合物复合转运系统等.本文对近年来聚合物介导的质粒DNA复合转运系统在骨组织工程中的应用进展做一综述.

  6. Loop VIII/IX of the Na+-citrate transporter CitS of Klebsiella pneumoniae folds into an amphipathic surface helix

    NARCIS (Netherlands)

    Sobczak, [No Value; Lolkema, JS; Sobczak, Iwona


    The sodium ion-dependent citrate transporter CitS of Klebsiella pneumoniae is a member of, the 2-hydroxycarboxylate transporter (2HCT) family whose members transport divalent citrate in symport with two sodium ions. Profiles of the hydrophobic moment suggested the presence of an amphipathic helical

  7. A unifying mechanism accounts for sensing of membrane curvature by BAR domains, amphipathic helices and membrane-anchored proteins

    DEFF Research Database (Denmark)

    Bhatia, Vikram Kjøller; Hatzakis, Nikos; Stamou, Dimitrios


    unrelated motifs: BAR domains, amphipathic helices and membrane-anchored proteins. We discuss the conclusion that the curvature of the BAR dimer is not responsible for sensing and that the sensing properties of all three motifs can be rationalized by the physicochemical properties of the curved membrane......The discovery of proteins that recognize membrane curvature created a paradigm shift by suggesting that membrane shape may act as a cue for protein localization that is independent of lipid or protein composition. Here we review recent data on membrane curvature sensing by three structurally...... itself. We thus anticipate that membrane curvature will promote the redistribution of proteins that are anchored in membranes through any type of hydrophobic moiety, a thesis that broadens tremendously the implications of membrane curvature for protein sorting, trafficking and signaling in cell biology....

  8. Structural determinants of salmon calcitonin bioactivity: the role of the Leu-based amphipathic alpha-helix. (United States)

    Andreotti, Giuseppina; Méndez, Blanca López; Amodeo, Pietro; Morelli, Maria A Castiglione; Nakamuta, Hiromichi; Motta, Andrea


    Salmon calcitonin (sCT) forms an amphipathic helix in the region 9-19, with the C-terminal decapeptide interacting with the helix (Amodeo, P., Motta, A., Strazzullo, G., Castiglione Morelli, M. A. (1999) J. Biomol. NMR 13, 161-174). To uncover the structural requirements for the hormone bioactivity, we investigated several sCT analogs. They were designed so as to alter the length of the central helix by removal and/or replacement of flanking residues and by selectively mutating or deleting residues inside the helix. The helix content was assessed by circular dichroism and NMR spectroscopies; the receptor binding affinity in human breast cancer cell line T 47D and the in vivo hypocalcemic activity were also evaluated. In particular, by NMR spectroscopy and molecular dynamics calculations we studied Leu(23),Ala(24)-sCT in which Pro(23) and Arg(24) were replaced by helix inducing residues. Compared with sCT, it assumes a longer amphipathic alpha-helix, with decreased binding affinity and one-fifth of the hypocalcemic activity, therefore supporting the idea of a relationship between a definite helix length and bioactivity. From the analysis of other sCT mutants, we inferred that the correct helix length is located in the 9-19 region and requires long range interactions and the presence of specific regions of residues within the sequence for high binding affinity and hypocalcemic activity. Taken together, the structural and biological data identify well defined structural parameters of the helix for sCT bioactivity.

  9. Immobilization and hybridization of DNA based on magnesium ion modified 2,6-pyridinedicarboxylic acid polymer and its application for label-free PAT gene fragment detection by electrochemical impedance spectroscopy

    Institute of Scientific and Technical Information of China (English)

    JIAO Kui; YANG Tao; YANG Jie; FENG YuanYuan


    A new approach for a simple electrochemical detection of PAT gene fragment is described. Poly(2,6-pyridinedicarboxylic acid) (PDC) modified glassy carbon electrode (GCE) was prepared by potential scan electropolymerization in an aqueous solution. Mg2+ ions were incorporated by immersion of the modified electrode in 0.5 mol/L aqueous solution of MgCl2 to complete the preparation of a generic "activated" electrode ready for binding the probe DNA. The ssDNA was linked to the conducting polymer by forming a bidentate complex between the carboxyl groups on the polymer and the phosphate groups of DNA via Mg2+. DNA immobilization and hybridization were characterized with differential pulse voltammetry (DPV) by using methylene blue (MB) as indicator and electrochemical impedance spectroscopy (EIS). The EIS was of higher sensitivity for DNA detection as compared with voltammetric methods in our strategy. The electron transfer resistance (Ret) of the electrode surface in EIS in [Fe(CN)6]3-/4- solution increased after the immobilization of the DNA probe on the Mg/PDC/GCE electrode. The hybridization of the DNA probe with complementary DNA (cDNA) made Ret increase further. The difference between the Ret at ssDNA/Mg/PDC/GCE and that at hybridization DNA modified electrode (dsDNA/Mg/PDC/GCE) was applied to determine the specific sequence related to the target PAT gene with the dynamic range comprised between 1.0×10-9 and 1.0×10-5 mol/L. A detection limit of 3.4×10-10 mol/L of oligonucleotides can be estimated.

  10. Fish DNA-modified clays: Towards highly flame retardant polymer nanocomposite with improved interfacial and mechanical performance (United States)

    Zabihi, Omid; Ahmadi, Mojtaba; Khayyam, Hamid; Naebe, Minoo


    Deoxyribonucleic Acid (DNA) has been recently found to be an efficient renewable and environmentally-friendly flame retardant. In this work, for the first time, we have used waste DNA from fishing industry to modify clay structure in order to increase the clay interactions with epoxy resin and take benefit of its additional thermal property effect on thermo-physical properties of epoxy-clay nanocomposites. Intercalation of DNA within the clay layers was accomplished in a one-step approach confirmed by FT-IR, XPS, TGA, and XRD analyses, indicating that d-space of clay layers was expanded from ~1.2 nm for pristine clay to ~1.9 nm for clay modified with DNA (d-clay). Compared to epoxy nanocomposite containing 2.5%wt of Nanomer I.28E organoclay (m-clay), it was found that at 2.5%wt d-clay loading, significant enhancements of ~14%, ~6% and ~26% in tensile strength, tensile modulus, and fracture toughness of epoxy nanocomposite can be achieved, respectively. Effect of DNA as clay modifier on thermal performance of epoxy nanocomposite containing 2.5%wt d-clay was evaluated using TGA and cone calorimetry analysis, revealing significant decreases of ~4000 kJ/m2 and ~78 kW/m2 in total heat release and peak of heat release rate, respectively, in comparison to that containing 2.5%wt of m-clay.

  11. Immobilization and hybridization of DNA based on magnesium ion modified 2,6-pyridinedicarboxylic acid polymer and its application for label-free PAT gene fragment detection by electrochemical impedance spectroscopy

    Institute of Scientific and Technical Information of China (English)


    A new approach for a simple electrochemical detection of PAT gene fragment is described. Poly(2,6-pyridinedicarboxylic acid) (PDC) modified glassy carbon electrode (GCE) was prepared by potential scan electropolymerization in an aqueous solution. Mg2+ ions were incorporated by immer-sion of the modified electrode in 0.5 mol/L aqueous solution of MgCl2 to complete the preparation of a generic "activated" electrode ready for binding the probe DNA. The ssDNA was linked to the conduct-ing polymer by forming a bidentate complex between the carboxyl groups on the polymer and the phosphate groups of DNA via Mg2+. DNA immobilization and hybridization were characterized with dif-ferential pulse voltammetry (DPV) by using methylene blue (MB) as indicator and electrochemical im-pedance spectroscopy (EIS). The EIS was of higher sensitivity for DNA detection as compared with voltammetric methods in our strategy. The electron transfer resistance (Ret) of the electrode surface in EIS in [Fe(CN)6]3-/4- solution increased after the immobilization of the DNA probe on the Mg/PDC/GCE electrode. The hybridization of the DNA probe with complementary DNA (cDNA) made Ret increase further. The difference between the Ret at ssDNA/Mg/PDC/GCE and that at hybridization DNA modified electrode (dsDNA/Mg/PDC/GCE) was applied to determine the specific sequence related to the target PAT gene with the dynamic range comprised between 1.0 × 10-9 and 1.0 × 105 mol/L. A detection limit of 3.4 × 10-10 mol/L of oligonucleotides can be estimated.

  12. Differential neuroprotective potential of CRMP2 peptide aptamers conjugated to cationic, hydrophobic, and amphipathic cell penetrating peptides

    Directory of Open Access Journals (Sweden)

    Aubin eMoutal


    Full Text Available The microtubule-associated axonal specification collapsin response mediator protein 2 (CRMP2 is a novel target for neuroprotection. A CRMP2 peptide (TAT-CBD3 conjugated to the HIV transactivator of transcription (TAT protein’s cationic cell penetrating peptide motif (CPP protected neurons in the face of toxic levels of Ca2+ influx leaked in via N-methyl-D-aspartate receptor (NMDAR hyperactivation. Here we tested whether replacing the hydrophilic TAT motif with alternative cationic (nona-arginine (R9, hydrophobic (membrane transport sequence (MTS of k-fibroblast growth factor or amphipathic (model amphipathic peptide (MAP CPPs could be superior to the neuroprotection bestowed by TAT-CBD3. In giant plasma membrane vesicles (GPMVs derived from cortical neurons, the peptides translocated across plasma membranes with similar efficiencies. Cortical neurons, acutely treated with peptides prior to a toxic glutamate challenge, demonstrated enhanced efflux of R9-CBD3 compared to others. R9-CBD3 inhibited N-methyl-D-aspartate (NMDA-evoked Ca2+ influx to a similar extent as TAT-CBD3 while MTS-CBD3 was ineffective which correlated with the ability of R9- and TAT-CBD3, but not MTS-CBD3, to block NMDAR interaction with CRMP2. Unrestricted Ca2+ influx through NMDARs leading to delayed calcium dysregulation and neuronal cell death was blocked by all peptides but MAP-CBD3. When applied acutely for 10 minutes, R9-CBD3 was more effective than TAT-CBD3 at neuroprotection while MTS- and MAP-CBD3 were ineffective. In contrast, long-term (> 24 hours treatment with MTS-CBD3 conferred neuroprotection where TAT-CBD3 failed. Neither peptide altered surface trafficking of NMDARs. Neuroprotection conferred by MTS-CBD3 peptide is likely due to its increased uptake coupled with decreased efflux when compared to TAT-CBD3. Overall, our results demonstrate that altering CPPs can bestow differential neuroprotective potential onto the CBD3 cargo.

  13. An amphipathic alpha-helix in the prodomain of cocaine and amphetamine regulated transcript peptide precursor serves as its sorting signal to the regulated secretory pathway.

    Directory of Open Access Journals (Sweden)

    Elías H Blanco

    Full Text Available Cocaine and Amphetamine Regulated Transcript (CART peptides are anorexigenic neuropeptides. The L34F mutation in human CART peptide precursor (proCART has been linked to obesity (Yanik et al. Endocrinology 147: 39, 2006. Decrease in CART peptide levels in individuals carrying the L34F mutation was attributed to proCART subcellular missorting. We studied proCART features required to enter the regulated secretory pathway. The subcellular localization and the secretion mode of monomeric EGFP fused to the full-length or truncated forms of human proCART transiently transfected in PC12 cells were analyzed. Our results showed that the N-terminal 1-41 fragment of proCART was necessary and sufficient to sort proCART to the regulated secretory pathway. In silico modeling predicted an alpha-helix structure located between residues 24-37 of proCART. Helical wheel projection of proCART alpha-helix showed an amphipathic configuration. The L34F mutation does not modify the amphipathicity of proCART alpha-helix and consistently proCARTL34F was efficiently sorted to the regulated secretory pathway. However, four additional mutations to proCARTL34F that reduced its alpha-helix amphipathicity resulted in the missorting of the mutated proCART toward the constitutive secretory pathway. These findings show that an amphipathic alpha-helix is a key cis-structure for the proCART sorting mechanism. In addition, our results indicate that the association between L34F mutation and obesity is not explained by proCART missorting.

  14. Oxyopinins, large amphipathic peptides isolated from the venom of the wolf spider Oxyopes kitabensis with cytolytic properties and positive insecticidal cooperativity with spider neurotoxins. (United States)

    Corzo, Gerardo; Villegas, Elba; Gómez-Lagunas, Froylan; Possani, Lourival D; Belokoneva, Olga S; Nakajima, Terumi


    Five amphipathic peptides with antimicrobial, hemolytic, and insecticidal activity were isolated from the crude venom of the wolf spider Oxyopes kitabensis. The peptides, named oxyopinins, are the largest linear cationic amphipathic peptides from the venom of a spider that have been chemically characterized at present. According to their primary structure Oxyopinin 1 is composed of 48 amino acid residues showing extended sequence similarity to the ant insecticidal peptide ponericinL2 and to the frog antimicrobial peptide dermaseptin. Oxyopinins 2a, 2b, 2c, and 2d have highly similar sequences. At least 27 out of 37 amino acid residues are conserved. They also show a segment of sequence similar to ponericinL2. Circular dichroism analyses showed that the secondary structure of the five peptides is essentially alpha-helical. Oxyopinins showed disrupting activities toward both biological membranes and artificial vesicles, particularly to those rich in phosphatidylcholine. Electrophysiological recordings performed on insect cells (Sf9) showed that the oxyopinins produce a drastic reduction of cell membrane resistance by opening non-selective ion channels. Additionally, a new paralytic neurotoxin named Oxytoxin 1 was purified from the same spider venom. It contains 69 amino acid residue cross-linked by five disulfide bridges. Application of mixtures containing oxyopinins and Oxytoxin 1 to insect larvae showed a potentiation phenomenon, by which an increase lethality effect is observed. These results suggest that the linear amphipathic peptides in spider venoms and neuropeptides cooperate to capture insects efficiently.

  15. Polymer films (United States)

    Granick, Steve; Sukhishvili, Svetlana A.


    A film contains a first polymer having a plurality of hydrogen bond donating moieties, and a second polymer having a plurality of hydrogen bond accepting moieties. The second polymer is hydrogen bonded to the first polymer.

  16. A polymer, random walk model for the size-distribution of large DNA fragments after high linear energy transfer radiation (United States)

    Ponomarev, A. L.; Brenner, D.; Hlatky, L. R.; Sachs, R. K.


    DNA double-strand breaks (DSBs) produced by densely ionizing radiation are not located randomly in the genome: recent data indicate DSB clustering along chromosomes. Stochastic DSB clustering at large scales, from > 100 Mbp down to energy transfer (LET) radiation, are obtained. They are found to be non-linear when the dose becomes so large that there is a significant probability of overlapping or close juxtaposition, along one chromosome, for different DSB clusters from different tracks. The non-linearity is more evident for large fragments than for small. The DNAbreak results furnish an example of the RLC (randomly located clusters) analytic formalism, which generalizes the broken-stick fragment-size distribution of the random-breakage model that is often applied to low-LET data.

  17. Amphipathic alpha-helices and putative cholesterol binding domains of the influenza virus matrix M1 protein are crucial for virion structure organisation. (United States)

    Tsfasman, Tatyana; Kost, Vladimir; Markushin, Stanislav; Lotte, Vera; Koptiaeva, Irina; Bogacheva, Elena; Baratova, Ludmila; Radyukhin, Victor


    The influenza virus matrix M1 protein is an amphitropic membrane-associated protein, forming the matrix layer immediately beneath the virus raft membrane, thereby ensuring the proper structure of the influenza virion. The objective of this study was to elucidate M1 fine structural characteristics, which determine amphitropic properties and raft membrane activities of the protein, via 3D in silico modelling with subsequent mutational analysis. Computer simulations suggest the amphipathic nature of the M1 α-helices and the existence of putative cholesterol binding (CRAC) motifs on six amphipathic α-helices. Our finding explains for the first time many features of this protein, particularly the amphitropic properties and raft/cholesterol binding potential. To verify these results, we generated mutants of the A/WSN/33 strain via reverse genetics. The M1 mutations included F32Y in the CRAC of α-helix 2, W45Y and W45F in the CRAC of α-helix 3, Y100S in the CRAC of α-helix 6, M128A and M128S in the CRAC of α-helix 8 and a double L103I/L130I mutation in both a putative cholesterol consensus motif and the nuclear localisation signal. All mutations resulted in viruses with unusual filamentous morphology. Previous experimental data regarding the morphology of M1-gene mutant influenza viruses can now be explained in structural terms and are consistent with the pivotal role of the CRAC-domains and amphipathic α-helices in M1-lipid interactions.

  18. Basic amphipathic model peptides: Structural investigations in solution, studied by circular dichroism, fluorescence, analytical ultracentrifugation and molecular modelling (United States)

    Mangavel, C.; Sy, D.; Reynaud, J. A.


    A twenty amino acid residue long amphipathic peptide made of ten leucine and ten lysine residues and four derivatives, in which a tryptophan, as a fluorescent probe, is substituted for a leucine, are studied. The peptides in water are mainly in an unordered conformation (~90%), and undergo a two state reversible transition upon heating, leading to a partially helical conformation (cold denaturation). Time resolved fluorescence results show that fluorescence decay for the four Trp containing peptides is best described by triple fluorescence decay kinetics. In TFE/water mixture, peptides adopt a single α-helix conformation but the Leu-Trp9 substitution leads to an effective helix destabilizing effect. In salted media, the peptides are fully helical and present a great tendency to self associate by bringing the hydrophobic faces of helices into close contact. This proceeds in non-cooperative multisteps leading to the formation of α helix aggregates with various degrees of complexation. Using modelling, the relative hydrophobic surface areas accessible to water molecules in n-mer structures are calculated and discussed. Nous avons étudié un peptide amphipathique composé de dix lysine et dix leucine, ainsi que quatre dérivés comportant un résidu tryptophane pour les études par fluorescence. Dans l'eau, les peptides ne sont pas structurés (~90%), et se structurent partiellement en hélice α par chauffage (dénaturation froide). Les mesures de déclin de fluorescence font apparaître une cinétique à trois temps de vie. Dans un mélange eau/TFE, les peptides adoptent une conformation en hélice α, mais la substitution Leu-Trp9 possède un effet déstabilisant. En mileu salin, les peptides sont totalement hélicoïdaux et ont tendance à s'agréger de façon à regrouper leur face hydrophobe. Ce processus se fait en plusieurs étapes avec des agrégats de taille variable. L'existence de tels agrégats est discutée sur la base de la modélisation mol

  19. Polymer fractionation

    Energy Technology Data Exchange (ETDEWEB)

    Hadermann, A. F.


    Soluble polymers are fractionated according to molecular weight by cryogenically comminuting the polymer and introducing the polymer particles, while still in the active state induced by cryogenic grinding, into a liquid having a solvent power selected to produce a coacervate fraction containing high molecular weight polymer species and a dilute polymer solution containing lower molecular weight polymer species. The coacervate may be physically separated from the solution and finds use in the production of antimisting jet fuels and the like.

  20. Intracellular segment between transmembrane helices S0 and S1 of BK channel α subunit contains two amphipathic helices connected by a flexible loop. (United States)

    Shi, Pan; Li, Dong; Lai, Chaohua; Zhang, Longhua; Tian, Changlin


    The BK channel, a tetrameric potassium channel with very high conductance, has a central role in numerous physiological functions. The BK channel can be activated by intracellular Ca(2+) and Mg(2+), as well as by membrane depolarization. Unlike other tetrameric potassium channels, the BK channel has seven transmembrane helices (S0-S6) including an extra helix S0. The intracellular segment between S0 and S1 (BK-IS1) is essential to BK channel functions and Asp99 in BK-IS1 is reported to be responsible for Mg(2+) coordination. In this study, BK-IS1 (44-113) was over-expressed using a bacterial system and purified in the presence of detergent micelles for multidimensional heteronuclear nuclear magnetic resonance (NMR) structural studies. Backbone resonance assignment and secondary structure analysis showed that BK-IS1 contains two amphipathic helices connected by a 36-residue loop. Amide (1)H-(15)N heteronuclear NOE analysis indicated that the loop is very flexible, while the two amphipathic helices are possibly stabilized through interaction with the membrane. A solution NMR-based titration assay of BK-IS1 was performed with various concentrations of Mg(2+). Two residues (Thr45 and Leu46) with chemical shift changes were observed but no, or very minor, chemical shift difference was observed for Asp99, indicating a possible site for binding divalent ions or other modulation partners.

  1. Synthesis and properties of amphipathic polymers (MCPP- g - PEG)%氯化聚丙烯接枝聚乙二醇的合成与性能

    Institute of Scientific and Technical Information of China (English)

    童身毅; 万敏; 张良均



  2. Biodegradable Polymers

    Directory of Open Access Journals (Sweden)

    Isabelle Vroman


    Full Text Available Biodegradable materials are used in packaging, agriculture, medicine and other areas. In recent years there has been an increase in interest in biodegradable polymers. Two classes of biodegradable polymers can be distinguished: synthetic or natural polymers. There are polymers produced from feedstocks derived either from petroleum resources (non renewable resources or from biological resources (renewable resources. In general natural polymers offer fewer advantages than synthetic polymers. The following review presents an overview of the different biodegradable polymers that are currently being used and their properties, as well as new developments in their synthesis and applications.

  3. Polymer electronics

    CERN Document Server

    Hsin-Fei, Meng


    Polymer semiconductor is the only semiconductor that can be processed in solution. Electronics made by these flexible materials have many advantages such as large-area solution process, low cost, and high performance. Researchers and companies are increasingly dedicating time and money in polymer electronics. This book focuses on the fundamental materials and device physics of polymer electronics. It describes polymer light-emitting diodes, polymer field-effect transistors, organic vertical transistors, polymer solar cells, and many applications based on polymer electronics. The book also disc

  4. Controlled release from recombinant polymers. (United States)

    Price, Robert; Poursaid, Azadeh; Ghandehari, Hamidreza


    Recombinant polymers provide a high degree of molecular definition for correlating structure with function in controlled release. The wide array of amino acids available as building blocks for these materials lend many advantages including biorecognition, biodegradability, potential biocompatibility, and control over mechanical properties among other attributes. Genetic engineering and DNA manipulation techniques enable the optimization of structure for precise control over spatial and temporal release. Unlike the majority of chemical synthetic strategies used, recombinant DNA technology has allowed for the production of monodisperse polymers with specifically defined sequences. Several classes of recombinant polymers have been used for controlled drug delivery. These include, but are not limited to, elastin-like, silk-like, and silk-elastinlike proteins, as well as emerging cationic polymers for gene delivery. In this article, progress and prospects of recombinant polymers used in controlled release will be reviewed.

  5. Polymer Science Pilot Program (United States)

    Maier, Mary L.


    Natural polymers such as cellulose, proteins, and DNA have been part of earth's store of chemicals long before chemists existed. However, polymers synthesized by chemists first appeared on this planet only sixty years ago. A veritable explosion of materials first known as plastics, later polymers, followed. Today polymers, natural and synthetic, are everywhere, and it is appropriate to include an introduction to polymers in the education of future scientists. The Polymer Science Pilot Program consists of a sequence of experiences with polymers, designed to focus upon the ways in which these materials resemble and/or compare with nonpolymers in physical properties, versatility, and function. The modular format makes it possible for educators to select specific sections of the program for integration into other college chemistry courses. The team learning aspect of he program can also be recommended to educators who select a specific module. When this program was presented at a Middle Atlantic Regional Meeting of the American Chemical Society, some attendees were concerned about the limited number of participants as compared with the seemingly large number of college instructors. It was explained that the concentrated format of the four day program necessitates this instructor-to-student ratio; one class consisting of eighteen participants was tried and it was found that some aspects of the program, especially the research paper preparation, were not as thoroughly moderated.


    NARCIS (Netherlands)

    Morichere, D; Malliaras, G.G; Krasnikov, V.V.; Bolink, H.J; Hadziioannou, G


    The use of polymers as photorefractive materials offers many advantages : flexibility in synthesis, doping, processing and low cost. The required functionalities responsible for photorefractivity, namely charge generation, transport, trapping and linear electrooptic effect are given in the polymer w

  7. Polymer Brushes

    NARCIS (Netherlands)

    Vos, de W.M.; Kleijn, J.M.; Keizer, de A.; Cosgrove, T.; Cohen Stuart, M.A.


    A polymer brush can be defined as a dense array of polymers end-attached to an interface that stretch out into the surrounding medium. Polymer brushes have been investigated for the past 30 years and have shown to be an extremely useful tool to control interfacial properties. This review is intended

  8. Polymer crowding and shape distributions in polymer-nanoparticle mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Wei Kang; Denton, Alan R., E-mail: [Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050 (United States)


    Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the influence of nanoparticle crowding on polymer shapes via Monte Carlo simulations and free-volume theory of a coarse-grained model of polymer-nanoparticle mixtures. Exploiting the geometry of random walks, we model polymer coils as effective penetrable ellipsoids, whose shapes fluctuate according to the probability distributions of the eigenvalues of the gyration tensor. Accounting for the entropic cost of a nanoparticle penetrating a larger polymer coil, we compute the crowding-induced shift in the shape distributions, radius of gyration, and asphericity of ideal polymers in a theta solvent. With increased nanoparticle crowding, we find that polymers become more compact (smaller, more spherical), in agreement with predictions of free-volume theory. Our approach can be easily extended to nonideal polymers in good solvents and used to model conformations of biopolymers in crowded environments.

  9. The random co-polymer glatiramer acetate rapidly kills primary human leukocytes through sialic-acid-dependent cell membrane damage

    DEFF Research Database (Denmark)

    Christiansen, Stig Hill; Zhang, Xianwei; Juul-Madsen, Kristian;


    The formulation glatiramer acetate (GA) is widely used in therapy of multiple sclerosis. GA consists of random copolymers of four amino acids, in ratios that produce a predominantly positive charge and an amphipathic character. With the extraordinary complexity of the drug, several pharmacological...... contacts, which is critical for the lytic properties. In our study, SAXS showed that GA also forms this type of contacts. Taken together, our study offers new insight on the immunomodulatory mode-of-action of positively charged co-polymers. The comparison of LL-37 and GA highlights a consistent requirement...

  10. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn


    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  11. Routing of individual polymers in designed patterns

    DEFF Research Database (Denmark)

    Knudsen, Jakob Bach; Liu, Lei; Kodal, Anne Louise Bank


    Synthetic polymers are ubiquitous in the modern world, but our ability to exert control over the molecular conformation of individual polymers is very limited. In particular, although the programmable self-assembly of oligonucleotides and proteins into artificial nanostructures has been...... demonstrated, we currently lack the tools to handle other types of synthetic polymers individually and thus the ability to utilize and study their single-molecule properties. Here we show that synthetic polymer wires containing short oligonucleotides that extend from each repeat can be made to assemble...... into arbitrary routings. The wires, which can be more than 200 nm in length, are soft and bendable, and the DNA strands allow individual polymers to self-assemble into predesigned routings on both two- and three-dimensional DNA origami templates. The polymers are conjugated and potentially conducting, and could...



    Ch. von Ferber; Yu.Holovatch


    It is our great pleasure to present a collection of papers devoted to theoretical, numerical, and experimental studies in the field of star polymers. Since its introduction in the early 80-ies, this field has attracted increasing interest and has become an important part of contemporary polymer physics. While research papers in this field appear regularly in different physical and chemical journals, the present collection is an attempt to join together the studies of star polymers showing the...

  13. Polymer Chemistry (United States)

    Williams, Martha; Roberson, Luke; Caraccio, Anne


    This viewgraph presentation describes new technologies in polymer and material chemistry that benefits NASA programs and missions. The topics include: 1) What are Polymers?; 2) History of Polymer Chemistry; 3) Composites/Materials Development at KSC; 4) Why Wiring; 5) Next Generation Wiring Materials; 6) Wire System Materials and Integration; 7) Self-Healing Wire Repair; 8) Smart Wiring Summary; 9) Fire and Polymers; 10) Aerogel Technology; 11) Aerogel Composites; 12) Aerogels for Oil Remediation; 13) KSC's Solution; 14) Chemochromic Hydrogen Sensors; 15) STS-130 and 131 Operations; 16) HyperPigment; 17) Antimicrobial Materials; 18) Conductive Inks Formulations for Multiple Applications; and 19) Testing and Processing Equipment.

  14. DNA Island Formation on Binary Block Copolymer Vesicles. (United States)

    Luo, Qingjie; Shi, Zheng; Zhang, Yitao; Chen, Xi-Jun; Han, Seo-Yeon; Baumgart, Tobias; Chenoweth, David M; Park, So-Jung


    Here, we report DNA-induced polymer segregation and DNA island formation in binary block copolymer assemblies. A DNA diblock copolymer of polymethyl acrylate-block-DNA (PMA-b-DNA) and a triblock copolymer of poly(butadiene)-block-poly(ethylene oxide)-block-DNA (PBD-b-PEO-b-DNA) were synthesized, and each was coassembled with a prototypical amphiphilic polymer of poly(butadiene)-block-poly(ethylene oxide) (PBD-b-PEO). The binary self-assembly of PMA-b-DNA and PBD-b-PEO resulted in giant polymersomes with DNA uniformly distributed in the hydrophilic PEO shell. When giant polymersomes were connected through specific DNA interactions, DNA block copolymers migrated to the junction area, forming DNA islands within polymersomes. These results indicate that DNA hybridization can induce effective lateral polymer segregation in mixed polymer assemblies. The polymer segregation and local DNA enrichment have important implications in DNA melting properties, as mixed block copolymer assemblies with low DNA block copolymer contents can still exhibit useful DNA melting properties that are characteristic of DNA nanostructures with high DNA density.

  15. Investigating the interaction between peptides of the amphipathic helix of Hcf106 and the phospholipid bilayer by solid-state NMR spectroscopy (United States)

    Zhang, Lei; Liu, Lishan; Maltsev, Sergey; Lorigan, Gary A.; Dabney-Smith, Carole


    The chloroplast twin arginine translocation (cpTat) system transports highly folded precursor proteins into the thylakoid lumen using the protonmotive force as its only energy source. Hcf106, as one of the core components of the cpTat system, is part of the precursor receptor complex and functions in the initial precursor-binding step. Hcf106 is predicted to contain a single amino terminal transmembrane domain followed by a Pro-Gly hinge, a predicted amphipathic α-helix (APH), and a loosely structured carboxy terminus. Hcf106 has been shown biochemically to insert spontaneously into thylakoid membranes. To better understand the membrane active capabilities of Hcf106, we used solid-state NMR spectroscopy to investigate those properties of the APH. In this study, synthesized peptides of the predicted Hcf106 APH (amino acids 28–65) were incorporated at increasing mol% into 1-palmitoyl-2-oleoyl-sn-glycero-phosphocholine (POPC) and POPC/MGDG (monogalactosyldiacylglycerol; mole ratio 85:15) multilamellar vesicles (MLVs) to probe the peptide-lipid interaction. Solid-state 31P NMR and 2H NMR spectroscopic experiments revealed that the peptide perturbs the headgroup and the acyl chain regions of phospholipids as indicated by changes in spectral lineshape, chemical shift anisotropy (CSA) line width, and 2H order SCD parameters. In addition, the comparison between POPC MLVs and POPC/MGDG MLVs indicated that the lipid bilayer composition affected peptide perturbation of the lipids, and such perturbation appeared to be more intense in a system more closely mimicking a thylakoid membrane. PMID:24144541

  16. Identification of an amphipathic helix important for the formation of ectopic septin spirals and axial budding in yeast axial landmark protein Bud3p. (United States)

    Guo, Jia; Gong, Ting; Gao, Xiang-Dong


    Correct positioning of polarity axis in response to internal or external cues is central to cellular morphogenesis and cell fate determination. In the budding yeast Saccharomyces cerevisiae, Bud3p plays a key role in the axial bud-site selection (axial budding) process in which cells assemble the new bud next to the preceding cell division site. Bud3p is thought to act as a component of a spatial landmark. However, it is not clear how Bud3p interacts with other components of the landmark, such as the septins, to control axial budding. Here, we report that overexpression of Bud3p causes the formation of small septin rings (∼1 µm in diameter) and arcs aside from previously reported spiral-like septin structures. Bud3p closely associates with the septins in vivo as Bud3p colocalizes with these aberrant septin structures and forms a complex with two septins, Cdc10p and Cdc11p. The interaction of Bud3p with the septins may involve multiple regions of Bud3p including 1-858, 850-1220, and 1221-1636 a.a. since they all target to the bud neck but exhibit different effects on septin organization when overexpressed. In addition, our study reveals that the axial budding function of Bud3p is mediated by the N-terminal region 1-858. This region shares an amphipathic helix (850-858) crucial for bud neck targeting with the middle portion 850-1103 involved in the formation of ectopic septin spirals and rings. Interestingly, the Dbl-homology domain located in 1-858 is dispensable for axial bud-site selection. Our findings suggest that multiple regions of Bud3p ensure efficient targeting of Bud3p to the bud neck in the assembly of the axial landmark and distinct domains of Bud3p are involved in axial bud-site selection and other cellular processes.

  17. An amphipathic alpha-helix controls multiple roles of brome mosaic virus protein 1a in RNA replication complex assembly and function.

    Directory of Open Access Journals (Sweden)

    Ling Liu


    Full Text Available Brome mosaic virus (BMV protein 1a has multiple key roles in viral RNA replication. 1a localizes to perinuclear endoplasmic reticulum (ER membranes as a peripheral membrane protein, induces ER membrane invaginations in which RNA replication complexes form, and recruits and stabilizes BMV 2a polymerase (2a(Pol and RNA replication templates at these sites to establish active replication complexes. During replication, 1a provides RNA capping, NTPase and possibly RNA helicase functions. Here we identify in BMV 1a an amphipathic alpha-helix, helix A, and use NMR analysis to define its structure and propensity to insert in hydrophobic membrane-mimicking micelles. We show that helix A is essential for efficient 1a-ER membrane association and normal perinuclear ER localization, and that deletion or mutation of helix A abolishes RNA replication. Strikingly, mutations in helix A give rise to two dramatically opposite 1a function phenotypes, implying that helix A acts as a molecular switch regulating the intricate balance between separable 1a functions. One class of helix A deletions and amino acid substitutions markedly inhibits 1a-membrane association and abolishes ER membrane invagination, viral RNA template recruitment, and replication, but doubles the 1a-mediated increase in 2a(Pol accumulation. The second class of helix A mutations not only maintains efficient 1a-membrane association but also amplifies the number of 1a-induced membrane invaginations 5- to 8-fold and enhances viral RNA template recruitment, while failing to stimulate 2a(Pol accumulation. The results provide new insights into the pathways of RNA replication complex assembly and show that helix A is critical for assembly and function of the viral RNA replication complex, including its central role in targeting replication components and controlling modes of 1a action.

  18. Organometallic Polymers. (United States)

    Carraher, Charles E., Jr.


    Reactions utilized to incorporate a metal-containing moiety into a polymer chain (addition, condensation, and coordination) are considered, emphasizing that these reactions also apply to smaller molecules. (JN)

  19. 两亲性结构修饰的非天然氨基酸及二肽的合成%Synthesis of Unusual Amino Acids and Dipeptides Modified with Amphipathic Betaine

    Institute of Scientific and Technical Information of China (English)

    吕玉健; 周宁; 刘克良


    目的 合成两亲性结构修饰的非天然氨基酸和二肽.方法 将具有两亲性结构特点的甜菜碱的羧基活化成酰氯,然后与对氨基苯丙氨酸的侧链氨基反应,制备甜菜碱修饰的非天然氨基酸构建单元和目标二肽,并进行油水分配系数的测定.结果 得到了1个甜菜碱修饰的非天然氨基酸和2个甜菜碱修饰的二肽.结论 甜菜碱修饰的二肽具有更强的两亲性,为增强药物两亲性,改善药学性质提供了一种新的选择.%Objective To synthesize unusual amino acid and dipeptides modified with an amphipathic structure. Methods The amphipathic betaine was activated as N-chlorobetainyl chloride and then coupled with to-a-mino of 4-amino phenylalanine to synthesize the target compound. The peptides were synthesized in the sold phase. Results One betaine-modified non-natural amino acid and two dipeptides were obtained. Conclusion One unusual amino acid and two dipeptides modified with betaine were synthesized. The carboxyl of betaine was activated with acyl chlorides and the reactivity of betaine was greatly increased. Betaine could smoothly couple with w-amino of amino acid, which provided a novel alternative for the amphipathic modification of peptides.

  20. Polymer inflation

    CERN Document Server

    Hassan, Syed Moeez; Seahra, Sanjeev S


    We consider the semi-classical dynamics of a free massive scalar field in a homogeneous and isotropic cosmological spacetime. The scalar field is quantized using the polymer quantization method assuming that it is described by a gaussian coherent state. For quadratic potentials, the semi-classical equations of motion yield a universe that has an early "polymer inflation" phase which is generic and almost exactly de Sitter, followed by a epoch of slow-roll inflation. We compute polymer corrections to the slow roll formalism, and discuss the probability of inflation in this model using a physical Hamiltonian arising from time gauge fixing. These results show the extent to which a quantum gravity motivated quantization method affects early universe dynamics.

  1. Antimocrobial Polymer

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, William F. (Utica, OH); Huang, Zhi-Heng (Walnut Creek, CA); Wright, Stacy C. (Columbus, GA)


    A polymeric composition having antimicrobial properties and a process for rendering the surface of a substrate antimicrobial are disclosed. The composition comprises a crosslinked chemical combination of (i) a polymer having amino group-containing side chains along a backbone forming the polymer, (ii) an antimicrobial agent selected from quaternary ammonium compounds, gentian violet compounds, substituted or unsubstituted phenols, biguanide compounds, iodine compounds, and mixtures thereof, and (iii) a crosslinking agent containing functional groups capable of reacting with the amino groups. In one embodiment, the polymer is a polyamide formed from a maleic anhydride or maleic acid ester monomer and alkylamines thereby producing a polyamide having amino substituted alkyl chains on one side of the polyamide backbone; the crosslinking agent is a phosphine having the general formula (A)3P wherein A is hydroxyalkyl; and the antimicrobial agent is chlorhexidine, dimethylchlorophenol, cetyl pyridinium chloride, gentian violet, triclosan, thymol, iodine, and mixtures thereof.

  2. Polymer electronics

    CERN Document Server

    Geoghegan, Mark


    Polymer electronics is the science behind many important new developments in technology, such as the flexible electronic display (e-ink) and many new developments in transistor technology. Solar cells, light-emitting diodes, and transistors are all areas where plastic electronics is likely to, or is already having, a serious impact on our daily lives. With polymer transistors and light-emitting diodes now being commercialised, there is a clear need for a pedagogic text thatdiscusses the subject in a clear and concise fashion suitable for senior undergraduate and graduate students. The content

  3. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan


    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  4. Sedimentation of Knotted Polymers

    CERN Document Server

    Piili, Joonas; Kaski, Kimmo; Linna, Riku


    We investigate the sedimentation of knotted polymers by means of the stochastic rotation dynamics, a molecular dynamics algorithm which takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number n_c of the corresponding ideal knot. To the best of our knowledge, this provides the first direct computational confirmation of this relation, postulated on the basis of experiments in "The effect of ionic conditions on the conformations of supercoiled DNA. I. sedimentation analysis" by Rybenkov et al., for the case of sedimentation. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of s on the inverse of the radius of gyration R_g^-1, more specifically with the inverse of the R_g component that is perpendicular to the direction along which the polymer sediments. Intriguingly, the linear de...

