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Sample records for amphipathic dna polymers

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

    Directory of Open Access Journals (Sweden)

    Juteau Jean-Marc

    2009-12-01

    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

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

    DEFF Research Database (Denmark)

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

    2003-01-01

    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...

  3. Supramolecular Polymers in DNA Nanotechnology

    OpenAIRE

    Vyborna, Yuliia; Vybornyi, Mykhailo; Häner, Robert

    2016-01-01

    Creation of biocompatible functional materials is an important task in supramolecular chemistry. In this contribution, we report on noncovalent synthesis of DNA-grafted supramolecular polymers (SPs). DNA-grafted SPs enable programmed arrangement of oligonucleotides in a regular, tightly packed one-dimensional array. Further interactions of DNA-grafted SPs with complementary DNA strands leads to the formation of networks through highly cooperative G-C blunt-end stacking interactions. The struc...

  4. Polymers for DNA Delivery

    Directory of Open Access Journals (Sweden)

    A. J. Domb

    2005-01-01

    Full Text Available Nucleic acid delivery has many applications in basic science, biotechnology, agriculture, and medicine. One of the main applications is DNA or RNA delivery for gene therapy purposes. Gene therapy, an approach for treatment or prevention of diseases associated with defective gene expression, involves the insertion of a therapeutic gene into cells, followed by expression and production of the required proteins. This approach enables replacement of damaged genes or expression inhibition of undesired genes. Following two decades of research, there are two major methods for delivery of genes. The first method, considered the dominant approach, utilizes viral vectors and is generally an efficient tool of transfection. Attempts, however, to resolve drawbacks related with viral vectors (e.g., high risk of mutagenicity, immunogenicity, low production yield, limited gene size, etc., led to the development of an alternative method, which makes use of non-viral vectors. This review describes non-viral gene delivery vectors, termed "self-assembled" systems, and are based on cationic molecules, which form spontaneous complexes with negatively charged nucleic acids. It introduces the most important cationic polymers used for gene delivery. A transition from in vitro to in vivo gene delivery is also presented, with an emphasis on the obstacles to achieve successful transfection in vivo.

  5. A conserved amphipathic helix in the N-terminal regulatory region of the papillomavirus E1 helicase is required for efficient viral DNA replication.

    Science.gov (United States)

    Morin, Geneviève; Fradet-Turcotte, Amélie; Di Lello, Paola; Bergeron-Labrecque, Fanny; Omichinski, James G; Archambault, Jacques

    2011-06-01

    The papillomavirus E1 helicase, with the help of E2, assembles at the viral origin into a double hexamer that orchestrates replication of the viral genome. The N-terminal region (NTR) of E1 is essential for DNA replication in vivo but dispensable in vitro, suggesting that it has a regulatory function. By deletion analysis, we identified a conserved region of the E1 NTR needed for efficient replication of viral DNA. This region is predicted to form an amphipathic α-helix (AH) and shows sequence similarity to portions of the p53 and herpes simplex virus (HSV) VP16 transactivation domains known as transactivation domain 2 (TAD2) and VP16C, which fold into α-helices upon binding their target proteins, including the Tfb1/p62 (Saccharomyces cerevisiae/human) subunit of general transcription factor TFIIH. By nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC), we found that a peptide spanning the E1 AH binds Tfb1 on the same surface as TAD2/VP16C and with a comparable affinity, suggesting that it does bind as an α-helix. Furthermore, the E1 NTRs from several human papillomavirus (HPV) types could activate transcription in yeast, and to a lesser extent in mammalian cells, when fused to a heterologous DNA-binding domain. Mutation of the three conserved hydrophobic residues in the E1 AH, analogous to those in TAD2/VP16C that directly contact their target proteins, decreased transactivation activity and, importantly, also reduced by 50% the ability of E1 to support transient replication of DNA in C33A cells, at a step following assembly of the E1-E2-ori preinitiation complex. These results demonstrate the existence of a conserved TAD2/VP16C-like AH in E1 that is required for efficient replication of viral DNA. PMID:21450828

  6. Polymers and polymer systems for DNA delivery

    Czech Academy of Sciences Publication Activity Database

    Ulbrich, Karel; Oupický, David; Koňák, Čestmír; Reschel, Tomáš; Seymour, L. W.

    London: The School of Pharmacy , University of London, 2000. s. 13. [International Symposium on Polymer Therapeutics /4./. 05.01.2000-07.01.2000, London] R&D Projects: GA ČR GV307/96/K226 Subject RIV: CE - Biochemistry

  7. Role of Polymer Loops in DNA Replication

    CERN Document Server

    Jun, S; Jun, Suckjoon; Bechhoefer, John

    2003-01-01

    Loop formation in long molecules occurs many places in nature, from solutions of carbon nanotubes to polymers inside a cell. In this article, we review theoretical studies of the static and dynamic properties of polymer loops. For example, long polymers must search many configurations to find a "target" binding site, while short polymers are stiff and resist bending. In between, there is an optimal loop size, which balances the entropy of long loops against the energetic cost of short loops. We show that such simple pictures of loop formation can explain several long-standing observations in DNA replication, quantitatively.

  8. Polymer microspheres carrying fluorescent DNA probes

    Science.gov (United States)

    Chen, Xiaoyu; Dai, Zhao; Zhang, Jimei; Xu, Shichao; Wu, Chunrong; Zheng, Guo

    2010-07-01

    A polymer microspheres carried DNA probe, which was based on resonance energy transfer, was presented in this paper when CdTe quantum dots(QDs) were as energy donors, Au nanoparticles were as energy accepters and poly(4- vinylpyrindine-co-ethylene glycol dimethacrylate) microspheres were as carriers. Polymer microspheres with functional group on surfaces were prepared by distillation-precipitation polymerization when ethylene glycol dimethacrylate was as crosslinker in acetonitrile. CdTe QDs were prepared when 3-mercaptopropionic acid(MPA) was as the stabilizer in aqueous solution. Because of the hydrogen-bonding between the carboxyl groups of MPA on QDs and the pyrindine groups on the microspheres, the QDs were self-assembled onto the surfaces of microspheres. Then, the other parts of DNA probe were finished according to the classic method. The DNA detection results indicated that this novel fluorescent DNA probe system could recognize the existence of complementary target DNA or not.

  9. Programmed Switching of Single Polymer Conformation on DNA Origami

    DEFF Research Database (Denmark)

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

    2016-01-01

    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......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...

  10. Polymer multilayer tattooing for enhanced DNA vaccination

    Science.gov (United States)

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

    2013-04-01

    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.

  11. 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

    Science.gov (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

    2015-04-01

    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

  12. Programmed Switching of Single Polymer Conformation on DNA Origami.

    Science.gov (United States)

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

    2016-02-23

    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. PMID:26766635

  13. The polymer physics of single DNA confined in nanochannels.

    Science.gov (United States)

    Dai, Liang; Renner, C Benjamin; Doyle, Patrick S

    2016-06-01

    In recent years, applications and experimental studies of DNA in nanochannels have stimulated the investigation of the polymer physics of DNA in confinement. Recent advances in the physics of confined polymers, using DNA as a model polymer, have moved beyond the classic Odijk theory for the strong confinement, and the classic blob theory for the weak confinement. In this review, we present the current understanding of the behaviors of confined polymers while briefly reviewing classic theories. Three aspects of confined DNA are presented: static, dynamic, and topological properties. The relevant simulation methods are also summarized. In addition, comparisons of confined DNA with DNA under tension and DNA in semidilute solution are made to emphasize universal behaviors. Finally, an outlook of the possible future research for confined DNA is given. PMID:26782150

  14. A two-dimensional DNA lattice implanted polymer solar cell

    International Nuclear Information System (INIS)

    A double crossover tile based artificial two-dimensional (2D) DNA lattice was fabricated and the dry-wet method was introduced to recover an original DNA lattice structure in order to deposit DNA lattices safely on the organic layer without damaging the layer. The DNA lattice was then employed as an electron blocking layer in a polymer solar cell causing an increase of about 10% up to 160% in the power conversion efficiency. Consequently, the resulting solar cell which had an artificial 2D DNA blocking layer showed a significant enhancement in power conversion efficiency compared to conventional polymer solar cells. It should be clear that the artificial DNA nanostructure holds unique physical properties that are extremely attractive for various energy-related and photonic applications.

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

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    Kathryn Regan

    2016-09-01

    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.