  5. Antimicrobial polymers. (United States)

    Jain, Anjali; Duvvuri, L Sailaja; Farah, Shady; Beyth, Nurit; Domb, Abraham J; Khan, Wahid


    Better health is basic requirement of human being, but the rapid growth of harmful pathogens and their serious health effects pose a significant challenge to modern science. Infections by pathogenic microorganisms are of great concern in many fields such as medical devices, drugs, hospital surfaces/furniture, dental restoration, surgery equipment, health care products, and hygienic applications (e.g., water purification systems, textiles, food packaging and storage, major or domestic appliances etc.) Antimicrobial polymers are the materials having the capability to kill/inhibit the growth of microbes on their surface or surrounding environment. Recently, they gained considerable interest for both academic research and industry and were found to be better than their small molecular counterparts in terms of enhanced efficacy, reduced toxicity, minimized environmental problems, resistance, and prolonged lifetime. Hence, efforts have focused on the development of antimicrobial polymers with all desired characters for optimum activity. In this Review, an overview of different antimicrobial polymers, their mechanism of action, factors affecting antimicrobial activity, and application in various fields are given. Recent advances and the current clinical status of these polymers are also discussed.

  6. Polymer physics

    CERN Document Server

    Gedde, Ulf W


    This book is the result of my teaching efforts during the last ten years at the Royal Institute of Technology. The purpose is to present the subject of polymer physics for undergraduate and graduate students, to focus the fundamental aspects of the subject and to show the link between experiments and theory. The intention is not to present a compilation of the currently available literature on the subject. Very few reference citations have thus been made. Each chapter has essentially the same structure: starling with an introduction, continuing with the actual subject, summarizing the chapter in 30D-500 words, and finally presenting problems and a list of relevant references for the reader. The solutions to the problems presented in Chapters 1-12 are given in Chapter 13. The theme of the book is essentially polymer science, with the exclusion of that part dealing directly with chemical reactions. The fundamentals in polymer science, including some basic polymer chemistry, are presented as an introduction in t...

  7. Sustained Release of Antibacterial Lipopeptides from Biodegradable Polymers against Oral Pathogens (United States)

    Eckhard, Lea H.; Houri-Haddad, Yael; Sol, Asaf; Zeharia, Rotem; Shai, Yechiel; Beyth, Shaul; Domb, Abraham J.


    The development of antibacterial drugs to overcome various pathogenic species, which inhabit the oral cavity, faces several challenges, such as salivary flow and enzymatic activity that restrict dosage retention. Owing to their amphipathic nature, antimicrobial peptides (AMPs) serve as the first line of defense of the innate immune system. The ability to synthesize different types of AMPs enables exploitation of their advantages as alternatives to antibiotics. Sustained release of AMPs incorporated in biodegradable polymers can be advantageous in maintaining high levels of the peptides. In this study, four potent ultra-short lipopeptides, conjugated to an aliphatic acid chain (16C) were incorporated in two different biodegradable polymers: poly (lactic acid co castor oil) (PLACO) and ricinoleic acid-based poly (ester-anhydride) (P(SA-RA)) for sustained release. The lipopeptide and polymer formulations were tested for antibacterial activity during one week, by turbidometric measurements of bacterial outgrowth, anti-biofilm activity by live/dead staining, biocompatibility by hemolysis and XTT colorimetric assays, mode of action by fluorescence-activated cell sorting (FACS) and release profile by a fluorometric assay. The results show that an antibacterial and anti-biofilm effect, as well as membrane disruption, can be achieved by the use of a formulation of lipopeptide incorporated in biodegradable polymer. PMID:27606830


    Energy Technology Data Exchange (ETDEWEB)



    During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.

  9. Domain Structures and Inter-Domain Interactions Defining the Holoenzyme Architecture of Archaeal D-Family DNA Polymerase


    Hideshi Yokoyama; Kazuhiko Yamasaki; Ikuo Matsui; Eriko Matsui


    Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large sub...

  10. Packaging stiff polymers in small containers: A molecular dynamics study

    CERN Document Server

    Rapaport, D C


    The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of the system -- the DNA polymer and the spherical viral capsid -- has been studied by molecular dynamics simulation. The results, involving longer polymers than in earlier work, show that as polymers become more rigid there is an increasing tendency to self-organize as spools that wrap from the inside out, rather than the inverse direction seen previously. In the final state, a substantial part of the polymer is packed into one or more coaxial spools, concentrically layered with different orientations, a form of packaging achievable without twisting the polymer.

  11. Polymer/Solvent and Polymer/Polymer Interaction Studies (United States)


    DCM and ATS are completely miscible. The sorption data described 1 2Jones, E. G., Pedrick , D. L., and Benadum, P. A., Polymer Characteri- zation Using...Encyclopedia of Polymer Science and Technology, Vol. 11, Wiley-Interscience, N.Y. (1969), p. 447. 12. Jones, E.G., Pedrick , D.L., and Benadum, P.A., Polymer

  12. Shape memory polymers (United States)

    Wilson, Thomas S.; Bearinger, Jane P.


    New shape memory polymer compositions, methods for synthesizing new shape memory polymers, and apparatus comprising an actuator and a shape memory polymer wherein the shape memory polymer comprises at least a portion of the actuator. A shape memory polymer comprising a polymer composition which physically forms a network structure wherein the polymer composition has shape-memory behavior and can be formed into a permanent primary shape, re-formed into a stable secondary shape, and controllably actuated to recover the permanent primary shape. Polymers have optimal aliphatic network structures due to minimization of dangling chains by using monomers that are symmetrical and that have matching amine and hydroxyl groups providing polymers and polymer foams with clarity, tight (narrow temperature range) single transitions, and high shape recovery and recovery force that are especially useful for implanting in the human body.

  13. DNA compaction by nonbinding macromolecules

    NARCIS (Netherlands)

    Vries, de R.J.


    Compaction of DNA by nonbinding macromolecules such as uncharged flexible polymer chains and negatively charged globular proteins is thought to have various applications in biophysics, for example in the formation of a nucleoid structure in bacteria. A simple experimental model that has been very we

  14. Polymer nanocomposites: polymer and particle dynamics

    KAUST Repository

    Kim, Daniel


    Polymer nanocomposites containing nanoparticles smaller than the random coil size of their host polymer chains are known to exhibit unique properties, such as lower viscosity and glass transition temperature relative to the neat polymer melt. It has been hypothesized that these unusual properties result from fast diffusion of the nanostructures in the host polymer, which facilitates polymer chain relaxation by constraint release and other processes. In this study, the effects of addition of sterically stabilized inorganic nanoparticles to entangled cis-1,4-polyisoprene and polydimethylsiloxane on the overall rheology of nanocomposites are discussed. In addition, insights about the relaxation of the host polymer chains and transport properties of nanoparticles in entangled polymer nanocomposites are presented. The nanoparticles are found to act as effective plasticizers for their entangled linear hosts, and below a critical, chemistry and molecular-weight dependent particle volume fraction, lead to reduced viscosity, glass transition temperature, number of entanglements, and polymer relaxation time. We also find that the particle motions in the polymer host are hyperdiffusive and at the nanoparticle length scale, the polymer host acts like a simple, ideal fluid and the composites\\' viscosity rises with increasing particle concentration. © 2012 The Royal Society of Chemistry.

  15. Premeltons in DNA. (United States)

    Sobell, Henry M


    Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A-DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A-transition), which differs from either A- or B-DNA. Called beta-DNA, this is both metastable and hyperflexible--and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A-DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5' and 3' ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions--all readily testable--as will be described in this review.

  16. MOLECULAR IMPRINTED POLYMERS--Novel Polymer Adsorbents

    Institute of Scientific and Technical Information of China (English)

    LI Haitao; XU Mancai; SHI Zuoqing; HE Binglin


    Molecular imprinted polymers (MIPs) are novel functional polymer materials and known as specific adsorbents for the template molecules. These novel functional polymers have promised potential applications in racemic resolution, sensor, chromatography, adsorptive separation and other fields. This review exhibits the approach for preparing MIPs, the features of MIPs obtained by different routes and the characteristics of adsorptive separations with MIPs. The molecular recognition mechanism and the idea of the present possibilities and limitations of molecular imprinting polymerization are discussed as well.

  17. Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities

    CERN Document Server

    Lu, Bing-Sui; Podgornik, Rudolf


    We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel $r^{-5}$ scaling behavior of the van der Waals interaction energy for small inter-polymer separation $r$, in contradistinction to the $r^{-4}$ scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently ali...

  18. Role for DNA polymerase beta in response to ionizing radiation.

    NARCIS (Netherlands)

    Vermeulen, C.; Verwijs-Janssen, M.; Cramers, P.; Begg, A.C.; Vens, C.


    Evidence for a role of DNA polymerase beta in determining radiosensitivity is conflicting. In vitro assays show an involvement of DNA polymerase beta in single strand break repair and base excision repair of oxidative damages, both products of ionizing radiation. Nevertheless the lack of DNA polymer

  19. Polymer Functionalized Nanoparticles in Polymer Nanocomposites (United States)

    Jayaraman, Arthi


    Significant interest has grown around the ability to control spatial arrangement of nanoparticles in a polymer nanocomposite to engineer materials with target properties. Past work has shown that one could achieve controlled assembly of nanoparticles in the polymer matrix by functionalizing nanoparticle surfaces with homopolymers. This talk will focus on our recent work using Polymer Reference Interaction Site Model (PRISM) theory and Monte Carlo simulations and GPU-based molecular dynamics simulations to specifically understand how heterogeneity in the polymer functionalization in the form of a) copolymers with varying monomer chemistry and monomer sequence, and b) polydispersity in homopolymer grafts can tune effective interactions between functionalized nanoparticles, and the assembly of functionalized nanoparticles.

  20. Conducting polymer materials

    Directory of Open Access Journals (Sweden)

    Jovanović Slobodan M.


    Full Text Available Conducting polymers represent a very interesting group of polymer materials Investigation of the synthesis, structure and properties of these materials has been the subject of considerable research efforts in the last twenty years. A short presentating of newer results obtained by investigating of the synthesis, structure and properties of two basic groups of conducting polymers: a conducting polymers the conductivity of which is the result of their molecular structure, and b conducting polymer composites (EPC, is given in this paper. The applications and future development of this group of polymer materials is also discussed.

  1. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger


    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  2. Polymer composites containing nanotubes (United States)

    Bley, Richard A. (Inventor)


    The present invention relates to polymer composite materials containing carbon nanotubes, particularly to those containing singled-walled nanotubes. The invention provides a polymer composite comprising one or more base polymers, one or more functionalized m-phenylenevinylene-2,5-disubstituted-p-phenylenevinylene polymers and carbon nanotubes. The invention also relates to functionalized m-phenylenevinylene-2,5-disubstituted-p-phenylenevinylene polymers, particularly to m-phenylenevinylene-2,5-disubstituted-p-phenylenevinylene polymers having side chain functionalization, and more particularly to m-phenylenevinylene-2,5-disubstituted-p-phenylenevinylene polymers having olefin side chains and alkyl epoxy side chains. The invention further relates to methods of making polymer composites comprising carbon nanotubes.

  3. Polymer Fluid Dynamics. (United States)

    Bird, R. Byron


    Problems in polymer fluid dynamics are described, including development of constitutive equations, rheometry, kinetic theory, flow visualization, heat transfer studies, flows with phase change, two-phase flow, polymer unit operations, and drag reduction. (JN)

  4. Dendritic polyurea polymers. (United States)

    Tuerp, David; Bruchmann, Bernd


    Dendritic polymers, subsuming dendrimers as well as hyperbranched or highly branched polymers are well established in the field of polymer chemistry. This review article focuses on urea based dendritic polymers and summarizes their synthetic routes through both isocyanate and isocyanate-free processes. Furthermore, this article highlights applications where dendritic polyureas show their specific chemical and physical potential. For these purposes scientific publications as well as patent literature are investigated to generate a comprehensive overview on this topic.

  5. Reducible, dibromomaleimide-linked polymers for gene delivery. (United States)

    Tan, James-Kevin Y; Choi, Jennifer L; Wei, Hua; Schellinger, Joan G; Pun, Suzie H


    Polycations have been successfully used as gene transfer vehicles both in vitro and in vivo; however, their cytotoxicity has been associated with increasing molecular weight. Polymers that can be rapidly degraded after internalization are typically better tolerated by mammalian cells compared to their non-degradable counterparts. Here, we report the use of a dibromomaleimide-alkyne (DBM-alkyne) linking agent to reversibly bridge cationic polymer segments for gene delivery and to provide site-specific functionalization by azide-alkyne cycloaddition chemistry. A panel of reducible and non-reducible, statistical copolymers of (2-dimethylamino)ethyl methacrylate (DMAEMA) and oligo(ethylene glycol)methyl ether methacrylate (OEGMA) were synthesized and evaluated. When complexed with plasmid DNA, the reducible and non-reducible polymers had comparable DNA condensation properties, sizes, and transfection efficiencies. When comparing cytotoxicity, the DBM-linked, reducible polymers were significantly less toxic than the non-reducible polymers. To demonstrate polymer functionalization by click chemistry, the DBM-linked polymers were tagged with an azide-fluorophore and were used to monitor cellular uptake. Overall, this polymer system introduces the use of a reversible linker, DBM-alkyne, to the area of gene delivery and allows for facile, orthogonal, and site-specific functionalization of gene delivery vehicles.

  6. Standardization of anti-DNA antibody assays. (United States)

    Pisetsky, David S


    Antibodies to DNA (anti-DNA) are the serological hallmark of systemic lupus erythematosus and represent important biomarkers for clinical and research purposes. These antibodies are part of a family of antibodies to nucleosomes and bind to conserved sites widely present on DNA. While the value of anti-DNA as a biomarker is well established, the assay for these antibodies has involved a variety of DNA sources and systems to detect DNA-anti-DNA interactions. The influence of these variations on antibody detection has complicated assay standardization. As an antigen, DNA has unique features since it is a highly charged polymer that has structural heterogeneity. This heterogeneity can affect antigenicity which can vary on the basis of DNA origin, size, conformation and mobility. In addition, as a polymer, DNA can promote patterns of antibody binding based on monogamous or bivalent interaction which require an extended polynucleotide structure. Understanding the nature of DNA as an antigen can facilitate interpretation of serological tests and underpin efforts at better standardization.

  7. Engineered Protein Polymers (United States)


    of each pure polymer, we plan to combine the various polymer solutions in different ratios to tune the composition and physico-chemical properties...protein materials as vehicles for storage and delivery of small molecules. Each protein polymer under concentrations for particle formation ( vida

  8. Microscopic and spectroscopic analysis of chitosan-DNA conjugates. (United States)

    Agudelo, D; Kreplak, L; Tajmir-Riahi, H A


    Conjugations of DNA with chitosans 15 kD (ch-15), 100 kD (ch-100) and 200 kD (ch-200) were investigated in aqueous solution at pH 5.5-6.5. Multiple spectroscopic methods and atomic force microscopy (AFM) were used to locate the chitosan binding sites and the effect of polymer conjugation on DNA compaction and particle formation. Structural analysis showed that chitosan-DNA conjugation is mainly via electrostatic interactions through polymer cationic charged NH2 and negatively charged backbone phosphate groups. As polymer size increases major DNA compaction and particle formation occurs. At high chitosan concentration major DNA structural changes observed indicating a partial B to A-DNA conformational transition.

  9. Fire-safe polymers and polymer composites (United States)

    Zhang, Huiqing

    The intrinsic relationships between polymer structure, composition and fire behavior have been explored to develop new fire-safe polymeric materials. Different experimental techniques, especially three milligram-scale methods---pyrolysis-combustion flow calorimetry (PCFC), simultaneous thermal analysis (STA) and pyrolysis GC/MS---have been combined to fully characterize the thermal decomposition and flammability of polymers and polymer composites. Thermal stability, mass loss rate, char yield and properties of decomposition volatiles were found to be the most important parameters in determining polymer flammability. Most polymers decompose by either an unzipping or a random chain scission mechanism with an endothermic decomposition of 100--900 J/g. Aromatic or heteroaromatic rings, conjugated double or triple bonds and heteroatoms such as halogens, N, O, S, P and Si are the basic structural units for fire-resistant polymers. The flammability of polymers can also be successfully estimated by combining pyrolysis GC/MS results or chemical structures with TGA results. The thermal decomposition and flammability of two groups of inherently fire-resistant polymers---poly(hydroxyamide) (PHA) and its derivatives, and bisphenol C (BPC II) polyarylates---have been systematically studied. PHA and most of its derivatives have extremely low heat release rates and very high char yields upon combustion. PHA and its halogen derivatives can completely cyclize into quasi-polybenzoxazole (PBO) structures at low temperatures. However, the methoxy and phosphate derivatives show a very different behavior during decomposition and combustion. Molecular modeling shows that the formation of an enol intermediate is the rate-determining step in the thermal cyclization of PHA. BPC II-polyarylate is another extremely flame-resistant polymer. It can be used as an efficient flame-retardant agent in copolymers and blends. From PCFC results, the total heat of combustion of these copolymers or blends

  10. DNA block copolymers: functional materials for nanoscience and biomedicine. (United States)

    Schnitzler, Tobias; Herrmann, Andreas


    We live in a world full of synthetic materials, and the development of new technologies builds on the design and synthesis of new chemical structures, such as polymers. Synthetic macromolecules have changed the world and currently play a major role in all aspects of daily life. Due to their tailorable properties, these materials have fueled the invention of new techniques and goods, from the yogurt cup to the car seat belts. To fulfill the requirements of modern life, polymers and their composites have become increasingly complex. One strategy for altering polymer properties is to combine different polymer segments within one polymer, known as block copolymers. The microphase separation of the individual polymer components and the resulting formation of well defined nanosized domains provide a broad range of new materials with various properties. Block copolymers facilitated the development of innovative concepts in the fields of drug delivery, nanomedicine, organic electronics, and nanoscience. Block copolymers consist exclusively of organic polymers, but researchers are increasingly interested in materials that combine synthetic materials and biomacromolecules. Although many researchers have explored the combination of proteins with organic polymers, far fewer investigations have explored nucleic acid/polymer hybrids, known as DNA block copolymers (DBCs). DNA as a polymer block provides several advantages over other biopolymers. The availability of automated synthesis offers DNA segments with nucleotide precision, which facilitates the fabrication of hybrid materials with monodisperse biopolymer blocks. The directed functionalization of modified single-stranded DNA by Watson-Crick base-pairing is another key feature of DNA block copolymers. Furthermore, the appropriate selection of DNA sequence and organic polymer gives control over the material properties and their self-assembly into supramolecular structures. The introduction of a hydrophobic polymer into DBCs

  11. Nanoporous polymer electrolyte (United States)

    Elliott, Brian [Wheat Ridge, CO; Nguyen, Vinh [Wheat Ridge, CO


    A nanoporous polymer electrolyte and methods for making the polymer electrolyte are disclosed. The polymer electrolyte comprises a crosslinked self-assembly of a polymerizable salt surfactant, wherein the crosslinked self-assembly includes nanopores and wherein the crosslinked self-assembly has a conductivity of at least 1.0.times.10.sup.-6 S/cm at C. The method of making a polymer electrolyte comprises providing a polymerizable salt surfactant. The method further comprises crosslinking the polymerizable salt surfactant to form a nanoporous polymer electrolyte.

  12. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  13. Polymer Based Biosensors for Medical Applications

    DEFF Research Database (Denmark)

    Cherré, Solène; Rozlosnik, Noemi


    The objective of this chapter is to give an overview about the newest developments in biosensors made of polymers for medical applications. Biosensors are devices that can recognize and detect a target with high selectivity. They are widely used in many fields such as medical diagnostic......, environmental monitoring and food safety. The detected element varies from a single molecule (such as glucose), a biopolymer (such as DNA or a protein) to a whole organism (such as bacteria). Due to their easy use and possible miniaturization, biosensors have a high potential to come out of the lab...... and be available for use by everybody. To fulfil these purposes, polymers represent very appropriate materials. Many nano- and microfabrication methods for polymers are available, allowing a fast and cheap production of devices. This chapter will present the general concept of a biosensor in a first part...

  14. Injection molded nanofluidic chips: Fabrication method and functional tests using single-molecule DNA experiments

    DEFF Research Database (Denmark)

    Utko, Pawel; Persson, Karl Fredrik; Kristensen, Anders;


    We demonstrate that fabrication of nanofluidic systems can be greatly simplified by injection molding of polymers. We functionally test our devices by single-molecule DNA experiments in nanochannels.......We demonstrate that fabrication of nanofluidic systems can be greatly simplified by injection molding of polymers. We functionally test our devices by single-molecule DNA experiments in nanochannels....

  15. Polymer dynamics from synthetic polymers to proteins

    Indian Academy of Sciences (India)

    D Richter; R Biehl; M Monkenbush; B Hoffmann; R Merkel


    Starting from the standard model of polymer motion - the Rouse model - we briefly present some key experimental results on the mesoscopic dynamics of polymer systems. We touch the role of topological confinement as expressed in the reptation model and discuss in some more detail processes limiting the confinement. In the second part we relate to some new developments concerning the measurement of large-scale internal dynamics of proteins by neutron spin echo.

  16. DNA Nanotechnology (United States)

    Taniguchi, Masateru; Kawai, Tomoji


    DNA is one candidate of promising molecules for molecular electronic devices, since it has the double helix structure with pi-electron bases for electron transport, the address at 0.4 nm intervals, and the self-assembly. Electrical conductivity and nanostructure of DNA and modified DNA molecules are investigated in order to research the application of DNA in nanoelectronic devices. It has been revealed that DNA is a wide-gap semiconductor in the absence of doping. The conductivity of DNA has been controlled by chemical doping, electric field doping, and photo-doping. It has found that Poly(dG)[middle dot]Poly(dC) has the best conductivity and can function as a conducting nanowire. The pattern of DNA network is controlled by changing the concentration of the DNA solution.

  17. Star-Branched Polymers (Star Polymers)

    KAUST Repository

    Hirao, Akira


    The synthesis of well-defined regular and asymmetric mixed arm (hereinafter miktoarm) star-branched polymers by the living anionic polymerization is reviewed in this chapter. In particular, much attention is being devoted to the synthetic development of miktoarm star polymers since 2000. At the present time, the almost all types of multiarmed and multicomponent miktoarm star polymers have become feasible by using recently developed iterative strategy. For example, the following well-defined stars have been successfully synthesized: 3-arm ABC, 4-arm ABCD, 5-arm ABCDE, 6-arm ABCDEF, 7-arm ABCDEFG, 6-arm ABC, 9-arm ABC, 12-arm ABC, 13-arm ABCD, 9-arm AB, 17-arm AB, 33-arm AB, 7-arm ABC, 15-arm ABCD, and 31-arm ABCDE miktoarm star polymers, most of which are quite new and difficult to synthesize by the end of the 1990s. Several new specialty functional star polymers composed of vinyl polymer segments and rigid rodlike poly(acetylene) arms, helical polypeptide, or helical poly(hexyl isocyanate) arms are introduced.

  18. DNA Methylation


    Alokail, Majed S.; Alenad, Amal M.


    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication e...

  19. CO2 -Responsive polymers. (United States)

    Lin, Shaojian; Theato, Patrick


    This Review focuses on the recent progress in the area of CO2 -responsive polymers and provides detailed descriptions of these existing examples. CO2 -responsive polymers can be categorized into three types based on their CO2 -responsive groups: amidine, amine, and carboxyl groups. Compared with traditional temperature, pH, or light stimuli-responsive polymers, CO2 -responsive polymers provide the advantage to use CO2 as a "green" trigger as well as to capture CO2 directly from air. In addition, the current challenges of CO2 -responsive polymers are discussed and the different solution methods are compared. Noteworthy, CO2 -responsive polymers are considered to have a prosperous future in various scientific areas.

  20. DNA packaging induced by micellar aggregates: a novel in vitro DNA condensation system. (United States)

    Ghirlando, R; Wachtel, E J; Arad, T; Minsky, A


    Evidence for a conceptually novel DNA packaging process is presented. X-ray scattering, electron microscopy, and circular dichroism measurements indicate that in the presence of positively charged micellar aggregates and flexible anionic polymers, such as negatively charged polypeptides or single-stranded RNA species, a complex is formed in which DNA molecules are partially embedded within a micellar scaffold and partially condensed into highly packed chiral structures. Based on studies of micelle-DNA and micelle-flexible anionic polymer systems, as well as on the known effects of a high charge density upon the micellar organization, a DNA packaging model is proposed. According to this model, the DNA induces the elongation of the micelles into rodlike aggregates, forming a closely packed matrix in which the DNA molecules are immobilized. In contrast, the flexible anionic polymers stabilize clusters of spherical micelles which are proposed to effect a capping of the rodlike micelles, thus arresting their elongation and creating surfactant-free segments of the DNA that are able to converge and collapse. Thus, unlike other in vitro DNA packaging systems, in which condensation follows encounters between charge-neutralized DNA molecules, a prepackaging phase where the DNA is immobilized within a matrix is proposed in this case. Cellular and nuclear membranes have been implicated in DNA packaging processes in vivo, and negatively charged polyelectrolytes were shown to be involved in the processes. These observations, combined with the basic tenets of the DNA condensation system described here, allow for the progression to the study of more elaborate model systems and thus might lead to insights into the nature and roles of the intricate in vivo DNA-membrane complexes.

  1. Development of potent anti-infective agents from Silurana tropicalis: conformational analysis of the amphipathic, alpha-helical antimicrobial peptide XT-7 and its non-haemolytic analogue [G4K]XT-7. (United States)

    Subasinghage, Anusha P; Conlon, J Michael; Hewage, Chandralal M


    Peptide XT-7 (GLLGP(5)LLKIA(10)AKVGS(15)NLL.NH(2)) is a cationic, leucine-rich peptide, first isolated from skin secretions of the frog, Silurana tropicalis (Pipidae). The peptide shows potent, broad-spectrum antimicrobial activity but its therapeutic potential is limited by haemolytic activity (LC(50)=140 microM). The analogue [G4K]XT-7, however, retains potent antimicrobial activity but is non-haemolytic (LC(50)>500 microM). In order to elucidate the molecular basis for this difference in properties, the three dimensional structures of XT-7 and the analogue have been investigated by proton NMR spectroscopy and molecular modelling. In aqueous solution, both peptides lack secondary structure. In a 2,2,2-trifluoroethanol (TFE-d(3))-H(2)O mixed solvent system, XT-7 is characterised by a right handed alpha-helical conformation between residues Leu(3) and Leu(17) whereas [G4K]XT-7 adopts a more restricted alpha-helical conformation between residues Leu(6) and Leu(17). A similar conformation for XT-7 in 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) micellular media was observed with a helical segment between Leu(3) and Leu(17). However, differences in side chain orientations restricting the hydrophilic residues to a smaller patch resulted in an increased hydrophobic surface relative to the conformation in TFE-H(2)O. Molecular modelling of the structures obtained in our study demonstrates the amphipathic character of the helical segments. It is proposed that the marked decrease in haemolytic activity produced by the substitution Gly(4)-->Lys in XT-7 arises from a decrease in both helicity and hydrophobicity. These studies may facilitate the development of potent but non-toxic anti-infective agents based upon the structure of XT-7.

  2. Macromolecular crowding increases binding of DNA polymerase to DNA: an adaptive effect

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, S.B.; Harrison, B.


    Macromolecular crowding extends the range of ionic conditions supporting high DNA polymerase reaction rates. Reactions tested were nick translation and gap-filling by DNA polymerase I of E. coli, nuclease and polymerase activities of the large fragment of that polymerase, and polymerization by the T4 DNA polymerase. For all of these reactions, high concentrations of nonspecific polymers increased enzymatic activity under otherwise inhibitory conditions resulting from relatively high ionic strength. The primary mechanism of the polymer effect seems to be to increase the binding of polymerase to DNA. They suggest that this effect of protein-DNA complexes is only one example of a general metabolic buffering action of crowded solutions on a variety of macromolecular interactions.

  3. Triclosan antimicrobial polymers


    Petersen, Richard C.


    Triclosan antimicrobial molecular fluctuating energies of nonbonding electron pairs for the oxygen atom by ether bond rotations are reviewed with conformational computational chemistry analyses. Subsequent understanding of triclosan alternating ether bond rotations is able to help explain several material properties in Polymer Science. Unique bond rotation entanglements between triclosan and the polymer chains increase both the mechanical properties of polymer toughness and strength that are ...

  4. BSA Hybrid Synthesized Polymer

    Institute of Scientific and Technical Information of China (English)

    Zong Bin LIU; Xiao Pei DENG; Chang Sheng ZHAO


    Bovine serum albumin (BSA), a naturally occurring biopolymer, was regarded as a polymeric material to graft to an acrylic acid (AA)-N-vinyl pyrrolidone (NVP) copolymer to form a biomacromolecular hybrid polymer. The hybrid polymer can be blended with polyethersulfone (PES) to increase the hydrophilicity of the PES membrane, which suggested that the hybrid polymer might have a wide application in the modification of biomaterials.

  5. Thermally conductive polymers (United States)

    Byrd, N. R.; Jenkins, R. K.; Lister, J. L. (Inventor)


    A thermally conductive polymer is provided having physical and chemical properties suited to use as a medium for potting electrical components. The polymer is prepared from hydroquinone, phenol, and formaldehyde, by conventional procedures employed for the preparation of phenol-formaldehyde resins. While the proportions of the monomers can be varied, a preferred polymer is formed from the monomers in a 1:1:2.4 molar or ratio of hydroquinone:phenol:formaldehyde.

  6. Nucleoid occlusion protein Noc recruits DNA to the bacterial cell membrane. (United States)

    Adams, David William; Wu, Ling Juan; Errington, Jeff


    To proliferate efficiently, cells must co-ordinate division with chromosome segregation. In Bacillus subtilis, the nucleoid occlusion protein Noc binds to specific DNA sequences (NBSs) scattered around the chromosome and helps to protect genomic integrity by coupling the initiation of division to the progression of chromosome replication and segregation. However, how it inhibits division has remained unclear. Here, we demonstrate that Noc associates with the cell membrane via an N-terminal amphipathic helix, which is necessary for function. Importantly, the membrane-binding affinity of this helix is weak and requires the assembly of nucleoprotein complexes, thus establishing a mechanism for DNA-dependent activation of Noc. Furthermore, division inhibition by Noc requires recruitment of NBS DNA to the cell membrane and is dependent on its ability to bind DNA and membrane simultaneously. Indeed, Noc production in a heterologous system is sufficient for recruitment of chromosomal DNA to the membrane. Our results suggest a simple model in which the formation of large membrane-associated nucleoprotein complexes physically occludes assembly of the division machinery.

  7. Dna Sequencing (United States)

    Tabor, Stanley; Richardson, Charles C.


    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  8. Characterisation of polymers, 1

    CERN Document Server

    Crompton, Roy


    This essential guide to Polymer Characterisation is a complete compendium of methodologies that have evolved for the determination of the chemical composition of polymers. This 478-page book gives an up-to-date and thorough exposition of the state-of-the-art theories and availability of instrumentation needed to effect chemical and physical analysis of polymers. This is supported by approximately 1200 references. Volume 1 covers the methodology used for the determination of metals, non-metals and organic functional groups in polymers, and for the determination of the ratio in which different m

  9. Biopolymers Versus Synthetic Polymers

    Directory of Open Access Journals (Sweden)

    Florentina Adriana Cziple


    Full Text Available This paper present an overview of important synthetic and natural polymers with emphasis on polymer structure, the chemistry of polymer formation. an introduction to polymer characterization. The biodegradation process can take place aerobically and anaerobically with or without the presence of light. These factors allow for biodegradation even in landfill conditions which are normally inconducive to any degradation. The sheeting used to make these packages differs significantly from other “degradable plastics” in the market as it does not attempt to replace the current popular materials but instead enhances them by rendering them biodegradable.

  10. Triclosan antimicrobial polymers

    Directory of Open Access Journals (Sweden)

    Richard C. Petersen


    Full Text Available Triclosan antimicrobial molecular fluctuating energies of nonbonding electron pairs for the oxygen atom by ether bond rotations are reviewed with conformational computational chemistry analyses. Subsequent understanding of triclosan alternating ether bond rotations is able to help explain several material properties in Polymer Science. Unique bond rotation entanglements between triclosan and the polymer chains increase both the mechanical properties of polymer toughness and strength that are enhanced even better through secondary bonding relationships. Further, polymer blend compatibilization is considered due to similar molecular relationships and polarities. With compatibilization of triclosan in polymers a more uniform stability for nonpolar triclosan in the polymer solid state is retained by the antimicrobial for extremely low release with minimum solubility into aqueous solution. As a result, triclosan is projected for long extended lifetimes as an antimicrobial polymer additive. Further, triclosan rapid alternating ether bond rotations disrupt secondary bonding between chain monomers in the resin state to reduce viscosity and enhance polymer blending. Thus, triclosan is considered for a polymer additive with multiple properties to be an antimicrobial with additional benefits as a nonpolar toughening agent and a hydrophobic wetting agent. The triclosan material relationships with alternating ether bond rotations are described through a complete different form of medium by comparisons with known antimicrobial properties that upset bacterial cell membranes through rapid fluctuating mechanomolecular energies. Also, triclosan bond entanglements with secondary bonding can produce structural defects in weak bacterial lipid membranes requiring pliability that can then interfere with cell division. Regarding applications with polymers, triclosan can be incorporated by mixing into a resin system before cure, melt mixed with thermoplastic polymers

  11. Triclosan antimicrobial polymers (United States)

    Petersen, Richard C.


    Triclosan antimicrobial molecular fluctuating energies of nonbonding electron pairs for the oxygen atom by ether bond rotations are reviewed with conformational computational chemistry analyses. Subsequent understanding of triclosan alternating ether bond rotations is able to help explain several material properties in Polymer Science. Unique bond rotation entanglements between triclosan and the polymer chains increase both the mechanical properties of polymer toughness and strength that are enhanced even better through secondary bonding relationships. Further, polymer blend compatibilization is considered due to similar molecular relationships and polarities. With compatibilization of triclosan in polymers a more uniform stability for nonpolar triclosan in the polymer solid state is retained by the antimicrobial for extremely low release with minimum solubility into aqueous solution. As a result, triclosan is projected for long extended lifetimes as an antimicrobial polymer additive. Further, triclosan rapid alternating ether bond rotations disrupt secondary bonding between chain monomers in the resin state to reduce viscosity and enhance polymer blending. Thus, triclosan is considered for a polymer additive with multiple properties to be an antimicrobial with additional benefits as a nonpolar toughening agent and a hydrophobic wetting agent. The triclosan material relationships with alternating ether bond rotations are described through a complete different form of medium by comparisons with known antimicrobial properties that upset bacterial cell membranes through rapid fluctuating mechanomolecular energies. Also, triclosan bond entanglements with secondary bonding can produce structural defects in weak bacterial lipid membranes requiring pliability that can then interfere with cell division. Regarding applications with polymers, triclosan can be incorporated by mixing into a resin system before cure, melt mixed with thermoplastic polymers that set on cooling

  12. Dispersing Zwitterions into Comb Polymers for Nonviral Transfection: Experiments and Molecular Simulation. (United States)

    Ghobadi, Ahmadreza F; Letteri, Rachel; Parelkar, Sangram S; Zhao, Yue; Chan-Seng, Delphine; Emrick, Todd; Jayaraman, Arthi


    Polymer-based gene delivery vehicles benefit from the presence of hydrophilic groups that mitigate the inherent toxicity of polycations and that provide tunable polymer-DNA binding strength and stable complexes (polyplexes). However, hydrophilic groups screen charge, and as such can reduce cell uptake and transfection efficiency. We report the effect of embedding zwitterionic sulfobetaine (SB) groups in cationic comb polymers, using a combination of experiments and molecular simulations. Ring-opening metathesis polymerization (ROMP) produced comb polymers with tetralysine (K4) and SB pendent groups. Dynamic light scattering, zeta potential measurements, and fluorescence-based experiments, together with coarse-grained molecular dynamics simulations, described the effect of SB groups on the size, shape, surface charge, composition, and DNA binding strength of polyplexes formed using these comb polymers. Experiments and simulations showed that increasing SB composition in the comb polymers decreased polymer-DNA binding strength, while simulations indicated that the SB groups distributed throughout the polyplex. This allows polyplexes to maintain a positive surface charge and provide high levels of gene expression in live cells. Notably, comb polymers with nearly 50 mol % SB form polyplexes that exhibit positive surface charge similarly as polyplexes formed from purely cationic comb polymers, indicating the ability to introduce an appreciable amount of SB functionality without screening surface charge. This integrated simulation-experimental study demonstrates the effectiveness of incorporating zwitterions in polyplexes, while guiding the design of new and effective gene delivery vectors.

  13. Visualization of large elongated DNA molecules. (United States)

    Lee, Jinyong; Kim, Yongkyun; Lee, Seonghyun; Jo, Kyubong


    Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.

  14. Streching of (DNA/functional molecules) complex between electrodes towards DNA molecular wire (United States)

    Kobayashi, Norihisa; Nishizawa, Makoto; Inoue, Shintarou; Nakamura, Kazuki


    DNA/functional molecules such as (Ru(bpy)32+ complex, conducting polymer etc.) complex was prepared to study molecular structure and I-V characteristics towards DNA molecular wire. For example, Ru(bpy)32+ was associated with duplex of DNA by not only electrostatic interaction but also intercalation in the aqueous solution. Singlemolecular structure of DNA/Ru(bpy)32+ complex was analyzed with AFM. We found a network structure of DNA/Ru(bpy)32+ complex on the mica substrate, which is similar to native DNA. The height of DNA/Ru(bpy)32+ complex on the mica substrate was ranging from 0.8 to 1.6 nm, which was higher than the naked DNA (0.5-1.0 nm). This indicates that single-molecular DNA/Ru(bpy)32+ complex also connects to each other to form network structure on a mica substrate. In order to stretch DNA complex between electrodes, we employed high frequency and high electric field stretching method proposed by Washizu et al. We stretched and immobilized DNA single molecules between a pair of electrodes and its structures were analyzed with AFM technique. The I-V characteristics of DNA single molecules between electrodes were improved by the association of functional molecules with DNA. The molecular structure and I-V characteristics of DNA complex were discussed.

  15. Doped Chiral Polymer Metamaterials Project (United States)

    National Aeronautics and Space Administration — Doped Chiral Polymer Metamaterials (DCPM) with tunable resonance frequencies have been developed by adding plasmonic inclusions into chiral polymers with variable...

  16. Melons are branched polymers

    CERN Document Server

    Gurau, Razvan


    Melonic graphs constitute the family of graphs arising at leading order in the 1/N expansion of tensor models. They were shown to lead to a continuum phase, reminiscent of branched polymers. We show here that they are in fact precisely branched polymers, that is, they possess Hausdorff dimension 2 and spectral dimension 4/3.

  17. Polymer Electronics, Quo Vadis?

    NARCIS (Netherlands)

    Chiechi, Ryan C.; Hummelen, Jan C.


    At the heart of polymer electronics lies more than three decades of research into conjugated polymers. The future of these materials is intimately tied to the development of organic photovoltaic (OPV) devices that can compete with traditional, inorganic devices in efficiency and cost. In addition to

  18. Stiff Quantum Polymers


    Kleinert, H


    At ultralow temperatures, polymers exhibit quantum behavior, which is calculated here for the second and fourth moments of the end-to-end distribution in the large-stiffness regime. The result should be measurable for polymers in wide optical traps.

  19. Tunable Optical Polymer Systems (United States)


    outperforms almost all other organic polymer systems reported thus far, the introduction of the first multiple color LBL electrochrome , and development...thin films outperform previously reported LBL assembled films and approach integration capability for a number of electrochromic , sensing and...Zacharia, N; Hammond, P. T. “ Electrochromism of LBL assembled thin polymer films containing metal oxide nanoparticles,” American Chemical Society

  20. Mechanically Invisible Polymer Coatings

    DEFF Research Database (Denmark)


    phase comprises particles, said particles comprising a filler material and an encapsulating coating of a second polymeric material, wherein the backbones of the first and second polymeric materials are the same. The composition may be used in electroactive polymers (EAPs) in order to obtain mechanically...... invisible polymer coatings....

  1. Polymers in Waveguide Packaging

    Institute of Scientific and Technical Information of China (English)

    Zhiyi Zhang; G. Z.Xiao; Jiaren Liu; C. P. Grover


    Polymers were successfully used in the packaging of waveguide-based photonic components in the area of fiber-to-waveguide coupling, waveguide die attachment, strain relief, and waveguide encapsulation. The application results of these polymers were described in this paper.

  2. General equilibrium shape equations of polymer chains. (United States)

    Zhang, Shengli; Zuo, Xianjun; Xia, Minggang; Zhao, Shumin; Zhang, Erhu


    The general equilibrium shape equations of polymer chains are analytically derived in this paper. This provides a unified description for many models, such as the well-known wormlike chain (WLC) model, the wormlike rod chain (WLRC) model, carbon nanotubes, and so on. Using the WLC model, we find that the pitch-to-radius ratio of coils, 4.443, agrees with Z-DNA, and the pitch-to-radius ratio from WLRC agrees with the data of B-DNA qualitatively. Using the general shape equations, we discuss a chiral model in which the solutions of straight, helical, and circular biopolymers are given, respectively. We also find that the model suggested by Helfrich [Langmuir 7, 567 (1991)] is very appropriate to describe B-DNA (or other biopolymers) if we choose the four phenomenological parameters as A=50 nm , C=60 nm(2) , alpha=40 nm(3) , and beta=50 nm(2) .

  3. Polymer electrolyte reviews. 1

    Energy Technology Data Exchange (ETDEWEB)

    Mac Callum, J.R.; Vincent, C.A.


    The development of polymer electrolytes which have potential applications in battery technology has resulted in an escalation of research into the synthesis of new macromolecular supports and the mechanisms of ionic transport within the solid matrix. Investigation of the properties of polymer electrolytes has brought together polymer chemists and electrochemists, and the understanding of the solubility and transport of electrolytes in organic polymers is now developing from this pooled experience. This book deals with experimental, theoretical and applied aspects of solid solutions of electrolytes used in coordinating polymer matrices. Attention is focused on the synthesis and properties of these new materials, the mechanisms of conduction processes and practical applications, especially with regard to battery technology.

  4. Polymer wear evaluation

    DEFF Research Database (Denmark)

    Lagerbon, Mikkel; Sivebæk, Ion Marius


    the safety of the patients. Prediction of the wear of polymers is complicated by the low thermal conductivity of this kind of material. It implies that any acceleration of testing conditions by increased contact pressure and/or sliding velocity will make the polymer fail due to exaggerated heat buildup......Polymer wear plays an increasing role in manufacturing of machine parts for e.g. medical devices. Some of these have an expected lifetime of five to eight years during which very little wear of the components is acceptable. Too much wear compromises the dosage accuracy of the device and thereby....... This is not the kind of wear observed in medical devices. In the present work a method was developed capable of evaluating the wear progression in polymer-polymer contacts. The configuration of the setup is injection moulded specimens consisting of an upper part having a toroid shape and a lower flat part. The sliding...

  5. Effect of anchor positioning on binding and diffusion of elongated 3D DNA nanostructures on lipid membranes (United States)

    Khmelinskaia, Alena; Franquelim, Henri G.; Petrov, Eugene P.; Schwille, Petra


    DNA origami is a state-of-the-art technology that enables the fabrication of nano-objects with defined shapes, to which functional moieties, such as lipophilic anchors, can be attached with a nanometre scale precision. Although binding of DNA origami to lipid membranes has been extensively demonstrated, the specific requirements necessary for membrane attachment are greatly overlooked. Here, we designed a set of amphipathic rectangular-shaped DNA origami structures with varying placement and number of chol-TEG anchors used for membrane attachment. Single- and multiple-cholesteryl-modified origami nanostructures were produced and studied in terms of their membrane localization, density and dynamics. We show that the positioning of at least two chol-TEG moieties near the corners is essential to ensure efficient membrane binding of large DNA nanostructures. Quantitative fluorescence correlation spectroscopy data further confirm that increasing the number of corner-positioned chol-TEG anchors lowers the dynamics of flat DNA origami structures on freestanding membranes. Taken together, our approach provides the first evidence of the importance of the location in addition to the number of hydrophobic moieties when rationally designing minimal DNA nanostructures with controlled membrane binding.

  6. Hybrid polymer-grafted multiwalled carbon nanotubes for in vitro gene delivery. (United States)

    Nunes, Antonio; Amsharov, Nadja; Guo, Chang; Van den Bossche, Jeroen; Santhosh, Padmanabhan; Karachalios, Theodoros K; Nitodas, Stephanos F; Burghard, Marko; Kostarelos, Kostas; Al-Jamal, Khuloud T


    Carbon nanotubes (CNTs) consist of carbon atoms arranged in sheets of graphene rolled up into cylindrical shapes. This class of nanomaterials has attracted attention because of their extraordinary properties, such as high electrical and thermal conductivity. In addition, development in CNT functionalization chemistry has led to an enhanced dispersibility in aqueous physiological media which indeed broadens the spectrum for their potential biological applications including gene delivery. The aim of this study is to determine the capability of different cationic polymer-grafted multiwalled carbon nanotubes (MWNTs) (polymer-g-MWNTs) to efficiently complex and transfer plasmid DNA (pCMV-βGal) in vitro without promoting cytotoxicity. Carboxylated MWNT is chemically conjugated to the cationic polymers polyethylenimine (PEI), polyallylamine (PAA), or a mixture of the two polymers. In order to explore the potential of these polymer-g-MWNTs as gene delivery systems, we first study their capacity to complex plasmid DNA (pDNA) using agarose gel electrophoresis. Gel migration studies confirm pDNA binding to polymer-g-MWNT with different affinities, highest for PEI-g-MWNT and PEI/PAA-g-CNT constructs. β-galactosidase expression is assessed in human lung epithelial (A549) cells, and the cytotoxicity is determined by modified LDH assay after 24 h incubation period. Additionally, PEI-g-MWNT and/or PEI/PAA-g-MWNT reveal an improvement in gene expression when compared to the naked pDNA or to the equivalent amounts of PEI polymer alone. Mechanistically, pDNA was delivered by the polymer-g-MWNT constructs via a different pathway compared to those used by polyplexes. In conclusion, polymer-g-MWNTs may be considered in the future as a versatile tool for efficient gene transfer in cancer cells in vitro, provided their toxicological profile is established.

  7. Wall depletion length of a channel-confined polymer (United States)

    Cheong, Guo Kang; Li, Xiaolan; Dorfman, Kevin D.


    Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well-defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths.

  8. Synthetic genetic polymers capable of heredity and evolution

    DEFF Research Database (Denmark)

    Pinheiro, Vitor B; Taylor, Alexander I; Cozens, Christopher


    Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored...... in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity...... for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage....

  9. Ion implantation in polymers (United States)

    Wintersgill, M. C.


    An introductory overview will be given of the effects of ion implantation on polymers, and certain areas will be examined in more detail. Radiation effects in general and ion implantation in particular, in the field of polymers, present a number of contrasts with those in ionic crystals, the most obvious difference being that the chemical effects of both the implanted species and the energy transfer to the host may profoundly change the nature of the target material. Common effects include crosslinking and scission of polymer chains, gas evolution, double bond formation and the formation of additional free radicals. Research has spanned the chemical processes involved, including polymerization reactions achievable only with the use of radiation, to applied research dealing both with the effects of radiation on polymers already in commercial use and the tailoring of new materials to specific applications. Polymers are commonly divided into two groups, in describing their behavior under irradiation. Group I includes materials which form crosslinks between molecules, whereas Group II materials tend to degrade. In basic research, interest has centered on Group I materials and of these polyethylene has been studied most intensively. Applied materials research has investigated a variety of polymers, particularly those used in cable insulation, and those utilized in ion beam lithography of etch masks. Currently there is also great interest in enhancing the conducting properties of polymers, and these uses would tend to involve the doping capabilities of ion implantation, rather than the energy deposition.

  10. Amphipathic silica nanoparticles induce cytotoxicity through oxidative stress mediated and p53 dependent apoptosis pathway in human liver cell line HL-7702 and rat liver cell line BRL-3A. (United States)

    Zuo, Daiying; Duan, Zhenfang; Jia, Yuanyuan; Chu, Tianxue; He, Qiong; Yuan, Juan; Dai, Wei; Li, Zengqiang; Xing, Liguo; Wu, Yingliang


    The aim of this study was to evaluate the potential cytotoxicity and the underlying mechanism of amphipathic silica nanoparticles (SiO2 NPs) exposure to human normal liver HL-7702 cells and rat normal liver BRL-3A cells. Prior to the cellular studies, transmission electron microscopy (TEM), dynamic light scattering (DLS), and X ray diffraction (XRD) were used to characterize SiO2 NPs, which proved the amorphous nature of SiO2 NPs with TEM diameter of 19.8±2.7nm. Further studies proved that exposure to SiO2 NPs dose-dependently induced cytotoxicity as revealed by cell counting kit (CCK-8) and lactate dehydrogenase (LDH) assays, with more severe cytotoxicity in HL-7702 cells than BRL-3A cells. Reactive oxygen species (ROS) and glutathione (GSH) assays showed elevated oxidative stress in both cells. Morphological studies by microscopic observation, Hochest 33258 and AO/EB staining indicated significant apoptotic changes after the cells being exposed to SiO2 NPs. Further studies by western blot indicated that SiO2 NPs exposure to both cells up-regulated p53, Bax and cleaved caspase-3 expression and down-regulated Bcl-2 and caspase-3 levels. Activated caspase-3 activity detected by colorimetric assay kit and caspase-3/7 activity detected by fluorescent real-time detection kit were significantly increased by SiO2 NPs exposure. In addition, antioxidant vitamin C significantly attenuated SiO2 NPs-induced caspase-3 activation, which indicated that SiO2 NPs-induced oxidative stress was involved in the process of HL-7702 and BRL-3A cell apoptosis. Taken together, these results suggested that SiO2 NPs-induced cytotoxicity in HL-7702 and BRL-3A cells was through oxidative stress mediated and p53, caspase-3 and Bax/Bcl-2 dependent pathway and HL-7702 cells were more sensitive to SiO2 NPs-induced cytotoxicity than BRL-3A cells.

  11. Revisiting blob theory for DNA diffusivity in slitlike confinement (United States)

    Dai, Liang; Tree, Douglas R.; van der Maarel, Johan R. C.; Dorfman, Kevin D.; Doyle, Patrick S.


    Blob theory has been widely applied to describe polymer conformations and dynamics in nanoconfinement. In slit confinement, blob theory predicts a scaling exponent of 2/3 for polymer diffusivity as a function of slit height, yet a large body of experimental studies using DNA produce a scaling exponent significantly less than 2/3. In this work, we develop a theory that predicts that this discrepancy occurs because the segment correlation function for a semiflexible chain such as DNA does not follow the Flory exponent for length scales smaller than the persistence length. We show that these short length scale effects contribute significantly to the scaling for the DNA diffusivity, but do not appreciably affect the scalings for static properties. Our theory is fully supported by Monte Carlo simulations, quantitative agreement with DNA experiments, and the results reconcile this outstanding problem for confined polymers. PMID:23679643

  12. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.


    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  13. Investigation of a thiolated polymer in gene delivery (United States)

    Bacalocostantis, Irene

    Thiol-containing bioreducible polymers show significant potential as delivery vectors in gene therapy, a rapidly growing field which seeks to treat genetic-based disorders by delivering functional synthetic genes to diseased cells. Studies have shown that thiolated polymers exhibit improved biodegradability and prolonged in vivo circulation times over non-thiolated polymers. However, the extent to which thiol concentrations impact the carrier's delivery potential has not been well explored. The aim of this dissertation is to investigate how relative concentrations of free thiols and disulfide crosslinks impact a polymeric carriers delivery performance with respect to DNA packaging, complex stability, cargo protection, gene release, internalization efficiency and cytotoxicity. To accomplish this goal, several fluorescent polymers containing varying concentrations of thiol groups were synthesized by conjugating thiol-pendant chains onto the primary amines of cationic poly(allylamine). In vitro delivery assays and characterization techniques were employed to assess the effect of thiols in gene delivery.

  14. Wireframe and tensegrity DNA nanostructures. (United States)

    Simmel, Stephanie S; Nickels, Philipp C; Liedl, Tim


    CONSPECTUS: Not only can triangulated wireframe network and tensegrity design be found in architecture, but it is also essential for the stability and organization of biological matter. Whether the scaffolding material is metal as in Buckminster Fuller's geodesic domes and Kenneth Snelson's floating compression sculptures or proteins like actin or spectrin making up the cytoskeleton of biological cells, wireframe and tensegrity construction can provide great stability while minimizing the material required. Given the mechanical properties of single- and double-stranded DNA, it is not surprising to find many variants of wireframe and tensegrity constructions in the emerging field of DNA nanotechnology, in which structures of almost arbitrary shape can be built with nanometer precision. The success of DNA self-assembly relies on the well-controlled hybridization of complementary DNA strands. Consequently, understanding the fundamental physical properties of these molecules is essential. Many experiments have shown that double-stranded DNA (in its most commonly occurring helical form, the B-form) behaves in a first approximation like a relatively stiff cylindrical beam with a persistence length of many times the length of its building blocks, the base pairs. However, it is harder to assign a persistence length to single-stranded DNA. Here, normally the Kuhn length is given, a measure that describes the length of individual rigid segments in a freely jointed chain. This length is on the order of a few nucleotides. Two immediate and important consequences arise from this high flexibility: single-stranded DNA is almost always present in a coiled conformation, and it behaves, just like all flexible polymers in solution, as an entropic spring. In this Account, we review the relation between the mechanical properties of DNA and design considerations for wireframe and tensegrity structures built from DNA. We illustrate various aspects of the successful evolution of DNA

  15. Biomedical applications of polymers

    CERN Document Server

    Gebelein, C G


    The biomedical applications of polymers span an extremely wide spectrum of uses, including artificial organs, skin and soft tissue replacements, orthopaedic applications, dental applications, and controlled release of medications. No single, short review can possibly cover all these items in detail, and dozens of books andhundreds of reviews exist on biomedical polymers. Only a few relatively recent examples will be cited here;additional reviews are listed under most of the major topics in this book. We will consider each of the majorclassifications of biomedical polymers to some extent, inclu

  16. Development of Silicate Polymers

    DEFF Research Database (Denmark)

    Søgaard, Erik Gydesen; Simonsen, Morten Enggrob

      The development of inorganic polymers is a new promising technology that may be used in many applications. The syntheses of inorganic polymers are normally carried out either by mixing an amorphous material for example silicium dioxide with a mineral base or dissolving metal oxids or metal...... hydroxide in acid and increase pH to saturation of the metal hydroxide. It is assumed that the syntheses of the inorganic polymer are carried out through polymerisation of oligomers (dimer, trimer) which provide the actual unit structures of the three dimensional macromolecular structure. In this work...

  17. Soluble porphyrin polymers (United States)

    Gust, Jr., John Devens; Liddell, Paul Anthony


    Porphyrin polymers of Structure 1, where n is an integer (e.g., 1, 2, 3, 4, 5, or greater) ##STR00001## are synthesized by the method shown in FIGS. 2A and 2B. The porphyrin polymers of Structure 1 are soluble in organic solvents such as 2-MeTHF and the like, and can be synthesized in bulk (i.e., in processes other than electropolymerization). These porphyrin polymers have long excited state lifetimes, making the material suitable as an organic semiconductor for organic electronic devices including transistors and memories, as well as solar cells, sensors, light-emitting devices, and other opto-electronic devices.

  18. Polymer artificial muscles

    Directory of Open Access Journals (Sweden)

    Tissaphern Mirfakhrai


    Full Text Available The various types of natural muscle are incredible material systems that enable the production of large deformations by repetitive molecular motions. Polymer artificial muscle technologies are being developed that produce similar strains and higher stresses using electrostatic forces, electrostriction, ion insertion, and molecular conformational changes. Materials used include elastomers, conducting polymers, ionically conducting polymers, and carbon nanotubes. The mechanisms, performance, and remaining challenges associated with these technologies are described. Initial applications are being developed, but further work by the materials community should help make these technologies applicable in a wide range of devices where muscle-like motion is desirable.

  19. Domain structures and inter-domain interactions defining the holoenzyme architecture of archaeal d-family DNA polymerase. (United States)

    Matsui, Ikuo; Matsui, Eriko; Yamasaki, Kazuhiko; Yokoyama, Hideshi


    Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information.

  20. Domain Structures and Inter-Domain Interactions Defining the Holoenzyme Architecture of Archaeal D-Family DNA Polymerase

    Directory of Open Access Journals (Sweden)

    Hideshi Yokoyama


    Full Text Available Archaea-specific D-family DNA polymerase (PolD forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information.

  1. Bioreducible cross-linked nanoshell enhances gene transfection of polycation/DNA polyplex in vivo. (United States)

    Piao, Ji-Gang; Ding, Sheng-Gang; Yang, Lu; Hong, Chun-Yan; You, Ye-Zi


    In this study, we have prepared a self-cross-linking PEG-based branched polymer, which easily forms a bioreducible nanoshell around polyplexes of cationic polymer and DNA, simply via heating the polyplex dispersions in the presence of this self-cross-linking branched polymer. This nanoshell can prevent the polyplex from dissociation and aggregation in physiological fluids without inhibiting the electrostatic interactions between the polymer and DNA. Furthermore, glutathione (GSH) can act as a stimulus to open the nanoshell after it has entered the cell. The polyplexes coated with the bioreducible nanoshell show an obvious enhancement in gene transfection in vivo compared with bare polyplexes.

  2. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger


    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  3. Water-Soluble Conjugated Polymers: Self-Assembly and Biosensor Applications (United States)

    Bazan, Guillermo


    Homogeneous assays can be designed which take advantage of the optical amplification of conjugated polymers and the self-assembly characteristic of aqueous polyelectrolytes. For example, a ssDNA sequence sensor comprises an aqueous solution containing a cationic water soluble conjugated polymer such as poly(9,9-bis(trimethylammonium)-hexyl)-fluorene phenylene) with a peptide nucleic acid (PNA) labeled with a dye (PNA-C*). Signal transduction is controlled by hybridization of the neutral PNA-C* probe and the negative ssDNA target, resulting in favorable electrostatic interactions between the hybrid complex and the cationic polymer. Distance requirements for Förster energy transfer are thus met only when ssDNA of complementary sequence to the PNA-C* probe is present. Signal amplification by the conjugated polymer provides fluorescein emission >25 times higher than that of the directly excited dye. Transduction by electrostatic interactions followed by energy transfer is a general strategy. Examples involving other biomolecular recognition events, such as DNA/DNA, RNA/protein and RNA/RNA, will also be provided. The mechanism of biosensing will be discussed, with special attention to the varying contributions of hydrophobic and electrostatic forces, polymer conformation, charge density, local concentration of C*s and tailored defect sites for aggregation-induced optical changes. Finally, the water solubility of these conjugated polymers opens possibilities for spin casting onto organic materials, without dissolving the underlying layers. This property is useful for fabricating multilayer organic optoelectronic devices by simple solution techniques.

  4. Fluorescence spectroscopic studies of DNA dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Scalettar, B.A.


    Random solvent induced motions of DNA are manifest as nanosecond torsional oscillations of the helix backbone, nanosecond through millisecond bending deformations and overall rotational and translational diffusion of the polymer. Fluorescence spectroscopy is used to study this spectrum of DNA motions while ethidium monoazide was covalently bounded. The steady state fluorescence depolarization data indicate that the covalent monoazide/DNA complex exhibits internal motions characterized by an average angular amplitude of 26 degrees confirming reports of fast torsional oscillations in noncovalent ethidium bromide/DNA systems. Data obtained by use of a new polarized photobleaching recovery technique (FPR) reflect both the rotational dynamics of the polymer and the reversible photochemistry of the dye. To isolate the reorientational motion of the DNA, the FPR experiments were ran in two modes that differ only in the polarization of the bleaching light. A quotient function constructed from the data obtained in these two modes monitors only the rotational component of the FPR recovery. In specific applications those bending deformations of long DNA molecules that have characteristic relaxation times on the order of 100 microseconds have been resolved. A fluorescence correlation technique that relates fluctuations in particle number to center-of-mass motion was used to measure translational diffusion on coefficients of the plasmid PBR322 and a short oligomeric DNA. A theory that describes angular correlation in systems exhibiting cyclic, biologically directed reorientation and random Brownian rotation is developed.

  5. DNA as a molecular local thermal probe for the analysis of magnetic hyperthermia. (United States)

    Dias, Jorge T; Moros, María; Del Pino, Pablo; Rivera, Sara; Grazú, Valeria; de la Fuente, Jesus M


    Too hot to handle: The surroundings of magnetic nanoparticles can be heated by applying a magnetic field. Polymer-coated magnetic nanoparticles were functionalized with single-stranded DNA molecules and further hybridized with DNA modified with different fluorophores. By correlating the denaturation profiles of the DNA with the local temperature, temperature gradients for the vicinity of the excited nanoparticles were determined.

  6. Shape-memory polymers

    Directory of Open Access Journals (Sweden)

    Marc Behl


    Full Text Available Shape-memory polymers are an emerging class of active polymers that have dual-shape capability. They can change their shape in a predefined way from shape A to shape B when exposed to an appropriate stimulus. While shape B is given by the initial processing step, shape A is determined by applying a process called programming. We review fundamental aspects of the molecular design of suitable polymer architectures, tailored programming and recovery processes, and the quantification of the shape-memory effect. Shape-memory research was initially founded on the thermally induced dual-shape effect. This concept has been extended to other stimuli by either indirect thermal actuation or direct actuation by addressing stimuli-sensitive groups on the molecular level. Finally, polymers are introduced that can be multifunctional. Besides their dual-shape capability, these active materials are biofunctional or biodegradable. Potential applications for such materials as active medical devices are highlighted.

  7. Rheology of Supramolecular Polymers

    DEFF Research Database (Denmark)

    Shabbir, Aamir

    efficient processes or biomedical areas. Design and development of supramolecular polymers using ionic, hydrogen bonding or transition metal complexes with tailored properties requires deep understanding of dynamics both in linear and non-linear deformations. While linear rheology is important to understand...... the dynamics under equilibrium conditions, extensional rheology is relevant during the processing or in the usage of polymers utilizing supramolecular associations for example, acrylic based pressure sensitive adhesives are subjected to extensional deformations during the peeling where strain hardening......) hydrogen bonding polymers, and (b) ionic bonding polymers (hereafter termed as ionomers). We study linear and non-linear rheology fora model system of entangled pure poly(n-butyl acrylate), PnBA, homopolymer andfour poly(acrylic acid), PnBA-PAA, copolymers with varying AA side groups synthesizedvia...

  8. Polymer semiconductor crystals

    Directory of Open Access Journals (Sweden)

    Jung Ah Lim


    Full Text Available One of the long-standing challenges in the field of polymer semiconductors is to figure out how long interpenetrating and entangled polymer chains self-assemble into single crystals from the solution phase or melt. The ability to produce these crystalline solids has fascinated scientists from a broad range of backgrounds including physicists, chemists, and engineers. Scientists are still on the hunt for determining the mechanism of crystallization in these information-rich materials. Understanding the theory and concept of crystallization of polymer semiconductors will undoubtedly transform this area from an art to an area that will host a bandwagon of scientists and engineers. In this article we describe the basic concept of crystallization and highlight some of the advances in polymer crystallization from crystals to nanocrystalline fibers.

  9. Electroactive polymers for sensing (United States)


    Electromechanical coupling in electroactive polymers (EAPs) has been widely applied for actuation and is also being increasingly investigated for sensing chemical and mechanical stimuli. EAPs are a unique class of materials, with low-moduli high-strain capabilities and the ability to conform to surfaces of different shapes. These features make them attractive for applications such as wearable sensors and interfacing with soft tissues. Here, we review the major types of EAPs and their sensing mechanisms. These are divided into two classes depending on the main type of charge carrier: ionic EAPs (such as conducting polymers and ionic polymer–metal composites) and electronic EAPs (such as dielectric elastomers, liquid-crystal polymers and piezoelectric polymers). This review is intended to serve as an introduction to the mechanisms of these materials and as a first step in material selection for both researchers and designers of flexible/bendable devices, biocompatible sensors or even robotic tactile sensing units. PMID:27499846

  10. Polymers for Protein Conjugation

    Directory of Open Access Journals (Sweden)

    Gianfranco Pasut


    Full Text Available Polyethylene glycol (PEG at the moment is considered the leading polymer for protein conjugation in view of its unique properties, as well as to its low toxicity in humans, qualities which have been confirmed by its extensive use in clinical practice. Other polymers that are safe, biodegradable and custom-designed have, nevertheless, also been investigated as potential candidates for protein conjugation. This review will focus on natural polymers and synthetic linear polymers that have been used for protein delivery and the results associated with their use. Genetic fusion approaches for the preparation of protein-polypeptide conjugates will be also reviewed and compared with the best known chemical conjugation ones.


    Institute of Scientific and Technical Information of China (English)

    A.Seeboth; A.Klukowska; R.Ruhmann; D.L(o)tzsch


    Thermochromic polymers will play an extremely important role in the next future.The physical background of thermochromism and the state of development of thermochromic polymers based on light absorption effects are reported.In detail.the interactions between the polymer matrix and the thermochromic composite-composed of leuco or indicator dyes-are discussed on a molecular level.Thermochromic hydrogels with extremely high transparency,an outstanding switching behavior from colorless to colored or between different colors is presented.Preparation of thermosetting and thermoplastic polymers,including the resulting optical,and,for the first time,the mechanical properties are discussed in relation to matrix tuned high-resistant microcapsules.

  12. Active Polymer Gel Actuators


    Shuji Hashimoto; Ryo Yoshida; Yusuke Hara; Shingo Maeda


    Many kinds of stimuli-responsive polymer and gels have been developed and applied to biomimetic actuators or artificial muscles. Electroactive polymers that change shape when stimulated electrically seem to be particularly promising. In all cases, however, the mechanical motion is driven by external stimuli, for example, reversing the direction of electric field. On the other hand, many living organisms can generate an autonomous motion without external driving stimuli like self-beating of he...

  13. Polymer optical motherboard technology (United States)

    Keil, N.; Yao, H.; Zawadzki, C.; Grote, N.; Schell, M.


    In this paper, different hybridly integrated optical devices including optical multiplexer/ demultiplexer and optical transceivers are described. The devices were made using polymer planar light wave circuit (P2LC) technology. Laser diodes, photodiodes, and thin-film filters have been integrated. Key issues involved in this technology, in particular the coupling between laser diodes and polymer waveguides, and between waveguides and photodiodes and also fibers are discussed.

  14. Polymer-Based Therapeutics


    Liu, Shuang; Maheshwari, Ronak; Kiick, Kristi L.


    Polymeric materials have been applied in therapeutic applications, such as drug delivery and tissue regeneration, for decades owing to their biocompatibility and suitable mechanical properties. In addition, select polymer–drug conjugates have been used as bioactive pharmaceuticals owing to their increased drug efficacy, solubility, and target specificity compared with small-molecule drugs. Increased synthetic control of polymer properties has permitted the production of polymer assemblies for...

  15. Branched Polymer Revisited

    CERN Document Server

    Aoki, H; Kawai, H; Kitazawa, Y; Aoki, Hajime; Iso, Satoshi; Kawai, Hikaru; Kitazawa, Yoshihisa


    We show that correlation functions for branched polymers correspond to those for $\\phi^3$ theory with a single mass insertion, not those for the $\\phi^3$ theory themselves, as has been widely believed. In particular, the two-point function behaves as 1/p^4, not as 1/p^2. This behavior is consistent with the fact that the Hausdorff dimension of the branched polymer is four.

  16. Voltammetry of conducting polymers


    Gulaboski, Rubin


    The search for new materials for enhancing electrical conductivity of various materials is one of the most active research areas today. Conducting polymers represent a unique class of organic materials that have been used in many applications such as bioelectronics, sensors, corrosion protection, electrocatalysis, and energy storage devices. Application of the conductive polymers in electrochemistry is almost inevitable in order to get better features of the voltammetric systems ...

  17. Transferases in Polymer Chemistry (United States)

    van der Vlist, Jeroen; Loos, Katja

    Transferases are enzymes that catalyze reactions in which a group is transferred from one compound to another. This makes these enzymes ideal catalysts for polymerization reactions. In nature, transferases are responsible for the synthesis of many important natural macromolecules. In synthetic polymer chemistry, various transferases are used to synthesize polymers in vitro. This chapter reviews some of these approaches, such as the enzymatic polymerization of polyesters, polysaccharides, and polyisoprene.

  18. Emergence of hairpins in the conformations of a confined polymer

    CERN Document Server

    Werner, E; Muralidhar, A; Frykholm, K; Smithe, T St Clere; Fritzsche, J; Westerlund, F; Dorfman, K D; Mehlig, B


    If a semiflexible polymer confined to a narrow channel bends around by 180 degrees, the polymer is said to exhibit a hairpin. The equilibrium extension statistics in either the limit where hairpins are rare or in the limit where they are common have been characterized in detail. In this article we consider the intermediate situation, where hairpins are rare but common enough to influence the extension statistics. We study the equilibrium distribution of the extension, as well as the approach to equilibrium, by a combination of theoretical analysis, Monte Carlo simulations, and experiments on DNA coated by the protein RecA, which enhances the stiffness of DNA by approximately one order of magnitude. We find good agreement between the model and simulations. The model also provides excellent agreement with experimental data provided that we assume a persistence length of 2 $\\mu$m for the RecA-DNA filament.

  19. Nanoimprinted polymer solar cell. (United States)

    Yang, Yi; Mielczarek, Kamil; Aryal, Mukti; Zakhidov, Anvar; Hu, Walter


    Among the various organic photovoltaic devices, the conjugated polymer/fullerene approach has drawn the most research interest. The performance of these types of solar cells is greatly determined by the nanoscale morphology of the two components (donor/acceptor) and the molecular orientation/crystallinity in the photoactive layer. A vertically bicontinuous and interdigitized heterojunction between donor and acceptor has been regarded as one of the ideal structures to enable both efficient charge separation and transport. Synergistic control of polymer orientation in the nanostructured heterojunction is also critical to improve the performance of polymer solar cells. Nanoimprint lithography has emerged as a new approach to simultaneously control both the heterojunction morphology and polymer chains in organic photovoltaics. Currently, in the area of nanoimprinted polymer solar cells, much progress has been achieved in the fabrication of nanostructured morphology, control of molecular orientation/crystallinity, deposition of acceptor materials, patterned electrodes, understanding of structure-property correlations, and device performance. This review article summarizes the recent studies on nanoimprinted polymer solar cells and discusses the outstanding challenges and opportunities for future work.

  20. Rapid Polymer Sequencer (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)


    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  1. Conductivity behaviour of polymer gel electrolytes: Role of polymer

    Indian Academy of Sciences (India)

    S S Sekhon


    Polymer is an important constituent of polymer gel electrolytes along with salt and solvent. The salt provides ions for conduction and the solvent helps in the dissolution of the salt and also provides the medium for ion conduction. Although the polymer added provides mechanical stability to the electrolytes yet its effect on the conductivity behaviour of gel electrolytes as well as the interaction of polymer with salt and solvent has not been conclusively established. The conductivity of lithium ion conducting polymer gel electrolytes decreases with the addition of polymer whereas in the case of proton conducting polymer gel electrolytes an increase in conductivity has been observed with polymer addition. This has been explained to be due to the role of polymer in increasing viscosity and carrier concentration in these gel electrolytes.

  2. East Coalinga polymer project: polymer comparisons. [California

    Energy Technology Data Exchange (ETDEWEB)

    Snell, G.


    Shell Oil Co. conducted a series of injection and filtration tests in the E. Colainga field, California, to determine the injection characteristics of biopolymer and polyacrylamides. The choice of Xanflood biopolymer was made in order to evaluate the relative merits of polymer flooding and waterflooding in the Temblor Zone II reservoir. Conclusions to the field injection tests were (1) Xanflood biopolymers maintain their mobility properties during these tests; (2) it is possible to remove unhydrated Xanflood biopolymer or unhydrated biopolymer and bacterial debris with DE Filtration without significant loss in biopolymer viscosity; (3) the introduction of an optimum level of shear in the biopolymer mixing process increases the mobility control available for a given concentration of polymer; (4) currently available commercial biopolymers cause well-bore impairment so that effective filtration of the polymer solution is required to maintain injectivity; (5) at test injection rates (33 bpd/ft), polyacrylamide loses most of its mobility control by shear degradation at the injection well perforations; (6) polyacrylamide can be delivered to the sand face without severe loss of viscosity; and (7) polyacrylamide will not impair the formation. (12 refs.)

  3. A tunable DNA spring in a nanochannel (United States)

    Riehn, Robert; Staunton, Rory; Lim, Shuang Fang; Bruinsma, Robijn; Reisner, Walter; Austin, Robert


    dsDNA becomes linearized when it is confined to nanofluidic channels with a cross-section of (100 nm)^2 or less, which has made them interesting for genomic DNA analyses. DNA is typically manipulated by means of electric fields. We have found that DNA undergoes a phase transition to a condensed state if an a.c. electric field is applied along the channel direction. The molecule collapses to about 1/4 of it's initial contour length. We will discuss how the effect depends on parameters such as frequency, field strength, channel dimensions, and will discuss the origin of the effect. Interestingly, DNA behaves like an artifical muscle that can be triggered by an a.c. electric field. Since the interaction is expected to hold for any solubilized polyelectrolyte, we speculate that the mechanism may lead to a new class of polymer-based mechanical actuators. These would not suffer from depolarization like piezo transducers.

  4. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian


    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  5. DNA data (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  6. DNA adductomics. (United States)

    Balbo, Silvia; Turesky, Robert J; Villalta, Peter W


    Systems toxicology is a broad-based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term exposome has been employed to refer to the totality of all exposures, and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics, and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the (32)P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. Although triple quadrupole and ion trap mass spectrometry, particularly when using multistage scanning (LC-MS(n)), have shown promise in the field of DNA adductomics, it is anticipated that high-resolution and accurate-mass LC-MS(n) instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should also benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other -omics tools will contribute greatly to the field of systems toxicology.

  7. Precursor polymer compositions comprising polybenzimidazole

    Energy Technology Data Exchange (ETDEWEB)

    Klaehn, John R.; Peterson, Eric S.; Orme, Christopher J.


    Stable, high performance polymer compositions including polybenzimidazole (PBI) and a melamine-formaldehyde polymer, such as methylated, poly(melamine-co-formaldehyde), for forming structures such as films, fibers and bulky structures. The polymer compositions may be formed by combining polybenzimidazole with the melamine-formaldehyde polymer to form a precursor. The polybenzimidazole may be reacted and/or intertwined with the melamine-formaldehyde polymer to form the polymer composition. For example, a stable, free-standing film having a thickness of, for example, between about 5 .mu.m and about 30 .mu.m may be formed from the polymer composition. Such films may be used as gas separation membranes and may be submerged into water for extended periods without crazing and cracking. The polymer composition may also be used as a coating on substrates, such as metal and ceramics, or may be used for spinning fibers. Precursors for forming such polymer compositions are also disclosed.

  8. Extração de DNA de materiais de arquivo e fontes escassas para utilização em reação de polimerização em cadeia (PCR Methods of DNA extraction from archived materials and rare sources for utilization in polymer chain reaction

    Directory of Open Access Journals (Sweden)

    Jaqueline A. Barea


    Full Text Available Este trabalho visou a comparação de cinco métodos diferentes de extração de DNA de materiais de arquivo (tecidos incluídos em parafina, esfregaços de sangue periférico - corados e não corados com Leishman, lâminas com mielogramas, gotas de sangue em Guthrie Card e de fontes escassas (células bucais, um e três bulbos capilares e 2 mL de urina, para que fossem avaliadas a facilidade de aplicação e a facilidade de amplificação deste DNA pela técnica da reação de polimerização em cadeia (PCR. Os métodos incluíram digestão por proteinase K, seguida ou não por purificação com fenol/clorofórmio; Chelex 100® (BioRad; Insta Gene® (BioRad e fervura em água estéril. O DNA obtido foi testado para amplificação de três fragmentos gênicos: Brain-derived neutrophic factor (764 pb, Factor V Leiden (220 pb e Abelson (106 pb. De acordo com o comprimento do fragmento gênico estudado, da fonte potencial de DNA e do método de extração utilizado, os resultados caracterizaram o melhor caminho para padronização de procedimentos técnicos a serem incluídos no manual de Procedimentos Operacionais Padrão do Laboratório de Biologia Molecular do Hemocentro - HC - Unesp - Botucatu.The present work aimed at comparing five different methods of DNA extraction of samples from archived materials (paraffin-embedded tissues, peripheral blood smears - stained or not with Leishman, aspired bone marrow smears and Guthrie card bloodspots and from rare sources (oral cells, one and three capillary bulbs, 2 mL of urine, to evaluate the ease of application and the possibility of amplification of this DNA by the polymerization chain reaction (PCR technique. The methods included proteinase K digestion - followed or not by phenol/chloroform purification, Chelex 100® (BioRad, InstaGene® (BioRad and boiling in the sterile water. The DNA obtained was tested for amplification of three genic fragments: the brain-derived neutrophic factor gene (764 bp

  9. High DNA-Binding Affinity and Gene-Transfection Efficacy of Bioreducible Cationic Nanomicelles with a Fluorinated Core. (United States)

    Wang, Long-Hai; Wu, De-Cheng; Xu, Hang-Xun; You, Ye-Zi


    During the last two decades, cationic polymers have become one of the most promising synthetic vectors for gene transfection. However, the weak interactions formed between DNA and cationic polymers result in low transfection efficacy. Furthermore, the polyplexes formed between cationic polymers and DNA generally exhibit poor stability and toxicity because of the large excess of cationic polymer typically required for complete DNA condensation. Herein, we report the preparation of a novel class of bioreducible cationic nanomicelles by the use of disulfide bonds to connect the cationic shell to the fluorocarbon core. These bioreducible nanomicelles form strong interactions with DNA and completely condense DNA at an N/P ratio of 1. The resulting nanomicelle/DNA polyplexes exhibited high biocompatibility and performed very effectively as a gene-delivery system.

  10. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van


    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  11. TH17 cells promote microbial killing and innate immune sensing of DNA via interleukin 26

    KAUST Repository

    Meller, Stephan


    Interleukin 17-producing helper T cells (TH 17 cells) have a major role in protection against infections and in mediating autoimmune diseases, yet the mechanisms involved are incompletely understood. We found that interleukin 26 (IL-26), a human TH17 cell-derived cytokine, is a cationic amphipathic protein that kills extracellular bacteria via membrane-pore formation. Furthermore, TH17 cell-derived IL-26 formed complexes with bacterial DNA and self-DNA released by dying bacteria and host cells. The resulting IL-26-DNA complexes triggered the production of type I interferon by plasmacytoid dendritic cells via activation of Toll-like receptor 9, but independently of the IL-26 receptor. These findings provide insights into the potent antimicrobial and proinflammatory function of TH17 cells by showing that IL-26 is a natural human antimicrobial that promotes immune sensing of bacterial and host cell death. © 2015 Nature America, Inc.

  12. Structural determinants of HIV-1 Vif susceptibility and DNA binding in APOBEC3F. (United States)

    Siu, Karen K; Sultana, Azmiri; Azimi, Farshad C; Lee, Jeffrey E


    The human APOBEC3 family of DNA cytosine deaminases serves as a front-line intrinsic immune response to inhibit the replication of diverse retroviruses. APOBEC3F and APOBEC3G are the most potent factors against HIV-1. As a countermeasure, HIV-1 viral infectivity factor (Vif) targets APOBEC3s for proteasomal degradation. Here we report the crystal structure of the Vif-binding domain in APOBEC3F and a novel assay to assess Vif-APOBEC3 binding. Our results point to an amphipathic surface that is conserved in APOBEC3s as critical for Vif susceptibility in APOBEC3F. Electrostatic interactions likely mediate Vif binding. Moreover, structure-guided mutagenesis reveals a straight ssDNA-binding groove distinct from the Vif-binding site, and an 'aromatic switch' is proposed to explain DNA substrate specificities across the APOBEC3 family. This study opens new lines of inquiry that will further our understanding of APOBEC3-mediated retroviral restriction and provides an accurate template for structure-guided development of inhibitors targeting the APOBEC3-Vif axis.