  16. Anisotropic Membrane Curvature Sensing by Amphipathic Peptides.

    Science.gov (United States)

    Gómez-Llobregat, Jordi; Elías-Wolff, Federico; Lindén, Martin

    2016-01-01

    Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodeling cell membranes. However, the molecular driving forces behind these processes are not well understood. Here, we describe an approach to study curvature sensing by simulating the interactions of single molecules with a buckled lipid bilayer. We analyze three amphipathic antimicrobial peptides, a class of membrane-associated molecules that specifically target and destabilize bacterial membranes, and find qualitatively different sensing characteristics that would be difficult to resolve with other methods. Our findings provide evidence for direction-dependent curvature sensing mechanisms in amphipathic peptides and challenge existing theories of hydrophobic insertion. The buckling approach is generally applicable to a wide range of curvature-sensing molecules, and our results provide strong motivation to develop new experimental methods to track position and orientation of membrane proteins. PMID:26745422

  17. Efficient Turing-Universal Computation with DNA Polymers

    Science.gov (United States)

    Qian, Lulu; Soloveichik, David; Winfree, Erik

    Bennett's proposed chemical Turing machine is one of the most important thought experiments in the study of the thermodynamics of computation. Yet the sophistication of molecular engineering required to physically construct Bennett's hypothetical polymer substrate and enzymes has deterred experimental implementations. Here we propose a chemical implementation of stack machines - a Turing-universal model of computation similar to Turing machines - using DNA strand displacement cascades as the underlying chemical primitive. More specifically, the mechanism described herein is the addition and removal of monomers from the end of a DNA polymer, controlled by strand displacement logic. We capture the motivating feature of Bennett's scheme: that physical reversibility corresponds to logically reversible computation, and arbitrarily little energy per computation step is required. Further, as a method of embedding logic control into chemical and biological systems, polymer-based chemical computation is significantly more efficient than geometry-free chemical reaction networks.

  18. Biological Sensing and DNA Templated Electronics Using Conjugated Polymers

    OpenAIRE

    Björk, Per

    2007-01-01

    Conjugated polymers have been found useful in a wide range of applications such as solar cells, sensor elements and printed electronics, due to their optical and electronic properties. Functionalization with charged side chains has enabled water solubility, resulting in an enhanced interaction with biomolecules. This thesis focus on the emerging research fields, where these conjugated polyelectrolytes (CPEs) are combined with biomolecules for biological sensing and DNA nanowire assembling. CP...

  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

    2016-01-01

    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

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    Md. Mahbubur Rahman

    2015-02-01

    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. Crystallization of a flexible polymer in melt in the presence of double-stranded DNA

    International Nuclear Information System (INIS)

    The behavior of a mixture of short fragments of double-stranded DNA and a flexible polymer is studied. The role of the DNA double helix in the formation of the crystalline phase in the flexible polymers melt is considered. It is shown that the presence of DNA rigid fragments in melt results in increase in the melting temperature. A shift of the melting temperature of a perfect crystal as compared to the pure polymer melt is calculated

  3. Charge transfer along DNA dimers, trimers and polymers

    CERN Document Server

    Simserides, Constantinos

    2013-01-01

    The transfer of electrons and holes along DNA dimers, trimers and polymers is described at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters between successive base-pairs. The temporal and spatial evolution of carriers along a $N$ base-pair DNA segment is determined, solving a system of $N$ coupled differential equations. Useful physical quantities are calculated including the pure mean carrier transfer rate $k$, the inverse decay length $\\beta$ used for exponential fit ($k = k_0 \\textrm{exp}(-\\beta d)$) of the transfer rate as a function of the charge transfer distance $d = N \\times$ 3.4 {\\AA} and the exponent $\\eta$ used for a power law fit ($k = k_0' N^{-\\eta}$) of the transfer rate as function of the number of monomers $N$. Among others, the electron and hole transfer along the polymers poly(dG)-poly(dC), poly(dA)-poly(dT), GCGCGC..., ATATAT... is studied. $\\beta$ ($\\eta$) falls in the range $\\approx$ 0.2 - 2 {\\AA}$^{-1}$ (1.7 - 17), $k_0$ ($k_0'$) is us...

  4. Tryptophan rotamer distributions in amphipathic peptides at a lipid surface.

    OpenAIRE

    Clayton, A H; Sawyer, W. H.

    1999-01-01

    The fluorescence decay of tryptophan is a sensitive indicator of its local environment within a peptide or protein. We describe the use of frequency domain fluorescence spectroscopy to determine the conformational and environmental changes associated with the interaction of single tryptophan amphipathic peptides with a phospholipid surface. The five 18-residue peptides studied are based on a class A amphipathic peptide known to associate with lipid bilayers. The peptides contain a single tryp...

  5. DNA immobilization on polymer-modified Si surface by controlling pH

    International Nuclear Information System (INIS)

    A novel approach based on polymer-modified Si surface as DNA sensor platforms is presented. The polymer-modified Si surface was prepared by using 3-(methacryloxypropyl)trimethoxysilane [γ-MPS] and poly(acrylamide) [PAAm]. Firstly, a layer of γ-MPS was formed on the hydroxylated silicon surface as a monolayer and then modified with different molecular weight of PAAm to form polymer-modified surface. The polymer-modified Si surface was used for dsDNA immobilization. All steps about formation of layer structure were characterized by ellipsometry, atomic force microscopy (AFM), attenuated total reflectance Fourier transformed infrared (ATR-FTIR), and contact angle (CA) measurements. We found that in this case the amount of dsDNA immobilized onto the surface was dictated by the electrostatic interaction between the substrate surface and the DNA. Our results thus demonstrated that DNA molecules could be immobilized differently onto the polymer-modified support surface via electrostatic interactions.

  6. DNA Microspheres Coated with Bioavailable Polymer as an Efficient Gene Expression Agent in Yeasts

    Directory of Open Access Journals (Sweden)

    Irena Reytblat

    2016-01-01

    Full Text Available Gene delivery is one of the steps necessary for gene therapy and for genetic modification. However, delivering DNA into cells is challenging due to its negative charge that leads to repulsion by the negative cell membrane. In the current research, DNA spheres with a DNA encoding to a certain gene were coated with bioavailable polymers, polyethylene imine (PEI and polycaprolactone (PCL, in a short, one-step sonochemical reaction. The polymers were used in order to neutralize the negative charge of the DNA. Our study shows that the DNA nanospheres not only managed to penetrate the cell without causing it any damage, but also expressed the desired gene inside it.

  7. Unbiased charge oscillations in DNA monomer-polymers and dimer-polymers

    CERN Document Server

    Lambropoulos, Konstantinos; Morphis, Andreas; Kaklamanis, Konstantinos; Theodorakou, Marina; Simserides, Constantinos

    2015-01-01

    We call {\\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a tight-binding (TB) approach at the base-pair level to readily determine the spatiotemporal evolution of a single extra carrier along a $N$ base-pair polymer. We study HOMO and LUMO eigenspectra as well as the mean over time probabilities to find the carrier at a particular monomer. We use the pure mean transfer rate $k$ to evaluate the easiness of charge transfer. The inverse decay length $\\beta$ for exponential fits $k(d)$, where $d$ is the charge transfer distance, and the exponent $\\eta$ for power law fits $k(N)$ are computed; generally power law fits are better. We illustrate that increasing the number of different parameters involved in the TB description, the fall of $k(d)$ or $k(N)$ becomes steeper and show the range covered by $\\beta$ and $\\eta$. Finally, both for the time-...

  8. Redox polymer and probe DNA tethered to gold electrodes for enzyme-amplified amperometric detection of DNA hybridization.

    Science.gov (United States)

    Kavanagh, Paul; Leech, Dónal

    2006-04-15

    The detection of nucleic acids based upon recognition surfaces formed by co-immobilization of a redox polymer mediator and DNA probe sequences on gold electrodes is described. The recognition surface consists of a redox polymer, [Os(2,2'-bipyridine)2(polyvinylimidazole)(10)Cl](+/2+), and a model single DNA strand cross-linked and tethered to a gold electrode via an anchoring self-assembled monolayer (SAM) of cysteamine. Hybridization between the immobilized probe DNA of the recognition surface and a biotin-conjugated target DNA sequence (designed from the ssrA gene of Listeria monocytogenes), followed by addition of an enzyme (glucose oxidase)-avidin conjugate, results in electrical contact between the enzyme and the mediating redox polymer. In the presence of glucose, the current generated due to the catalytic oxidation of glucose to gluconolactone is measured, and a response is obtained that is binding-dependent. The tethering of the probe DNA and redox polymer to the SAM improves the stability of the surface to assay conditions of rigorous washing and high salt concentration (1 M). These conditions eliminate nonspecific interaction of both the target DNA and the enzyme-avidin conjugate with the recognition surfaces. The sensor response increases linearly with increasing concentration of target DNA in the range of 1 x 10(-9) to 2 x 10(-6) M. The detection limit is approximately 1.4 fmol, (corresponding to 0.2 nM of target DNA). Regeneration of the recognition surface is possible by treatment with 0.25 M NaOH solution. After rehybridization of the regenerated surface with the target DNA sequence, >95% of the current is recovered, indicating that the redox polymer and probe DNA are strongly bound to the surface. These results demonstrate the utility of the proposed approach. PMID:16615783

  9. Cationic polymers for DNA origami coating - examining their binding efficiency and tuning the enzymatic reaction rates.