  13. Swelling properties of cross-linked DNA gels. (United States)

    Costa, Diana; Miguel, M Graça; Lindman, Björn


    This work represents our contribution to the field of physical chemistry of DNA gels, and concerns the synthesis and study of novel chemically cross-linked DNA gels. The use of covalent DNA gels is a very promising way to study DNA-cosolute interactions, as well as the dynamic behaviour of DNA and cationic compacting agents, like lipids, surfactants and polycations. Manipulating DNA in new ways, like DNA networks, allows a better understanding and characterization of DNA-cosolute complexes at the molecular level, and also allows us to follow the assembly structures of these complexes. The use of responsive polymer gels for targeted delivery of toxic and/or labile drugs has, during the past few years, shown to be a promising concept. The features found in the proposed system would find applications in a broader field of gel/drug interaction, for the development of controlled release and targeted delivery devices.

  14. DNA and RNA sensor

    Institute of Scientific and Technical Information of China (English)

    LIU; Tao; LIN; Lin; ZHAO; Hong; JIANG; Long


    This review summarizes recent advances in DNA sensor. Major areas of DNA sensor covered in this review include immobilization methods of DNA, general techniques of DNA detection and application of nanoparticles in DNA sensor.

  15. What Is Mitochondrial DNA? (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  16. Microrheology of concentrated DNA solutions using optical tweezers

    Indian Academy of Sciences (India)

    Arun S Rajkumar; B M Jaffar Ali


    Semiflexible biopolymers play a vital role in shaping cellular structure and rigidity. In this work, we report the determination of microrheological properties of concentrated, double-stranded calf thymus DNA (CT-DNA) solutions using passive, laser-scattering based particle-tracking methodology. From power spectral analysis, we obtain dynamic shear moduli of the polymer solutions stretching over three decades of frequency (100–103 Hz) and over concentration ranges spanning from very dilute to concentrated regime. We also study the effects of altered ionic strength and denaturation on the shear modulus. Our results indicate that (CT-DNA) exhibits predominantly elastic behaviour in the concentration range we probed. From the measurements of the plateau shear modulus, p, we conclude that DNA generally behaves like a semiflexible polymer in a good solvent even at low ionic strength. We have thus demonstrated application of passive microrheological method using optical tweezers to DNA solutions. Further extensions of the technique and its applications are discussed.

  17. Preparation and separation of DNA-wrapped carbon nanotubes. (United States)

    Ao, Geyou; Zheng, Ming


    Purification of single-chirality single-wall carbon nanotubes (SWCNTs) from their synthetic mixture is a prerequisite for many applications. DNA-controlled carbon nanotube (CNT) purification has evolved over a decade along with other separation techniques utilizing different types of dispersing agents such as surfactants and polymers. The size of single-stranded DNA (ssDNA) libraries affords practically unlimited ways of coating SWCNTs. Recent developments in separating surfactant-dispersed SWCNTs by polymer aqueous two-phase (ATP) extraction has enabled rapid and efficient SWCNT separation on a larger volume scale. Applying the ATP separation method to DNA-SWCNT hybrids opens a new route for effective sorting of nanotubes into each and every single-chirality species. Here, we report protocols for purifying as many as 15 single-chirality nanotube species from a synthetic mixture based on the separation of DNA-SWCNTs by the aqueous two-phase (ATP) method.

  18. Designing new strategy for controlling DNA orientation in biosensors (United States)

    Feng, Chao; Ding, Hong-ming; Ren, Chun-lai; Ma, Yu-qiang


    Orientation controllable DNA biosensors hold great application potentials in recognizing small molecules and detecting DNA hybridization. Though electric field is usually used to control the orientation of DNA molecules, it is also of great importance and significance to seek for other triggered methods to control the DNA orientation. Here, we design a new strategy for controlling DNA orientation in biosensors. The main idea is to copolymerize DNA molecules with responsive polymers that can show swelling/deswelling transitions due to the change of external stimuli, and then graft the copolymers onto an uncharged substrate. In order to highlight the responsive characteristic, we take thermo-responsive polymers as an example, and reveal multi-responsive behavior and the underlying molecular mechanism of the DNA orientation by combining dissipative particle dynamics simulation and molecular theory. Since swelling/deswelling transitions can be also realized by using other stimuli-responsive (like pH and light) polymers, the present strategy is universal, which can enrich the methods of controlling DNA orientation and may assist with the design of the next generation of biosensors. PMID:26400770

  19. Jamming of Semiflexible Polymers (United States)

    Hoy, Robert S.


    We study jamming in model freely rotating polymers as a function of chain length N and bond angle θ0. The volume fraction at jamming ϕJ(θ0) is minimal for rigid-rodlike chains (θ0=0 ), and increases monotonically with increasing θ0≤π /2 . In contrast to flexible polymers, marginally jammed states of freely rotating polymers are highly hypostatic, even when bond and angle constraints are accounted for. Large-aspect-ratio (small θ0) chains behave comparably to stiff fibers: resistance to large-scale bending plays a major role in their jamming phenomenology. Low-aspect-ratio (large θ0) chains behave more like flexible polymers, but still jam at much lower densities due to the presence of frozen-in three-body correlations corresponding to the fixed bond angles. Long-chain systems jam at lower ϕ and are more hypostatic at jamming than short-chain systems. Implications of these findings for polymer solidification are discussed.

  20. Modelling polymer draft gears (United States)

    Wu, Qing; Yang, Xiangjian; Cole, Colin; Luo, Shihui


    This paper developed a new and simple approach to model polymer draft gears. Two types of polymer draft gears were modelled and compared with experimental data. Impact characteristics, in-train characteristics and frequency responses of these polymer draft gears were studied and compared with those of a friction draft gear. The impact simulations show that polymer draft gears can withstand higher impact speeds than the friction draft gear. Longitudinal train dynamics simulations show that polymer draft gears have significantly longer deflections than friction draft gears in normal train operations. The maximum draft gear working velocities are lower than 0.2 m/s, which are significantly lower than the impact velocities during shunting operations. Draft gears' in-train characteristics are similar to their static characteristics but are very different from their impact characteristics; this conclusion has also been reached from frequency response simulations. An analysis of gangway bridge plate failures was also conducted and it was found that they were caused by coupler angling behaviour and long draft gear deflections.

  1. Effects of long DNA folding and small RNA stem-loop in thermophoresis. (United States)

    Maeda, Yusuke T; Tlusty, Tsvi; Libchaber, Albert


    In thermophoresis, with the fluid at rest, suspensions move along a gradient of temperature. In an aqueous solution, a PEG polymer suspension is depleted from the hot region and builds a concentration gradient. In this gradient, DNA polymers of different sizes can be separated. In this work the effect of the polymer structure for genomic DNA and small RNA is studied. For genome-size DNA, individual single T4 DNA is visualized and tracked in a PEG solution under a temperature gradient built by infrared laser focusing. We find that T4 DNA follows steps of depletion, ring-like localization, and accumulation patterns as the PEG volume fraction is increased. Furthermore, a coil-globule transition for DNA is observed for a large enough PEG volume fraction. This drastically affects the localization position of T4 DNA. In a similar experiment, with small RNA such as ribozymes we find that the stem-loop folding of such polymers has important consequences. The RNA polymers having a long and rigid stem accumulate, whereas a polymer with stem length less than 4 base pairs shows depletion. Such measurements emphasize the crucial contribution of the double-stranded parts of RNA for thermal separation and selection under a temperature gradient. Because huge temperature gradients are present around hydrothermal vents in the deep ocean seafloor, this process might be relevant, at the origin of life, in an RNA world hypothesis. Ribozymes could be selected from a pool of random sequences depending on the length of their stems.

  2. Fluctuation modes of nanoconfined DNA. (United States)

    Karpusenko, Alena; Carpenter, Joshua H; Zhou, Chunda; Lim, Shuang Fang; Pan, Junhan; Riehn, Robert


    We report an experimental investigation of the magnitude of length and density fluctuations in DNA that has been stretched in nanofluidic channels. We find that the experimental data can be described using a one-dimensional overdamped oscillator chain with nonzero equilibrium spring length and that a chain of discrete oscillators yields a better description than a continuous chain. We speculate that the scale of these discrete oscillators coincides with the scale at which the finite extensibility of the polymer manifests itself. We discuss how the measurement process influences the apparent measured dynamic properties, and outline requirements for the recovery of true physical quantities.

  3. DNA vaccines (United States)

    Gregersen, Jens-Peter


    Immunization by genes encoding immunogens, rather than with the immunogen itself, has opened up new possibilities for vaccine research and development and offers chances for new applications and indications for future vaccines. The underlying mechanisms of antigen processing, immune presentation and regulation of immune responses raise high expectations for new and more effective prophylactic or therapeutic vaccines, particularly for vaccines against chronic or persistent infectious diseases and tumors. Our current knowledge and experience of DNA vaccination is summarized and critically reviewed with particular attention to basic immunological mechanisms, the construction of plasmids, screening for protective immunogens to be encoded by these plasmids, modes of application, pharmacokinetics, safety and immunotoxicological aspects. DNA vaccines have the potential to accelerate the research phase of new vaccines and to improve the chances of success, since finding new immunogens with the desired properties is at least technically less demanding than for conventional vaccines. However, on the way to innovative vaccine products, several hurdles have to be overcome. The efficacy of DNA vaccines in humans appears to be much less than indicated by early studies in mice. Open questions remain concerning the persistence and distribution of inoculated plasmid DNA in vivo, its potential to express antigens inappropriately, or the potentially deleterious ability to insert genes into the host cell's genome. Furthermore, the possibility of inducing immunotolerance or autoimmune diseases also needs to be investigated more thoroughly, in order to arrive at a well-founded consensus, which justifies the widespread application of DNA vaccines in a healthy population.

  4. DNA nanotechnology

    Directory of Open Access Journals (Sweden)

    Nadrian C Seeman


    We are all aware that the DNA found in cells is a double helix consisting of two antiparallel strands held together by specific hydrogen-bonded base pairs; adenine (A always pairs with thymine (T, and guanine (G always pairs with cytosine (C. The specificity of this base pairing and the ability to ensure that it occurs in this fashion (and not some other1 is key to the use of DNA in materials applications. The double helical arrangement of the two molecules leads to a linear helix axis, linear not in the geometrical sense of being a straight line, but in the topological sense of being unbranched. Genetic engineers discovered in the 1970s how to splice together pieces of DNA to add new genes to DNA molecules2, and synthetic chemists worked out convenient syntheses for short pieces of DNA (up to ∼100–150 units in the 1980s3. Regardless of the impact of these technologies on biological systems, hooking together linear molecules leads only to longer linear molecules, with circles, knots, and catenanes perhaps resulting from time to time.

  5. Antiviral Polymer Therapeutics

    DEFF Research Database (Denmark)

    Smith, Anton Allen Abbotsford


    The field of drug delivery is in essence an exercise in engineered pharmacokinetics. Methods of doing so have been developed through the introduction of a vehicle carrying the drug, either by encapsulation or covalent attachment. The emergence of polymer therapeutics in anticancer therapy has...... the examples of polymer therapeutics being applied as an antiviral treatment are few and far in-between. This work aims to explore antiviral therapeutics, specifically in context of hepatitis virus C (HCV) and HIV. The current treatment of hepatitis C consists of a combination of drugs, of which ribavirin....... Curiously, the therapeutic window of ribavirin was vastly improved in several of these polymers suggesting altered pharmacodynamics. The applicability of liver-targeting sugar moieties is likewise tested in a similarly methodical approach. The same technique of synthesis was applied with zidovudine to make...

  6. Nanostructured silicate polymer concrete

    Directory of Open Access Journals (Sweden)

    Figovskiy Oleg L'vovich


    Full Text Available It has been known that acid-resistant concretes on the liquid glass basis have high porosity (up to 18~20 %, low strength and insufficient water resistance. Significant increasing of silicate matrix strength and density was carried out by incorporation of special liquid organic alkali-soluble silicate additives, which block superficial pores and reduce concrete shrinkage deformation. It was demonstrated that introduction of tetrafurfuryloxisilane additive sharply increases strength, durability and shock resistance of silicate polymer concrete in aggressive media. The experiments showed, that the strength and density of silicate polymer concrete increase in case of decreasing liquid glass content. The authors obtained optimal content of silicate polymer concrete, which possesses increased strength, durability, density and crack-resistance. Diffusive permeability of concrete and its chemical resistance has been investigated in various corroding media.

  7. Doped Chiral Polymer Metamaterials (United States)

    Park, Cheol (Inventor); Kang, Jin Ho (Inventor); Gordon, Keith L. (Inventor); Sauti, Godfrey (Inventor); Lowther, Sharon E. (Inventor); Bryant, Robert G. (Inventor)


    Some implementations provide a composite material that includes a first material and a second material. In some implementations, the composite material is a metamaterial. The first material includes a chiral polymer (e.g., crystalline chiral helical polymer, poly-.gamma.-benzyl-L-glutamate (PBLG), poly-L-lactic acid (PLA), polypeptide, and/or polyacetylene). The second material is within the chiral polymer. The first material and the second material are configured to provide an effective index of refraction value for the composite material of 1 or less. In some implementations, the effective index of refraction value for the composite material is negative. In some implementations, the effective index of refraction value for the composite material of 1 or less is at least in a wavelength of one of at least a visible spectrum, an infrared spectrum, a microwave spectrum, and/or an ultraviolet spectrum.

  8. Polymer Photovoltaic Cells

    Institute of Scientific and Technical Information of China (English)

    Jianhui Hou; Chunhe Yang; Erjun Zhou; Chang He; Zhan'ao Tan; Youjun He; Yongfang Li


    @@ 1Introduction Polymer photovoltaic cells (PPVCs) have attracted much attention recently because of its easy fabrication, low cost and possibility to make flexible devices[1]. PPVC is composed of a conjugated polymer/C60blend layer (photosensitive layer) sandwiched between a transparent ITO electrode and a metal electrode.When a light through ITO electrode irradiates on the photosensitive layer, the photons with appropriate energy will be absorbed by the conjugated polymer (CP) and excitons (electron-hole pair) are produced. The excitons move to the interface of CP/C60 where the electrons transfer to the LUMO of C60 and holes leave on the HOMO of the CP. The separated electrons migrate through the C60 network to and are collected by the metal electrode, and the holes migrate through the CP network to and are collected by the ITO electrode, so that the photocurrent and photovoltage are attained.

  9. 'Stuffed' conducting polymers

    DEFF Research Database (Denmark)

    Winther-Jensen, Bjørn; Chen, Jun; West, Keld


    Conducting polymers (CP) obtained by oxidative polymerization using iron(III) salts shrink when Fe(II) and the excess counter ions are washed out after polymerization. This phenomenon can be used to incorporate active molecules into the CP matrix via their addition to the wash liquid. In the pres......Conducting polymers (CP) obtained by oxidative polymerization using iron(III) salts shrink when Fe(II) and the excess counter ions are washed out after polymerization. This phenomenon can be used to incorporate active molecules into the CP matrix via their addition to the wash liquid....... In the present work we demonstrate this principle on three different CP's: polypyrrole (PPy), poly-terthiophene (PTTh) and poly(3,4-ethylenedioxy thiophene) (PEDT), using ferrocene as a model molecule to be trapped in the polymer films. (c) 2005 Elsevier Ltd. All rights reserved....

  10. Active Polymer Gel Actuators

    Directory of Open Access Journals (Sweden)

    Shuji Hashimoto


    Full Text Available Many kinds of stimuli-responsive polymer and gels have been developed and applied to biomimetic actuators or artificial muscles. Electroactive polymers that change shape when stimulated electrically seem to be particularly promising. In all cases, however, the mechanical motion is driven by external stimuli, for example, reversing the direction of electric field. On the other hand, many living organisms can generate an autonomous motion without external driving stimuli like self-beating of heart muscles. Here we show a novel biomimetic gel actuator that can walk spontaneously with a wormlike motion without switching of external stimuli. The self-oscillating motion is produced by dissipating chemical energy of oscillating reaction. Although the gel is completely composed of synthetic polymer, it shows autonomous motion as if it were alive.

  11. Polymer Chemistry in High School. (United States)

    Stucki, Roger


    Discusses why polymer chemistry should be added to the general chemistry curriculum and what topics are appropriate (listing traditional with related polymer topics). Also discusses when and how these topics should be taught. (JN)

  12. Composite solid polymer electrolyte membranes

    Energy Technology Data Exchange (ETDEWEB)

    Formato, Richard M. (Shrewsbury, MA); Kovar, Robert F. (Wrentham, MA); Osenar, Paul (Watertown, MA); Landrau, Nelson (Marlborough, MA); Rubin, Leslie S. (Newton, MA)


    The present invention relates to composite solid polymer electrolyte membranes (SPEMs) which include a porous polymer substrate interpenetrated with an ion-conducting material. SPEMs of the present invention are useful in electrochemical applications, including fuel cells and electrodialysis.

  13. Conducting polymer 3D microelectrodes

    DEFF Research Database (Denmark)

    Sasso, Luigi; Vazquez, Patricia; Vedarethinam, Indumathi


    Conducting polymer 3D microelectrodes have been fabricated for possible future neurological applications. A combination of micro-fabrication techniques and chemical polymerization methods has been used to create pillar electrodes in polyaniline and polypyrrole. The thin polymer films obtained...

  14. Polymers and colloids

    Energy Technology Data Exchange (ETDEWEB)

    Schurtenberger, P. [ETH Zurich, Inst. fuer Polymere, Zurich (Switzerland)


    A wealth of structural information from colloid and polymer solutions on a large range of length scales can be obtained using small angle neutron scattering (SANS) experiments. After a general introduction to the field of soft condensed matter, I shall give a few selected examples on how SANS combined with suitable contrast variation schemes can be used to extract information on the size and conformation of polymer coils in solution and in the melt, and on the local structure and flexibility of polymerlike micelles and microemulsions. (author) 8 figs., tabs., 44 refs.

  15. Shape memory polymer foams (United States)

    Santo, Loredana


    Recent advances in shape memory polymer (SMP) foam research are reviewed. The SMPs belong to a new class of smart polymers which can have interesting applications in microelectromechanical systems, actuators and biomedical devices. They can respond to specific external stimulus changing their configuration and then remember the original shape. In the form of foams, the shape memory behaviour can be enhanced because they generally have higher compressibility. Considering also the low weight, and recovery force, the SMP foams are expected to have great potential applications primarily in aerospace. This review highlights the recent progress in characterization, evaluation, and proposed applications of SMP foams mainly for aerospace applications.

  16. Delocalization in polymer models

    CERN Document Server

    Jitomirskaya, S Yu; Stolz, G


    A polymer model is a one-dimensional Schroedinger operator composed of two finite building blocks. If the two associated transfer matrices commute, the corresponding energy is called critical. Such critical energies appear in physical models, an example being the widely studied random dimer model. Although the random models are known to have pure-point spectrum with exponentially localized eigenstates for almost every configuration of the polymers, the spreading of an initially localized wave packet is here proven to be at least diffusive for every configuration.

  17. Antibacterial polymer coatings.

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Mollye C.; Allen, Ashley N.; Barnhart, Meghan; Tucker, Mark David; Hibbs, Michael R.


    A series of poly(sulfone)s with quaternary ammonium groups and another series with aldehyde groups are synthesized and tested for biocidal activity against vegetative bacteria and spores, respectively. The polymers are sprayed onto substrates as coatings which are then exposed to aqueous suspensions of organisms. The coatings are inherently biocidal and do not release any agents into the environment. The coatings adhere well to both glass and CARC-coated coupons and they exhibit significant biotoxicity. The most effective quaternary ammonium polymers kills 99.9% of both gram negative and gram positive bacteria and the best aldehyde coating kills 81% of the spores on its surface.

  18. Electrically Conducting Polymers. (United States)


    polypyrrole, the oxidized polythiophene is also unstable in air. A rather different class of conducting polymers lies outside the scope of this review but...AD-A129 488 ELECTRICALLY CONDUCTING POLYNERS(U) IBM RESEARCH LAB / SAN JOSE CA W D GILL ET RL. 97 APR 83 TR-B UNCLASSIFIED F/G 7/3 N I Ihhhhhhhhhhhhl...00 Contract N00014-80-C-0779 Technical Report No. 8 *Electrically Conducting Polymers by W. D. Gill, T. C. Clarke, and G. B. Street Prepared for

  19. Nanoparticles from Renewable Polymers (United States)

    Wurm, Frederik; Weiss, Clemens


    The use of polymers from natural resources can bring many benefits for novel polymeric nanoparticle systems. Such polymers have a variety of beneficial properties such as biodegradability and biocompatibility, they are readily available on large scale and at low cost. As the amount of fossil fuels decrease, their application becomes more interesting even if characterization is in many cases more challenging due to structural complexity, either by broad distribution of their molecular weights polysaccharides, polyesters, lignin) or by complex structure (proteins, lignin). This review summarizes different sources and methods for the preparation of biopolymer-based nanoparticle systems for various applications.

  20. Polymers at cryogenic temperatures

    CERN Document Server

    Fu, Shao-Yun


    Kalia and Fu's novel monograph covers cryogenic treatment, properties and applications of cryo-treated polymer materials. Written by numerous international experts, the twelve chapters in this book offer the reader a comprehensive picture of the latest findings and developments, as well as an outlook on the field. Cryogenic technology has seen remarkable progress in the past few years and especially cryogenic properties of polymers are attracting attention through new breakthroughs in space, superconducting, magnetic and electronic techniques. This book is a valuable resource for researchers, educators, engineers and graduate students in the field and at technical institutions.

  1. DNA Confined in Nanochannels and Nanoslits (United States)

    Tree, Douglas R.

    It has become increasingly apparent in recent years that next-generation sequencing (NGS) has a blind spot for large scale genomic variation, which is crucial for understanding the genotype-phenotype relationship. Genomic mapping methods attempt to overcome the weakesses of NGS by providing a coarse-grained map of the distances between restriction sites to aid in sequence assembly. From such methods, one hopes to realize fast and inexpensive de novo sequencing of human and plant genomes. One of the most promising methods for genomic mapping involves placing DNA inside a device only a few dozen nanometers wide called a nanochannel. A nanochannel stretches the DNA so that the distance between fluorescently labeled restriction sites can be measured en route to obtaining an accurate genome map. Unfortunately for those who wish to design devices, the physics of how DNA stretches when confined in a nanochannel is still an active area of research. Indeed, despite decades old theories from polymer physics regarding weakly and strongly stretched polymers, seminal experiments in the mid-2000s have gone unexplained until very recently. With a goal of creating a realistic engineering model of DNA in nanochannels, this dissertation addresses a number of important outstanding research topics in this area. We first discuss the physics of dilute solutions of DNA in free solution, which show distinctive behavior due to the stiff nature of the polymer. We then turn our attention to the equilibrium regimes of confined DNA and explore the effects of stiff chains and weak excluded volume on the confinement free energy and polymer extension. We also examine dynamic properties such as the diffusion coefficient and the characteristic relaxation time. Finally, we discuss a sister problem related to DNA confined in nanoslits, which shares much of the same physics as DNA confined in channels. Having done this, we find ourselves with a well-parameterized wormlike chain model that is

  2. Shape memory polymer medical device (United States)

    Maitland, Duncan; Benett, William J.; Bearinger, Jane P.; Wilson, Thomas S.; Small, IV, Ward; Schumann, Daniel L.; Jensen, Wayne A.; Ortega, Jason M.; Marion, III, John E.; Loge, Jeffrey M.


    A system for removing matter from a conduit. The system includes the steps of passing a transport vehicle and a shape memory polymer material through the conduit, transmitting energy to the shape memory polymer material for moving the shape memory polymer material from a first shape to a second and different shape, and withdrawing the transport vehicle and the shape memory polymer material through the conduit carrying the matter.

  3. Polymer-solvent molecular compounds

    CERN Document Server

    Guenet, Jean-Michel


    Crystallisable polymers represent a large share of the polymers used for manufacturing a wide variety of objects, and consequently have received continuous attention from scientists these past 60 years. Molecular compounds from crystallisable polymers, particularly from synthetic polymers, are receiving growing interest due to their potential application in the making of new materials such as multiporous membranes capable of capturing large particles as well as small pollutant molecules. The present book gives a detailed description of these promising systems. The first chapter

  4. Adsorption theory for polydisperse polymers.

    NARCIS (Netherlands)

    Roefs, S.P.F.M.; Scheutjens, J.M.H.M.; Leermakers, F.A.M.


    Most polymers are polydisperse. We extend the self-consistent field polymer adsorption theory due to Scheutjens and Fleer to account for an arbitrary polymer molecular weight distribution with a cutoff chain length Nmax. In this paper, the treatment is restricted to homopolymers. For this case a ver

  5. Self-assembled alignment of nanorod by using DNA brush (Conference Presentation) (United States)

    Ijiro, Kuniharu; Nakamura, Satoshi; Mitomo, Hideyuki; Pike, Andrew; Matsuo, Yasutaka; Niikura, Kenichi


    Surface modification with polymer is widely applied to various kinds of applications. Recently, polymer brushes, which is a layer of polymers attached with one end to a surface, have attracted much attention as functionalized surfaces. In particular, ionic polymer brushes provide ultra-low friction or anti-fouling because they act as highly hydrated soft film. Almost ionic polymer brushes have been prepared from synthetic polymers. Few biopolymers have been investigated for polymer brush studies. DNA which is one of ionic biopolymers has unique functions and conformations which synthetic polymers don't have. We found that cationic gold nanorods (30 x 10 nm) were adsorbed to DNA bush (148 bp) prepared on a glass surface in an aqueous solution by observation using extinction spectra. When the cationic charge density of gold nanorods were decreased, nanorods were immobilized perpendicularly to the substrate by binding to DNA elongated. This indicates that self-assembled alignment of gold nanorods can be achieved by using DNA brush. Formed aligned gold nanorods can be used for plasmonic color analysis.

  6. DNA origami nanopores for controlling DNA translocation. (United States)

    Hernández-Ainsa, Silvia; Bell, Nicholas A W; Thacker, Vivek V; Göpfrich, Kerstin; Misiunas, Karolis; Fuentes-Perez, Maria Eugenia; Moreno-Herrero, Fernando; Keyser, Ulrich F


    We combine DNA origami structures with glass nanocapillaries to reversibly form hybrid DNA origami nanopores. Trapping of the DNA origami onto the nanocapillary is proven by imaging fluorescently labeled DNA origami structures and simultaneous ionic current measurements of the trapping events. We then show two applications highlighting the versatility of these DNA origami nanopores. First, by tuning the pore size we can control the folding of dsDNA molecules ("physical control"). Second, we show that the specific introduction of binding sites in the DNA origami nanopore allows selective detection of ssDNA as a function of the DNA sequence ("chemical control").

  7. Synthesis of polymer-biohybrids: from small to giant surfactants. (United States)

    Reynhout, Irene C; Cornelissen, Jeroen J L M; Nolte, Roeland J M


    Amphiphiles or surfactants, more popularly known as soaps, are among the oldest known chemical compounds used by man. Written text on a clay tablet dated to 2200 B.C. indicates that the Babylonians were familiar with soap-like substances. According to the Ebers papyrus (1550 B.C.), the ancient Egyptians bathed regularly in a mixture of animal oils, vegetable extracts, and alkaline salts, and a soap factory with bars of scented soap was found in the ruins of Pompeii (79 A.D.). In modern times, the use of soap has become universal, and we now understand reasonably well what happens when soap molecules are dispersed in aqueous solution and how the cleaning properties of soap work. The latter is related to the surface-active behavior of soap molecules, which is a result of their amphiphilic, also called amphipathic, character. Although the cleaning aspect is still an important issue, scientists are increasingly focusing on other properties of soaps, for example, self-assembling behavior and how this can be used in the design and non-covalent synthesis of new (macro)molecular architectures. These new molecules can be employed in nanotechnology and drug delivery, among other applications. This Account will focus on three different classes of amphiphiles. The first is the low molecular weight amphiphiles, also called classical amphiphiles in this context. A short overview will be given on the research carried out by our group and others on the self-assembly behavior and properties of these compounds; in particular, we focus on the ones that can be stabilized by polymerization (polymerized vesicles). Next, we will introduce the still relatively young field of superamphiphiles, macromolecules consisting of a hydrophobic and a hydrophilic polymeric block. Finally, and this constitutes the main part of this Account, we will provide an overview of a new class of amphiphiles, the so-called giant amphiphiles. These macromolecules have an enzyme or protein as the polar head group

  8. Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement

    DEFF Research Database (Denmark)

    Hong, Sun-Hae; Toro, Esteban; Mortensen, Kim;


    is the contour length, and cell-to-cell distribution of the interloci distance r is a universal function of r/n0.22 with broad cell-to-cell variability. For DNA segments greater than about 300 kb, the mean interloci distances scale as n, in agreement with previous observations. The 0.22 value of the scaling......We measured the distance between fluorescent-labeled DNA loci of various interloci contour lengths in Caulobacter crescentus swarmer cells to determine the in vivo configuration of the chromosome. For DNA segments less than about 300 kb, the mean interloci distances, 〈r〉, scale as n0.22, where n...... exponent for short DNA segments is consistent with theoretical predictions for a branched DNA polymer structure. Predictions from Brownian dynamics simulations of the packing of supercoiled DNA polymers in an elongated cell-like confinement are also consistent with a branched DNA structure, and simulated...

  9. Dynamics of Polaron at Polymer/Polymer Interface

    Institute of Scientific and Technical Information of China (English)

    DI Bing; MENG Yan; AN Zhong; LI You-Cheng


    The migration of a polaron at polymer/polymer interface is believed to be of fundamental importance for the transport and light-emitting properties of conjugated polymer-based light emitting diodes.Based on the onedimensional tight-binding Su-Schrieffer-Heeger(SSH)model,we have investigated polaron dynamics in a onedimensional polymer/polymer system by using a nonadiabatic evolution method.In particular,we focus on how a polaron migrates through the conjugated polymer/polymer interface in the presence of external electric field.The results show that the migration of polaron at the interface depends sensitively on the hopping integrals,the potential barrier induced by the energy mismatch,and the strength of applied electric field which increases the polaron kinetic energy.

  10. Primordial polymer perturbations

    Energy Technology Data Exchange (ETDEWEB)

    Seahra, Sanjeev S.; Husain, Viqar [Department of Mathematics and Statistics, University of New Brunswick, Fredericton, NB, E3B 5A3 (Canada); Brown, Iain A. [Institute of Theoretical Astrophysics, University of Oslo, P.O. Box 1029 Blindern, N-0315 Oslo (Norway); Hossain, Golam Mortuza, E-mail:, E-mail:, E-mail:, E-mail: [Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, P.O. Krishi Viswavidyalaya, Nadia 741 252, WB (India)


    We study the generation of primordial fluctuations in pure de Sitter inflation where the quantum scalar field dynamics are governed by polymer (not Schroedinger) quantization. This quantization scheme is related to, but distinct from, the structures employed in Loop Quantum Gravity; and it modifies standard results above a polymer energy scale M{sub *}. We recover the scale invariant Harrison Zel'dovich spectrum for modes that have wavelengths bigger than M{sub *}{sup −1} at the start of inflation. The primordial spectrum for modes with initial wavelengths smaller than M{sub *}{sup −1} exhibits oscillations superimposed on the standard result. The amplitude of these oscillations is proportional to the ratio of the inflationary Hubble parameter H to the polymer energy scale. For reasonable choices of M{sub *}, we find that polymer effects are likely unobservable in CMB angular power spectra due to cosmic variance uncertainty, but future probes of baryon acoustic oscillations may be able to directly constrain the ratio H/M{sub *}.

  11. Glass Fibre Reinforced Polymers

    NARCIS (Netherlands)

    Nikolaou, N.; Karagianni, L.; Sarakiniatti, M.V.


    This "designers' manual" is made during the TIDO-course AR0533 Innovation & Sustainability. Fibre reinforced polymers (FRPs) have been used in many applications over the years, from new construction to retrofitting. They are lightweight, no-corrosive, exhibit high specific strength and specific sti

  12. Semi-metallic polymers

    DEFF Research Database (Denmark)

    Bubnova, Olga; Khan, Zia Ullah; Wang, Hui


    Polymers are lightweight, flexible, solution-processable materials that are promising for low-cost printed electronics as well as for mass-produced and large-area applications. Previous studies demonstrated that they can possess insulating, semiconducting or metallic properties; here we report th...... a Fermi glass to a semi-metal. The high Seebeck value, the metallic conductivity at room temperature and the absence of unpaired electron spins makes polymer semi-metals attractive for thermoelectrics and spintronics.......Polymers are lightweight, flexible, solution-processable materials that are promising for low-cost printed electronics as well as for mass-produced and large-area applications. Previous studies demonstrated that they can possess insulating, semiconducting or metallic properties; here we report...... that polymers can also be semi-metallic. Semi-metals, exemplified by bismuth, graphite and telluride alloys, have no energy bandgap and a very low density of states at the Fermi level. Furthermore, they typically have a higher Seebeck coefficient and lower thermal conductivities compared with metals, thus being...

  13. Segmented conjugated polymers

    Indian Academy of Sciences (India)

    G Padmanaban; S Ramakrishnan


    Segmented conjugated polymers, wherein the conjugation is randomly truncated by varying lengths of non-conjugated segments, form an interesting class of polymers as they not only represent systems of varying stiffness, but also ones where the backbone can be construed as being made up of chromophores of varying excitation energies. The latter feature, especially when the chromophores are fluorescent, like in MEHPPV, makes these systems particularly interesting from the photophysics point of view. Segmented MEHPPV- samples, where x represents the mole fraction of conjugated segments, were prepared by a novel approach that utilizes a suitable precursor wherein selective elimination of one of the two eliminatable groups is affected; the uneliminated units serve as conjugation truncations. Control of the composition x of the precursor therefore permits one to prepare segmented MEHPPV- samples with varying levels of conjugation (elimination). Using fluorescence spectroscopy, we have seen that even in single isolated polymer chains, energy migration from the shorter (higher energy) chromophores to longer (lower energy) ones occurs – the extent of which depends on the level of conjugation. Further, by varying the solvent composition, it is seen that the extent of energy transfer and the formation of poorly emissive inter-chromophore excitons are greatly enhanced with increasing amounts of non-solvent. A typical S-shaped curve represents the variation of emission yields as a function of composition suggestive of a cooperative collapse of the polymer coil, reminiscent of conformational transitions seen in biological macromolecules.

  14. Cyclic polymers from alkynes (United States)

    Roland, Christopher D.; Li, Hong; Abboud, Khalil A.; Wagener, Kenneth B.; Veige, Adam S.


    Cyclic polymers have dramatically different physical properties compared with those of their equivalent linear counterparts. However, the exploration of cyclic polymers is limited because of the inherent challenges associated with their synthesis. Conjugated linear polyacetylenes are important materials for electrical conductivity, paramagnetic susceptibility, optical nonlinearity, photoconductivity, gas permeability, liquid crystallinity and chain helicity. However, their cyclic analogues are unknown, and therefore the ability to examine how a cyclic topology influences their properties is currently not possible. We have solved this challenge and now report a tungsten catalyst supported by a tetraanionic pincer ligand that can rapidly polymerize alkynes to form conjugated macrocycles in high yield. The catalyst works by tethering the ends of the polymer to the metal centre to overcome the inherent entropic penalty of cyclization. Gel-permeation chromatography, dynamic and static light scattering, viscometry and chemical tests are all consistent with theoretical predictions and provide unambiguous confirmation of a cyclic topology. Access to a wide variety of new cyclic polymers is now possible by simply choosing the appropriate alkyne monomer.

  15. Conformational properties of polymers

    Indian Academy of Sciences (India)

    A R Singh; D Giri; S Kumar


    We discuss exact enumeration technique and its application to polymers and biopolymers. Using this method one can obtain phase diagram in thermodynamic limit. The method works quite well in describing the outcomes of single molecule force spectroscopy results where finite size effects play a crucial role.

  16. Transferases in Polymer Chemistry

    NARCIS (Netherlands)

    van der Vlist, Jeroen; Loos, Katja; Palmans, ARA; Heise, A


    Transferases are enzymes that catalyze reactions in which a group is transferred from one compound to another. This makes these enzymes ideal catalysts for polymerization reactions. In nature, transferases are responsible for the synthesis of many important natural macromolecules. In synthetic polym

  17. Ion Implantation of Polymers

    DEFF Research Database (Denmark)

    Popok, Vladimir


    are discussed. Related to that, the effects of radiothermolysis, degassing and carbonisation are considered. Specificity of depth distributions of implanted into polymers impurities is analysed and the case of high-fluence implantation is emphasised. Within rather broad topic of ion bombardment, the focus...

  18. Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics

    CERN Document Server

    Alizadehheidari, M; Noble, C; Reiter-Schad, M; Nyberg, L K; Fritzsche, J; Mehlig, B; Tegenfeldt, J O; Ambjörnsson, T; Persson, F; Westerlund, F


    Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA....

  19. Frictional properties of confined polymers

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N; Persson, Bo N J


    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force...

  20. Gel polymer electrolytes for batteries (United States)

    Balsara, Nitash Pervez; Eitouni, Hany Basam; Gur, Ilan; Singh, Mohit; Hudson, William


    Nanostructured gel polymer electrolytes that have both high ionic conductivity and high mechanical strength are disclosed. The electrolytes have at least two domains--one domain contains an ionically-conductive gel polymer and the other domain contains a rigid polymer that provides structure for the electrolyte. The domains are formed by block copolymers. The first block provides a polymer matrix that may or may not be conductive on by itself, but that can soak up a liquid electrolyte, thereby making a gel. An exemplary nanostructured gel polymer electrolyte has an ionic conductivity of at least 1.times.10.sup.-4 S cm.sup.-1 at C.


    DEFF Research Database (Denmark)


    A method for preparing polybenzimidazole or polybenzimidazole blend membranes and fabricating gas diffusion electrodes and membrane-electrode assemblies is provided for a high temperature polymer electrolyte membrane fuel cell. Blend polymer electrolyte membranes based on PBI and various...... thermoplastic polymers for high temperature polymer electrolyte fuel cells have also been developed. Miscible blends are used for solution casting of polymer membranes (solid electrolytes). High conductivity and enhanced mechanical strength were obtained for the blend polymer solid electrolytes...... electrolyte membrane by hot-press. The fuel cell can operate at temperatures up to at least 200 °C with hydrogen-rich fuel containing high ratios of carbon monoxide such as 3 vol% carbon monoxide or more, compared to the carbon monoxide tolerance of 10-20 ppm level for Nafion$m(3)-based polymer electrolyte...

  2. DNA nanostructure immobilization to lithographic DNA arrays (United States)

    Negrete, Omar D.

    Although DNA is well known for its genetic role in biology, DNA has also been sought-after as a material for the self-assembly of biological and electronic devices. Examples of DNA nanostructure construction include DNA tiled self-assembly and DNA Origami, where by controlling the sequence and concentration of DNA molecules, the rational design of geometric DNA nanostructures is possible. The assembly of DNA nanostructures takes place in solution and thus they are in disorder and require further organization to construct circuitry or devices. Hence, it is essential for future applications of this technology to develop methods to direct the placement of DNA nanostructures on a surface. To address this challenge my research examines the use of DNA microarrays to capture DNA nanostructures via DNA hybridization. Modern DNA arrays offer a high-density of sequence-specific molecular recognition sites where the addressable placement of DNA nanostructures can be achieved. Using Maskless Array Synthesizer (MAS) technology, I have characterized photolithographic DNA arrays for the hybridization of DNA complexes like large DNA molecules (> 1 kb), DNA-gold nanoparticle conjugates, and DNA Origami. Although modern photolithographic DNA arrays can possess a high-density of sequence (106/cm2), the printed DNA areas are on the order of tens of microns. Thus, I have also developed a method to reduce the DNA array spot size to nanoscale dimensions through the combined use of electron beam lithography with photolithographic DNA synthesis. This work addresses the key elements towards developing a surface patterning technology that takes advantage of DNA base-pairing for both molecular sub-assembly and surface patterning.