    Science.gov (United States)

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

    2016-06-01

    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. PMID:27219684

  10. Polymers modified with double-tailed fluorous compounds for efficient DNA and siRNA delivery.

    Science.gov (United States)

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

    2015-08-01

    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. PMID:25937003

  11. Synthetic Polymer Hybridization with DNA and RNA Directs Nanoparticle Loading, Silencing Delivery, and Aptamer Function

    OpenAIRE

    Zhou, Zhun; Xia, Xin; Bong, Dennis

    2015-01-01

    We report herein discrete triplex hybridization of DNA and RNA with polyacrylates. Length-monodisperse triazine-derivatized polymers were prepared on gram-scale by reversible addition–fragmentation chain-transfer polymerization. Despite stereoregio backbone heterogeneity, the triazine polymers bind T/U-rich DNA or RNA with nanomolar affinity upon mixing in a 1:1 ratio, as judged by thermal melts, circular dichroism, gel-shift assays, and fluorescence quenching. We call these polyacrylates “bi...

  12. Synthetic Polymer Hybridization with DNA and RNA Directs Nanoparticle Loading, Silencing Delivery, and Aptamer Function.

    Science.gov (United States)

    Zhou, Zhun; Xia, Xin; Bong, Dennis

    2015-07-22

    We report herein discrete triplex hybridization of DNA and RNA with polyacrylates. Length-monodisperse triazine-derivatized polymers were prepared on gram-scale by reversible addition-fragmentation chain-transfer polymerization. Despite stereoregio backbone heterogeneity, the triazine polymers bind T/U-rich DNA or RNA with nanomolar affinity upon mixing in a 1:1 ratio, as judged by thermal melts, circular dichroism, gel-shift assays, and fluorescence quenching. We call these polyacrylates "bifacial polymer nucleic acids" (bPoNAs). Nucleic acid hybridization with bPoNA enables DNA loading onto polymer nanoparticles, siRNA silencing delivery, and can further serve as an allosteric trigger of RNA aptamer function. Thus, bPoNAs can serve as tools for both non-covalent bioconjugation and structure-function nucleation. It is anticipated that bPoNAs will have utility in both bio- and nanotechnology. PMID:26138550

  13. Cationic polymers for DNA origami coating - examining their binding efficiency and tuning the enzymatic reaction rates

    Science.gov (United States)

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

    2016-06-01

    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

  14. DNA-sensors based on functionalized conducting polymers and quantum dots

    Science.gov (United States)

    Kjällman, Tanja; Peng, Hui; Travas-Sejdic, Jadranka; Soeller, Christian

    2007-12-01

    The availability of rapid and specific biosensors is of great importance for many areas of biomedical research and modern biotechnology. This includes a need for DNA sensors where the progress of molecular biology demands routine detection of minute concentrations of specific gene fragments. A promising alternative approach to traditional DNA essays utilizes novel smart materials, including conducting polymers and nanostructured materials such as quantum dots. We have constructed a number of DNA sensors based on smart materials that allow rapid one-step detection of unlabeled DNA fragments with high specificity. These sensors are based on functionalized conducting polymers derived from polypyrrole (PPy) and poly(p-phenylenevinylene) (PPV). PPy based sensors provide intrinsic electrical readout via cyclic voltammetry and electrochemical impedance spectroscopy. The performance of these sensors is compared to a novel self-assembled monolayer-PNA construct on a gold electrode. Characterization of the novel PNA based sensor shows that it has comparable performance to the PPy based sensors and can also be read out effectively using AC cyclic voltammetry. Complementary to such solid substrate sensors we have developed a novel optical DNA essay based on a new PPV derived cationic conducting polymer. DNA detection in this essay results from sample dependent fluorescence resonance energy transfer changes between the cationic conducting polymer and Cy3 labeled probe oligonucleotides. As an alternative to such fluorochrome based sensors we discuss the use of inorganic nanocrystals ('quantum dots') and present data from water soluble CdTe quantum dots synthesized in an aqueous environment.

  15. Equilibrium properties of DNA and other semiflexible polymers confined in nanochannels

    Science.gov (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

  16. Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer.

    Science.gov (United States)

    Kinoshita, Kenji; Fujimoto, Kentaro; Yakabe, Toru; Saito, Shin; Hamaguchi, Yuzo; Kikuchi, Takayuki; Nonaka, Ken; Murata, Shigenori; Masuda, Daisuke; Takada, Wataru; Funaoka, Sohei; Arai, Susumu; Nakanishi, Hisao; Yokoyama, Kanehisa; Fujiwara, Kazuhiko; Matsubara, Kenichi

    2007-01-01

    DNA microarrays are routinely used to monitor gene expression profiling and single nucleotide polymorphisms (SNPs). However, for practically useful high performance, the detection sensitivity is still not adequate, leaving low expression genes undetected. To resolve this issue, we have developed a new plastic S-BIO PrimeSurface with a biocompatible polymer; its surface chemistry offers an extraordinarily stable thermal property for a lack of pre-activated glass slide surface. The oligonucleotides immobilized on this substrate are robust in boiling water and show no significant loss of hybridization activity during dissociation treatment. This allowed us to hybridize the templates, extend the 3' end of the immobilized DNA primers on the S-Bio by DNA polymerase using deoxynucleotidyl triphosphates (dNTP) as extender units, release the templates by denaturalization and use the same templates for a second round of reactions similar to that of the PCR method. By repeating this cycle, the picomolar concentration range of the template oligonucleotide can be detected as stable signals via the incorporation of labeled dUTP into primers. This method of Multiple Primer EXtension (MPEX) could be further extended as an alternative route for producing DNA microarrays for SNP analyses via simple template preparation such as reverse transcript cDNA or restriction enzyme treatment of genome DNA. PMID:17135189

  17. Surface modification of polyelectrolyte DNA complexes with degradable polymers

    Czech Academy of Sciences Publication Activity Database

    Laga, Richard; Braunová, Alena; Koňák, Čestmír; Pechar, Michal; Šubr, Vladimír; Ulbrich, Karel

    Prague : Institute of Macromolecular Chemistry AS CR, 2006. s. 66. ISBN 80-85009-52-8. [Microsymposium on Structure and Dynamics of Self-organized Macromolecular Systems /45./. 09.07.2006-13.07.2006, Prague] EU Projects: European Commission(XE) 512087 - GIANT Institutional research plan: CEZ:AV0Z40500505 Keywords : poly(L- lysine ) * DNA * Polyelectrolyte complex Subject RIV: CD - Macromolecular Chemistry

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    ) using a 4 inch diameter two-level hybrid stamp. The fluidic structures were sealed using thermal polymer fusion bonding. The stamp has nanometer-and micrometer-sized protrusions defined in a thermally grown SiO2 layer and the sol - gel process derived duromeric hybrid polymer Ormocomp, respectively. The...... 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....

  19. Controlling self-assembly of DNA-polymer conjugates for applications in imaging and drug delivery.

    Science.gov (United States)

    Peterson, Amberlyn M; Heemstra, Jennifer M

    2015-01-01

    Amphiphilic supramolecular structures such as micelles and vesicles can be formed through phase-driven self-assembly of monomer units having discrete hydrophilic and hydrophobic blocks. These structures show great promise for use in medical and biological applications, and incorporating DNA as the hydrophilic block of the amphiphilic monomers enables the creation of assemblies that also take advantage of the unique information storage and molecular recognition capabilities of DNA. Recently, significant advances have been made in the synthesis of DNA-polymer conjugates (DPCs), controlling the morphology of DPC assemblies by altering monomer structure, and probing the effect of assembly on DNA stability and hybridization. Together, these investigations have laid the framework for using DPCs in drug delivery, cellular imaging, and other applications in materials science and chemistry. PMID:25327363

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

    International Nuclear Information System (INIS)

    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

  1. Electric field induced charge transfer through single and double-stranded DNA polymer molecules

    OpenAIRE

    Ramos, Marta M. D.; Correia, Helena M. G.