  3. DNA Packaging in Bacteriophage: Is Twist Important?


    Spakowitz, Andrew James; Wang, Zhen-Gang


    We study the packaging of DNA into a bacteriophage capsid using computer simulation, specifically focusing on the potential impact of twist on the final packaged conformation. We perform two dynamic simulations of packaging a polymer chain into a spherical confinement: one where the chain end is rotated as it is fed, and one where the chain is fed without end rotation. The final packaged conformation exhibits distinct differences in these two cases: the packaged conformation from feeding with...

  4. The dynamics of the DNA denaturation transition

    CERN Document Server

    van Erp, Titus S


    The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate shows a minimum, but then increases as function of length. We also examine the influence of sequence and solvent friction. Molecules having the same number of weak and strong base-pairs can have significantly different opening rates depending on the order of base-pairs.

  5. Adsorption and flocculation by polymers and polymer mixtures. (United States)

    Gregory, John; Barany, Sandor


    Polymers of various types are in widespread use as flocculants in several industries. In most cases, polymer adsorption is an essential prerequisite for flocculation and kinetic aspects are very important. The rates of polymer adsorption and of re-conformation (relaxation) of adsorbed chains are key factors that influence the performance of flocculants and their mode of action. Polyelectrolytes often tend to adopt a rather flat adsorbed configuration and in this state their action is mainly through charge effects, including 'electrostatic patch' attraction. When the relaxation rate is quite low, particle collisions may occur while the adsorbed chains are still in an extended state and flocculation by polymer bridging may occur. These effects are now well understood and supported by much experimental evidence. In recent years there has been considerable interest in the use of multi-component flocculants, especially dual-polymer systems. In the latter case, there can be significant advantages over the use of single polymers. Despite some complications, there is a broad understanding of the action of dual polymer systems. In many cases the sequence of addition of the polymers is important and the pre-adsorbed polymer can have two important effects: providing adsorption sites for the second polymer or causing a more extended adsorbed conformation as a result of 'site blocking'.

  6. Synthesis and Evaluation of Tetramethylguanidinium-Polyethylenimine Polymers as Efficient Gene Delivery Vectors

    Directory of Open Access Journals (Sweden)

    Manohar Mahato


    Full Text Available Previously, we demonstrated that 6-(N,N,N′,N′-tetramethylguanidinium chloride-hexanoyl-polyethylenimine (THP polymers exhibited significantly enhanced transfection efficiency and cell viability. Here, in the present study, we have synthesized a series of N,N,N′,N′-tetramethylguanidinium-polyethylenimine (TP1-TP5 polymers via a single-step reaction involving peripheral primary amines of bPEI and varying amounts of 2-(1H-benzotriazol-1-yl-1,1,3,3-tetramethyluronium hexafluorophosphate (HBTU. These polymers were found to interact efficiently with negatively charged pDNA and formed stable complexes in the size range of ~240–450 nm. Acid-base titration profiles revealed improved buffering capacity of TP polymers as compared to bPEI. Transfection and cytotoxicity assays performed with TP/pDNA complexes on HEK293, CHO, and HeLa cells showed significantly higher transfection efficiency and cell viability with one of the complexes, TP2/pDNA complex, exhibited the highest transfection efficiency (~1.4–2.3-fold outcompeting native bPEI and the commercially available transfection reagent, Lipofectamine 2000. Compared to previously reported THP polymers, the transfection efficiency of TP/pDNA complexes was found to be lower, as examined by flow cytometry. These results highlight the importance of the hydrophobic C-6 linker in THP polymers in forming compact nanostructures with pDNA, which might lead to efficient uptake and internalization of the complexes; however, the projected TP polymers offer an advantage of their rapid and economical one-step synthesis.

  7. Generation of a Focused Poly(amino ether Library: Polymer-mediated Transgene Delivery and Gold-Nanorod based Theranostic Systems

    Directory of Open Access Journals (Sweden)

    Lucas Vu, James Ramos, Thrimoorthy Potta, Kaushal Rege


    Full Text Available A focused library of twenty-one cationic poly(amino ethers was synthesized following ring-opening polymerization of two diglycidyl ethers by different oligoamines. The polymers were screened in parallel for plasmid DNA (pDNA delivery, and transgene expression efficacies of individual polymers were compared to those of 25 kDa polyethylenimine (PEI, a current standard for polymer-mediated transgene delivery. Seven lead polymers that demonstrated higher transgene expression than PEI in pancreatic and prostate cancer cells lines were identified from the screen. All seven lead polymers showed highest transgene expression at a polymer:pDNA weight ratio of 5:1 in the MIA PaCa-2 pancreatic cancer cell line. Among the conditions studied, transgene expression efficacy correlated with minimal polymer cytotoxicity but not polyplex sizes. In addition, this study indicated that methylene spacing between amine centers in the monomers, amine content, and molecular weight of the polymers are all significant factors and should be considered when designing polymers for transgene delivery. A lead effective polymer was employed for coating gold nanorods, leading to theranostic nanoassemblies that possess combined transgene delivery and optical imaging capabilities, leading to potential theranostic systems.

  8. Gene analysis of multiple oral bacteria by the polymerase chain reaction coupled with capillary polymer electrophoresis. (United States)

    Liu, Chenchen; Yamaguchi, Yoshinori; Sekine, Shinichi; Ni, Yi; Li, Zhenqing; Zhu, Xifang; Dou, Xiaoming


    Capillary polymer electrophoresis is identified as a promising technology for the analysis of DNA from bacteria, virus and cell samples. In this paper, we propose an innovative capillary polymer electrophoresis protocol for the quantification of polymerase chain reaction products. The internal standard method was modified and applied to capillary polymer electrophoresis. The precision of our modified internal standard protocol was evaluated by measuring the relative standard deviation of intermediate capillary polymer electrophoresis experiments. Results showed that the relative standard deviation was reduced from 12.4-15.1 to 0.6-2.3%. Linear regression tests were also implemented to validate our protocol. The modified internal standard method showed good linearity and robust properties. Finally, the ease of our method was illustrated by analyzing a real clinical oral sample using a one-run capillary polymer electrophoresis experiment.

  9. Photogenerating work from polymers

    Directory of Open Access Journals (Sweden)

    Hilmar Koerner


    Full Text Available The ability to control the creation of mechanical work remotely, with high speed and spatial precision, over long distances, offers many intriguing possibilities. Recent developments in photoresponsive polymers and nanocomposite concepts are at the heart of these future devices. Whether driving direct conformational changes, initiating reversible chemical reactions to release stored strain, or converting a photon to a local temperature increase, combinations of photoactive units, nanoparticles, ordered mesophases, and polymeric networks are providing an expansive array of photoresponsive polymer options for mechanical devices. Framing the typically geometry-specific observations into an applied engineering vocabulary will ultimately define the role of these materials in future actuator applications, ranging from microfluidic valves in medical devices to optically controlled mirrors in displays.

  10. How do polymers degrade? (United States)

    Lyu, Suping


    Materials derived from agricultural products such as cellulose, starch, polylactide, etc. are more sustainable and environmentally benign than those derived from petroleum. However, applications of these polymers are limited by their processing properties, chemical and thermal stabilities. For example, polyethylene terephthalate fabrics last for many years under normal use conditions, but polylactide fabrics cannot due to chemical degradation. There are two primary mechanisms through which these polymers degrade: via hydrolysis and via oxidation. Both of these two mechanisms are related to combined factors such as monomer chemistry, chain configuration, chain mobility, crystallinity, and permeation to water and oxygen, and product geometry. In this talk, we will discuss how these materials degrade and how the degradation depends on these factors under application conditions. Both experimental studies and mathematical modeling will be presented.

  11. Semiconducting polymers: the Third Generation. (United States)

    Heeger, Alan J


    There has been remarkable progress in the science and technology of semiconducting polymers during the past decade. The field has evolved from the early work on polyacetylene (the First Generation material) to a proper focus on soluble and processible polymers and co-polymers. The soluble poly(alkylthiophenes) and the soluble PPVs are perhaps the most important examples of the Second Generation of semiconducting polymers. Third Generation semiconducting polymers have more complex molecular structures with more atoms in the repeat unit. Important examples include the highly ordered and crystalline PDTTT and the ever-growing class of donor-acceptor co-polymers that has emerged in the past few years. Examples of the latter include the bithiophene-acceptor co-polymers pioneered by Konarka and the polycarbazole-acceptor co-polymers pioneered by Leclerc and colleagues. In this tutorial review, I will summarize progress in the basic physics, the materials science, the device science and the device performance with emphasis on the following recent studies of Third Generation semiconducting polymers: stable semiconducting polymers; self-assembly of bulk heterojunction (BHJ) materials by spontaneous phase separation; bulk heterojunction solar cells with internal quantum efficiency approaching 100%; high detectivity photodetectors fabricated from BHJ materials.

  12. Significance of bending restraints for the stability of helical polymer conformations (United States)

    Williams, Matthew J.; Bachmann, Michael


    We performed parallel-tempering Monte Carlo simulations to investigate the formation and stability of helical tertiary structures for flexible and semiflexible polymers, employing a generic coarse-grained model. Structural conformations exhibit helical order with tertiary ordering into single helices, multiple helical segments organized into bundles, and disorganized helical arrangements. For both bending-restrained semiflexible and bending-unrestrained flexible helical polymers, the stability of the structural phases is discussed systematically by means of hyperphase diagrams parametrized by suitable order parameters, temperature, and torsion strength. This exploration lends insight into the restricted flexibility of biological polymers such as double-stranded DNA and proteins.


    Institute of Scientific and Technical Information of China (English)

    Guanghui Ma


    Much attention has in recent years been paid to fine applications of polymer particles, e.g., carrier for enzyme, separation media for protein, DNA and cell, and carrier for drug in Drug Delivery System (DDS). Control of polymer particle size is especially important in such fine applications. For instance, when the particles are used as a carrier of anti-cancer agents, the locations of particles containing anti-cancer agents also depend on the size of the particles. In this paper, various techniques of controlling polymer particle size are described, with emphasis on Shirasu Porous Glass (SPG) membrane emulsification, as carried out in our research group.

  14. Significance of bending restraints for the stability of helical polymer conformations. (United States)

    Williams, Matthew J; Bachmann, Michael


    We performed parallel-tempering Monte Carlo simulations to investigate the formation and stability of helical tertiary structures for flexible and semiflexible polymers, employing a generic coarse-grained model. Structural conformations exhibit helical order with tertiary ordering into single helices, multiple helical segments organized into bundles, and disorganized helical arrangements. For both bending-restrained semiflexible and bending-unrestrained flexible helical polymers, the stability of the structural phases is discussed systematically by means of hyperphase diagrams parametrized by suitable order parameters, temperature, and torsion strength. This exploration lends insight into the restricted flexibility of biological polymers such as double-stranded DNA and proteins.

  15. Electrochemical polymer electrolyte membranes

    CERN Document Server

    Fang, Jianhua; Wilkinson, David P


    Electrochemical Polymer Electrolyte Membranes covers PEMs from fundamentals to applications, describing their structure, properties, characterization, synthesis, and use in electrochemical energy storage and solar energy conversion technologies. Featuring chapters authored by leading experts from academia and industry, this authoritative text: Discusses cutting-edge methodologies in PEM material selection and fabricationPoints out important challenges in developing PEMs and recommends mitigation strategies to improve PEM performanceAnalyzes the cur

  16. Conducting Thermoset Polymers. (United States)


    polymers conducting. The acetylene-terminated Schiff base and acetylene-terminated polythiophene monomers were first cured, then doped with iodine... Schiff base thermoset was implanted with high energy argon ions using a commercial ion implanter. Electron spin resonance, photoluminescence, and...photoabsorption data suggest that polarons can form in the doped and undoped forms of the acetylene-terminated Schiff base and polythiophene thermoset

  17. Dynamics of polymers

    Energy Technology Data Exchange (ETDEWEB)

    Buchenau, U. [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Energieverfahrenstechnik


    Neutron scattering from amorphous polymers allows to switch from incoherent to coherent scattering in the same substance. The power of the tool for the study of the picosecond dynamics of disordered matter is illustrated for polybutadiene, polycarbonate and polystyrene. The results suggest a mixture of sound waves and localized modes, strongly interacting with each other, in the picosecond range. (author) 8 figs., tabs., 39 refs.

  18. Advanced Polymer Network Structures (United States)


    Std. Z39.18 Approved for public release; distribution is unlimited. iii Contents List of Figures iv List of Tables v 1. Introduction 1 2...unlimited. v black and blue lines correspond to the single network composed of the first (system 10) and second networks (system 11), respectively...aggregation also contributes significantly to the tensile behavior, where the H- and comb - polymers with long spikes have a considerably higher

  19. Photogenerating work from polymers


    Hilmar Koerner; White, Timothy J.; Nelson V. Tabiryan; Timothy J. Bunning; Vaia, Richard A.


    The ability to control the creation of mechanical work remotely, with high speed and spatial precision, over long distances, offers many intriguing possibilities. Recent developments in photoresponsive polymers and nanocomposite concepts are at the heart of these future devices. Whether driving direct conformational changes, initiating reversible chemical reactions to release stored strain, or converting a photon to a local temperature increase, combinations of photoactive units, nanoparticle...


    Directory of Open Access Journals (Sweden)

    I. I. Karpunin


    Full Text Available The executed investigations have made it possible to ascertain that a morphological structure of starch granules mainly determine technological peculiarities of starch isolation from raw material, its modification and its later use. Morphological structure of starch granules primarily depends on type of plant starch-containing raw material which has been used for its isolation. Class of raw material exerts a strong impact on the shape and size of the granules. Linear “light” amylose chains and “heavy” amylopectin branch chains form a starch granule ultrastructure. X-ray research has proved that starch granules are characterized by presence of interlacing amorphous and crystalline regions. In this case polymer orientation using stretching of the obtained end product influences on its physical and mechanical  indices which are increasing due to polymer orientation. For the purpose of packaging orientation of polymer films can solve such important problems as significant improvement of operational properties, creation of  thermosetting film materials, improvement of qualitative indices of the recycled film.Results of the conducted research have proved the fact that it is necessary to make changes in technology in order to increase biological degradability of the recycled packaging made from polymers and improve physical and mechanical indices. In this regard film production technology presupposes usage of such substances as stark and others which are characterized by rather large presence of branch chains of molecules and interlacing amorphous and crystalline regions. Such approach makes it possible to obtain after-use package which is strong and quickly degradable by micro-organisms.

  1. Polymer Stretching by Turbulence

    CERN Document Server

    Chertkov, M


    The stretching of a polymer chain by a large scale chaotic flow is considered. The steady state which emerges as a balance of the turbulent stretching and anharmonic resistance of the chain is quantitatively described, i.e. the dependency on the flow parameters (Lyapunov exponent statistics) and the chain characteristics (the number of beads and the inter-bead elastic potential) is made explicit. Implications for the drag reduction theory are discussed.

  2. Absorbable and biodegradable polymers

    CERN Document Server

    Shalaby, Shalaby W


    INTRODUCTION NOTES: Absorbable/Biodegradable Polymers: Technology Evolution. DEVELOPMENT AND APPLICATIONOF NEW SYSTEMS: Segmented Copolyesters with Prolonged Strength Retention Profiles. Polyaxial Crystalline Fiber-Forming Copolyester. Polyethylene Glycol-Based Copolyesters. Cyanoacrylate-Based Systems as Tissue Adhesives. Chitosan-Based Systems. Hyaluronic Acid-Based Systems. DEVELOPMENTS IN PREPARATIVE, PROCESSING, AND EVALUATION METHODS: New Approaches to the Synthesis of Crystalline. Fiber-Forming Aliphatic Copolyesters. Advances in Morphological Development to Tailor the Performance of Me

  3. Conjugated Polymer Solar Cells (United States)


    oxygen since their EPR and conductivity data indicated the presence of unpaired charges. On the other hand, intramolecular CT complexes have recently...been reported for polythiophene [2], where weak CT occurs from a polymer unit cell to the covalently bonded acceptor molecule. Nevertheless, it was...intracavity optical doubler (532 nm), diode lasers (670, 810 nm) and light emitting diodes (490, 630 nm). Measurements were conducted for pump intensity 0.1

  4. Synthesis of Energetic Polymers. (United States)


    50 system is a flowable oil at room temperature. The 75/25 mol% BAMO/THF is comparable in melting point to PEG 4000 (mp 550C). Although THF is a...conversion whereas THF reached a steady state of 85% after 38 hours. Based on the amount of monomers remaining, the final polymer composition was...elastomeric binders for use in propellant and explosive compositions . The copolymerization of 3,3-bis(azidomethyl) oxetane (BAMO) with tetrahydrofuran

  5. Solution Processing - Rodlike Polymers (United States)


    side it necessary and identify by block number) Para-ordered Polymers High Modulus Fibers and Films Polybenzobisoxazoles Polybenzobisthiazoles 20...considerations important in solution processing are considered, with special emphasis on the dry-jet wet spinning process used to form fibers . Pertinent...Company, Summit, N.J. iii TABLE OF CONTENTS 1. INTRODUCTION ................ .......................... .. 1 2. REMARKS ON DRY-JET WET SPUN FIBER

  6. Scratch behaviors in polymers (United States)

    Xiang, Chen


    As part of a large effort toward the fundamental understanding of scratch behaviors in polymeric materials, studies were carried out on a broad range of polymers, with an emphasis on automotive thermoplastic olefins (TPOs). Two types of scratch tests were performed in this research, i.e., Ford constant load and instrumented progressive load scratch tests. A scratch model proposed by Hamilton and Goodman was applied to understand the fundamental mechanics of the scratch process. Several characterization techniques were used to investigate the scratch damage mechanisms in polymers. Both testing results and the scratch model analysis indicate that certain rigidity in polymers is essential to give good scratch resistance. Fundamental understanding of the scratching process in terms of basic material characteristics such as Young's modulus, yield stress, tensile strength, friction coefficient, scratch hardness, penetration recovery and fracture toughness are discussed. Scratch damage investigation, on both surface and subsurface, shows that shear yielding is the main cause of the plastics flow scratch pattern, while tensile tear on the surface and shear induced fracture on the subsurface are the main damage mechanisms in the fracture scratch pattern. This study explains why automotive TPOs are susceptible to scratch under the current scratch test practiced in automotive industry. Shear deformation and fracture behavior in model TPOs are also studied using the Iosipescu shear test. Iosipescu shear deformation in terms of shear stress-strain curves of model TPOs is obtained experimentally. Shear fracture process and damage mechanisms in TPOs are also demonstrated and revealed. Further studies on the scratch damage in TPOs based on the roles of additives and fillers in the scratch behavior are addressed. The effects of phase morphology and toughening mechanisms on scratch behavior in TPOs are also discussed. This research has resulted in an increased understanding of the

  7. Knots in polymers

    Indian Academy of Sciences (India)

    Yacov Kantov


    Knots and topological entanglements play an important role in the statistical mechanics of polymers. While topological entanglement is a global property, it is possible to study the size of a knotted region both numerically and analytically. It can be shown that long-range repulsive interactions, as well as entropy favor small knots in dilute systems. However, in dense systems and at the -point in two dimensions the uncontracted knot configuration is the most likely.

  8. Frustrated polymer crystal structures (United States)

    Lotz, B.; Strasbourg, 67083


    Several crystal structures or polymorphs of chiral or achiral polymers and biopolymers with three fold conformation of the helix have been found to conform to a common and -with one exception(Puterman, M. et al, J. Pol. Sci., Pol. Phys. Ed., 15, 805 (1977))- hitherto unsuspected packing scheme. The trigonal unit-cell contains three isochiral helices; the azimuthal setting of one helix differs significantly from that of the other two, leading to a so-called frustrated packing scheme, in which the environment of conformationally identical helices differs. Two variants of the frustrated scheme are analyzed. Similarities with frustrated two dimensional magnetic systems are underlined. Various examples of frustration in polymer crystallography are illustrated via the elucidation or reinterpretation of crystal phases or polymorphs of polyolefins, polyesters, cellulose derivatives and polypeptides. Structural manifestations (including AFM evidence) and morphological consequences of frustration are presented, which help diagnose the existence of this original packing of polymers.(Work done with L. Cartier, D. Dorset, S. Kopp, T. Okihara, M. Schumacher, W. Stocker.)

  9. Semi-metallic polymers (United States)

    Bubnova, Olga; Khan, Zia Ullah; Wang, Hui; Braun, Slawomir; Evans, Drew R.; Fabretto, Manrico; Hojati-Talemi, Pejman; Dagnelund, Daniel; Arlin, Jean-Baptiste; Geerts, Yves H.; Desbief, Simon; Breiby, Dag W.; Andreasen, Jens W.; Lazzaroni, Roberto; Chen, Weimin M.; Zozoulenko, Igor; Fahlman, Mats; Murphy, Peter J.; Berggren, Magnus; Crispin, Xavier


    Polymers are lightweight, flexible, solution-processable materials that are promising for low-cost printed electronics as well as for mass-produced and large-area applications. Previous studies demonstrated that they can possess insulating, semiconducting or metallic properties; here we report that polymers can also be semi-metallic. Semi-metals, exemplified by bismuth, graphite and telluride alloys, have no energy bandgap and a very low density of states at the Fermi level. Furthermore, they typically have a higher Seebeck coefficient and lower thermal conductivities compared with metals, thus being suitable for thermoelectric applications. We measure the thermoelectric properties of various poly(3,4-ethylenedioxythiophene) samples, and observe a marked increase in the Seebeck coefficient when the electrical conductivity is enhanced through molecular organization. This initiates the transition from a Fermi glass to a semi-metal. The high Seebeck value, the metallic conductivity at room temperature and the absence of unpaired electron spins makes polymer semi-metals attractive for thermoelectrics and spintronics.

  10. Hyperbranched Polymer-Based Electrolyte for Lithium Polymer Batteries

    Institute of Scientific and Technical Information of China (English)

    Takahito Itoh


    @@ 1Introduction Solid polymer electrolytes have attracted much attention as electrolyte materials for all solid-state recharge able lithium batteries, and poly ( ethylene oxide) ( PEO)-based polymer electrolytes are among the most intensively studied systems[1-3]. Hyperbranched polymers have unique properties such as completely amorphous, highly soluble in common organic solvent and processible because of the highly branched nature[4,5].

  11. Nonequilibrium thermodynamics of dilute polymer solutions in flow. (United States)

    Latinwo, Folarin; Hsiao, Kai-Wen; Schroeder, Charles M


    Modern materials processing applications and technologies often occur far from equilibrium. To this end, the processing of complex materials such as polymer melts and nanocomposites generally occurs under strong deformations and flows, conditions under which equilibrium thermodynamics does not apply. As a result, the ability to determine the nonequilibrium thermodynamic properties of polymeric materials from measurable quantities such as heat and work is a major challenge in the field. Here, we use work relations to show that nonequilibrium thermodynamic quantities such as free energy and entropy can be determined for dilute polymer solutions in flow. In this way, we determine the thermodynamic properties of DNA molecules in strong flows using a combination of simulations, kinetic theory, and single molecule experiments. We show that it is possible to calculate polymer relaxation timescales purely from polymer stretching dynamics in flow. We further observe a thermodynamic equivalence between nonequilibrium and equilibrium steady-states for polymeric systems. In this way, our results provide an improved understanding of the energetics of flowing polymer solutions.

  12. Dynamic Polymer Brush at Polymer/Water Interface (United States)

    Yokoyama, Hideaki; Inoue, Kazuma; Ito, Kohzo; Inutsuka, Manabu; Tanaka, Keiji; Yamada, Norifumi


    A layer of polymer chains tethered by one end to a surface is called polymer brush and known to show various unique properties such as anti-fouling. The surface segregation phenomena of copolymers with surface-active blocks should be useful for preparing such a brush layer in spontaneous process. We report hydrophilic polymer brushes formed at the interface between water and polymer by the segregation of amphiphilic diblock copolymers blended in a crosslinked rubbery matrix and call it ``dynamic polymer brush.'' In this system, the hydrophilic block with high surface energy avoids air surface, but segregates to cover the interface between hydrophobic elastomer and water. The structures of the brush layers at D2O/polymer interfaces were measured by neutron reflectivity. The dynamic polymer brush layer surprisingly reached 75% of the contour length of the chain and 2.7 chains/nm2. The brush density was surprisingly comparable to the polymer brush fabricated by the ``grafting-from'' method. We will discuss the dependence of the brush structure on molecular weight and block fraction of amphiphilic block copolymers. Such a surprisingly thick and dense polymer brush were induced by the large enthalpy gain of hydration of hydrophilic block.

  13. Bacterial DNA segregation by dynamic SopA polymers



    Many bacterial plasmids and chromosomes rely on ParA ATPases for proper positioning within the cell and for efficient segregation to daughter cells. Here we demonstrate that the F-plasmid-partitioning protein SopA polymerizes into filaments in an ATP-dependent manner in vitro, and that the filaments elongate at a rate that is similar to that of plasmid separation in vivo. We show that SopA is a dynamic protein within the cell, undergoing cycles of polymerization and depolymerization, and shut...

  14. Electronic Activation of a DNA Nanodevice Using a Multilayer Nanofilm. (United States)

    Jeong, Hyejoong; Ranallo, Simona; Rossetti, Marianna; Heo, Jiwoong; Shin, Jooseok; Park, Kwangyong; Ricci, Francesco; Hong, Jinkee


    A method to control activation of a DNA nanodevice by supplying a complementary DNA (cDNA) strand from an electro-responsive nanoplatform is reported. To develop functional nanoplatform, hexalayer nanofilm is precisely designed by layer-by-layer assembly technique based on electrostatic interaction with four kinds of materials: Hydrolyzed poly(β-amino ester) can help cDNA release from the film. A cDNA is used as a key building block to activate DNA nanodevice. Reduced graphene oxides (rGOs) and the conductive polymer provide conductivity. In particular, rGOs efficiently incorporate a cDNA in the film via several interactions and act as a barrier. Depending on the types of applied electronic stimuli (reductive and oxidative potentials), a cDNA released from the electrode can quantitatively control the activation of DNA nanodevice. From this report, a new system is successfully demonstrated to precisely control DNA release on demand. By applying more advanced form of DNA-based nanodevices into multilayer system, the electro-responsive nanoplatform will expand the availability of DNA nanotechnology allowing its improved application in areas such as diagnosis, biosensing, bioimaging, and drug delivery.

  15. Correlation-induced DNA adsorption on like-charged membranes (United States)

    Buyukdagli, Sahin; Blossey, Ralf


    The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates for further analysis, e.g., by force microscopy, or the pulling of polyelectrolytes into membrane nanopores, as in sequencing applications. In this paper, we present a theoretical analysis of such scenarios based on the self-consistent field theory approach, which allows us to address the important effect of charge correlations. We calculate the grand potential of a stiff polyelectrolyte immersed in an electrolyte in contact with a negatively charged dielectric membrane. For the sake of conciseness, we neglect conformational polymer fluctuations and model the molecule as a rigid charged line. At strongly charged membranes, the adsorbed counterions enhance the screening ability of the interfacial region. In the presence of highly charged polymers such as double-stranded DNA molecules close to the membrane, this enhanced interfacial screening dominates the mean-field level DNA-membrane repulsion and results in the adsorption of the DNA molecule to the surface. This picture provides a simple explanation for the recently observed DNA binding onto similarly charged substrates [G. L.-Caballero et al., Soft Matter 10, 2805 (2014), 10.1039/c3sm52428k] and points out charge correlations as a non-negligible ingredient of polymer-surface interactions.

  16. Dynamics of Polymer Chains. (United States)

    Hong, Tzay-Ming

    A major objective of this research is to establish at a more fundamental level some of the qualitative or semi-quantitative treatments in use at the present time, such as the Doi-Edwards tube picture, the switch from non -ideal to ideal behavior, and dynamical aspects of the reptation model. The main topics are: (I) An attempt was made to determine the order of magnitude of the elastic time interval of a viscoelastic polymer melt, defining it as the reciprocal of the average rate at which the total entanglement (clockwise plus anticlockwise) passes through zero due to thermal agitation. We calculated the case of a free chain winding about a straight rod both in friction-independent regime and in high friction regime. (II) By successively coarse -graining and rescaling the monomer-monomer interaction (using a modified Wilson recursion formula) we found that the interaction is driven to a very strong but short-ranged one. This verifies the observation that polymers in dilute solutions tend to curl up and behave like hard spheres. (III) We studied the case of chemical equilibrium of i-mers with their nucleating monomers and on the basis of a Flory-Huggins -type mean field theory find that in the dilute limit the swelling of the i-mers takes on the traditional N ^{3over5} law only for sufficiently small monomer chemical potential. When that potential is large enough, then, assuming a Flory law of chain propagation, the law seems to become N^{1over3 }. This is distinct from the problem of changeover from dilute to semidilute polymer system, which we also studied by imposing total polymer density as a constraint equation. (IV) Another item examined concerns the form of the space curve that a very long polymer must assume in order to minimize its free energy (we found that a family of helices with a definite functional relation between pitch and radius renders the free energy stationary). Because a chain is a one-dimensional object, this does not mean that helical shapes

  17. Biomolecule-functionalized polymer brushes. (United States)

    Jiang, Hui; Xu, Fu-Jian


    Functional polymer brushes have been utilized extensively for the immobilization of biomolecules, which is of crucial importance for the development of biosensors and biotechnology. Recent progress in polymerization methods, in particular surface-initiated atom transfer radical polymerization (ATRP), has provided a unique means for the design and synthesis of new biomolecule-functionalized polymer brushes. This current review summarizes such recent research activities. The different preparation strategies for biomolecule immobilization through polymer brush spacers are described in detail. The functional groups of the polymer brushes used for biomolecule immobilization include epoxide, carboxylic acid, hydroxyl, aldehyde, and amine groups. The recent research activities indicate that functional polymer brushes become versatile and powerful spacers for immobilization of various biomolecules to maximize their functionalities. This review also demonstrates that surface-initiated ATRP is used more frequently than other polymerization methods in the designs of new biomolecule-functionalized polymer brushes.

  18. Supramolecular control over thermoresponsive polymers

    Directory of Open Access Journals (Sweden)

    Victor R. de la Rosa


    Full Text Available Thermoresponsive polymers facilitate the development of a wide range of applications in multiple areas spanning from construction or water management to lab-on-a-chip technologies and biomedical sciences. The combination of thermoresponsive polymers with supramolecular chemistry, inspired by the molecular mechanisms behind natural systems, is resulting in adaptive and smart materials with unprecedented properties. This work reviews the past advances on the combination of this young field of research with polymer chemistry that is enabling a high level of control on polymer architecture and stimuli-responsiveness in solution. We will discuss how such polymer systems are able to store thermal information, respond to multiple stimuli in a reversible manner, or adapt their morphology on demand, all powered by the synergy between polymer chemistry and supramolecular chemistry.

  19. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer. (United States)

    Perlmutter, Jason D; Drasler, William J; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N


    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.

  20. Functional Coatings with Polymer Brushes


    König, Meike


    The scope of this work is to fathom different possibilities to create functional coatings with polymer brushes. The immobilization of nanoparticles and enzymes is investigated, as well as the affection of their properties by the stimuli-responsiveness of the brushes. Another aspect is the coating of 3D-nanostructures by polymer brushes and the investigation of the resulting functional properties of the hybrid material. The polymer brush coatings are characterized by a variety of microscopic a...

  1. Polymer multilayer tattooing for enhanced DNA vaccination. (United States)

    DeMuth, Peter C; Min, Younjin; Huang, Bonnie; Kramer, Joshua A; Miller, Andrew D; Barouch, Dan H; Hammond, Paula T; Irvine, Darrell J


    DNA vaccines have many potential benefits but have failed to generate robust immune responses in humans. Recently, methods such as in vivo electroporation have demonstrated improved performance, but an optimal strategy for safe, reproducible, and pain-free DNA vaccination remains elusive. Here we report an approach for rapid implantation of vaccine-loaded polymer films carrying DNA, immune-stimulatory RNA, and biodegradable polycations into the immune-cell-rich epidermis, using microneedles coated with releasable polyelectrolyte multilayers. Films transferred into the skin following brief microneedle application promoted local transfection and controlled the persistence of DNA and adjuvants in the skin from days to weeks, with kinetics determined by the film composition. These 'multilayer tattoo' DNA vaccines induced immune responses against a model HIV antigen comparable to electroporation in mice, enhanced memory T-cell generation, and elicited 140-fold higher gene expression in non-human primate skin than intradermal DNA injection, indicating the potential of this strategy for enhancing DNA vaccination.

  2. Crystal structure of a DNA catalyst. (United States)

    Ponce-Salvatierra, Almudena; Wawrzyniak-Turek, Katarzyna; Steuerwald, Ulrich; Höbartner, Claudia; Pena, Vladimir


    Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules. In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold. Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14) at 2.8 Å resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms.

  3. Wear of polymers and composites

    CERN Document Server

    Abdelbary, Ahmed


    In the field of tribology, the wear behaviour of polymers and composite materials is considered a highly non-linear phenomenon. Wear of Polymers and Composites introduces fundamentals of polymers and composites tribology. The book suggests a new approach to explore the effect of applied load and surface defects on the fatigue wear behaviour of polymers, using a new tribometer and thorough experiments. It discusses effects of surface cracks, under different static and cyclic loading parameters on wear, and presents an intelligent algorithm, in the form of a neural network, to map the relations

  4. Small angle scattering and polymers

    Energy Technology Data Exchange (ETDEWEB)

    Cotton, J.P. [Laboratoire Leon Brillouin (LLB) - Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France)


    The determination of polymer structure is a problem of interest for both statistical physics and industrial applications. The average polymer structure is defined. Then, it is shown why small angle scattering, associated with isotopic substitution, is very well suited to the measurement of the chain conformation. The corresponding example is the old, but pedagogic, measurement of the chain form factor in the polymer melt. The powerful contrast variation method is illustrated by a recent determination of the concentration profile of a polymer interface. (author) 12 figs., 48 refs.

  5. Progress in polymer solar cell

    Institute of Scientific and Technical Information of China (English)

    LI LiGui; LU GuangHao; YANG XiaoNiu; ZHOU EnLe


    This review outlines current progresses in polymer solar cell. Compared to traditional silicon-based photovoltaic (PV) technology, the completely different principle of optoelectric response in the polymer cell results in a novel configuration of the device and more complicated photovoltaic generation process. The conception of bulk-heterojunction (BHJ) is introduced and its advantage in terms of morphology is addressed. The main aspects including the morphology of photoactive layer, which limit the efficiency and stability of polymer solar cell, are discussed in detail. The solutions to boosting up both the efficiency and stability (lifetime) of the polymer solar cell are highlighted at the end of this review.

  6. Polymer-based solar cells

    Directory of Open Access Journals (Sweden)

    Alex C. Mayer


    Full Text Available A significant fraction of the cost of solar panels comes from the photoactive materials and sophisticated, energy-intensive processing technologies. Recently, it has been shown that the inorganic components can be replaced by semiconducting polymers capable of achieving reasonably high power conversion efficiencies. These polymers are inexpensive to synthesize and can be solution-processed in a roll-to-roll fashion with high throughput. Inherently poor polymer properties, such as low exciton diffusion lengths and low mobilities, can be overcome by nanoscale morphology. We discuss polymer-based solar cells, paying particular attention to device design and potential improvements.

  7. Sustainable polymers from renewable resources (United States)

    Zhu, Yunqing; Romain, Charles; Williams, Charlotte K.


    Renewable resources are used increasingly in the production of polymers. In particular, monomers such as carbon dioxide, terpenes, vegetable oils and carbohydrates can be used as feedstocks for the manufacture of a variety of sustainable materials and products, including elastomers, plastics, hydrogels, flexible electronics, resins, engineering polymers and composites. Efficient catalysis is required to produce monomers, to facilitate selective polymerizations and to enable recycling or upcycling of waste materials. There are opportunities to use such sustainable polymers in both high-value areas and in basic applications such as packaging. Life-cycle assessment can be used to quantify the environmental benefits of sustainable polymers.

  8. Polymer Processing and Characterization Laboratory (United States)

    Federal Laboratory Consortium — The purpose is to process and evaluate polymers for use in nonlinear optical, conductive and structural Air Force applications. Primary capabilities are extrusion of...

  9. Investigation of the charge effect on the electrochemical transduction in a quinone-based DNA sensor

    DEFF Research Database (Denmark)

    Reisberg, S.; Piro, B.; Noel, V.;


    To elucidate the mechanism involved in the electrochemical transduction process of a conducting polymer-based DNA sensor, peptide nucleic acids (PNA) were used. PNA are DNA analogues having similar hybridization properties but are neutral. This allows to discriminate the electrostatic effect of D...

  10. A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction (United States)

    Johnson, J.; Brackley, C. A.; Cook, P. R.; Marenduzzo, D.


    We present computer simulations of the phase behaviour of an ensemble of proteins interacting with a polymer, mimicking non-specific binding to a piece of bacterial DNA or eukaryotic chromatin. The proteins can simultaneously bind to the polymer in two or more places to create protein bridges. Despite the lack of any explicit interaction between the proteins or between DNA segments, our simulations confirm previous results showing that when the protein-polymer interaction is sufficiently strong, the proteins come together to form clusters. Furthermore, a sufficiently large concentration of bridging proteins leads to the compaction of the swollen polymer into a globular phase. Here we characterise both the formation of protein clusters and the polymer collapse as a function of protein concentration, protein-polymer affinity and fibre flexibility.

  11. Counterion effects on fluorescence energy transfer in conjugated polyelectrolyte-based DNA detection. (United States)

    Nag, Okhil Kumar; Kang, Mijeong; Hwang, Sungu; Suh, Hongsuk; Woo, Han Young


    Cationic poly[9,9'-bis[6''-(N,N,N-trimethylammonium)hexyl]fluorene-co-alt-phenylene]s with five different counterions (CIs) were synthesized and studied as fluorescence resonance energy transfer (FRET) donors (D) to dye-labeled DNA (FRET acceptor, A). The polymers with different CIs show the same pi-conjugated electronic structure with similar absorption (lambda(abs) = approximately 380 nm) and photoluminescence (lambda(PL) = approximately 420 nm) emission spectra in water. The CIs accompanying the polymer chain are expected to affect the D/A complexation and modify the D-A intermolecular separation by acting as a spacer. Polymers with different CIs function differently as FRET excitation donors to fluorescein (Fl)-labeled single-stranded DNA (ssDNA-Fl). The FRET-induced Fl emission was enhanced significantly by the larger CI-exchanged polymers. The polymers with the CIs of tetrakis(1-imidazolyl)borate (FPQ-IB) and tetraphenylborate (FPQ-PB) showed a 2-4-fold enhancement in the FRET-induced signal compared with the polymer with bromide (FPQ-BR). The delayed FRET signal saturation and low association constants (K(a)) with ssDNA-Fl (3.53 x 10(6) M(-1) for FPQ-BR and 1.80 x 10(6) M(-1) for FPQ-PB) were measured for the polymers with larger CIs. The delayed acceptor saturation strengthens the antenna effect and reduces self-quenching of Fl by increasing the polymer concentration near Fl. The weak polymer/ssDNA-Fl association reduces the amount of energy-wasting charge transfer by increasing D-A intermolecular separation. The combined effects lead to increase the overall FRET-induced signal.

  12. DNA meets synthetic polymers—highly versatile hybrid materials

    NARCIS (Netherlands)

    Alemdaroglu, Fikri E.; Herrmann, Andreas


    The combination of synthetic polymers and DNA has provided biologists, chemists and materials scientists with a fascinating new hybrid material. The challenges in preparing these molecular chimeras were overcome by different synthetic strategies that rely on coupling the nucleic acid moiety and the

  13. DNA nanostructure meets nanofabrication. (United States)

    Zhang, Guomei; Surwade, Sumedh P; Zhou, Feng; Liu, Haitao


    Recent advances in DNA nanotechnology have made it possible to construct DNA nanostructures of almost arbitrary shapes with 2-3 nm of precision in their dimensions. These DNA nanostructures are ideal templates for bottom-up nanofabrication. This review highlights the challenges and recent advances in three areas that are directly related to DNA-based nanofabrication: (1) fabrication of large scale DNA nanostructures; (2) pattern transfer from DNA nanostructure to an inorganic substrate; and (3) directed assembly of DNA nanostructures.

  14. DNA repair in Chromobacterium violaceum. (United States)

    Duarte, Fábio Teixeira; Carvalho, Fabíola Marques de; Bezerra e Silva, Uaska; Scortecci, Kátia Castanho; Blaha, Carlos Alfredo Galindo; Agnez-Lima, Lucymara Fassarella; Batistuzzo de Medeiros, Silvia Regina


    Chromobacterium violaceum is a Gram-negative beta-proteobacterium that inhabits a variety of ecosystems in tropical and subtropical regions, including the water and banks of the Negro River in the Brazilian Amazon. This bacterium has been the subject of extensive study over the last three decades, due to its biotechnological properties, including the characteristic violacein pigment, which has antimicrobial and anti-tumoral activities. C. violaceum promotes the solubilization of gold in a mercury-free process, and has been used in the synthesis of homopolyesters suitable for the production of biodegradable polymers. The complete genome sequence of this organism has been completed by the Brazilian National Genome Project Consortium. The aim of our group was to study the DNA repair genes in this organism, due to their importance in the maintenance of genomic integrity. We identified DNA repair genes involved in different pathways in C. violaceum through a similarity search against known sequences deposited in databases. The phylogenetic analyses were done using programs of the PHILYP package. This analysis revealed various metabolic pathways, including photoreactivation, base excision repair, nucleotide excision repair, mismatch repair, recombinational repair, and the SOS system. The similarity between the C. violaceum sequences and those of Neisserie miningitidis and Ralstonia solanacearum was greater than that between the C. violaceum and Escherichia coli sequences. The peculiarities found in the C. violaceum genome were the absence of LexA, some horizontal transfer events and a large number of repair genes involved with alkyl and oxidative DNA damage.


    Institute of Scientific and Technical Information of China (English)

    ZHANG Xinghua; Robert West


    Polysilane polymers containing cyclotetramethylenesilylene units were synthesized by sodium coupling of diorganodichlorosilanes in toluene. These polymers are soluble in common solvents, can be formed into a variety of shapes by molding, casting, coating or potting. They can be crosslinked by irradiation and oxidation at moderate or room temperature.

  16. Thermoresponsive Polymers for Nuclear Medicine: Which Polymer Is the Best? (United States)

    Sedláček, Ondřej; Černoch, Peter; Kučka, Jan; Konefal, Rafał; Štěpánek, Petr; Vetrík, Miroslav; Lodge, Timothy P; Hrubý, Martin


    Thermoresponsive polymers showing cloud point temperatures (CPT) in aqueous solutions are very promising for the construction of various systems in biomedical field. In many of these applications these polymers get in contact with ionizing radiation, e.g., if they are used as carriers for radiopharmaceuticals or during radiation sterilization. Despite this fact, radiosensitivity of these polymers is largely overlooked to date. In this work, we describe the effect of electron beam ionizing radiation on the physicochemical and phase separation properties of selected thermoresponsive polymers with CPT between room and body temperature. Stability of the polymers to radiation (doses 0-20 kGy) in aqueous solutions increased in the order poly(N-vinylcaprolactam) (PVCL, the least stable) ≪ poly[N-(2,2-difluoroethyl)acrylamide] (DFP) polymer radiotherapeutics and sterilization of biomedical systems, cause significant increase in molecular weight due to cross-linking (except for POX, where this effect is weak). In the case of PVCL irradiated with low doses, the increase in molecular weight induced an increase in the CPT of the polymer. For PNIPAM and DFP, there is strong chain hydrophilization leading to an increase in CPT. From this perspective, POX is the most suitable polymer for the construction of delivery systems that experience exposure to radiation, while PVCL is the least suitable and PNIPAM and DFP are suitable only for low radiation demands.

  17. Efimov-Like Behaviour in Low-Dimensional Polymer Models (United States)

    Mura, Federica; Bhattacharjee, Somendra M.; Maji, Jaya; Masetto, Mario; Seno, Flavio; Trovato, Antonio


    In the quantum Efimov effect, identical bosons form infinitely many bound trimer states at the bound dimer dissociation threshold, with their energy spectrum obeying a universal geometrical scaling law. Inspired by the formal correspondence between the possible trajectories of a quantum particle and the possible conformations of a polymer chain, the existence of a triple-stranded DNA bound state when a double-stranded DNA is not stable was recently predicted by modelling three directed polymer chains in low-dimensional lattices, both fractal (ddouble-stranded DNA requires in d≤ 2 the introduction of a weighting factor penalizing the formation of denaturation bubbles, that is non-base paired portions of DNA. The details of how bubble weighting is defined for a three-chain system were shown to crucially affect the presence of Efimov-like behaviour on a fractal lattice. Here we assess the same dependence on the euclidean 1+1 lattice, by setting up the transfer matrix method for three infinitely long chains confined in a finite size geometry. This allows us to discriminate unambiguously between the absence of Efimov-like behaviour and its presence in a very narrow temperature range, in close correspondence with what was already found on the fractal lattice. When present, however, no evidence is found for triple-stranded bound states other than the ground state at the two-chain melting temperature.

  18. Quantitative analysis of reptation of partially extended DNA in sub-30 nm nanoslits

    CERN Document Server

    Yeh, Jia-Wei; Taloni, Alessandro; Chen, Yeng-Long; Chou, Chia-Fu


    We observed reptation of single DNA molecules in fused silica nanoslits of sub-30 nm height. The reptation behavior and the effect of confinement are quantitatively characterized using orientation correlation and transverse fluctuation analysis. We show tube-like polymer motion arises for a tense polymer under strong quasi-2D confinement and interaction with surface- passivating polyvinylpyrrolidone (PVP) molecules in nanoslits, while etching- induced device surface roughness, chip bonding materials and DNA-intercalated dye-surface interaction, play minor roles. These findings have strong implications for the effect of surface modification in nanofluidic systems with potential applications for single molecule DNA analysis.

  19. The Statistics of DNA Capture by a Solid-State Nanopore

    CERN Document Server

    Mihovilovic, Mirna; Stein, Derek


    A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm wide nanopore reveals a strong bias favoring the capture of molecules near their ends. A theoretical model shows that bias to be a consequence of configurational entropy, rather than a search by the polymer for an energetically favorable configuration. We also quantified the fluctuations and length-dependence of the speed of simultaneously translocating polymer segments from our study of folded DNA configurations.

  20. Chiral conducting polymers. (United States)

    Kane-Maguire, Leon A P; Wallace, Gordon G


    This critical review describes the preparation and properties of a relatively new class of chiral macromolecules, namely chiral conducting polymers. It focuses in particular on examples based on polypyrrole, polythiophene and polyaniline. They possess remarkable properties, combining not only chirality with electrical conductivity but also the ability to undergo facile redox and pH switching. These unique properties have opened up a range of exciting new potential applications, including as chiral sensors, as novel stationary phases for chiral separations, and as chiral electrodes for electrochemical asymmetric synthesis (153 references).

  1. Polymer Blends. Volume 1 (United States)



  2. Modeling DNA beacons at the mesoscopic scale

    CERN Document Server

    Errami, Jalal; Theodorakopoulos, Nikos


    We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are...

  3. Electrophoresis of a DNA Coil Near a Nanopore

    CERN Document Server

    Rowghanian, Payam


    Motivated by DNA electrophoresis near a nanopore, we consider the flow field around an "elongated jet", a long thin source which injects momentum into a liquid. This solution qualitatively describes the electro-osmotic flow around a long rigid polymer, where due to electrohydrodynamic coupling, the solvent receives momentum from the electric field. Based on the qualitative behavior of the elongated jet solution, we develop a coarse-grained scheme which reproduces the known theoretical results regarding the electrophoretic behavior of a long rigid polymer and a polymer coil in a uniform field, which we then exploit to analyze the electrophoresis of a polymer coil in the non-uniform field near a nanopore.

  4. Direct measurements reveal non-Markovian fluctuations of DNA threading through a solid-state nanopore

    CERN Document Server

    Bell, Nicholas A W


    The threading of a polymer chain through a small pore is a classic problem in polymer dynamics and underlies nanopore sensing technology. However important experimental aspects of the polymer motion in a solid-state nanopore, such as an accurate measurement of the velocity variation during translocation, have remained elusive. In this work we analysed the translocation through conical quartz nanopores of a 7 kbp DNA double-strand labelled with six markers equally spaced along its contour. These markers, constructed from DNA hairpins, give direct experimental access to the translocation dynamics. On average we measure a 5% reduction in velocity during the translocation. We also find a striking correlation in velocity fluctuations with a decay constant of 100s of {\\mu}s. These results shed light on hitherto unresolved problems in the dynamics of DNA translocation and provide guidance for experiments seeking to determine positional information along a DNA strand.

  5. Torsional dynamics and orientation of DNA-DAPI complexes


    Barcellona, ML; Gratton, E


    The flexibility of calf thymus DNA and several polynucleotides was measured using the anisotropy decay of DAPI bound to DNA, a minor groove probe. DNA torsional dynamics were analyzed using the Schurr model [Allison, S. A., and Schutt, J. M. (1979) Chem. Phys. 41, 35-44] in the infinite polymer length approximation. Time-resolved fluorescence depolarization was measured using a frequency-doubled mode-locked dye laser and frequency- domain acquisition methods. At very high P/D ratios, the anis...

  6. DNA-based materials and their device applications (Conference Presentation) (United States)

    Rau, Ileana; Kajzar, François; Grote, James G.


    In the last decade a lot of interest was paid to DNA materials in view of their practical applications in photonics and in electronics. This aspect is especially due to the fact that this polymer is eco-friendly, originating from renewable resources and can be obtained from any animal or vegetable waste. In this respect many studies have shown that DNA is an intriguing biopolymer which can find applications in many fields. In this paper we will review and discuss the functionalization of DNA and some practical applications.

  7. Oil and fat absorbing polymers (United States)

    Marsh, H. E., Jr. (Inventor)


    A method is described for forming a solid network polymer having a minimal amount of crosslinking for use in absorbing fats and oils. The polymer remains solid at a swelling ratio in oil or fat of at least ten and provides an oil absorption greater than 900 weight percent.

  8. All-Polymer Electrochemical Sensors

    DEFF Research Database (Denmark)

    Kafka, Jan Robert

    This thesis presents fabrication strategies to produce different types of all-polymer electrochemical sensors based on electrodes made of the highly conductive polymer poly(3,4-ethylenedioxythiophene) (PEDOT). Three different systems are presented, fabricated either by using microdrilling or by hot...


    Institute of Scientific and Technical Information of China (English)

    Ingolf Buethe


    At the turn of the century, the global polymer industry is undergoing the most rapid and dramatic changes in its history. Emerging markets, particularly in Asia, and their polymer consumption are catching up with other parts of the world,creating new business opportunities. Economy of scale, combined with optimized logistic concepts, is becoming a key economic success factor, thus forcing smaller suppliers out of business and creating a major hurdle for newcomers and the introduction of new products. Globalization of polymer customers and cost pressure lead to a consolidation of suppliers and products. Today standard thermoplastics have a dominant position in the market and they will retain this position in future.Engineering thermoplastics are facing growing competition due to the increased efficiency of standard polymers. This leads to a displacement process where standard polymers substitute engineering thermoplastics. Simultaneously engineering polymers are pushing into new markets or applications or displacing materials like glass, wood or metal. The recent history and future trends have a strong impact on R&D activity in the polymer industry. Competition on a global scale and increasing cost pressure are turning innovation into an essential precondition of commercial success, thus determining the objectives of industrial polymer research and development.

  10. Ring closure in actin polymers (United States)

    Sinha, Supurna; Chattopadhyay, Sebanti


    We present an analysis for the ring closure probability of semiflexible polymers within the pure bend Worm Like Chain (WLC) model. The ring closure probability predicted from our analysis can be tested against fluorescent actin cyclization experiments. We also discuss the effect of ring closure on bend angle fluctuations in actin polymers.

  11. Fifty years of polymer science

    NARCIS (Netherlands)

    Prez, Du Filip; Hoogenboom, Richard; Klumperman, Bert; Meier, Michael; Monteiro, Michael; Müller, Alejandro; Vancso, Julius


    The European Polymer Journal (EPJ) has been serving the scientific community for 50 years, which makes it one of the older macromolecular journals with a broad focus. Since its launch 50 years ago, EPJ has provided a distinguished forum for publications in polymer research, including chemistry, phys

  12. Supramolecular networks of telechelic polymers

    NARCIS (Netherlands)

    Bohdan, M.A.


    This thesis focuses on the fundamental understanding of phenomena associated with the gelation of end-functionalized polymers and the dynamic processes occurring inside of the gel network. To address particular questions we use two types of telechelic polymers, in which the assembly occurs due to th

  13. Engineering the Structure and Properties of DNA-Nanoparticle Superstructures Using Polyvalent Counterions. (United States)

    Chou, Leo Y T; Song, Fayi; Chan, Warren C W


    DNA assembly of nanoparticles is a powerful approach to control their properties and prototype new materials. However, the structure and properties of DNA-assembled nanoparticles are labile and sensitive to interactions with counterions, which vary with processing and application environment. Here we show that substituting polyamines in place of elemental counterions significantly enhanced the structural rigidity and plasmonic properties of DNA-assembled metal nanoparticles. These effects arose from the ability of polyamines to condense DNA and cross-link DNA-coated nanoparticles. We further used polyamine wrapped DNA nanostructures as structural templates to seed the growth of polymer multilayers via layer-by-layer assembly, and controlled the degree of DNA condensation, plasmon coupling efficiency, and material responsiveness to environmental stimuli by varying polyelectrolyte composition. These results highlight counterion engineering as a versatile strategy to tailor the properties of DNA-nanoparticle assemblies for various applications, and should be applicable to other classes of DNA nanostructures.

  14. Organizing DNA origami tiles into larger structures using preformed scaffold frames. (United States)

    Zhao, Zhao; Liu, Yan; Yan, Hao


    Structural DNA nanotechnology utilizes DNA molecules as programmable information-coding polymers to create higher order structures at the nanometer scale. An important milestone in structural DNA nanotechnology was the development of scaffolded DNA origami in which a long single-stranded viral genome (scaffold strand) is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides (staple strands). The achievable dimensions of the DNA origami tile units are currently limited by the length of the scaffold strand. Here we demonstrate a strategy referred to as "superorigami" or "origami of origami" to scale up DNA origami technology. First, this method uses a collection of bridge strands to prefold a single-stranded DNA scaffold into a loose framework. Subsequently, preformed individual DNA origami tiles are directed onto the loose framework so that each origami tile serves as a large staple. Using this strategy, we demonstrate the ability to organize DNA origami nanostructures into larger spatially addressable architectures.

  15. Polymer dye lasers

    DEFF Research Database (Denmark)

    Balslev, Søren


    , elektronstrålelithografi og Röntgenstrålelithografi. Andre polymerer er også blevet formgivet via ”nanoimprint” lithografi for at skabe laserresonatorer. En række lasere, både baseret på et flydende forstærkningsmedium og et faststof forstærkningsrmedium er blevet udviklet. Laserne giver både lys i flere ”modes” og i een......Formålet med dette Ph.D. arbejde har været at udvikle miniaturiserede polymer farvestoflasere, egnet til at blive integreret i mikrochips som også indeholder andre polymerstrukturer – som for eksempel kan findes i ”Laboratorie-på-en-chip” kredsløb. Lasernes funktion skal være at levere lys til...... meget følsomme sensorformål, og at undgå at skulle opliniere eksterne lyskilder til sensorer på polymerchips. En enkelt type gennemsigtig ”resist” (SU-8) er blevet brugt til at udvikle en række laserresonatorer i polymer. ”Resisten” er blevet formgivet via en række lithografiske teknikker: UV lithografi...

  16. Graphene/Polymer Nanocomposites (United States)

    Macosko, Chris


    Graphite has attracted large attention as a reinforcement for polymers due to its ability to modify electrical conductivity, mechanical and gas barrier properties of host polymers and its potentially lower cost than carbon nanotubes. If graphite can be exfoliated into atomically thin graphene sheets, it is possible to achieve the highest property enhancements at the lowest loading. However, small spacing and strong van der Waals forces between graphene layers make exfoliation of graphite via conventional composite manufacturing strategies challenging. Recently, two different approaches to obtain exfoliated graphite prior to blending were reported: thermal treatment (Schniepp et al., JACS 2006) and chemical modification (Stankovich et al., J Mat Chem 2006). Both start from graphite oxide. We will describe and evaluate these exfoliation approaches and the methods used to produce graphene reinforced thermoplastics, particularly polyester, polycarbonate and polyurethane nanocomposites. Three different dispersion methods - melt blending, solution mixing and in-situ polymerization -- are compared. Characterization of dispersion quality is illustrated with TEM, rheology and in electrical conductivity, tensile modulus and gas barrier property improvement.

  17. Luminescent DNA- and agar-based membranes. (United States)

    Leones, R; Fernandes, M; Ferreira, R A S; Cesarino, I; Lima, J F; Carlos, L D; Bermudez, V de Zea; Magon, C J; Donoso, J P; Silva, M M; Pawlicka, A


    Luminescent materials containing europium ions are investigated for different optical applications. They can be obtained using bio-macromolecules, which are promising alternatives to synthetic polymers based on the decreasing oil resources. This paper describes studies of the DNA- and Agar-europium triflate luminescent membranes and its potential technological applications are expanded to electroluminescent devices. Polarized optical microscopy demonstrated that the samples are birefringent with submicrometer anisotropy. The X-ray diffraction analysis revealed predominantly amorphous nature of the samples and the atomic force microscopy images showed a roughness of the membranes of 409.0 and 136.1 nm for the samples of DNA10Eu and Agar1.11Eu, respectively. The electron paramagnetic resonance spectra of the DNA(n)Eu membranes with the principal lines at g ≈ 2.0 and g ≈ 4.8 confirmed uniform distribution of rare earth ions in a disordered matrix. Moreover, these strong and narrow resonance lines for the samples of DNA(n)Eu when compared to the Agar(n)Eu suggested a presence of paramagnetic radicals arising from the DNA matrix. The emission spectra suggested that the Eu3+ ions occupy a single local environment in both matrices and the excitation spectra monitored around the Eu emission lines pointed out that the Eu3+ ions in the Agar host were mainly excited via the broad band component rather than by direct intra-4f(6) excitation, whereas the opposite case occurred for the DNA-based sample.

  18. DNA ligase I, the replicative DNA ligase. (United States)

    Howes, Timothy R L; Tomkinson, Alan E


    Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each of the domains contacting the DNA. The non-catalytic N-terminal region of eukaryotic DNA ligase I is responsible for the specific participation of these enzymes in DNA replication. This proline-rich unstructured region contains the nuclear localization signal and a PCNA interaction motif that is critical for localization to replication foci and efficient joining of Okazaki fragments. DNA ligase I initially engages the PCNA trimer via this interaction motif which is located at the extreme N-terminus of this flexible region. It is likely that this facilitates an additional interaction between the DNA binding domain and the PCNA ring. The similar size and shape of the rings formed by the PCNA trimer and the DNA ligase I catalytic region when it engages a DNA nick suggest that these proteins interact to form a double-ring structure during the joining of Okazaki fragments. DNA ligase I also interacts with replication factor C, the factor that loads the PCNA trimeric ring onto DNA. This interaction, which is regulated by phosphorylation of the non-catalytic N-terminus of DNA ligase I, also appears to be critical for DNA replication.

  19. Accelerated Characterization of Polymer Properties

    Energy Technology Data Exchange (ETDEWEB)

    R. Wroczynski; l. Brewer; D. Buckley; M. Burrell; R. Potyrailo


    This report describes the efforts to develop a suite of microanalysis techniques that can rapidly measure a variety of polymer properties of industrial importance, including thermal, photo-oxidative, and color stability; as well as ductility, viscosity, and mechanical and antistatic properties. Additional goals of the project were to direct the development of these techniques toward simultaneous measurements of multiple polymer samples of small size in real time using non-destructive and/or parallel or rapid sequential measurements, to develop microcompounding techniques for preparing polymers with additives, and to demonstrate that samples prepared in the microcompounder could be analyzed directly or used in rapid off-line measurements. These enabling technologies are the crucial precursors to the development of high-throughput screening (HTS) methodologies for the polymer additives industry whereby the rate of development of new additives and polymer formulations can be greatly accelerated.

  20. Electrochemical synthesis of electroconducting polymers

    Directory of Open Access Journals (Sweden)

    Gvozdenović Milica M.


    Full Text Available Electroconducting polymers from the group of synthetic metals are extensively investigated due to numerous properties perspective in practical application. These materials may be synthesized by both chemical and electrochemical procedures. Chemical synthesis is suitable when bulk quantities of the polymer are needed and up to date it presents dominant commercial method of producing electroconducting polymers. Nevertheless, electrochemical synthesis has its advantages; it avoids usage of oxidants since conducting polymeric material is obtained at anode upon application of positive potential, leading to increased purity. On the other hand, since the polymer is deposited onto electrode, further electrochemical characterization is facilitated. Owing to actuality of the research in the field this texts aims to describe important aspects of electrochemical synthesis of electroconducting polymers, with special emphasis to polyaniline and polypyrrole. [Projekat Ministarstva nauke Republike Srbije, br. 172046

  1. Polymer in Agriculture: a Review

    Directory of Open Access Journals (Sweden)

    Francesco Puoci


    Full Text Available In agricultural field, polymers are widely used for many applications. Although they were used, in the first time, just as structural materials (inhert polymers, in the last decades functionalized polymers revolutionized the agricultural and food industry with new tools for several applications. Smart polymeric materials and smart delivery systems helped the agricultural industryto combat viruses and other crop pathogens, functionalized polymers were used to increase the efficiency of pesticides and herbicides, allowing lower doses to be used and to indirectly protect the environment through filters or catalysts to reduce pollution and clean-up existing pollutants. This report will review the key aspects of used polymers in agricultural area, highlighting current research in this field and the future impacts they may have.

  2. Review of polymer MEMS micromachining (United States)

    Kim, Brian J.; Meng, Ellis


    The development of polymer micromachining technologies that complement traditional silicon approaches has enabled the broadening of microelectromechanical systems (MEMS) applications. Polymeric materials feature a diverse set of properties not present in traditional microfabrication materials. The investigation and development of these materials have opened the door to alternative and potentially more cost effective manufacturing options to produce highly flexible structures and substrates with tailorable bulk and surface properties. As a broad review of the progress of polymers within MEMS, major and recent developments in polymer micromachining are presented here, including deposition, removal, and release techniques for three widely used MEMS polymer materials, namely SU-8, polyimide, and Parylene C. The application of these techniques to create devices having flexible substrates and novel polymer structural elements for biomedical MEMS (bioMEMS) is also reviewed.

  3. Soft Confinement for Polymer Solutions

    CERN Document Server

    Oya, Yutaka


    As a model of soft confinement for polymers, we investigated equilibrium shapes of a flexible vesicle that contains a phase-separating polymer solution. To simulate such a system, we combined the phase field theory (PFT) for the vesicle and the self-consistent field theory (SCFT) for the polymer solution. We observed a transition from a symmetric prolate shape of the vesicle to an asymmetric pear shape induced by the domain structure of the enclosed polymer solution. Moreover, when a non-zero spontaneous curvature of the vesicle is introduced, a re-entrant transition between the prolate and the dumbbell shapes of the vesicle is observed. This re-entrant transition is explained by considering the competition between the loss of conformational entropy and that of translational entropy of polymer chains due to the confinement by the deformable vesicle. This finding is in accordance with the recent experimental result reported by Terasawa, et al.

  4. Mechanisms of Morphology Development and Control in Polymer- Polymer Blends (United States)

    Macosko, Christopher W.


    Polymer-polymer blends continue to be the most important method for achieving optimization of properties in plastics products. Over 30 percent of all plastics are blends. While miscible blends generally give average properties between the components, immiscible blends offer synergistic possibilities such as high modulus with high toughness; high flow with high impact strength or diffusion barriers with good mechanical properties and low cost. The key to performance of these immiscible blends is their morphology. There are several important types of morphology which can lead to valuable property improvement: emulsion - small polymer spheres well dispersed in a polymer matrix. double emulsion - spheres inside spheres which are dispersed in another matrix. microlayer - thin, parallel layers of one polymer in a matrix. cocontinuous - two (or more) continuous, interpenetrating polymer phases. To be economical it is desirable to create these morphologies via melt mixing of powder or pellets in conventional compounding equipment. The melting stage during compounding is very important for morphology development. This presentation will demonstrate the role of melting or softening of each phase as well as their viscosity, elasticity and interfacial tension in morphology development. Interfacial modification with premade block copolymers or reactively formed copolymers can greatly alter morphology formation and stability. Experimental results will be presented which quantify the role of these additives. References to recent work in this area by our group are listed below: DeBrule, M. B., L. Levitt and C.W. Macosko, "The Rheology and Morphology of Layered Polymer Melts in Shear," Soc. Plastics Eng. Tech Papers (ANTEC), 84-89 (1996). Guegan, P., C. W. Macosko, T. Ishizone, A. Hirao and S. Nakahama, "Kinetics of Chain Coupling at Melt Interfaces, Macromol. 27, 4993-4997 (1994). Lee, M. S., T.P. Lodge, and C. W. Macosko, "Can Random Copolymers Serve as Effective Polymeric

  5. Effect of inhibitors of cellular metabolism on postradiation repair and degradation of DNA in rat thymocytes

    Energy Technology Data Exchange (ETDEWEB)

    Ivannik, B.P.; Golubeva, R.V.; Proskuryakov, S.Ya.; Murzaev, V.I.; Ryabchenko, N.I.


    The viscosimetric method was used to determine the molecular weight of high polymer single-stranded DNA in alkaline nuclear lysates for the study of the effects of a number of inhibitors of synthesis of DNA (hydroxyurea), macroergic elements (2,4-dinitrophenol, EDTA) and DNAase (Na/sup +/ citrate, Ca/sup + +/ ions) on the process of repair and secondary post-radiation degradation of DNA of rat thymocytes exposed to radiation in a dosage of 3 kR.

  6. Communication: Origin of the contributions to DNA structure in phages. (United States)

    Myers, Christopher G; Pettitt, B Montgomery


    Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies.

  7. Polymers – A New Open Access Scientific Journal on Polymer Science

    Directory of Open Access Journals (Sweden)

    Shu-Kun Lin


    Full Text Available Polymers is a new interdisciplinary, Open Access scientific journal on polymer science, published by Molecular Diversity Preservation International (MDPI. This journal welcomes manuscript submissions on polymer chemistry, macromolecular chemistry, polymer physics, polymer characterization and all related topics. Both synthetic polymers and natural polymers, including biopolymers, are considered. Manuscripts will be thoroughly peer-reviewed in a timely fashion, and papers will be published, if accepted, within 6 to 8 weeks after submission. [...

  8. Polymer nanoassemblies for cancer treatment and imaging. (United States)

    Lee, Hyun Jin; Ponta, Andrei; Bae, Younsoo


    Amphiphilic polymers represented by block copolymers self-assemble into well-defined nanostructures capable of incorporating therapeutics. Polymer nanoassemblies currently developed for cancer treatment and imaging are reviewed in this article. Particular attention is paid to three representative polymer nanoassemblies: polymer micelles, polymer micellar aggregates and polymer vesicles. Rationales, design and performance of these polymer nanoassemblies are addressed, focusing on increasing the solubility and chemical stability of drugs. Also discussed are polymer nanoassembly formation, the distribution of polymer materials in the human body and applications of polymer nanoassemblies for combined therapy and imaging of cancer. Updates on tumor-targeting approaches, based on preclinical and clinical results are provided, as well as solutions for current issues that drug-delivery systems have, such as in vivo stability, tissue penetration and therapeutic efficacy. These are discussed to provide insights on the future development of more effective polymer nanoassemblies for the delivery of therapeutics in the body.

  9. A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

    Directory of Open Access Journals (Sweden)

    Nikolay Korolev


    Full Text Available Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra- and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1–100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

  10. Synthesis of DNA (United States)

    Mariella, Jr., Raymond P.


    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  11. EDITORIAL: Electroactive polymer materials (United States)

    Bar-Cohen, Yoseph; Kim, Kwang J.; Ryeol Choi, Hyouk; Madden, John D. W.


    Imitating nature's mechanisms offers enormous potential for the improvement of our lives and the tools we use. This field of the study and imitation of, and inspiration from, nature's methods, designs and processes is known as biomimetics. Artificial muscles, i.e. electroactive polymers (EAPs), are one of the emerging technologies enabling biomimetics. Polymers that can be stimulated to change shape or size have been known for many years. The activation mechanisms of such polymers include electrical, chemical, pneumatic, optical and magnetic. Electrical excitation is one of the most attractive stimulators able to produce elastic deformation in polymers. The convenience and practicality of electrical stimulation and the continual improvement in capabilities make EAP materials some of the most attractive among activatable polymers (Bar-Cohen Y (ed) 2004 Electroactive Polymer (EAP) Actuators as Artificial Muscles—Reality, Potential and Challenges 2nd edn, vol PM136 (Bellingham, WA: SPIE Press) pp 1-765). As polymers, EAP materials offer many appealing characteristics that include low weight, fracture tolerance and pliability. Furthermore, they can be configured into almost any conceivable shape and their properties can be tailored to suit a broad range of requirements. These capabilities and the significant change of shape or size under electrical stimulation while being able to endure many cycles of actuation are inspiring many potential possibilities for EAP materials among engineers and scientists in many different disciplines. Practitioners in biomimetics are particularly excited about these materials since they can be used to mimic the movements of animals and insects. Potentially, mechanisms actuated by EAPs will enable engineers to create devices previously imaginable only in science fiction. For many years EAP materials received relatively little attention due to their poor actuation capability and the small number of available materials. In the last fifteen

  12. Conjugated polymer-assisted dispersion of single-wall carbon nanotubes: the power of polymer wrapping. (United States)

    Samanta, Suman Kalyan; Fritsch, Martin; Scherf, Ullrich; Gomulya, Widianta; Bisri, Satria Zulkarnaen; Loi, Maria Antonietta


    coordinates [(n,m) indices]. The polymer wrapping strategy enables the generation of SWNT dispersions containing exclusively semiconducting nanotubes. Toward the applications in electronic devices, until now most applied approach is a direct processing of such SWNT dispersions into the active layer of network-type thin film field effect transistors. However, to achieve promising transistor performance (high mobility and on-off ratio) careful removal of the wrapping polymer chains seems crucial, for example, by washing or ultracentrifugation. More defined positioning of the SWNTs can be accomplished in directed self-assembly procedures. One possible strategy uses diblock copolymers containing a conjugated polymer block as dispersing moiety and a second block for directed self-assembly, for example, a DNA block for specific interaction with complementary DNA strands. Another strategy utilizes reactive side chains for controlled anchoring onto patterned surfaces (e.g., by interaction of thiol-terminated alkyl side chains with gold surfaces). A further promising application of purified SWNT dispersions is the field of organic (all-carbon) or hybrid solar cell devices.

  13. Mechanically strong, fluorescent hydrogels from zwitterionic, fully π-conjugated polymers. (United States)

    Elmalem, Einat; Biedermann, Frank; Scherer, Maik R J; Koutsioubas, Alexandros; Toprakcioglu, Chris; Biffi, Giulia; Huck, Wilhelm T S


    Mechanically strong supramolecular hydrogels (up to 98.9% water content) were obtained by the combination of a rigid, fully π-conjugated polymer backbone and zwitterionic side chains. The gels were characterized by SAXS, SEM and rheology measurements and are fluorescent, stimuli responsive (temperature, salts) and bind DNA.

  14. Polymers in Curved Boxes

    CERN Document Server

    Yaman, K; Solis, F J; Witten, T A


    We apply results derived in other contexts for the spectrum of the Laplace operator in curved geometries to the study of an ideal polymer chain confined to a spherical annulus in arbitrary space dimension D and conclude that the free energy compared to its value for an uncurved box of the same thickness and volume, is lower when $D < 3$, stays the same when $D = 3$, and is higher when lowers the effective bending elasticity of the walls, and might induce spontaneous symmetry breaking, i.e. bending. (Actually, the above mentioned results show that {\\em {any}} shell in $D = 3$ induces this effect, except for a spherical shell). We compute the contribution of this effect to the bending rigidities in the Helfrich free energy expression.

  15. Polymer Infiltration Studies

    Energy Technology Data Exchange (ETDEWEB)

    Marchello, J.M.


    Significant progress has been made on the preparation of carbon fiber composites using advanced polymer resins during the past three months. Current and ongoing research activities reported herein include: (1) Prepregger Hot Sled Operation; (2) Ribbonizing Powder-Impregnated Towpreg; (3) Textile Composites from Powder-Coated Towpreg: Role of Bulk Factor; and (4) Powder Curtain Prepreg Process. During the coming months research will be directed toward further development of the new powder curtain prepregging method and on ways to customize dry powder towpreg for textile and robotic applications in aircraft part fabrication. Studies of multi-tow powder prepregging and ribbon preparation will be conducted in conjunction with continued development of prepegging technology and the various aspects of composite part fabrication using customized towpreg. Also, work will continue on the analysis of the new solution prepegger.

  16. Protein Polymers and Amyloids

    DEFF Research Database (Denmark)

    Risør, Michael Wulff


    , underlining the importance of understanding this relationship. The monomeric C-36 peptide was investigated by liquid-state NMR spectroscopy and found to be intrinsically disordered with minor propensities towards β-sheet structure. The plasticity of such a peptide makes it suitable for a whole range......, is a general hallmark. They also include the α1-antitrypsin deficiency, where disease-causing mutations in the serine protease inhibitor, α1-antitrypsin (α1AT), leads to accumulation of the aberrant protein in the liver of these patients. The native metastable structure of α1AT constitutes a molecular trap...... of this mechanism were investigated through a series of interaction experiments. Despite a very buried location in the native structure, evidence here suggest that the C-terminal tail is labile under slightly destabilizing conditions, providing new detail to this matter. A small infectious polymer unit was also...

  17. Self-healing polymers (United States)

    Klein, Daniel J. (Inventor)


    A three dimensional structure fabricated from a self-healing polymeric material, comprising poly(ester amides) obtained from ethylene glycol, azelaic acid and 1,1-aminoundecanoic acid, wherein polymeric material has a melt index above 2.5 g/10 min. as determined by ASTM D1238 at C. and 2.16kg, impact resistance and ductility sufficient to resist cracking and brittle fracture upon impact by a 9 mm bullet fired at a temperature of about C. at subsonic speed in a range from about 800 feet/sec to about 1000 feet/sec. It has been determined that the important factors necessary for self-healing behavior of polymers include sufficient impact strength, control of the degree of crystallinity, low melting point and the ability to instantly melt at impacted area.

  18. All Polymer Micropump

    DEFF Research Database (Denmark)

    Hansen, Thomas Steen


    (ACEO) micropump. The ACEO pump consists of an array of interdigitated small and large PEDOTjPMMA encapsulated in a polyurethane (PUR) channel system. The pumping velocity was detected using fluorescent microspheres and a confocal microscope. The pump characteristics resembled those of pumps based...... polymer was developed by mixing polyurethane in to the solution from which the PEDOT was cast. The resulting PEDOTjPUR material showed good conductivity. The film was elongated 50 % ten times and apart from a small irreversible increase in resistance during the first elongation, the film resistance was...... a new short chained polyurethane. The resolution of the inkjet printer was in the order of 200 J-tm. The inkjet printed pattern is compared with the agarose stamping technique in a setup where the conductivity perpendicular to the stretching direction is measured on two electrodes fabricated by the two...

  19. Polymer optical fiber fuse

    CERN Document Server

    Mizuno, Yosuke; Tanaka, Hiroki; Nakamura, Kentaro


    Although high-transmission-capacity optical fibers are in demand, the problem of the fiber fuse phenomenon needs to be resolved to prevent the destruction of fibers. As polymer optical fibers become more prevalent, clarifying their fuse properties has become important. Here, we experimentally demonstrate a fuse propagation velocity of 21.9 mm/s, which is 1 to 2 orders of magnitude slower than that in standard silica fibers. The achieved threshold power density and proportionality constant between the propagation velocity and the power density are respectively 1/186 of and 16.8 times the values for silica fibers. An oscillatory continuous curve instead of periodic voids is formed after the passage of the fuse. An easy fuse termination method is presented herein, along with its potential plasma applications.

  20. Elastic Behavior of Polymer Chains

    Institute of Scientific and Technical Information of China (English)

    Teng Lu; Tao Chen; Hao-jun Liang


    The elastic behavior of the polymer chain was investigated in a three-dimensional off-lattice model. We sample more than 109 conformations of each kind of polymer chain by using a Monte Carlo algorithm, then analyze them with the non-Gaussian theory of rubberlike elasticity, and end with a statistical study. Through observing the effect of the chain flexibility and the stretching ratio on the mean-square end-to-end distance,the average energy, the average Helmholtz free energy, the elastic force, the contribution of energy to the elastic force, and the entropy contribution to elastic force of the polymer chain, we find that a rigid polymer chain is much easier to stretch than a flexible polymer chain. Also, a rigid polymer chain will become difficult to stretch only at a quite high stretching ratio because of the effect of the entropy contribution.These results of our simulation calculation may explain some of the macroscopic phenomena of polymer and biomacromolecular elasticity.

  1. Model membrane interaction and DNA-binding of antimicrobial peptide Lasioglossin II derived from bee venom. (United States)

    Bandyopadhyay, Susmita; Lee, Meryl; Sivaraman, J; Chatterjee, Chiradip


    Lasioglossins, a new family of antimicrobial peptide, have been shown to have strong antimicrobial activity with low haemo-lytic and mast cell degranulation activity, and exhibit cytotoxic activity against various cancer cells in vitro. In order to understand the active conformation of these pentadecapeptides in membranes, we have studied the interaction of Lasioglossin II (LL-II), one of the members of Lasioglossins family with membrane mimetic micelle Dodecylphosphocholine (DPC) by fluorescence, Circular Dichroism (CD) and two dimensional (2D) (1)H NMR spectroscopy. Fluorescence experiments provide evidence of interaction of the N-terminal tryptophan residue of LL-II with the hydrophobic core of DPC micelle. CD results show an extended chain conformation of LL-II in water which is converted to a partial helical conformation in the presence of DPC micelle. Moreover we have determined the first three-dimensional NMR structure of LL-II bound to DPC micelle with rmsd of 0.36Å. The solution structure of LL-II shows hydrophobic and hydrophilic core formation in peptide pointing towards different direction in the presence of DPC. This amphipathic structure may allow this peptide to penetrate deeply into the interfacial region of negatively charged membranes and leading to local membrane destabilization. Further we have elucidated the DNA binding ability of LL-II by agarose gel retardation and fluorescence quenching experiments.

  2. The elastic theory of a single DNA molecule

    Indian Academy of Sciences (India)

    Haijun Zhou; Yang Zhang; Zhang-Can Ou-Yang


    We study the elastic responses of double- (ds) and single-stranded (ss) DNA at external force fields. A double-strand-polymer elastic model is constructed and solved by path integral methods and Monte Carlo simulations to understand the entropic elasticity, cooperative extensibility, and supercoiling property of dsDNA. The good agreement with experiments indicates that shortranged base-pair stacking interaction is crucial for the stability and the high deformability of dsDNA. Hairpin-coil transition in ssDNA is studied with generating function method. A threshold force is needed to pull the ssDNA hairpin patterns, stabilized by base pairing and base-pair stacking, into random coils. This phase transition is predicted to be of first order for stacking potential higher than some critical level, in accordance with experimental observations.