    2011-01-01

    The charge transfer through single-stranded and double-stranded DNA polymer molecules has been the subject of numerous experimental and theoretical studies concerning their applications in molecular electronics. However, the underlying mechanisms responsible for their different electrical conductivity observed in the experiments are poorly understood. Here we use a self-consistent quantum molecular dynamics method to study the effect of an applied electric field along the molecular axis on ch...

  2. 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

    2003-01-01

    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.

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

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    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.

  4. Using temperature-sensitive smart polymers to regulate DNA-mediated nanoassembly and encoded nanocarrier drug release.

    Science.gov (United States)

    Hamner, Kristen L; Alexander, Colleen M; Coopersmith, Kaitlin; Reishofer, David; Provenza, Christina; Maye, Mathew M

    2013-08-27

    In this paper we describe the use of a temperature-responsive polymer to regulate DNA interactions in both a DNA-mediated assembly system and a DNA-encoded drug delivery system. A thermoresponsive pNIPAAm-co-pAAm polymer, with a transition temperature (TC) of 51 °C, was synthesized with thiol modification and grafted onto gold nanoparticles (Au NPs) also containing single-stranded oligonucleotides (ssDNA). The thermoresponsive behavior of the polymer regulated the accessibility of the sequence-specific hybridization between complementary DNA-functionalized Au NPs. At T TC, the polymer shell undergoes a hydrophilic to -phobic phase transition and collapses, shrinking below the outer ssDNA, allowing for the sequence-specific hybridization to occur. The potential application of this dynamic interface for drug delivery is shown, in which the chemotherapy drug doxorubicin (DOX) is bound to double-stranded DNA (dsDNA)-functionalized Au NPs whose sequences are known to be high-affinity intercalation points for it. The presence of the polymer capping is shown to decrease drug release kinetics and equilibrium at T TC, thus improving the cytotoxicity of the encoded nanocarrier design. PMID:23899347

  5. Neutron diffraction studies of amphipathic helices in phospholipid bilayers

    International Nuclear Information System (INIS)

    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

  6. 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)

    1994-12-31

    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.

  7. Synthesis of a new conjugated polymer for DNA alkylation and gene regulation.

    Science.gov (United States)

    Nie, Chenyao; Zhu, Chunlei; Feng, Liheng; Lv, Fengting; Liu, Libing; Wang, Shu

    2013-06-12

    A new polyfluorene derivative containing pendent alkylating chlorambucil (PFP-Cbl) was synthesized and characterized. Under direct incubation with DNA in vitro, PFP-Cbl could undergo an efficient DNA alkylating reaction and induce DNA cross-linking. In vitro transcription and translation experiment exhibited that the PFP-Cbl significantly down-regulated the gene expression of luciferase reporter plasmid. The down-regulation of gene expression was also verified through the transfection experiment of p-EGFP plasmid, which showed decreased green fluorescent protein (GFP) in cells. Meanwhile, the self-luminous property of PFP-Cbl could make it able to trace the internalized PFP-Cbl and plasmid complexes resulted from cross-linking in cells by fluorescent microscopy. Combining the features of alkylating function, multivalent binding sites, and fluorescent characteristics, PFP-Cbl provides a new insight in the area of gene regulation and extends the new applications of conjugated polymers (CPs). PMID:23548104

  8. Protein-based polymers that bond to DNA : design of virus-like particles and supramolecular nanostructures

    NARCIS (Netherlands)

    Hernandez Garcia, A.

    2014-01-01

     In this thesis it is demonstrated that it is possible to use Protein-based Polymers (PbPs) as synthetic binders of DNA (or any other negatively charged polyelectrolyte). The PbPs co-assemble with their DNA templates to form highly organized virus-like particles and supramolecular structures. A

  9. Potent catenation of supercoiled and gapped DNA circles by topoisomerase I in the presence of a hydrophilic polymer.

    Science.gov (United States)

    Low, R L; Kaguni, J M; Kornberg, A

    1984-04-10

    An exceptionally potent DNA catenation activity, identified in an extract from Escherichia coli, has been purified and partially characterized. Catenation results from the sequential action of the following two polypeptides: beta, 34 kDa and identical to exonuclease III; and alpha, 101 kDa and identical to DNA topoisomerase I (omega protein). An additional requirement is that a small proportion of the circles be nicked in order to provide the substrate for exonuclease III to generate gaps, estimated to be about 100 nucleotides long. Following exonuclease III digestion, one molecule of topoisomerase I can interlock per minute at 30 degrees C about 20 supercoiled and gapped DNA circles into a massively catenated network. The reaction requires Mg2+ and a hydrophilic polymer (polyvinyl alcohol or polyethylene glycol) at about 7%, but neither ATP nor spermidine. The hydrophilic polymer appears to drive catenation by condensing the DNA; decatenation by topoisomerase I proceeds upon removal of the polymer. PMID:6323479

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

    Science.gov (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

    2016-05-01

    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. PMID:27058968

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

    International Nuclear Information System (INIS)

    Highlights: • We systematically study carrier transfer along DNA dimers, trimers and polymers. • We define max transfer percentage, pure max transfer rate, pure mean transfer rate. • For exponential (power-law) fit, the inverse decay length β (exponent η) is computed. • The results are compared with theoretical and experimental works. • The method assesses the extent a specific DNA segment can serve for charge transfer. - Abstract: A systematic study of carrier transfer along DNA dimers, trimers and polymers including poly(dG)–poly(dC), poly(dA)–poly(dT), GCGCGC…, ATATAT… is presented allowing to determine the spatiotemporal evolution of electrons or holes along a N base-pair DNA segment. Physical quantities are defined including maximum transfer percentage p and pure maximum transfer rate p/T when a period T is defined; pure mean transfer rate k and speed u=kd, where d is the charge transfer distance. The inverse decay length β for the exponential fit k=k0exp(-βd) and the exponent η for the power-law fit k=k0′N-η are computed. β≈ 0.2–2 Å−1, k0 is usually 10−2–10−1 PHz, generally ≈10−4–10 PHz. η≈1.7–17, k0′ is usually 10−2–10−1 PHz, generally ≈10−4–103 PHz. The results are compared with theoretical and experimental works. This method allows to assess the extent at which a specific DNA segment can serve for charge transfer

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

    Directory of Open Access Journals (Sweden)

    Glass John I

    2010-07-01

    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

  13. Formulation of nucleic acid with pH-responsive amphipathic peptides for pulmonary delivery

    OpenAIRE

    Liang, Wanling; 梁婉玲

    2014-01-01

    Nucleic acids could be used as therapeutic agents for the treatment of many different diseases, but poor delivery limits their clinical application. A series of pH-responsive amphipathic peptides containing histidine or 2,3-diaminopropionic acid (Dap) derivatives, LAH and LADap peptides, were investigated in this study as nucleic acid carriers for the treatment of respiratory infectious disease. LAH and LADap peptides are cationic, amphipathic pH-responsive peptides. The major attractive ...

  14. Persistent draining crossover in DNA and other semi-flexible polymers: Evidence from hydrodynamic models and extensive measurements on DNA solutions.