  3. Binding and Transformation of Extracellular DNA in Soil

    Institute of Scientific and Technical Information of China (English)

    CAI Peng; HUANG Qiao-Yun; ZHANG Xue-Wen; CHEN Hao


    DNA is the genetic material of various organisms. Extracellular DNA adsorbed or bound on surface-active particles in soils has been shown to persist for long periods against nucleases degradation and still retain the ability to transform competent cells. This paper reviews some recent advances on the binding and transformation of extracellular DNA in soils,which is fundamental to understanding the nature of the soil, regulating biodiversity, and assessing the risk of releasing genetically engineered microorganisms (GEMs) as well as being helpful for development of the genetic evolutional theory of bacteria. Several influencing factors, such as soil pH, ionic strength, soil surface properties, and characteristics of the DNA polymer, are discussed. To date, the understanding of the type of molecular binding sites and the conformation of adsorbed and bound DNA to soil particles is still in its infancy.

  4. Molecular DNA switches and DNA chips (United States)

    Sabanayagam, Chandran R.; Berkey, Cristin; Lavi, Uri; Cantor, Charles R.; Smith, Cassandra L.


    We present an assay to detect single-nucleotide polymorphisms on a chip using molecular DNA switches and isothermal rolling- circle amplification. The basic principle behind the switch is an allele-specific oligonucleotide circularization, mediated by DNA ligase. A DNA switch is closed when perfect hybridization between the probe oligonucleotide and target DNA allows ligase to covalently circularize the probe. Mismatches around the ligation site prevent probe circularization, resulting in an open switch. DNA polymerase is then used to preferentially amplify the closed switches, via rolling-circle amplification. The stringency of the molecular switches yields 102 - 103 fold discrimination between matched and mismatched sequences.

  5. Physical properties of polymers handbook

    CERN Document Server


    This book offers concise information on the properties of polymeric materials, particularly those most relevant to physical chemistry and chemical physics. Extensive updates and revisions to each chapter include eleven new chapters on novel polymeric structures, reinforcing phases in polymers, and experiments on single polymer chains. The study of complex materials is highly interdisciplinary, and new findings are scattered among a large selection of scientific and engineering journals. This book brings together data from experts in the different disciplines contributing to the rapidly growing area of polymers and complex materials.

  6. Bioderadable Polymers in Food Packaging

    Directory of Open Access Journals (Sweden)



    Full Text Available In recent years, there has been a marked increase in the interest in use of biodegradable materials in packaging. The principal function of packaging is protection and preservation of food from external contamination. This function involves retardation of deterioration, extension of shelf life, and maintenance of quality and safety of packaged food. Biodegradable polymers are the one which fulfill all these functions without causing any threat to the environment. The belief is that biodegradable polymer materials will reduce the need for synthetic polymer production (thus reducing pollution at a low cost, thereby producing a positive effect both environmentally and economically.

  7. Physics of photorefraction in polymers

    CERN Document Server

    West, Dave


    Photorefractive polymer composites are an unusually sensitive class of photopolymers. Physics of Photorefraction in Polymers describes our current understanding of the physical processes that produce a photorefractive effect in key composite materials. Topics as diverse as charge generation, dispersive charge transport, charge compensation and trapping, molecular diffusion, organic composite structure, and nonlinear optical wave coupling are all developed from a physical perspective. Emphasis is placed on explaining how these physical processes lead to observable properties of the polymers, and the authors discuss various applications, including holographic archiving.

  8. Multilayer Electroactive Polymer Composite Material (United States)

    Ounaies, Zoubeida (Inventor); Park, Cheol (Inventor); Harrison, Joycelyn S. (Inventor); Holloway, Nancy M. (Inventor); Draughon, Gregory K. (Inventor)


    An electroactive material comprises multiple layers of electroactive composite with each layer having unique dielectric, electrical and mechanical properties that define an electromechanical operation thereof when affected by an external stimulus. For example, each layer can be (i) a 2-phase composite made from a polymer with polarizable moieties and an effective amount of carbon nanotubes incorporated in the polymer for a predetermined electromechanical operation, or (ii) a 3-phase composite having the elements of the 2-phase composite and further including a third component of micro-sized to nano-sized particles of an electroactive ceramic incorporated in the polymer matrix.

  9. Statistical properties of curved polymer

    Indian Academy of Sciences (India)

    Surya Kanta Ghosh; Anirban Sain


    Intrinsic curvature of biopolymers is emerging as an essential feature in various biological phenomena. Examples of polymers with intrinsic curvature are microtubule in eukaryotic cells or FtsZ filaments in prokaryotic cells. We consider the general model for polymers with intrinsic curvature. We aim to study both equilibrium and dynamic properties of such polymers. Here we report preliminary results on the equilibrium distribution function $P({\\mathbf{R}})$ of the end-to-end distance ${\\mathbf{R}}$. We employ transfer matrix method for this study.

  10. Scaling Behaviors of Branched Polymers

    CERN Document Server

    Aoki, H; Kawai, H; Kitazawa, Y; Aoki, Hajime; Iso, Satoshi; Kawai, Hikaru; Kitazawa, Yoshihisa


    We study the thermodynamic behavior of branched polymers. We first study random walks in order to clarify the thermodynamic relation between the canonical ensemble and the grand canonical ensemble. We then show that correlation functions for branched polymers are given by those for $\\phi^3$ theory with a single mass insertion, not those for the $\\phi^3$ theory themselves. In particular, the two-point function behaves as $1/p^4$, not as $1/p^2$, in the scaling region. This behavior is consistent with the fact that the Hausdorff dimension of the branched polymer is four.

  11. Turbulence in dilute polymer solutions (United States)

    Liberzon, A.; Guala, M.; Lüthi, B.; Kinzelbach, W.; Tsinober, A.


    The work reported below is a comparative study of the properties of turbulence with weak mean flow in a Newtonian fluid and in a dilute polymer solution with an emphasis on the small scale phenomena. The main tool used is a three-dimensional particle tracking system allowing to measure and follow in a Lagrangian manner the field of velocities, as well as velocity derivatives, and thus vorticity, strain, and a variety of related and dynamically significant quantities. The comparison of data from the two flows allows to directly observe the influence of polymers on these quantities as well as the evolution of material elements in the presence of polymers.

  12. Thermoresponsive Polymers for Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Theoni K. Georgiou


    Full Text Available Thermoresponsive polymers are a class of “smart” materials that have the ability to respond to a change in temperature; a property that makes them useful materials in a wide range of applications and consequently attracts much scientific interest. This review focuses mainly on the studies published over the last 10 years on the synthesis and use of thermoresponsive polymers for biomedical applications including drug delivery, tissue engineering and gene delivery. A summary of the main applications is given following the different studies on thermoresponsive polymers which are categorized based on their 3-dimensional structure; hydrogels, interpenetrating networks, micelles, crosslinked micelles, polymersomes, films and particles.

  13. Principles of polymer processing modelling

    Directory of Open Access Journals (Sweden)

    Agassant Jean-François


    Full Text Available Polymer processing involves three thermo-mechanical stages: Plastication of solid polymer granules or powder to an homogeneous fluid which is shaped under pressure in moulds or dies and finally cooled and eventually drawn to obtain the final plastic part. Physical properties of polymers (high viscosity, non-linear rheology, low thermal diffusivity as well as the complex shape of most plastic parts make modelling a challenge. Several examples (film blowing extrusion dies, injection moulding, blow moulding are presented and discussed.

  14. Wetting of brushes by polymer melts

    NARCIS (Netherlands)

    Maas, J.


    The scientific and practical importance of thin polymer films is evident and in many applications polymer films are required. Hence, studying properties of polymer films is relevant. Adsorption of polymer at liquid/solid interfaces can stabilise particles in a matrix. Homopolymers are often used for

  15. Carbon nanotube-polymer composite actuators (United States)

    Gennett, Thomas; Raffaelle, Ryne P.; Landi, Brian J.; Heben, Michael J.


    The present invention discloses a carbon nanotube (SWNT)-polymer composite actuator and method to make such actuator. A series of uniform composites was prepared by dispersing purified single wall nanotubes with varying weight percents into a polymer matrix, followed by solution casting. The resulting nanotube-polymer composite was then successfully used to form a nanotube polymer actuator.

  16. Migration and sensory evaluation of irradiated polymers

    NARCIS (Netherlands)

    Stoffers, N.H.; Linssen, J.P.H.; Franz, R.; Welle, F.


    The effects on ionising irradiation on polymer additives, monomers and polymers themselves have been investigated. Changes of initial concentrations of certain additives and monomers, a change in their specific migration as well as sensory changes of the polymers were examined. Polymer stabilizers s

  17. The Workshop on Conductive Polymers: Final Report (United States)


    Reports are made by groups on: polyacetylene, polyphenylene, polyaniline, and related systems; molecular, crystallographic, and defect structures in conducting polymers; heterocyclic polymers; synthesis of new and improved conducting polymers; future applications possibilities for conducting polymers; and challenges for improved understanding of properties. (DLC)

  18. Carbon dioxide foaming of glassy polymers

    NARCIS (Netherlands)

    Wessling, M.; Borneman, Z.; Boomgaard, van den Th.; Smolders, C.A.


    The mechanism of foaming a glassy polymer using sorbed carbon dioxide is studied in detail. A glassy polymer supersaturated with nitrogen forms a microcellular foam, if the polymer is quickly heated above its glass transition temperature. A glassy polymer supersaturated with CO2 forms this foam-like

  19. Method for bonding a thermoplastic polymer to a thermosetting polymer component

    NARCIS (Netherlands)

    Van Tooren, M.J.L.


    The invention relates to a method for bonding a thermoplastic polymer to a thermosetting polymer component, the thermoplastic polymer having a melting temperature that exceeds the curing temperature of the thermosetting polymer. The method comprises the steps of providing a cured thermosetting polym

  20. Water Soluble Polymers for Pharmaceutical Applications

    Directory of Open Access Journals (Sweden)

    Veeran Gowda Kadajji


    Full Text Available Advances in polymer science have led to the development of novel drug delivery systems. Some polymers are obtained from natural resources and then chemically modified for various applications, while others are chemically synthesized and used. A large number of natural and synthetic polymers are available. In the present paper, only water soluble polymers are described. They have been explained in two categories (1 synthetic and (2 natural. Drug polymer conjugates, block copolymers, hydrogels and other water soluble drug polymer complexes have also been explained. The general properties and applications of different water soluble polymers in the formulation of different dosage forms, novel delivery systems and biomedical applications will be discussed.

  1. Inkjet printing of electroactive polymer actuators on polymer substrates (United States)

    Pabst, O.; Perelaer, J.; Beckert, E.; Schubert, U. S.; Eberhardt, R.; Tünnermann, A.


    Electroactive polymers (EAP) are promising materials for actuators in different application areas. This paper reports inkjet printing as a versatile tool for manufacturing EAP actuators. Drop-on-demand inkjet printing can be used for additive deposition of functional materials onto substrates. Cantilever bending actuators with lateral dimensions in the mm range are described here. A commercially available solution of electroactive polymers is dispensed onto metalized polycarbonate substrates using inkjet printing. These polymers exhibit piezoelectric behavior. Multiple layers are printed resulting in a film thickness of 5 to 10 μm. After printing, the polymer layers are annealed thermally at 130 °C. Top electrodes are deposited onto the EAP layer by inkjet printing a silver nanoparticle ink. The as-printed silver layers are sintered using an argon plasma - a recently developed sintering technique that is compatible with low TG polymer foils. After printing the EAP layers are poled. When applying an electric field across the polymer layer, piezoelectric strain in the EAP leads to a bending deflection of the structures. With driving voltages of 200 V the actuators generate displacements of 20 μm and blocking forces of approximately 3 mN. The first resonance frequency occurs at 230 Hz.

  2. Polymer and Polymer Gel of Liquid Crystalline Semiconductors

    Institute of Scientific and Technical Information of China (English)

    Teppei Shimakawa; Naoki Yoshimoto; Jun-ichi Hanna


    It prepared a polymer and polymer gel of a liquid crystalline (LC) semiconductor having a 2-phenylnaphthalene moiety and studied their charge carrier transport properties by the time-of-flight technique. It is found that polyacrylate having the mesogenic core moiety of 2-phenylnaphtalene (PNP-acrylate) exhibited a comparable mobility of 10-4cm2/Vs in smectic A phase to those in smectic A (SmA) phase of small molecular liquid crystals with the same core moiety, e.g., 6-(4'-octylphenyl)- 2-dodecyloxynaphthalene (8-PNP-O12), and an enhanced mobility up to 10-3cm2/Vs in the LC-glassy phase at room temperature, when mixed with a small amount of 8-PNP-O12. On the other hand, the polymer gel consisting of 20 wt %-hexamethylenediacrylate (HDA)-based cross-linked polymer and 8-PNP-O12 exhibited no degraded mobility when cross-linked at the mesophase. These results indicate that the polymer and polymer composite of liquid crystalline semiconductors provide us with an easy way to realize a quality organic semiconductor thin film for the immediate device applications.

  3. Comparative study of the electrochemical behavior and analytical applications of (bio)sensing platforms based on the use of multi-walled carbon nanotubes dispersed in different polymers. (United States)

    Primo, E N; Gutierrez, F A; Luque, G L; Dalmasso, P R; Gasnier, A; Jalit, Y; Moreno, M; Bracamonte, M V; Rubio, M Eguílaz; Pedano, M L; Rodríguez, M C; Ferreyra, N F; Rubianes, M D; Bollo, S; Rivas, G A


    This review present a critical comparison of the electrochemical behavior and analytical performance of glassy carbon electrodes (GCE) modified with carbon nanotubes (CNTs) dispersed in different polymers: polyethylenimine (PEI), PEI functionalized with dopamine (PEI-Do), polyhistidine (Polyhis), polylysine (Polylys), glucose oxidase (GOx) and double stranded calf-thymus DNA (dsDNA). The comparison is focused on the analysis of the influence of the sonication time, solvent, polymer/CNT ratio, and nature of the polymer on the efficiency of the dispersions and on the electrochemical behavior of the resulting modified electrodes. The results allow to conclude that an adequate selection of the polymers makes possible not only an efficient dispersion of CNTs but also, and even more important, the building of successful analytical platforms for the detection of different bioanalytes like NADH, glucose, DNA and dopamine.

  4. Approaches for Making High Performance Polymer Materials from Commodity Polymers

    Institute of Scientific and Technical Information of China (English)

    Xu Xi


    A brief surrey of ongoing research work done for improving and enhancing the properties of commodity polymers by the author and author's colleagues is given in this paper. A series of high performance polymers and polymer nanomaterials were successfully prepared through irradiation and stress-induced reactions of polymers and hydrogen bonding. The methods proposed are viable, easy in operation, clean and efficient.1. The effect of irradiation source (UV light, electron beam, γ -ray and microwave), irradiation dose, irradiation time and atmosphere etc. on molecular structure of polyolefine during irradiation was studied. The basic rules of dominating oxidation, degradation and cross-linking reactions were mastered. Under the controlled conditions, cross-linking reactions are prevented, some oxygen containing groups are introduced on the molecular chain of polyolefine to facilitate the interface compatibility of their blends. A series of high performance polymer materials: u-HDPE/PA6,u-HDPE/CaCO3, u-iPP/STC, γ-HDPE/STC, γ-LLDPE/ATH, e-HDPE, e-LLDPE and m-HDPEfilled system were prepared (u- ultraviolet light irradiated, γ- γ-ray irradiated, e- electron beam irradiated, m- microwave irradiated)2. The effect of ultrasonic irradiation, jet and pan-milling on structure and changes in properties of polymers were studied. Imposition of critical stress on polymer chain can cause the scission of bonds to form macroradicals. The macroradicals formed in this way may recombine or react with monomer or other radicals to form linear, branched or cross-linked polymers or copolymers. About 20 kinds of block/graft copolymers have been synthesized from polymer-polymer or polymer-monomer through ultrasonic irradiation.Through jet-milling, the molecular weight of PVC is decreased somewhat, the intensity of its crystalline absorption bonds becomes indistinct. The processability, the yield strength, strength at break and elongation at break of PVC get increased quite a lot after

  5. Polymer-phyllosilicate nanocomposites and their preparation (United States)

    Chaiko, David J.


    Polymer-phyllosilicate nanocomposites that exhibit superior properties compared to the polymer alone, and methods-for producing these polymer-phyllosilicate nanocomposites, are provided. Polymeric surfactant compatabilizers are adsorbed onto the surface of hydrophilic or natural phyllosilicates to facilitate the dispersal and exfoliation of the phyllosilicate in a polymer matrix. Utilizing polymeric glycol based surfactants, polymeric dicarboxylic acids, polymeric diammonium surfactants, and polymeric diamine surfactants as compatabilizers facilitates natural phyllosilicate and hydrophilic organoclay dispersal in a polymer matrix to produce nanocomposites.

  6. Physical Organic Chemistry of Supramolecular Polymers (United States)

    Serpe, Michael J.; Craig, Stephen L.


    Unlike the case of traditional covalent polymers, the entanglements that determine properties of supramolecular polymers are defined by very specific, intermolecular interactions. Recent work using modular molecular platforms to probe the mechanisms underlying mechanical response of supramolecular polymers is reviewed. The contributions of supramolecular kinetics, thermodynamics, and conformational flexibility to supramolecular polymer properties in solutions of discrete polymers, in networks, and at interfaces, are described. Molecule-to-material relationships are established through methods reminiscent of classic physical organic chemistry. PMID:17279638

  7. Polymer useful for an ion exchange membrane

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Siwei; Lynd, Nathaniel A.


    The present invention provides for a polymer formed by reacting a first reactant polymer, or a mixture of first reactant polymers comprising different chemical structures, comprising a substituent comprising two or more nitrogen atoms (or a functional group/sidechain comprising a two or more nitrogen atoms) with a second reactant polymer, or a mixture of second reactant polymers comprising different chemical structures, comprising a halogen substituent (or a functional group/sidechain comprising a halogen).

  8. Conducting Polymer 3D Microelectrodes

    Directory of Open Access Journals (Sweden)

    Jenny Emnéus


    Full Text Available Conducting polymer 3D microelectrodes have been fabricated for possible future neurological applications. A combination of micro-fabrication techniques and chemical polymerization methods has been used to create pillar electrodes in polyaniline and polypyrrole. The thin polymer films obtained showed uniformity and good adhesion to both horizontal and vertical surfaces. Electrodes in combination with metal/conducting polymer materials have been characterized by cyclic voltammetry and the presence of the conducting polymer film has shown to increase the electrochemical activity when compared with electrodes coated with only metal. An electrochemical characterization of gold/polypyrrole electrodes showed exceptional electrochemical behavior and activity. PC12 cells were finally cultured on the investigated materials as a preliminary biocompatibility assessment. These results show that the described electrodes are possibly suitable for future in-vitro neurological measurements.

  9. Functionalised Polymers by Surface Modification

    Institute of Scientific and Technical Information of China (English)

    Jon-Paul Griffiths; M. G. Moloney


    @@ 1Introduction Surface-active polymers are of substantial importance in many diverse aspects of modern technology, with applications ranging from solid phase chemical synthesis related to drug discovery and chemical catalysis to biocompatible/bioactive medical implants and prostheses, and to surface-modified fabrics. Whilst there are a number of existing physical (e. g. corona or plasma discharge, ion beam irradiation[1] ) and chemical (e. g.silanisation, oxidation, chlorination, acylation and quaternisation[2-4]) methods for the surface modification of polymers, the frequent requirement for significant infrastructure, harsh reaction conditions, and limitation to specific polymer types (e. g. polybutadiene[5] ), which must possess suitable chemical functionality capable of direct modification, led us to consider alternative chemical methods. Desirable was an alternative that would be amenable to a large range of polymers, permitting direct chemical modification under mild conditions and using inexpensive reagents.

  10. Polymer Bose–Einstein condensates

    Energy Technology Data Exchange (ETDEWEB)

    Castellanos, E., E-mail: [Departamento de Física, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, A.P. 14-740, México D.F. 07000 (Mexico); Chacón-Acosta, G., E-mail: [Departamento de Matemáticas Aplicadas y Sistemas, Universidad Autónoma Metropolitana-Cuajimalpa, Artificios 40, México D.F. 01120 (Mexico)


    In this work we analyze a non-interacting one-dimensional polymer Bose–Einstein condensate in a harmonic trap within the semiclassical approximation. We use an effective Hamiltonian coming from the polymer quantization that arises in loop quantum gravity. We calculate the number of particles in order to obtain the critical temperature. The Bose–Einstein functions are replaced by series, whose high order terms are related to powers of the polymer length. It is shown that the condensation temperature presents a shift respect to the standard case, for small values of the polymer scale. In typical experimental conditions, it is possible to establish a bound for λ{sup 2} up to ≲10{sup −16} m{sup 2}. To improve this bound we should decrease the frequency of the trap and also decrease the number of particles.

  11. Color Changes Mark Polymer Reactions. (United States)

    Krieger, James H.


    Describes how polydiacetylenes can be used as educational aids. These polymers have conjugated backbones, which cause changes in color when the polydiacetylenes undergo various chemical and physical processes. Diagrams summarize all chemical reactions and their associated color changes. (CS)

  12. Conductive polymer-based material (United States)

    McDonald, William F.; Koren, Amy B.; Dourado, Sunil K.; Dulebohn, Joel I.; Hanchar, Robert J.


    Disclosed are polymer-based coatings and materials comprising (i) a polymeric composition including a polymer having side chains along a backbone forming the polymer, at least two of the side chains being substituted with a heteroatom selected from oxygen, nitrogen, sulfur, and phosphorus and combinations thereof; and (ii) a plurality of metal species distributed within the polymer. At least a portion of the heteroatoms may form part of a chelation complex with some or all of the metal species. In many embodiments, the metal species are present in a sufficient concentration to provide a conductive material, e.g., as a conductive coating on a substrate. The conductive materials may be useful as the thin film conducting or semi-conducting layers in organic electronic devices such as organic electroluminescent devices and organic thin film transistors.

  13. Polyphosphazine-based polymer materials (United States)

    Fox, Robert V.; Avci, Recep; Groenewold, Gary S.


    Methods of removing contaminant matter from porous materials include applying a polymer material to a contaminated surface, irradiating the contaminated surface to cause redistribution of contaminant matter, and removing at least a portion of the polymer material from the surface. Systems for decontaminating a contaminated structure comprising porous material include a radiation device configured to emit electromagnetic radiation toward a surface of a structure, and at least one spray device configured to apply a capture material onto the surface of the structure. Polymer materials that can be used in such methods and systems include polyphosphazine-based polymer materials having polyphosphazine backbone segments and side chain groups that include selected functional groups. The selected functional groups may include iminos, oximes, carboxylates, sulfonates, .beta.-diketones, phosphine sulfides, phosphates, phosphites, phosphonates, phosphinates, phosphine oxides, monothio phosphinic acids, and dithio phosphinic acids.


    Institute of Scientific and Technical Information of China (English)

    Lin-ping Ke; Mei-li Guo; De-lu Zhao


    For a system of flexible polymer molecules, the concepts of two concentrations, namely the segmental and the molecular concentrations, have been proposed in this paper. The former is equivalent to the volume fraction. The latter can be defined as the number of the gravity centers of macromolecules in a unit volume. The two concentrations should be correlated with each other by the conformational function of the polymer chain and should be discussed in different thermodynamic equations. On the basis of these concepts it has been proved that the Flory-Huggins entropy of mixing should be the result of the mixing "ideal gases of the gravity centers of macromolecules". The general correlation between the free energy of mixing and the scattering function (structural factor) of polymer blends has been studied based on the general fluctuation theory. When the Flory-Huggins free energy of mixing is adopted, the de Gennes scattering function of a polymer blend can be derived.

  15. Polymer electronic devices and materials.

    Energy Technology Data Exchange (ETDEWEB)

    Schubert, William Kent; Baca, Paul Martin; Dirk, Shawn M.; Anderson, G. Ronald; Wheeler, David Roger


    Polymer electronic devices and materials have vast potential for future microsystems and could have many advantages over conventional inorganic semiconductor based systems, including ease of manufacturing, cost, weight, flexibility, and the ability to integrate a wide variety of functions on a single platform. Starting materials and substrates are relatively inexpensive and amenable to mass manufacturing methods. This project attempted to plant the seeds for a new core competency in polymer electronics at Sandia National Laboratories. As part of this effort a wide variety of polymer components and devices, ranging from simple resistors to infrared sensitive devices, were fabricated and characterized. Ink jet printing capabilities were established. In addition to promising results on prototype devices the project highlighted the directions where future investments must be made to establish a viable polymer electronics competency.

  16. Recent advances in photorefractive polymers (United States)

    Thomas, Jayan; Christenson, C. W.; Lynn, B.; Blanche, P.-A.; Voorakaranam, R.; Norwood, R. A.; Yamamoto, M.; Peyghambarian, N.


    Photorefractive composites derived from conducting polymers offer the advantage of dynamically recording holograms without the need for processing of any kind. Thus, they are the material of choice for many cutting edge applications, such as updatable three-dimensional (3D) displays and 3D telepresence. Using photorefractive polymers, 3D images or holograms can be seen with the unassisted eye and are very similar to how humans see the actual environment surrounding them. Absence of a large-area and dynamically updatable holographic recording medium has prevented realization of the concept. The development of a novel nonlinear optical chromophore doped photoconductive polymer composite as the recording medium for a refreshable holographic display is discussed. Further improvements in the polymer composites could bring applications in telemedicine, advertising, updatable 3D maps and entertainment.

  17. Modeling the polymer product maceration (United States)

    Ahunov, D. N.; Karpova, M. N.


    The article contains a view of mass transmission simulation procedure conformably to control of manufacturing method's automation, and also is shown a simulator of polymer product maceration process, and results of developed for this simulator realization program system

  18. Temperature, Humidity, And Polymer Aging (United States)

    Cuddihy, Edward F.


    Report presents analysis of experimental data on electrical resistivity of polymer (polyvinyl butyral) as function of temperature and relative humidity. Resulting theoretical expression for electrical resistivity resembles generally accepted empirical law for the corrosion rate.

  19. Deformation of Linked Polymer Coils

    Institute of Scientific and Technical Information of China (English)

    董朝霞; 李明远; 吴肇亮; 林梅钦


    Linked polymer solution (LPS) is defined as the solution of linked polymer coils (LPCs) dispersed in water, composed of low concentration partially hydrolyzed polyacrylamide (HPAM) and aluminum citrate (crosslinker). In the work, the conformational changes of LPCs under different conditions were investigated by the methods of membrane filtering under low pressure, dynamic light scattering and core flooding experiments. The results showed that in some conditions the LPCs could be compressed mechanically to 1/158.5 of their original volume because of relatively lower HPAM cross-linking. The hydration property of LPCs was similar to that of normal polymer coils. The deformation of LPCs was more restricted than that of ordinary polymer coils under the flow shear stress or the shift of hydration equilibrium caused in the variation of the electrolyte concentration which is responsible for the effective plugging in the throats of porous media when LPCs are used for deep diverting.

  20. Conjugated Polymers for Energy Production

    DEFF Research Database (Denmark)

    Livi, Francesco

    arylation (DAr) and direct arylation polymerization (DArP) have been applied to the preparation of PPDTBT, making this polymer readily available in only 4 synthetic steps and thus easily transferable to a large scale-production setup. DArP avoids organometallic species and therefore is an appealing......This dissertation is aimed at developing materials for flexible, large area, ITO-free polymer solar cells (PSCs) fully printed under ambient conditions. A large screening of conjugated polymers, both novel and well-known materials, has been carried out in order to find suitable candidates...... for scalable PSCs fully printed under ambient conditions [Adv. Energy Mater. 2015, 5, 1402186]. PPDTBT resulted to be the conjugated polymer with the best photovoltaic performance within the 104 synthesized macromolecules. Therefore, further studies have been done on such material. The impact of side chain...

  1. Semiconducting-polymer photonic devices (United States)

    Ho, Peter; Tessler, Nir; Friend, Richard H.


    The last decade has seen tremendous advances in the field of semiconducting-polymer optoelectronics as a result of a concerted chemistry, physics and engineering effort. For example, ink-jet-printed full-color active-matrix thin-film display prototypes with semiconducting polymers as the active layers have already been demonstrated. The key advantages of this technology lie in its full-color capability, scalability to both large-area and micro- displays, as well as low-cost associated with simplicity and solution processability. In a number of related inorganic device technologies, the control of optical properties using photonic structures has ben crucial to the performance of the devices. In principle, polymer devices can also benefit from such control if appropriate polymer optical building blocks that retain the processing advantages can be found. Here we will show that the refractive index of poly(p- phenylenevinuylene) (PPV) can be tuned over remarkable ranges from 1.6 to 2.7 at 550-nm wavelength by dispersing 50-angstrom-diameter silica nanoparticles into its matrix. This is achieved without incurring significant optical scattering losses. Using these semiconducting-polymer composites, we have demonstrated efficient distributed Bragg reflectors in the green spectral region from relatively few periods of quarterwave stacks of the high- and low-index materials. Controlled chemical doping of these photonic structures fabricated polymer microcavity light-emitting diodes in which current is injected through the polymer DBR with adequate confinement of photons and electron-hole pairs. We have also fabricated photo pumped all-polymer microcavity structures.

  2. Automatic Coarse Graining of Polymers


    Faller, Roland


    Several recently proposed semi--automatic and fully--automatic coarse--graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi--atom units or super--atoms from atomistic simulations. These include techniques relying on single chain simulations in vacuum and self--consistent optimizations from the melt like the simplex method and the inverted Boltzmann method. The focus is on matching the polymer structure on different scales. Several ...

  3. Biocompatible and Bioeliminable Hydrophilic Polymers

    Institute of Scientific and Technical Information of China (English)

    Paolo; FerrutiUniversità


    1 Introduction This presentation will report on some recent results obtained in Milan on two polymer families of biomedical interest, namely poly(N-vinyl-2-pyrrolidinone) and polyamidoamines. 2 Results and DiscussionPoly(N-vinyl-2-pyrrolidinone) (PVP) is a well known bioactive and biocompatible polymer. In its soluble form, it is largely used as excipient of oral pharmaceutical formulations, especially for its high water solubilising power.In its crosslinked form, it plays a relevant role as biomateria...

  4. Thermophysical Properties of Irradiated Polymers (United States)

    Briskman, Boris A.


    The effect of ionising radiation on the specific heat, thermal conductivity, thermal diffusivity, and density of partially crystalline (polyethylene, polypropylene, polytetrafluoro-ethylene) and of amorphous polymers (polystyrene, poly(methyl methacrylate)) is discussed. Analytical models of the mechanism of heat conduction, and the development of anisotropic thermal conductivity in amorphous polymers, are examined. The influence of ionising radiation on the thermophysical properties of composite materials is analysed. 79 references.

  5. Thermal expansion of glassy polymers. (United States)

    Davy, K W; Braden, M


    The thermal expansion of a number of glassy polymers of interest in dentistry has been studied using a quartz dilatometer. In some cases, the expansion was linear and therefore the coefficient of thermal expansion readily determined. Other polymers exhibited non-linear behaviour and values appropriate to different temperature ranges are quoted. The linear coefficient of thermal expansion was, to a first approximation, a function of both the molar volume and van der Waal's volume of the repeating unit.

  6. Characterization of Nanostructured Polymer Films (United States)


    AFRL-OSR-VA-TR-2015-0059 Characterization of Nanostructured Polymer Films RODNEY PRIESTLEY TRUSTEES OF PRINCETON UNIVERSITY Final Report 12/23/2014...Report 3. DATES COVERED (From - To) 06/01/2012-08/31/2014 4. TITLE AND SUBTITLE Characterization of Nanostructured Polymer Films 5a. is due to the film morphology, i.e., the films are nanostructured . The aim of this proposal was to understand the mechanism of film formation and

  7. Nanoporous polymer liquid core waveguides

    DEFF Research Database (Denmark)

    Gopalakrishnan, Nimi; Christiansen, Mads Brøkner; Ndoni, Sokol


    We demonstrate liquid core waveguides defined by UV to enable selective water infiltration in nanoporous polymers, creating an effective refractive index shift Δn=0.13. The mode confinement and propagation loss in these waveguides are presented.......We demonstrate liquid core waveguides defined by UV to enable selective water infiltration in nanoporous polymers, creating an effective refractive index shift Δn=0.13. The mode confinement and propagation loss in these waveguides are presented....

  8. Polymer-Layer Silicate Nanocomposites

    DEFF Research Database (Denmark)

    Potarniche, Catalina-Gabriela

    Nowadays, some of the material challenges arise from a performance point of view as well as from recycling and biodegradability. Concerning these aspects, the development of polymer layered silicate nanocomposites can provide possible solutions. This study investigates how to obtain polymer layered...... silicate nanocomposites and their structure-properties relationship. In the first part of the thesis, thermoplastic layered silicates were obtained by extrusion. Different modification methods were tested to observe the intercalation treatment effect on the silicate-modifier interactions. The silicate...

  9. Finite-size corrections for confined polymers in the extended de Gennes regime (United States)

    Smithe, T. St Clere; Iarko, V.; Muralidhar, A.; Dorfman, K. D.; Mehlig, B.


    Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in this asymptotic limit. We calculate the statistics of the span and the end-to-end distance of a semiflexible polymer of finite length in the extended de Gennes regime, exploiting the fact that the problem can be mapped to a one-dimensional weakly self-avoiding random walk. The results thus obtained compare favourably with pruned-enriched Rosenbluth method (PERM) simulations of a three-dimensional discrete wormlike chain model of DNA confined in a nanochannel. We discuss the implications for experimental studies of linear λ-DNA confined to nanochannels at the high ionic strengths used in many experiments. PMID:26764718

  10. Effect of temperature on DNA double helix: An insight from molecular dynamics simulation

    Indian Academy of Sciences (India)

    Sangeeta Kundu; Sanchita Mukherjee; Dhananjay Bhattacharyya


    The three-dimensional structure of DNA contains various sequence-dependent structural information, which control many cellular processes in life, such as replication, transcription, DNA repair, etc. For the above functions, DNA double helices need to unwind or melt locally, which is different from terminal melting, as often seen in molecular dynamics (MD) simulations or even in many DNA crystal structures. We have carried out detailed MD simulations of DNA double helices of regular oligonucleotide fragments as well as in polymeric constructs with water and charge-neutralizing counter-ions at several different temperatures. We wanted to eliminate the end-effect or terminal melting propensity by employing MD simulation of DNA oligonucleotides in such a manner that gives rise to properties of polymeric DNA of infinite length. The polymeric construct is expected to allow us to see local melting at elevated temperatures. Comparative structural analysis of oligonucleotides and its corresponding virtual polymer at various temperatures ranging from 300 K to 400 K is discussed. The general behaviour, such as volume expansion coefficients of both the simulations show high similarity, indicating polymeric construct, does not give many artificial constraints. Local melting of a polymer, even at elevated temperature, may need a high nucleation energy that was not available in the short (7 ns) simulations. We expected to observe such nucleation followed by cooperative melting of the polymers in longer MD runs. Such simulations of different polymeric sequences would facilitate us to predict probable melting origins in a polymeric DNA.

  11. Disposable polyester-toner electrophoresis microchips for DNA analysis. (United States)

    Duarte, Gabriela R M; Coltro, Wendell K T; Borba, Juliane C; Price, Carol W; Landers, James P; Carrilho, Emanuel


    Microchip electrophoresis has become a powerful tool for DNA separation, offering all of the advantages typically associated with miniaturized techniques: high speed, high resolution, ease of automation, and great versatility for both routine and research applications. Various substrate materials have been used to produce microchips for DNA separations, including conventional (glass, silicon, and quartz) and alternative (polymers) platforms. In this study, we perform DNA separation in a simple and low-cost polyester-toner (PeT)-based electrophoresis microchip. PeT devices were fabricated by a direct-printing process using a 600 dpi-resolution laser printer. DNA separations were performed on PeT chip with channels filled with polymer solutions (0.5% m/v hydroxyethylcellulose or hydroxypropylcellulose) at electric fields ranging from 100 to 300 V cm(-1). Separation of DNA fragments between 100 and 1000 bp, with good correlation of the size of DNA fragments and mobility, was achieved in this system. Although the mobility increased with increasing electric field, separations showed the same profile regardless of the electric field. The system provided good separation efficiency (215,000 plates per m for the 500 bp fragment) and the separation was completed in 4 min for 1000 bp fragment ladder. The cost of a given chip is approximately $0.15 and it takes less than 10 minutes to prepare a single device.

  12. Fabrication of highly uniform conductive polypyrrole nanowires with DNA template. (United States)

    Moon, Hock Key; Kim, Hyung Jin; Kim, Nam-Hoon; Roh, Yonghan


    Deoxyribonucleic acid (DNA) is considered as one of the alternative materials for electronic device applications; however, DNA has critical limitation to electronic device applications due to its low electrical conductivity and unreliability. Therefore, it is required for electronic devices to prepare the well defined conductive polymer nanowires with DNA as a template. Polypyrrole (PPy) is an attractive polymer due to its high conductivity and environmental stability in bulk; although it is well known that ammonium persulfate (APS) used for the polymerization of pyrrole causes the deformation of DNA molecules. We minimized the damage of immobilized DNA strands on (3-aminopropyl) triethoxysilane (APTES) modified silicon wafer during APS polymerization. Atomic force microscopy (AFM) images from different APS treatment times and from using the vortex process obviously showed the effect on the synthesis of individual and continuous polypyrrole nanowires (PPy NWs). The PPy NWs at various pyrrole concentrations had similar height; however, the higher concentration gave more residues. Fourier transform-infrared spectroscopy (FT-IR) spectroscopy provided the strong evidence that PPy NWs were successfully synthesized on the DNA strands.

  13. Metal-conductive polymer hybrid nanostructures: preparation and electrical properties of palladium-polyimidazole nanowires. (United States)

    Al-Hinai, Mariam; Hassanien, Reda; Watson, Scott M D; Wright, Nicholas G; Houlton, Andrew; Horrocks, Benjamin R


    A simple, convenient method for the formation of hybrid metal/conductive polymer nanostructures is described. Polyimidazole (PIm) has been templated on λ-DNA via oxidative polymerisation of imidazole using FeCl3 to produce conductive PIm/DNA nanowires. The PIm/DNA nanowires were decorated with Pd (Pd/PIm/DNA) by electroless reduction of PdCl4(-2) with NaBH4 in the presence of PIm/DNA; the choice of imidazole was motivated by the potential Pd(II) binding site at the pyridinic N atom. The formation of PIm/DNA and the presence of metallic Pd on Pd/PIm/DNA nanowires were verified by FTIR, UV-vis and XPS spectroscopy techniques. AFM studies show that the nanowires have diameters in the range 5-45 nm with a slightly greater mean diameter (17.1 ± 0.75 nm) for the Pd-decorated nanowires than the PIm/DNA nanowires (14.5 ± 0.89 nm). After incubation for 24 h in the polymerisation solution, the PIm/DNA nanowires show a smooth, uniform morphology, which is retained after decoration with Pd. Using a combination of scanned conductance microscopy, conductive AFM and two-terminal measurements we show that both types of nanowire are conductive and that it is possible to discriminate different possible mechanisms of transport. The conductivity of the Pd/PIm/DNA nanowires, (0.1-1.4 S cm(-1)), is comparable to the PIm/DNA nanowires (0.37 ± 0.029 S cm(-1)). In addition, the conductance of Pd/PIm/DNA nanowires exhibits Arrhenius behaviour (E(a )= 0.43 ± 0.02 eV) as a function of temperature in contrast to simple Pd/DNA nanowires. These results indicate that although the Pd crystallites on Pd/PIm/DNA nanowires decorate the PIm polymer, the major current pathway is through the polymer rather than the Pd.

  14. Nucleic Acid-Peptide Complex Phase Controlled by DNA Hybridization (United States)

    Vieregg, Jeffrey; Lueckheide, Michael; Leon, Lorraine; Marciel, Amanda; Tirrell, Matthew

    When polyanions and polycations are mixed, counterion release drives formation of polymer-rich complexes that can either be solid (precipitates) or liquid (coacervates) depending on the properties of the polyelectrolytes. These complexes are important in many fields, from encapsulation of industrial polymers to membrane-free segregation of biomolecules such as nucleic acids and proteins. Condensation of long double-stranded DNA has been studied for several decades, but comparatively little attention has been paid to the polyelectrolyte behavior of oligonucleotides. We report here studies of DNA oligonucleotides (10 - 88 nt) complexed with polylysine (10 - 100 aa). Unexpectedly, we find that the phase of the resulting complexes is controlled by the hybridization state of the nucleic acid, with double-stranded DNA forming precipitates and single-stranded DNA forming coacervates. Stability increases with polyelectrolyte length and decreases with solution salt concentration, with complexes of the longer double-stranded polymers undergoing precipitate/coacervate/soluble transitions as ionic strength is increased. Mixing coacervates formed by complementary single-stranded oligonucleotides results in precipitate formation, raising the possibility of stimulus-responsive material design.

  15. DNA hybridization sensing for cytogenetic analysis

    DEFF Research Database (Denmark)

    Kwasny, Dorota; Dapra, Johannes; Brøgger, Anna Line;


    Cytogenetic analysis focuses on studying the cell structure, mainly in respect to chromosome content and their structure. Chromosome abnormalities, such as translocations may cause various genetic disorders, but are also associated with heametological malignancies. Chromosome translocations...... for cheaper detection a label-free approach has been investigated using electrochemical impedance spectroscopy as a sensing method. We present here our recent results in regards to DNA sensing on metallic and conductive polymer electrodes for translocation detection. Our sensors are inexpensive and can...... be successfully applied in cytogenetic analysis as a replacement of standard techniques....

  16. Electrostatics of polymer translocation events in electrolyte solutions. (United States)

    Buyukdagli, Sahin; Ala-Nissila, T


    We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based membranes are driven by a competition between the repulsive DNA-image-charge interactions and the attractive coupling between the DNA segments on the trans and the cis sides of the membrane. The latter effect is induced by the reduction of the coupling by the dielectric membrane. In strong salt solutions where the repulsive image-charge effects dominate the attractive trans-cis coupling, the DNA molecule encounters a translocation barrier of ≈10 kBT. In dilute electrolytes, the trans-cis coupling takes over image-charge forces and the membrane becomes a metastable attraction point that can trap translocating polymers over long time intervals. This mechanism can be used in translocation experiments in order to control DNA motion by tuning the salt concentration of the solution.

  17. Microfabricated polymer filter device for bio-applications (United States)

    Atkin, Micah; Poetter, Karl; Cattrall, Robert; Harvey, Erol


    The need for disposable diagnostic sensors in the health care industry has been a major driver in the development of low-cost polymer microfluidic devices. Of crucial importance to many of these devices is the incorporation of sieves and filters for the pretreatment of biological samples. Much of the previous work on integrating filtration systems in microdevices has focused on silicon and glass technologies. Of more difficulty, due to the different manufacturing methodology and lower mechanical strength, is the integration of filtration systems in polymer microfluidic chips. This paper presents a design and construction methodology to fabricate such integrated devices in polyethylene terepthalate (PET) and describes their characterization for particle filtration. To demonstrate the application of these systems, DNA extraction from whole blood was investigated. This currently represents a major stumbling block for point-of-care diagnostics. To this end two approaches were taken; the isolation of leucocytes for subsequent DNA extraction, and the trapping of silica microspheres for DNA adsorption. The polymer surfaces of the fluidic chips were modified by UV exposure and chemical etching to increase their surface energy for improved non-specific binding and electroosmotic flow characteristics. Integrated filtration devices were successfully fabricated with excimer laser machined membranes having pore dimensions down to 1μm, and contact angles from 75° down to less than 25° were achieved using UV modification, and from 75° down to 16° by chemical modification of PET. White blood cells were filtered from whole blood and silica particle retention was demonstrated successfully.

  18. The Extraction and Partial Purification of Bacterial DNA as a Practical Exercise for GCE Advanced Level Students. (United States)

    Falconer, A. C.; Hayes, L. J.


    Describes a relatively simple method of extraction and purification of bacterial DNA. This technique permits advanced secondary-level science students to obtain adequate amounts of DNA from very small pellets of bacteria and to observe some of its polymer properties. (ML)

  19. Efficiency Improvement of Heterojunction Polymer Photovoltaic Cells through Controlling the Morphology of the Polymer Film

    Institute of Scientific and Technical Information of China (English)


    1 Results Polymer photovoltaic cells, which provide clean and renewable energy sources, have gained more and more attention. Polymer photovoltaic cells have the advantage of low fabrication cost and high mechanical flexibility. Polymers can be processed through a solution process, so that a homogeneous polymer film could be readily prepared in a large area. Recently, the light-to-electricity conversion efficiency of the polymer photovoltaic cells was improved significantly[1-2]. Polymer donor and organi...

  20. Fabrication of combined-scale nano- and microfluidic polymer systems using a multilevel dry etching, electroplating and molding process

    DEFF Research Database (Denmark)

    Tanzi, Simone; Østergaard, Peter Friis; Matteucci, Marco;


    Microfabricated single-cell capture and DNA stretching devices have been produced by injection molding. The fabrication scheme employed deep reactive ion etching in a silicon substrate, electroplating in nickel and molding in cyclic olefin polymer. This work proposes technical solutions to fabric......Microfabricated single-cell capture and DNA stretching devices have been produced by injection molding. The fabrication scheme employed deep reactive ion etching in a silicon substrate, electroplating in nickel and molding in cyclic olefin polymer. This work proposes technical solutions...

  1. Photosensitizer-doped conjugated polymer nanoparticles with high cross-sections for one- and two-photon excitation. (United States)

    Grimland, Jennifer L; Wu, Changfeng; Ramoutar, Ria R; Brumaghim, Julia L; McNeill, Jason


    We report a novel nanoparticle that is promising for photodynamic therapy applications, which consists of a π-conjugated polymer doped with a singlet oxygen photosensitizer. The nanoparticles exhibit highly efficient collection of excitation light due to the large excitation cross-section of the polymer. A quantum efficiency of singlet oxygen production of 0.5 was determined. Extraordinarily large two-photon excitation cross-sections were determined, indicating promise for near infrared multiphoton photodynamic therapy. Gel electrophoresis of DNA after near-UV irradiation in the presence of nanoparticles indicated both purine base and backbone DNA damage.

  2. A simple approach for producing highly efficient DNA carriers with reduced toxicity based on modified polyallylamine

    Energy Technology Data Exchange (ETDEWEB)

    Oskuee, Reza Kazemi [Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad (Iran, Islamic Republic of); Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad (Iran, Islamic Republic of); Dosti, Fatemeh [School of Pharmacy, Mashhad University of Medical Sciences, Mashhad (Iran, Islamic Republic of); Gholami, Leila [Targeted Drug Delivery Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad (Iran, Islamic Republic of); Malaekeh-Nikouei, Bizhan, E-mail: [Nanotechnology Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad (Iran, Islamic Republic of)


    Nowadays gene delivery is a topic in many research studies. Non-viral vectors have many advantages over viral vectors in terms of safety, immunogenicity and gene carrying capacity but they suffer from low transfection efficiency and high toxicity. In this study, polyallylamine (PAA), the cationic polymer, has been modified with hydrophobic branches to increase the transfection efficiency of the polymer. Polyallylamine with molecular weights of 15 and 65 kDa was selected and grafted with butyl, hexyl and decyl acrylate at percentages of 10, 30 and 50. The ability of the modified polymer to condense DNA was examined by ethidium bromide test. The complex of modified polymer and DNA (polyplex) was characterized for size, zeta potential, transfection efficiency and cytotoxicity in Neuro2A cell lines. The results of ethidium bromide test showed that grafting of PAA decreased its ability for DNA condensation but vectors could still condense DNA at moderate and high carrier to DNA ratios. Most of polyplexes had particle size between 150 and 250 nm. The prepared vectors mainly showed positive zeta potential but carriers composed of PAA with high percentage of grafting had negative zeta potential. The best transfection activity was observed in vectors with hexyl acrylate chain. Grafting of polymer reduced its cytotoxicity especially at percentages of 30 and 50. The vectors based of PAA 15 kDa had better transfection efficiency than the vectors made of PAA 65 kDa. In conclusion, results of the present study indicated that grafting PAA 15 kDa with high percentages of hexyl acrylate can help to prepare vectors with better transfection efficiency and less cytotoxicity. - Highlights: • The modified polyallylamine was synthesized as a gene carrier. • Modification of polyallylamine (15 kDa) with high percentages of hexyl acrylate improved transfection activity remarkably. • Grafting of polymer with acrylate derivatives reduced polymer cytotoxicity especially at percentages of

  3. Recent developments in Inorganic polymers: A Review with focus on Si-Al based inorganic polymers

    Directory of Open Access Journals (Sweden)

    Shrray Srivastava


    Full Text Available Inorganic polymers are a unique classification of polymers. They contain inorganic atoms in the main chain. Hybrids with organic polymers as well as those chains that contain metals as pendant groups are considered in a special sub-classification as organo-metallic polymers. The networks containing only inorganic elements in main chain are called inorganic polymers. The silicone rubber is the most commercial inorganic polymer. The organo-metallic and inorganic polymers have a different set of applications. The current paper is a review of current applications of polymers with inorganic back-bone networks, especially focusing on Si and Al based inorganic polymeric materials.

  4. Nanostructured polymer membranes for proton conduction (United States)

    Balsara, Nitash Pervez; Park, Moon Jeong


    Polymers having an improved ability to entrain water are characterized, in some embodiments, by unusual humidity-induced phase transitions. The described polymers (e.g., hydrophilically functionalized block copolymers) have a disordered state and one or more ordered states (e.g., a lamellar state, a gyroid state, etc.). In one aspect, the polymers are capable of undergoing a disorder-to-order transition while the polymer is exposed to an increasing temperature at a constant relative humidity. In some aspects the polymer includes a plurality of portions, wherein a first portion forms proton-conductive channels within the membrane and wherein the channels have a width of less than about 6 nm. The described polymers are capable of entraining and preserving water at high temperature and low humidity. Surprisingly, in some embodiments, the polymers are capable of entraining greater amounts of water with the increase of temperature. The polymers can be used in Polymer Electrolyte Membranes in fuel cells.

  5. Dihydroxybenzene/benzoquinone-containing polymers: organic redox polymers

    Energy Technology Data Exchange (ETDEWEB)

    Moulay, S. [Universite de Blida, Lab. de Chimie-Physique Macromoleculaire, Institut de Chimie Industrielle (Algeria)


    Polymers containing hydroquinone, catechol or their corresponding benzoquinones are a special class of redox polymers. Three pathways of their syntheses are possible: condensation polymerization of suitable monomers, addition polymerization of vinyl monomers containing redox moiety, and chemical attachment of redox unit onto pre-made polymeric matrix. A range of functionalized matrices have been employed such as polyethers, polyesters, polycarbonates, polyurethanes, polyamides and others. Protection of their phenolic functionality has conducted to chemically interesting redox polymer precursors. The presence of a redox moiety coupled with the extant functionalization of the polymer matrix makes the materials very valuable, of wide properties and consequently of vast applicability. For instance, in the oil field, some polymers such as carboxy-methyl-cellulose (CMC) are often applied as to bring about a viscosity improvement and therefore to facilitate the oil drilling. In this regard, Patel evaluated sulfo-alkylated polymeric catechol, namely sulfo-methylated and sulfo-ethylated resins. Indeed, polymeric catechol chemically modified as such exhibited a marked ability to control the viscosity, the gel strength, as well as the filtrate loss of aqueous oil drilling fluids.

  6. DNA fragmentation in apoptosis

    Institute of Scientific and Technical Information of China (English)


    Cleavage of chromosomal DNA into oligonucleosomal size fragments is an integral part of apoptosis. Elegant biochemical work identified the DNA fragmentation factor (DFF) as a major apoptotic endonuclease for DNA fragmentation in vitro. Genetic studies in mice support the importance of DFF in DNA fragmentation and possibly in apoptosis in vivo. Recent work also suggests the existence of additional endonucleases for DNA degradation. Understanding the roles of individual endonucleases in apoptosis, and how they might coordinate to degrade DNA in different tissues during normal development and homeostasis, as well as in various diseased states, will be a major research focus in the near future.

  7. ex vivo DNA assembly

    Directory of Open Access Journals (Sweden)

    Adam B Fisher


    Full Text Available Even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. Advances in cloning techniques have resulted in powerful in vitro and in vivo assembly of DNA. However, monetary and time costs have limited these approaches. Here, we report an ex vivo DNA assembly method that uses cellular lysates derived from a commonly used laboratory strain of Escherichia coli for joining double-stranded DNA with short end homologies embedded within inexpensive primers. This method concurrently shortens the time and decreases costs associated with current DNA assembly methods.

  8. Editorial of the Special Issue Antimicrobial Polymers

    Directory of Open Access Journals (Sweden)

    Iolanda Francolini


    Full Text Available The special issue “Antimicrobial Polymers” includes research and review papers concerning the recent advances on preparation of antimicrobial polymers and their relevance to industrial settings and biomedical field. Antimicrobial polymers have recently emerged as promising candidates to fight microbial contamination onto surfaces thanks to their interesting properties. In this special issue, the main strategies pursued for developing antimicrobial polymers, including polymer impregnation with antimicrobial agents or synthesis of polymers bearing antimicrobial moieties, were discussed. The future application of these polymers either in industrial or healthcare settings could result in an extremely positive impact not only at the economic level but also for the improvement of quality of life.

  9. Method of Thermocleaving a Polymer Layer

    DEFF Research Database (Denmark)


    A method of thermocleaving a thermocleavable polymer layer which is in thermal contact with a heat sensitive component that is not tolerant of the temperature required for thermocleavage of the thermocleavable polymer layer, in which the thermocleavable polymer layer is illuminated with a light...... source having a wavelength range more strongly absorbed by the thermocleavable polymer and substantially less strongly absorbed by the heat sensitive component, such that the thermocleavable polymer layer reaches a temperature sufficient to cause thermocleavage of the polymer without causing detrimental...

  10. Polymers for energy storage and conversion

    CERN Document Server

    Mittal, Vikas


    One of the first comprehensive books to focus on the role of polymers in the burgeoning energy materials market Polymers are increasingly finding applications in the areas of energy storage and conversion. A number of recent advances in the control of the polymer molecular structure which allows the polymer properties to be more finely tuned have led to these advances and new applications. Polymers for Energy Storage and Conversion assimilates these advances in the form of a comprehensive text that includes the synthesis and properties of a large number of polymer systems for

  11. Selection of polymers for application in scaffolds applicable for human pancreatic islet transplantation. (United States)

    Smink, Alexandra M; de Haan, Bart J; Paredes-Juarez, Genaro A; Wolters, Anouk H G; Kuipers, Jeroen; Giepmans, Ben N G; Schwab, Leendert; Engelse, Marten A; van Apeldoorn, Aart A; de Koning, Eelco; Faas, Marijke M; de Vos, Paul


    The liver is currently the site for transplantation of islets in humans. This is not optimal for islets, but alternative sites in humans are not available. Polymeric scaffolds in surgically accessible areas are a solution. As human donors are rare, the polymers should not interfere with functional survival of human-islets. We applied a novel platform to test the adequacy of polymers for application in scaffolds for human-islet transplantation. Viability, functionality, and immune parameters were included to test poly(D,L-lactide-co-ε-caprolactone) (PDLLCL), poly(ethylene oxide terephthalate)/polybutylene terephthalate (PEOT/PBT) block copolymer, and polysulfone. The type of polymer influenced the functional survival of human islets. In islets cultured on PDLLCL the glucagon-producing α-cells and insulin-producing β-cells contained more hormone granules than in islets in contact with PEOT/PBT or polysulfone. This was studied with ultrastructural analysis by electron microscopy (nanotomy) during 7 d of culture. PDLLCL was also associated with statistically significant lower release of double-stranded DNA (dsDNA, a so called danger-associate molecular pattern (DAMP)) from islets on PDLLCL when compared to the other polymers. DAMPs support undesired immune responses. Hydrophilicity of the polymers did not influence dsDNA release. Islets on PDLLCL also showed less cellular outgrowth. These outgrowing cells were mainly fibroblast and some β-cells undergoing epithelial to mesenchymal cell transition. None of the polymers influenced the glucose-stimulated insulin secretion. As PDLLCL was associated with less release of DAMPs, it is a promising candidate for creating a scaffold for human islets. Our study demonstrates that for sensitive, rare cadaveric donor tissue such as pancreatic islets it might be necessary to first select materials that do not influence functionality before proposing the biomaterial for in vivo application. Our presented platform may facilitate

  12. A High-Fidelity Codon Set for the T4 DNA Ligase-Catalyzed Polymerization of Modified Oligonucleotides. (United States)

    Lei, Yi; Kong, Dehui; Hili, Ryan


    In vitro selection of nucleic acid polymers can readily deliver highly specific receptors and catalysts for a variety of applications; however, it is suspected that the functional group deficit of nucleic acids has limited their potential with respect to proteinogenic polymers. This has stimulated research toward expanding their chemical diversity to bridge the functional gap between nucleic acids and proteins to develop a superior biopolymer. In this study, we investigate the effect of codon library size and composition on the sequence specificity of T4 DNA ligase in the DNA-templated polymerization of both unmodified and modified oligonucleotides. Using high-throughput DNA sequencing of duplex pairs, we have uncovered a 256-membered codon set that yields sequence-defined modified ssDNA polymers in high yield and with high fidelity.

  13. Cavity approach for modeling and fitting polymer stretching

    CERN Document Server

    Massucci, Francesco Alessandro; Vicente, Conrad J Pérez


    The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly studied force--elongation relation is typically hard. Here we draw from techniques developed in the context of disordered systems to solve models for single and double--stranded DNA stretching in the limit of a long polymeric chain. Since we directly derive the marginals for the molecule local orientation, our approach allows us to readily calculate the experimental elongation as well as other observables at wish. As an example, we evaluate the correlation length as a function of the stretching force. Furthermore, we are able to fit successfully our solution to real experimental data. Although the model is admittedly phenomenological, our findings are very sound. For single--stranded DNA our solution yields the correct (monomer) scale and, yet more importantly, the right pers...

  14. Synthesis and Characterization of Polymer-Templated Magnetic Nanoparticles (United States)

    Tamakloe, Beatrice

    This research reports on the investigation into the synthesis and stabilization of iron oxide nanoparticles for theranostic applications using amine-epoxide polymers. Although theranostic agents such as magnetic nanoparticles have been designed and developed for a few decades, there is still more work that needs to be done with the type of materials that can be used to stabilize or functionalize these particles if they are to be used for applications such as drug delivery, imaging and hyperthermia. For in-vivo applications, it is crucial that organic coatings enclose the nanoparticles in order to prevent aggregation and facilitate efficient removal from the body as well as protect the body from toxic material. The objective of this thesis is to design polymer coated magnetite nanoparticles with polymers that are biocompatible and can stabilize the iron oxide nanoparticle to help create mono-dispersed particles in solution. It is desirable to also have these nanoparticles possess high magnetic susceptibility in response to an applied magnetic field. The co-precipitation method was selected because it is probably the simplest and most efficient chemical pathway to obtain magnetic nanoparticles. In literature, cationic polymers such as Polyethylenimine (PEI), which is the industry standard, have been used to stabilize IONPs because they can be used in magnetofections to deliver DNA or RNA. PEI however is known to interact very strongly with proteins and is cytotoxic, so as mentioned previously the Iron Oxide nanoparticles (IONPs) synthesized in this study were stabilized with amine-epoxide polymers because of the limitations of PEI. Four different amine-epoxide polymers which have good water solubility, biodegradability and less toxic than PEI were synthesized and used in the synthesis and stabilization of the magnetic nanoparticles and compared to PEI templated IONPs. These polymer-templated magnetic nanoparticles were also characterized by size, surface charge, Iron

  15. Photoluminescence of Conjugated Star Polymers (United States)

    Ferguson, J. B.; Prigodin, N. V.; Epstein, A. J.; Wang, F.


    Higher dimensionality "star" polymers provide new properties beyond those found in their linear analogs. They have been used to improving electronic properties for nonlinear optics through exciton transfer and molecular antenna structures for example (M. Kawa, J. M. J. Frechet, Chem. Mater. 10, 286 (1998).). We report on photoluminescence properties of star polymers with a hyperbranched core (both hyperbranched phenlyene and hyperbranched triphenylamine) and polyhexylthiophene arms. The arm is a conjugated oligomer of polythiophene that has been investigated extensively for metallic like conductivity when doped as well as utilized in field effect transistors in its undoped form (A. Tsumara, H. Koezuka, T. Ando, Appl. Phys. Lett. 49, 1210 (1986).). The cores are respectively, a nonconjugated polymer in the case of hyperbranched phenlyene and a conjugated polymer in the case of hyperbranched triphenylamine. The photoluminesce spectrum (λ_max at 575 nm) is identical for both star polymers with the two electronically different hyperbranched cores and for linear polythiophene alone. We conclude the wave functions of the core and arms do not strongly interact to form states different from their individual states and excitons formed on the hyperbranched cores migrate to the lower bandgap polythiophene before recombining.

  16. Ring polymers in confined geometries

    CERN Document Server

    Usatenko, Z; Kuterba, P


    The investigation of a dilute solution of phantom ideal ring polymers and ring polymers with excluded volume interactions (EVI) in a good solvent confined in a slit geometry of two parallel repulsive walls and in a solution of colloidal particles of big size were performed. Taking into account the correspondence between the field theoretical $\\phi^4$ $O(n)$-vector model in the limit $n\\to 0$ and the behavior of long-flexible polymer chains in a good solvent the correspondent depletion interaction potentials, depletion forces and the forces which exert phantom ideal ring and ring polymer chains with EVI on the walls were obtained in the framework of the massive field theory approach at fixed space dimensions d=3 up to one-loop order. Additionally, the investigation of a dilute solution of phantom ideal ring polymers in a slit geometry of two inert walls and mixed walls with one repulsive and other one inert wall were performed and correspondent depletion interaction potentials and the depletion forces were cal...

  17. Systematic Multiscale Modeling of Polymers (United States)

    Faller, Roland; Huang, David; Bayramoglu, Beste; Moule, Adam


    The systematic coarse-graining of heterogeneous soft matter systems is an area of current research. We show how the Iterative Boltzmann Inversion systematically develops models for polymers in different environments. We present the scheme and a few applications. We study polystyrene in various environments and compare the different models from the melt, the solution and polymer brushes to validate accuracy and efficiency. We then apply the technique to a complex system needed as active layer in polymer-based solar cells. Nano-scale morphological information is difficult to obtain experimentally. On the other hand, atomistic computer simulations are only feasible to studying systems not much larger than an exciton diffusion length. Thus, we develop a coarse-grained (CG) simulation model, in which collections of atoms from an atomistic model are mapped onto a smaller number of ``superatoms.'' We study mixtures of poly(3-hexylthiophene) and C60 . By comparing the results of atomistic and CG simulations, we demonstrate that the model, parametrized at one temperature and two mixture compositions, accurately reproduces the system structure at other points of the phase diagram. We use the CG model to characterize the microstructure as a function of polymer:fullerene mole fraction and polymer chain length for systems approaching the scale of photovoltaic devices.

  18. [Uracil-DNA glycosylases]. (United States)

    Pytel, Dariusz; Słupianek, Artur; Ksiazek, Dominika; Skórski, Tomasz; Błasiak, Janusz


    Uracil is one of four nitrogen bases, most frequently found in normal RNA. Uracyl can be found also in DNA as a result of enzymatic or non-enzymatic deamination of cytosine as well as misincorporation of dUMP instead of dTMP during DNA replication. Uracil from DNA can be removed by DNA repair enzymes with apirymidine site as an intermediate. However, if uracil is not removed from DNA a pair C:G in parental DNA can be changed into a T:A pair in the daughter DNA molecule. Therefore, uracil in DNA may lead to a mutation. Uracil in DNA, similarly to thymine, forms energetically most favorable hydrogen bonds with adenine, therefore uracil does not change the coding properties of DNA. Uracil in DNA is recognized by uracil DNA glycosylase (UDGs), which initiates DNA base excision repair, leading to removing of uracil from DNA and replacing it by thymine or cytosine, when arose as a result of cytosine deamination. Eukaryotes have at least four nuclear UDGs: UNG2, SMUG1, TDG i MBD4, while UNG1 operates in the mitochondrium. UNG2 is involved in DNA repair associated with DNA replication and interacts with PCNA and RPA proteins. Uracil can also be an intermediate product in the process of antigen-dependent antibody diversification in B lymphocytes. Enzymatic deamination of viral DNA by host cells can be a defense mechanism against viral infection, including HIV-1. UNG2, MBD4 and TDG glycosylases may cooperate with mismatch repair proteins and TDG can be involved in nucleotide excision repair system.

  19. DNA damage and autophagy

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States); Panayiotidis, Mihalis I. [School of Community Health Sciences, University of Nevada, Reno, NV 89557 (United States); Franco, Rodrigo, E-mail: [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States)


    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  20. Green polymer chemistry: enzyme catalysis for polymer functionalization. (United States)

    Sen, Sanghamitra; Puskas, Judit E


    Enzyme catalyzed reactions are green alternative approaches to functionalize polymers compared to conventional methods. This technique is especially advantageous due to the high selectivity, high efficiency, milder reaction conditions, and recyclability of enzymes. Selected reactions can be conducted under solventless conditions without the application of metal catalysts. Hence this process is becoming more recognized in the arena of biomedical applications, as the toxicity created by solvents and metal catalyst residues can be completely avoided. In this review we will discuss fundamental aspects of chemical reactions biocatalyzed by Candida antarctica lipase B, and their application to create new functionalized polymers, including the regio- and chemoselectivity of the reactions.

  1. Green Polymer Chemistry: Enzyme Catalysis for Polymer Functionalization

    Directory of Open Access Journals (Sweden)

    Sanghamitra Sen


    Full Text Available Enzyme catalyzed reactions are green alternative approaches to functionalize polymers compared to conventional methods. This technique is especially advantageous due to the high selectivity, high efficiency, milder reaction conditions, and recyclability of enzymes. Selected reactions can be conducted under solventless conditions without the application of metal catalysts. Hence this process is becoming more recognized in the arena of biomedical applications, as the toxicity created by solvents and metal catalyst residues can be completely avoided. In this review we will discuss fundamental aspects of chemical reactions biocatalyzed by Candida antarctica lipase B, and their application to create new functionalized polymers, including the regio- and chemoselectivity of the reactions.

  2. Dynamic in situ chromosome immobilisation and DNA extraction using localized poly(N-isopropylacrylamide) phase transition

    DEFF Research Database (Denmark)

    Eriksen, Johan; Thilsted, Anil Haraksingh; Marie, Rodolphe


    A method of in situ chromosome immobilisation and DNA extraction in a microfluidic polymer chip was presented. Light-induced local heating was used to induce poly(N-isopropylacrylamide) phase transition in order to create a hydrogel and embed a single chromosome such that it was immobilised....... This was achieved with the use of a near-infrared laser focused on an absorption layer integrated in the polymer chip in close proximity to the microchannel. It was possible to proceed to DNA extraction while holding on the chromosome at an arbitrary location by introducing protease K into the microchannel. © 2011...

  3. Translocation frequency of double-stranded DNA through a solid-state nanopore

    CERN Document Server

    Bell, Nicholas A W; Keyser, Ulrich F


    Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of double-stranded DNA translocations through conical quartz nanopores with mean opening diameter 15 nm. We observe an entropic barrier limited, length dependent translocation frequency at 4M LiCl salt concentration and a drift-dominated, length independent translocation frequency at 1M KCl salt concentration. These observations are described by a unifying convection-diffusion equation which includes the contribution of an entropic barrier for polymer entry.

  4. Extension of DNA in a Nanochannel as a Rod-to-Coil Transition (United States)

    Tree, Douglas R.; Wang, Yanwei; Dorfman, Kevin D.


    DNA confinement in nanochannels is emerging as an important tool for genomics and an excellent platform for testing the theories of confined wormlike polymers. Using cutting-edge, large scale Monte Carlo simulations of asymptotically long wormlike chains, we show that, in analogy to the rod-to-coil transition for free wormlike polymers, there exists a universal, Gauss-de Gennes regime that connects the classic Odijk and de Gennes regimes of channel-confined chains. For DNA in a nanochannel, this Gauss-de Gennes regime spans practically the entire experimentally relevant range of channel sizes, including the nanochannels used in an incipient genome mapping technology. PMID:25167455

  5. Direct measurement of the intermolecular forces confining a single molecule in an entangled polymer solution. (United States)

    Robertson, Rae M; Smith, Douglas E


    We use optical tweezers to directly measure the intermolecular forces acting on a single polymer imposed by surrounding entangled polymers (115 kbp DNA, 1 mg/ml). A tubelike confining field was measured in accord with the key assumption of reptation models. A time-dependent harmonic potential opposed transverse displacement, in accord with recent simulation findings. A tube radius of 0.8 microm was determined, close to the predicted value (0.5 microm). Three relaxation modes (approximately 0.4, 5, and 34 s) were measured following transverse displacement, consistent with predicted relaxation mechanisms.

  6. Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity

    CERN Document Server

    Brackley, C A; Marenduzzo, D; 10.1103/PhysRevLett.109.168103


    We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in 3D, and of sequence heterogeneity. We find that in a network of DNA loops, as are thought to be present in bacterial DNA, the search process is very sensitive to the spatial location of the target within such loops. Therefore, specific genes might be repressed or promoted by changing the local topology of the genome. On the other hand, sequence heterogeneity creates traps which normally slow down facilitated diffusion. When suitably positioned, though, these traps can, surprisingly, render the search process much more efficient.

  7. Shape changing thin films powered by DNA hybridization (United States)

    Shim, Tae Soup; Estephan, Zaki G.; Qian, Zhaoxia; Prosser, Jacob H.; Lee, Su Yeon; Chenoweth, David M.; Lee, Daeyeon; Park, So-Jung; Crocker, John C.


    Active materials that respond to physical and chemical stimuli can be used to build dynamic micromachines that lie at the interface between biological systems and engineered devices. In principle, the specific hybridization of DNA can be used to form a library of independent, chemically driven actuators for use in such microrobotic applications and could lead to device capabilities that are not possible with polymer- or metal-layer-based approaches. Here, we report shape changing films that are powered by DNA strand exchange reactions with two different domains that can respond to distinct chemical signals. The films are formed from DNA-grafted gold nanoparticles using a layer-by-layer deposition process. Films consisting of an active and a passive layer show rapid, reversible curling in response to stimulus DNA strands added to solution. Films consisting of two independently addressable active layers display a complex suite of repeatable transformations, involving eight mechanochemical states and incorporating self-righting behaviour.

  8. The effect of solvent dynamics on the low frequency collectivemotions of DNA in solution and unoriented films

    Energy Technology Data Exchange (ETDEWEB)

    Woods, K.N.; Lee, S.A.; Holman, H.-Y.N.; Wiedemann, H.


    Infrared spectroscopy is used to probe the dynamics of invitro samples of DNA prepared as solutions and as solid unoriented films.The lowest frequency DNA mode identified in the far-infrared spectra ofthe DNA samples is found to shift in frequency when the solvent influencein the hydration shell is altered. The lowest frequency mode also hascharacteristics that are similar to beta - relaxations identified inother glass forming polymers.

  9. Preparation of polysulfone hollow microspheres encapsulating DNA and their functional utilization. (United States)

    Zhao, C; Liu, X D; Nomizu, M; Nishi, N


    Polysulfone hollow microspheres encapsulating DNA were prepared using a liquid-liquid phase separation technique. The microspheres were then used to absorb a DNA-binding intercalating material--ethidium bromide. The amount of DNA encapsulated in the microspheres depended on the concentration of the DNA solution used to prepare the microspheres, and the microsphere morphology depended on both the polymer concentration and the preparation conditions. The amount of ethidium bromide in the microspheres depended mainly on the amount of encapsulated DNA, and the microsphere morphology also affected the removal of the ethidium bromide. The new method of DNA encapsulation is proposed, and the microspheres encapsulating the DNA have the potential to be used in environmental applications.

  10. DNA tagged microparticles

    Energy Technology Data Exchange (ETDEWEB)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth


    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  11. Modeling DNA Replication. (United States)

    Bennett, Joan


    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  12. Configurational transitions in Fourier series-represented DNA supercoils. (United States)

    Liu, G; Schlick, T; Olson, A J; Olson, W K


    A new Fourier series representation of supercoiled DNA is employed in Langevin dynamics simulations to study large-scale configurational motions of intermediate-length chains. The polymer is modeled as an ideal elastic rod subject to long-range van der Waals' interactions. The van der Waals' term prevents the self-contact of distant chain segments and also mimics attractive forces thought to stabilize the association of closely spaced charged rods. The finite Fourier series-derived polymer formulation is an alternative to the piecewise B-spline curves used in past work to describe the motion of smoothly deformed supercoiled DNA in terms of a limited number of independent variables. This study focuses on two large-scale configurational events: the interconversion between circular and figure-8 forms at a relatively low level of supercoiling, and the transformation between branched and interwound structures at a higher superhelical density.

  13. DNA packaging in bacteriophage: is twist important? (United States)

    Spakowitz, Andrew James; Wang, Zhen-Gang


    We study the packaging of DNA into a bacteriophage capsid using computer simulation, specifically focusing on the potential impact of twist on the final packaged conformation. We perform two dynamic simulations of packaging a polymer chain into a spherical confinement: one where the chain end is rotated as it is fed, and one where the chain is fed without end rotation. The final packaged conformation exhibits distinct differences in these two cases: the packaged conformation from feeding with rotation exhibits a spool-like character that is consistent with experimental and previous theoretical work, whereas feeding without rotation results in a folded conformation inconsistent with a spool conformation. The chain segment density shows a layered structure, which is more pronounced for packaging with rotation. However, in both cases, the conformation is marked by frequent jumps of the polymer chain from layer to layer, potentially influencing the ability to disentangle during subsequent ejection. Ejection simulations with and without Brownian forces show that Brownian forces are necessary to achieve complete ejection of the polymer chain in the absence of external forces.

  14. Photoconductive properties of conjugated polymers

    CERN Document Server

    Halls, J J M


    The research described in my dissertation has involved the fabrication and characterisation of photovoltaic cells based on conjugated polymers, including the widely studied polymer poly(p-phenylenevinylene). These materials have semiconducting properties which arise from the delocalisation of electrons along the pi-electron systems of the polymer chains. Research into these materials is motivated both by their novel electronic properties, and also their potential for use in a wide range of applications including light-emitting diodes (LEDs), thin-film transistors, and photovoltaic cells (solar cells and light detectors). Light absorbed in a photovoltaic cell generates opposite charges which are collected at two different electrodes, giving rise to an electric current

  15. Polymer network stretching during electrospinning (United States)

    Greenfeld, Israel; Arinstein, Arkadii; Fezzaa, Kamel; Rafailovich, Miriam; Zussman, Eyal


    Fast X-ray phase contrast imaging is used to observe the flow of a semi-dilute polyethylene oxide solution during electrospinning. Micron-size glass particles mixed in the polymer solution allow viewing of the jet flow field, and reveal a high-gradient flow that has both longitudinal and radial components that grow rapidly along the jet. The resulting hydrodynamic forces cause substantial longitudinal stretching and transversal contraction of the polymer network within the jet, as confirmed by random walk simulation and theoretical modeling. The polymer network therefore concentrates towards the jet center, and its conformation may transform from a free state to a fully-stretched state within a short distance from the jet start. We acknowledge the financial support of the United States - Israel Bi-National Science Foundation (grant 2006061).

  16. Polyamide 6 single polymer composites

    Directory of Open Access Journals (Sweden)


    Full Text Available Combining the two basic techniques used for the preparation of single polymer composites (SPCs, hot compaction and film stacking, a polyamide 6 (PA 6 single polymer composite was manufactured. The starting materials were PA 6 high tenacity yarn (reinforcement and PA 6 film prepared via melt quenching (matrix, both expected to be the two principal polymorphic modifications of PA 6 and thus differing in their melting temperatures. The prepared single polymer composite is characterized by a layered structure and shows superior mechanical properties due to the good wetting – tensile modulus is improved by 200% and the ultimate tensile strength – by 300–400% as compared to the isotropic matrix film. Improvement of the interfacial adhesion via transreactions promoted by Sb2O3 as a catalyst was also undertaken.

  17. Thermoplastic dry polymer powder prepregging

    Energy Technology Data Exchange (ETDEWEB)

    Bucher, R.A.; Loos, A.C.; Meyer, G. [Virginia Polytechnic Institute and State Univ., Blacksburg, VA (United States)] [and others


    Thermoplastic resin systems have shown potential for reducing the manufacturing costs and improving the damage tolerance of composite structures. Current methods for thermoplastic resin impregnation of fiber bundles are limited by various difficulties and thus produce poor quality prepregs. The emerging technology of fiber is one of the most promising options, producing excellent matrix drape, and feasibility for a wide variety of matrix systems. An electrostatic dry polymer powder prepregging system was developed at the NSF Science and Technology Center at Virginia Tech, and has been used to produce high quality thermoplastic towpreg from a wide variety o polymer matrices. Additionally, a modification of the system allows for the production of towpreg from 15 gram polymer samples. This is ideal for the production of composites from resin systems under development, allowing early feedback concerning processing and composite mechanical performance.

  18. Development of environmental adaptable polymer

    Energy Technology Data Exchange (ETDEWEB)

    Yoshii, Fumio [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment


    Biodegradable polymers were modified by radiation crosslinking tequniques to develop environmental adaptable polymer. Poly({epsilon}-caprolactone), OCL, (melting temperature, 60 deg C) by irradiation in the supercooled state led to the highest gel content and this polymer has high heat resistance. Relatively smaller dose such as 15 and 30 kGy were effective to improve process ability of aliphatic polyester by formation of branch structure during irradiation. It was found that sodium carboxymethyl cellulose (CMC-Na) with degree of substitution (DS) from 0.7 to 2.2 and sodium carboxymethyl starch (CMS-Na) with DS 0.15 caused crosslinking at past like condition by irradiation. The condition with higher concentration such as 50-60% was most effective for crosslinking of CMC-Na and CMS-Na. Crosslinked CMC-Na and CMS-Na formed hydrogel. PCL, CMC-Na, and CMS-Na had biodegradability even after crosslinking in irradiation. (author)

  19. Water Soluble Responsive Polymer Brushes

    Directory of Open Access Journals (Sweden)

    Andrew J. Parnell


    Full Text Available Responsive polymer brushes possess many interesting properties that enable them to control a range of important interfacial behaviours, including adhesion, wettability, surface adsorption, friction, flow and motility. The ability to design a macromolecular response to a wide variety of external stimuli makes polymer brushes an exciting class of functional materials, and has been made possible by advances in modern controlled polymerization techniques. In this review we discuss the physics of polymer brush response along with a summary of the techniques used in their synthesis. We then review the various stimuli that can be used to switch brush conformation; temperature, solvent quality, pH and ionic strength as well as the relatively new area of electric field actuation We discuss examples of devices that utilise brush conformational change, before highlighting other potential applications of responsive brushes in real world devices.

  20. Click chemistry with DNA


    El-Sagheer, Afaf H.; Brown, Tom


    The advent of click chemistry has led to an influx of new ideas in the nucleic acids field. The copper catalysed alkyne–azide cycloaddition (CuAAC) reaction is the method of choice for DNA click chemistry due to its remarkable efficiency. It has been used to label oligonucleotides with fluorescent dyes, sugars, peptides and other reporter groups, to cyclise DNA, to synthesise DNA catenanes, to join oligonucleotides to PNA, and to produce analogues of DNA with modified nucleobases and backbone...