    Science.gov (United States)

    Mansfield, Marc L; Tsortos, Achilleas; Douglas, Jack F

    2015-09-28

    Although the scaling theory of polymer solutions has had many successes, this type of argument is deficient when applied to hydrodynamic solution properties. Since the foundation of polymer science, it has been appreciated that measurements of polymer size from diffusivity, sedimentation, and solution viscosity reflect a convolution of effects relating to polymer geometry and the strength of the hydrodynamic interactions within the polymer coil, i.e., "draining." Specifically, when polymers are expanded either by self-excluded volume interactions or inherent chain stiffness, the hydrodynamic interactions within the coil become weaker. This means there is no general relationship between static and hydrodynamic size measurements, e.g., the radius of gyration and the hydrodynamic radius. We study this problem by examining the hydrodynamic properties of duplex DNA in solution over a wide range of molecular masses both by hydrodynamic modeling using a numerical path-integration method and by comparing with extensive experimental observations. We also considered how excluded volume interactions influence the solution properties of DNA and confirm that excluded volume interactions are rather weak in duplex DNA in solution so that the simple worm-like chain model without excluded volume gives a good leading-order description of DNA for molar masses up to 10(7) or 10(8) g/mol or contour lengths between 5 μm and 50 μm. Since draining must also depend on the detailed chain monomer structure, future work aiming to characterize polymers in solution through hydrodynamic measurements will have to more carefully consider the relation between chain molecular structure and hydrodynamic solution properties. In particular, scaling theory is inadequate for quantitative polymer characterization. PMID:26429037

  15. Contribution of Amphipathicity and Hydrophobicity to the Antimicrobial Activity and Cytotoxicity of β-Hairpin Peptides

    Science.gov (United States)

    2016-01-01

    Bacteria have acquired extensive resistance mechanisms to protect themselves against antibiotic action. Today the bacterial membrane has become one of the “final frontiers” in the search for new compounds acting on novel targets to address the threat of multi-drug resistant (MDR) and XDR bacterial pathogens. β-Hairpin antimicrobial peptides are amphipathic, membrane-binding antibiotics that exhibit a broad range of activities against Gram-positive, Gram-negative, and fungal pathogens. However, most members of the class also possess adverse cytotoxicity and hemolytic activity that preclude their development as candidate antimicrobials. We examined peptide hydrophobicity, amphipathicity, and structure to better dissect and understand the correlation between antimicrobial activity and toxicity, membrane binding, and membrane permeability. The hydrophobicity, pI, net charge at physiological pH, and amphipathic moment for the β-hairpin antimicrobial peptides tachyplesin-1, polyphemusin-1, protegrin-1, gomesin, arenicin-3, and thanatin were determined and correlated with key antimicrobial activity and toxicity data. These included antimicrobial activity against five key bacterial pathogens and two fungi, cytotoxicity against human cell lines, and hemolytic activity in human erythrocytes. Observed antimicrobial activity trends correlated with compound amphipathicity and, to a lesser extent, with overall hydrophobicity. Antimicrobial activity increased with amphipathicity, but unfortunately so did toxicity. Of note, tachyplesin-1 was found to be 8-fold more amphipathic than gomesin. These analyses identify tachyplesin-1 as a promising scaffold for rational design and synthetic optimization toward an antibiotic candidate.

  16. Release of cationic polymer-DNA complexes from the endosome: A theoretical investigation of the proton sponge hypothesis.

    Science.gov (United States)

    Yang, Shuang; May, Sylvio

    2008-11-14

    Polyplexes are complexes composed of DNA and cationic polymers; they are promising transport vehicles for nonviral gene delivery. Cationic polymers that contain protonatable groups, such as polyethylenimine, have been suggested to trigger endosomal escape of polyplexes according to the "proton sponge hypothesis." Here, osmotic swelling is induced by a decrease in the endosomal pH value, leading to an accumulation of polymer charge accompanied by the influx of Cl(-) ions to maintain overall electroneutrality. We study a theoretical model of the proton sponge mechanism. The model is based on the familiar Poisson-Boltzmann approach, modified so as to account for the presence of ionizable polyelectrolytes within self-consistent field theory with assumed ground state dominance. We consider polyplexes, composed of fixed amounts of DNA and cationic polymer, to coexist with uncomplexed cationic polymer in an enclosing vesicle of fixed volume. For such a system, we calculate the increase in osmotic pressure upon moderately decreasing the pH value and relate that pressure to the rupture tension of the enclosing membrane. Our model predicts membrane rupture upon pH decrease only within a certain range of free polymer content in the vesicle. That range narrows with increasing amount of DNA. Consequently, there exists a maximal amount of DNA that can be incorporated into a vesicle while maintaining the ability of content release through the proton sponge mechanism. PMID:19045433

  17. POLYSACCHARIDES AND eDNA AID BACTERIAL ATTACHMENT TO POLYMER BRUSH COATINGS (PLL-g-PEG)

    DEFF Research Database (Denmark)

    Zeng, Guanghong; Ogaki, Ryosuke; Regina, Viduthalai R.; Meyer, Rikke Louise

    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...... in complete absence of bacterial colonization from Pseudomonas aeruginosa, Staphylococcus aureus and Staphylococcus epidermis, whereas the conventional PLL-g-PEG coatings only resisted colonization by P. aeruginosa and S. aureus, but not S. epidermidis. Colonization patterns were also reflected in...... of the conventional coating. These results explain why S. epidermidis, which produces polysaccharides and extracellular DNA, could successfully colonize the conventional PLL-g-PEG coatings. The ability of high-density PLL-g-PEG to resist polysaccharides, DNA, and bacterial adhesion of all strains is...

  18. Manipulating lipid bilayer material properties using biologically active amphipathic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Ashrafuzzaman, Md [Department of Physiology and Biophysics, Weill Medical College of University of Cornell, New York, NY 10021 (United States); Lampson, M A [Department of Physiology and Biophysics, Weill Medical College of University of Cornell, New York, NY 10021 (United States); Greathouse, D V [Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701 (United States); II, R E Koeppe [Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701 (United States); Andersen, O S [Department of Physiology and Biophysics, Weill Medical College of University of Cornell, New York, NY 10021 (United States)

    2006-07-19

    Lipid bilayers are elastic bodies with properties that can be manipulated/controlled by the adsorption of amphipathic molecules. The resulting changes in bilayer elasticity have been shown to regulate integral membrane protein function. To further understand the amphiphile-induced modulation of bilayer material properties (thickness, intrinsic monolayer curvature and elastic moduli), we examined how an enantiomeric pair of viral anti-fusion peptides (AFPs)-Z-Gly-D-Phe and Z-Gly-Phe, where Z denotes a benzyloxycarbonyl group, as well as Z-Phe-Tyr and Z-D-Phe-Phe-Gly-alters the function of enantiomeric pairs of gramicidin channels of different lengths in planar bilayers. For both short and long channels, the channel lifetimes and appearance frequencies increase as linear functions of the aqueous AFP concentration, with no apparent effect on the single-channel conductance. These changes in channel function do not depend on the chirality of the channels or the AFPs. At pH 7.0, the relative changes in channel lifetimes do not vary when the channel length is varied, indicating that these compounds exert their effects primarily by causing a positive-going change in the intrinsic monolayer curvature. At pH 4.0, the AFPs are more potent than at pH 7.0 and have greater effects on the shorter channels, indicating that these compounds now change the bilayer elastic moduli. When AFPs of different anti-fusion potencies are compared, the rank order of the anti-fusion activity and the channel-modifying activity is similar, but the relative changes in anti-fusion potency are larger than the changes in channel-modifying activity. We conclude that gramicidin channels are useful as molecular force transducers to probe the influence of small amphiphiles upon lipid bilayer material properties.

  19. Conducting polymer based DNA biosensor for the detection of the Bacillus cereus group species

    Science.gov (United States)

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

    2009-05-01

    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.

  20. Cholesteric liquid crystalline phases given by three helical biological polymers : DNA, PBLG and xanthan. A comparative analysis of their textures

    OpenAIRE

    Livolant, F.

    1986-01-01

    The cholesteric liquid crystalline phases of three polymers of biological interest have been investigated: PBLG (a polypeptide), DNA (a polynucleotide) and xanthan (a polysaccharide). The textures (and the defects which they contain) of these three mesophases are analysed and compared The main difference concerns focal lines which apparently do not occur in PBLG, are rare in DNA but occur frequently in xanthan. The frequency of occurrence of the different types of rotation and translation dis...

  1. Role of amphipathic helix of a herpesviral protein in membrane deformation and T cell receptor downregulation.

    Directory of Open Access Journals (Sweden)

    Chan-Ki Min

    2008-11-01

    Full Text Available Lipid rafts are membrane microdomains that function as platforms for signal transduction and membrane trafficking. Tyrosine kinase interacting protein (Tip of T lymphotropic Herpesvirus saimiri (HVS is targeted to lipid rafts in T cells and downregulates TCR and CD4 surface expression. Here, we report that the membrane-proximal amphipathic helix preceding Tip's transmembrane (TM domain mediates lipid raft localization and membrane deformation. In turn, this motif directs Tip's lysosomal trafficking and selective TCR downregulation. The amphipathic helix binds to the negatively charged lipids and induces liposome tubulation, the TM domain mediates oligomerization, and cooperation of the membrane-proximal helix with the TM domain is sufficient for localization to lipid rafts and lysosomal compartments, especially the mutivesicular bodies. These findings suggest that the membrane-proximal amphipathic helix and TM domain provide HVS Tip with the unique ability to deform the cellular membranes in lipid rafts and to downregulate TCRs potentially through MVB formation.

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

    Directory of Open Access Journals (Sweden)

    Kaushik Naveen K

    2012-08-01

    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.

  3. Biogenesis and the growth of DNA-like polymer chains: a computer simulation

    International Nuclear Information System (INIS)

    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-p sub (CG)), as ξ ∝ 1/r1-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. (author)

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

    CERN Document Server

    Simserides, Constantinos

    2014-01-01

    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. Highly sensitive colorimetric sensor for Hg(2+) detection based on cationic polymer/DNA interaction.

    Science.gov (United States)

    Zhu, Yingyue; Cai, Yilin; Zhu, Yibo; Zheng, Lixue; Ding, Jianying; Quan, Ying; Wang, Limei; Qi, Bin

    2015-07-15

    The detection of ultralow concentrations of mercury is a currently significant challenge. Here, a novel strategy is proposed: the colorimetric detection of Hg(2+) based on the aggregation of gold nanoparticles (AuNPs) driven by a cationic polymer. In this three-component system, DNA combines electrostatically with phthalic diglycol diacrylate (PDDA) in a solution of AuNPs. In the presence of Hg(2+), thymine (T)-Hg(2+)-T induced hairpin turns are formed in the DNA strands, which then do not interact with PDDA, enabling the freed PDDA to subsequently facilitate aggregation of the AuNPs. Thus, according to the change in color from wine-red to blue-purple upon AuNPs aggregation, a colorimetric sensor is established to detect Hg(2+). Under optimal conditions, the color change is clearly seen with the naked eye. A linear range of 0.25-500nM was obtained by absorption spectroscopy with a detection limit of approximately 0.15nM. Additionally, the proposed method shows high selectivity toward Hg(2+) in the presence of other heavy metal ions. Real sample analysis was evaluated with the use of lake water and the results suggest good potential for practical application. PMID:25727033

  6. Increasing polymer diffusivity by increasing the contour length: The surprising effect of YOYO-1 on DNA dynamics

    Science.gov (United States)

    Shin, Seunghwan; Dorfman, Kevin; Cheng, Xiang

    2015-03-01

    Double-stranded DNA (dsDNA) labeled with cyanine dyes such as YOYO-1 has been extensively used as a model to study equilibrium and dynamic properties of semiflexible polyelectrolytes. The ability to directly visualize the polymer dynamics is an attractive feature of these experiments, but positively charged cyanine dyes affect the physical properties of dsDNA, distorting the double helix and counterbalancing the intrinsic negative charge of the backbone. A variety of studies have been conducted to reveal the effect of the dye on the contour length and the persistence length of dsDNA. However, fewer efforts have been made to directly quantify the effect of dye on the diffusion behavior of dsDNA. In order to resolve this issue, we measured the in-plane diffusion coefficient of unconfined dsDNA using confocal microscopy. Although there is widespread consensus that intercalation increases the contour length of dsDNA, we find that increasing the dye:base pair ratio for YOYO-1 actually enhances the diffusion of dsDNA. This enhancement is more significant at lower ionic strengths, which implies that the increase in the diffusion coefficient by dye-DNA intercalation is mainly due to a reduction of excluded volume effect resulting from charge neutralization on the backbone.

  7. 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

    2004-01-01

    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).

  8. Rectangular Coordination Polymer Nanoplates: Large-Scale, Rapid Synthesis and Their Application as a Fluorescent Sensing Platform for DNA Detection

    OpenAIRE

    Yingwei Zhang; Yonglan Luo; Jingqi Tian; Asiri, Abdullah M.; Al-Youbi, Abdulrahman O.; Xuping Sun

    2012-01-01

    In this paper, we report on the large-scale, rapid synthesis of uniform rectangular coordination polymer nanoplates (RCPNs) assembled from Cu(II) and 4,4'-bipyridine for the first time. We further demonstrate that such RCPNs can be used as a very effective fluorescent sensing platform for multiple DNA detection with a detection limit as low as 30 pM and a high selectivity down to single-base mismatch. The DNA detection is accomplished by the following two steps: (1) RCPN binds dye-labeled sin...

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...

  10. Charge transport in poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

    OpenAIRE

    Hennig, Dirk; Starikov, Eugen B.; Archilla, Juan F. R.; Palmero Acebedo, Faustino

    2003-01-01

    We investigate the charge transport in synthetic DNA polymers built up from single types of base pairs. In the context of a polaron-like model, for which an electronic tight-binding system and bond vibrations of the double helix are coupled, we present estimates for the electron-vibration coupling strengths utilizing a quantum-chemical procedure. Subsequent studies concerning the mobility of polaron solutions, representing the state of a localized charge in unison with its a...

  11. 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

    2013-01-01

    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 ...... microanalytical systems, including polystyrene (PS), cyclic olefin copolymer (COC), liquid crystalline polymer (LCP), and polyimide (PI)....

  12. Rectangular coordination polymer nanoplates: large-scale, rapid synthesis and their application as a fluorescent sensing platform for DNA detection.

    Directory of Open Access Journals (Sweden)

    Yingwei Zhang

    Full Text Available In this paper, we report on the large-scale, rapid synthesis of uniform rectangular coordination polymer nanoplates (RCPNs assembled from Cu(II and 4,4'-bipyridine for the first time. We further demonstrate that such RCPNs can be used as a very effective fluorescent sensing platform for multiple DNA detection with a detection limit as low as 30 pM and a high selectivity down to single-base mismatch. The DNA detection is accomplished by the following two steps: (1 RCPN binds dye-labeled single-stranded DNA (ssDNA probe, which brings dye and RCPN into close proximity, leading to fluorescence quenching; (2 Specific hybridization of the probe with its target generates a double-stranded DNA (dsDNA which detaches from RCPN, leading to fluorescence recovery. It suggests that this sensing system can well discriminate complementary and mismatched DNA sequences. The exact mechanism of fluorescence quenching involved is elucidated experimentally and its use in a human blood serum system is also demonstrated successfully.

  13. A Soybean Oil-Based Liposome-Polymer Transfection Complex as a Co delivery System for DNA and Subunit Vaccines

    International Nuclear Information System (INIS)

    Inexpensive liposome-polymer transfection complexes (LPTCs) were developed and used as for DNA or protein delivery. The particle sizes of the LPTCs were in the range of 212.2 to 312.1 m, and the zeta potential was +38.7 mV. LPTCs condensed DNA and protected DNA from DNase I digestion and efficiently delivered LPTC/DNA complexes in Balb/3T3 cells. LPTCs also enhanced the cellular uptake of antigen in mouse macrophage cells and stimulated TNF-α release in naive mice splenocytes, both indicating the potential of LPTCs as adjuvants for vaccines. In vivo studies were performed using H. pylori relative heat shock protein 60 as an antigen model. The vaccination of BALB/c mice with LPTC-complexed DNA and protein enhanced the humoral immune response. Therefore, we developed a DNA and protein delivery system using LPTCs that is inexpensive, and we successfully applied it to the development of a DNA and subunit vaccine.

  14. Optical mapping of single-molecule human DNA in disposable, mass-produced all-polymer devices

    Science.gov (United States)

    Østergaard, Peter Friis; Lopacinska-Jørgensen, Joanna; Nyvold Pedersen, Jonas; Tommerup, Niels; Kristensen, Anders; Flyvbjerg, Henrik; Silahtaroglu, Asli; Marie, Rodolphe; Taboryski, Rafael

    2015-10-01

    We demonstrate all-polymer injection molded devices for optical mapping of denaturation-renaturation (DR) patterns on long, single DNA-molecules from the human genome. The devices have channels with ultra-low aspect ratio, only 110 nm deep while 20 μm wide, and are superior to the silica devices used previously in the field. With these polymer devices, we demonstrate on-chip recording of DR images of DNA-molecules stretched to more than 95% of their contour length. The stretching is done by opposing flows Marie et al (2013 Proc. Natl Acad. Sci. USA 110 4893-8). The performance is validated by mapping 20 out of 24 Mbp-long DNA fragments to the human reference genome. We optimized fabrication of the devices to a yield exceeding 95%. This permits a substantial economies-of-scale driven cost-reduction, leading to device costs as low as 3 USD per device, about a factor 70 lower than the cost of silica devices. This lowers the barrier to a wide use of DR mapping of native, megabase-size DNA molecules, which has a huge potential as a complementary method to next-generation sequencing.

  15. Optical mapping of single-molecule human DNA in disposable, mass-produced all-polymer devices

    International Nuclear Information System (INIS)

    We demonstrate all-polymer injection molded devices for optical mapping of denaturation–renaturation (DR) patterns on long, single DNA-molecules from the human genome. The devices have channels with ultra-low aspect ratio, only 110 nm deep while 20 μm wide, and are superior to the silica devices used previously in the field. With these polymer devices, we demonstrate on-chip recording of DR images of DNA-molecules stretched to more than 95% of their contour length. The stretching is done by opposing flows Marie et al (2013 Proc. Natl Acad. Sci. USA 110 4893–8). The performance is validated by mapping 20 out of 24 Mbp-long DNA fragments to the human reference genome. We optimized fabrication of the devices to a yield exceeding 95%. This permits a substantial economies-of-scale driven cost-reduction, leading to device costs as low as 3 USD per device, about a factor 70 lower than the cost of silica devices. This lowers the barrier to a wide use of DR mapping of native, megabase-size DNA molecules, which has a huge potential as a complementary method to next-generation sequencing. (paper)

  16. A mathematically defined motif for the radial distribution of charged residues on apolipoprotein amphipathic alpha helixes.

    OpenAIRE

    Hazelrig, J B; Jones, M. K.; Segrest, J P

    1993-01-01

    Multiple amphipathic alpha-helical candidate domains have been identified in exchangeable apolipoproteins by sequence analysis and indirect experimental evidence. The distribution of charged residues can differ within and between these apolipoproteins. Segrest et al. (Segrest, J. P., H. DeLoof, J. G. Dohlman, C. G. Brouillette, and G. M. Anantharamaiah. 1990. Proteins. 8:103-117.) argued that these differences are correlated with lipid affinity. A mathematically defined motif for the particul...

  17. An amphipathic motif at the transmembrane-cytoplasmic junction prevents autonomous activation of the thrombopoietin receptor.

    OpenAIRE

    Staerk, Judith; Lacout, Catherine; Sato, Takeshi; Smith, Steven O.; Vainchenker, William; Constantinescu, Stefan

    2006-01-01

    Ligand binding to the thrombopoietin receptor (TpoR) is thought to impose a dimeric receptor conformation(s) leading to hematopoietic stem cell renewal, megakaryocyte differentiation, and platelet formation. Unlike other cytokine receptors, such as the erythropoietin receptor, TpoR contains an amphipathic KWQFP motif at the junction between the transmembrane (TM) and cytoplasmic domains. We show here that a mutant TpoR (delta5TpoR), where this sequence was deleted, is constitutively active. I...

  18. Design and synthesis of basic peptides having amphipathic beta-structure and their interaction with phospholipid membranes.

    Science.gov (United States)

    Ono, S; Lee, S; Mihara, H; Aoyagi, H; Kato, T; Yamasaki, N

    1990-02-28

    Basic amphipathic beta-structural peptides, Ac-(Ser-Val-Lys-Val)n-NHCH3 (1n, n = 1-3) and Ac-(Lys-Val)n-NHCH3 (2n, n = 2-4), were synthesized and their interaction with DPPC and DPPC-DPPG (3:1) bilayers was studied by CD, dye-leakage and fluorescence experiments. The CD data indicated that oligopeptides consisting of more than eight residues with alternating hydrophobic (Val) and hydrophilic amino acids (Ser and Lys) were able to form an amphipathic beta-structure in acidic phospholipid bilayers, but not or weakly in aqueous solution and in neutral phospholipid bilayers. The dye-leakage experiment showed that the basic amphipathic beta-structural peptides interact with acidic phospholipid bilayers to perturb them, but less effectively compared with basic amphipathic alpha-helical peptides. Fluorescent spectroscopic data suggest that hydrophobic side of the amphipathic peptides may immerse into membrane without deep penetration. Based on these results, we postulate that the formation of the basic amphipathic beta-structure on acidic lipid bilayers may be due to the combined effect of electrostatic and hydrophobic interactions between basic peptides and acidic lipid bilayers. PMID:2306456

  19. A study on the plasma polymer thin film surface modification for DNA alignment by using high energy electron beam irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Sang-Jin, E-mail: bluescreen@skku.edu [Department of Chemistry and Institute of Basic Science, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Kim, Hyung Jin; Hong, Byungyou [School of Information and Communication Engineering, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Boo, Jin-Hyo, E-mail: jhboo@skku.edu [Department of Chemistry and Institute of Basic Science, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2011-08-01

    The plasma polymer thin films were deposited on Si(100) substrate by PECVD (plasma enhanced chemical vapor deposition) method. Liquid cyclohexene was used as single organic precursor. It was heated up to 60 deg. C and bubbled up by hydrogen gas, which flow rate was 50 sccm (standard cubic centimeters per min). Deposition temperature was room temperature. Plasma was ignited by a radio frequency (RF; 13.56 MHz) of 10 W. As-deposited plasma polymer thin films were treated by e-beam of 300 keV with various adsorption radiation doses. The plasma polymer films, which were treated by high energy e-beam (HEEB), were investigated by FT-IR (Fourier Transform Infrared), XPS (X-ray Photoelectron Spectroscopy), AFM (Atomic Force Microscopy), and the water contact angles. From IR spectra, the intensity of -OH functional group is increased by increasing electron dose rate. XPS results also show that the intensity of O{sub 1s} peak is increased by increasing electron dose rate. C{sub 1s} peak shows that oxygen bonded at carbon site. The water contact angles are decreased by increasing electron dose rate. From the AFM analysis, we observed the formation of {lambda}-DNA (deoxyribonucleic acid) array on plasma polymer film, which was treated by HEEB with 14 kGy of adsorption radiation dose.

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

    Science.gov (United States)

    Larsen, Esben Kjær Unmack; Larsen, Niels B

    2013-02-21

    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 including hydrophobic and hydrophilic drugs (0.23 8) in their pharmaceutically relevant concentration range ≤100 nM. The low adsorption is mediated by photochemical conjugation, where polyethylene glycol (PEG) polymers in aqueous solution are covalently bound to the surface by UV illumination of dissolved benzophenone and a functionalized PEG. The method can coat the interior of polymer systems made from a range of materials commonly used in microanalytical systems, including polystyrene (PS), cyclic olefin copolymer (COC), liquid crystalline polymer (LCP), and polyimide (PI). PMID:23254780

  1. Filling the void in confined polymer nematics: phase transitions in a minimal model of dsDNA packing

    OpenAIRE

    Shin, Homin; Grason, Gregory M.

    2011-01-01

    Inspired to understand the complex spectrum of space-filling organizations the dsDNA genome within the capsid of bacterial viruses, we study a minimal, coarse-grained model of single chains densely-packed into a finite spherical volume. We build the three basic elements of the model--i) the absence of chain ends ii) the tendency of parallel-strand alignment and iii) a preference of uniform areal density of chain segments--into a polymer nematic theory for confined chains. Given the geometric ...

  2. 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

    2016-01-01

    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...

  3. Cationic Polymer Intercalation into the Lipid Membrane Enables Intact Polyplex DNA Escape from Endosomes for Gene Delivery.

    Science.gov (United States)

    Vaidyanathan, Sriram; Chen, Junjie; Orr, Bradford G; Banaszak Holl, Mark M

    2016-06-01

    Developing improved cationic polymer-DNA polyplexes for gene delivery requires improved understanding of DNA transport from endosomes into the nucleus. Using a FRET-capable oligonucleotide molecular beacon (OMB), we monitored the transport of intact DNA to cell organelles. We observed that for effective (jetPEI) and ineffective (G5 PAMAM) vectors, the fraction of cells displaying intact OMB in the cytosol (jetPEI ≫ G5 PAMAM) quantitatively predicted the fraction expressing transgene (jetPEI ≫ G5 PAMAM). Intact OMB delivered with PAMAM and confined to endosomes could be released to the cytosol by the subsequent addition of L-PEI, with a corresponding 10-fold increase in transgene expression. These results suggest that future vector development should optimize vectors for intercalation into, and destabilization of, the endosomal membrane. Finally, the study highlights a two-step strategy in which the pDNA is loaded in cells using one vector and endosomal release is mediated by a second agent. PMID:27111496

  4. Efficient Capture and Isolation of Tumor-Related Circulating Cell-Free DNA from Cancer Patients Using Electroactive Conducting Polymer Nanowire Platforms

    Science.gov (United States)

    Jeon, SeungHyun; Lee, HyungJae; Bae, Kieun; Yoon, Kyong-Ah; Lee, Eun Sook; Cho, Youngnam

    2016-01-01

    Circulating cell-free DNA (cfDNA) is currently recognized as a key non-invasive biomarker for cancer diagnosis and progression and therapeutic efficacy monitoring. Because cfDNA has been detected in patients with diverse types of cancers, the use of efficient strategies to isolate cfDNA not only provides valuable insights into tumour biology, but also offers the potential for developing new cancer-specific targets. However, the challenges associated with conventional cfDNA extraction methods prevent their further clinical applications. Here, we developed a nanostructured conductive polymer platform for the efficient capture and release of circulating cfDNA and demonstrated its potential clinical utility using unprocessed plasma samples from patients with breast and lung cancers. Our results confirmed that the platform's enhanced efficiency allows tumor-specific circulating cfDNA to be recovered at high yield and purity. PMID:27162553

  5. 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

    2007-05-01

    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.

  6. Carbon nanotube/polymer composite electrodes for flexible, attachable electrochemical DNA sensors.

    Science.gov (United States)

    Li, Jianfeng; Lee, Eun-Cheol

    2015-09-15

    All-solution-processed, easily-made, flexible multi-walled carbon nanotube (MWCNT)/polydimethylsiloxane (PDMS)-based electrodes were fabricated and used for electrochemical DNA sensors. These electrodes could serve as a recognition layer for DNA, without any surface modification, through π-π interactions between the MWCNTs and DNA, greatly simplifying the fabrication process for DNA sensors. The electrodes were directly connected to an electrochemical analyzer in the differential pulse voltammetry (DPV) and cyclic voltammetry (CV) measurements, where methylene blue was used as a redox indicator. Since neither functional groups nor probe DNA were immobilized on the surfaces of the electrodes, the sensor can be easily regenerated by washing these electrodes with water. The limit of detection was found to be 1.3 × 10(2)pM (S/N=3), with good DNA sequence differentiation ability. Fast fabrication of a DNA sensor was also achieved by cutting and attaching the MWCNT-PDMS composite electrodes at an analyte solution-containable region. Our results pave the way for developing user-fabricated easily attached DNA sensors at low costs. PMID:25950937

  7. 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

    2009-01-01

    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.

  8. 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

    2010-01-01

    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...

  9. 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

    2009-06-01

    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.

  10. Polymers & People

    Science.gov (United States)

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

    2004-01-01

    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…

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

    DEFF Research Database (Denmark)

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

    2005-01-01

    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...

  12. Optical mapping of single-molecule human DNA in disposable, mass-produced all-polymer

    DEFF Research Database (Denmark)

    Østergaard, Peter Friis; Lopacinska-Jørgensen, Joanna; Pedersen, Jonas Nyvold;

    2015-01-01

    mapping 20 out of 24 Mbp-long DNA fragments to the human reference genome. We optimized fabrication of the devices to a yield exceeding 95%. This permits a substantial economies-of-scale driven cost-reduction, leading to device costs as low as 3 USD per device, about a factor 70 lower than the cost of...

  13. 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

    2013-01-01

    including hydrophobic and hydrophilic drugs (0.23 DNA. The coating is shown to limit the adsorption of even highly hydrophobic drugs (ClogP > 8) in their pharmaceutically relevant concentration range ≤100 nM. The low adsorption is mediated...

  14. N,N,N-trimethylchitosan modified with well defined multifunctional polymer modules used as pDNA delivery vector.

    Science.gov (United States)

    Ren, Hongqi; Liu, Shuai; Yang, Jixiang; Zhang, Xian; Zhou, Hao; Chen, Jiatong; Guo, Tianying

    2016-02-10

    A novel non-viral gene carrier based on N,N,N-trimethylchitosan (TMC) has been fabricated. First, well-defined copolymer P(PEGMA-co-DMAEMA) was synthesized through reversible addition fragmentation chain transfer (RAFT) polymerization of poly(ethylene glycol) methyl ether methacrylate (PEGMA) and N,N-(2-dimethylamino)ethyl methacrylamide (DMAEMA). Then allyl group grafting N,N,N-trimethylchitosan (Allyl-TMC) was synthesized via the reaction between allyl bromide and hydroxyl of TMC. Finally, P(PEGMA-co-DMAEMA) and folate were ordinally grafted onto Allyl-TMC to obtain TMC-g-P(PEGMA-co-DMAEMA)-FA. In comparison with pristine chitosan, TMC-g-P(PEGMA-co-DMAEMA)-FA has achieved both better water solubility and stronger pDNA packaging ability, which can contribute to improving gene transfection. Gene delivery efficiency of a series of TMC based functional polymers with different chitosan molecular weights has been tested. The results show that 20k-TMC-g-P(PEGMA-co-DMAEMA)-FA/pDNA complex at the weight ratio of 20 achieve the highest transfection efficiency in 293 T cells. This work presents a new strategy to modify chitosan efficiently as gene carrier material. PMID:26686124

  15. Using Temperature-Sensitive Smart Polymers to Regulate DNA-mediated Nanoassembly

    Science.gov (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 chains extended beyond the hydrodynamic reach of the single stranded DNA and prohibited recognition, while 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.

  16. 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

    2008-01-01

    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.

  17. Improving membrane binding as a design strategy for amphipathic peptide hormones

    DEFF Research Database (Denmark)

    Pedersen, Søren Ljungberg; Bhatia, Vikram Kjøller; Jurt, Simon;

    2012-01-01

    It has been hypothesized that amphipathic peptides might bind to membranes prior to activating their cognate receptors, but this has proven difficult to test. The peptide hormone PYY3-36 is believed to perform its appetite-suppressing actions through binding to hypothalamic Y2 receptors. It has...... by paramagnetic relaxation enhancement using a spin label, which confirmed that the hydrophobic residues bound to the membrane. Our studies further support the hypothesis that PYY3-36 associates with the membrane and indicate that this can be used in the design of novel molecules with high receptor binding...... potency. These observations are likely to be generally important for peptide hormones and biopharmaceutical drugs derived from them. This new 2-helix variant of PYY3-36 will be useful as a tool compound for studying peptide-membrane interactions....

  18. Membrane topology of a 14-mer model amphipathic peptide: a solid-state NMR spectroscopy study.

    Science.gov (United States)

    Ouellet, Marise; Doucet, Jean-Daniel; Voyer, Normand; Auger, Michèle

    2007-06-01

    We have investigated the interaction between a synthetic amphipathic 14-mer peptide and model membranes by solid-state NMR. The 14-mer peptide is composed of leucines and phenylalanines modified by the addition of crown ethers and forms a helical amphipathic structure in solution and bound to lipid membranes. To shed light on its membrane topology, 31P, 2H, 15N solid-state NMR experiments have been performed on the 14-mer peptide in interaction with mechanically oriented bilayers of dilauroylphosphatidylcholine (DLPC), dimyristoylphosphatidylcholine (DMPC), and dipalmitoylphosphatidylcholine (DPPC). The 31P, 2H, and 15N NMR results indicate that the 14-mer peptide remains at the surface of the DLPC, DMPC, and DPPC bilayers stacked between glass plates and perturbs the lipid orientation relative to the magnetic field direction. Its membrane topology is similar in DLPC and DMPC bilayers, whereas the peptide seems to be more deeply inserted in DPPC bilayers, as revealed by the greater orientational and motional disorder of the DPPC lipid headgroup and acyl chains. 15N{31P} rotational echo double resonance experiments have also been used to measure the intermolecular dipole-dipole interaction between the 14-mer peptide and the phospholipid headgroup of DMPC multilamellar vesicles, and the results indicate that the 14-mer peptide is in contact with the polar region of the DMPC lipids. On the basis of these studies, the mechanism of membrane perturbation of the 14-mer peptide is associated to the induction of a positive curvature strain induced by the peptide lying on the bilayer surface and seems to be independent of the bilayer hydrophobic thickness. PMID:17487978

  19. Bacterial DNA isolation using new magnetic polymer microspheres containing carboxyl groups

    Czech Academy of Sciences Publication Activity Database

    Rittich, B.; Španová, A.; Horák, Daniel

    Egmond aan Zee : Netherlands Society for Microbiology and Federation of European Microbiological Societies, 2005. B049. [Symposium on Lactic Acid Bacteria /8./. 28.8.2005-1.9.2005, Egmond aan Zee] R&D Projects: GA ČR GA203/05/2256; GA MZe 1G46045; GA MZe 1G57037 Keywords : polymerase chain reaction * magnetic * DNA Subject RIV: EE - Microbiology, Virology

  20. A zwitterionic 1D/2D polymer co-crystal and its polymorphic sub-components: a highly selective sensing platform for HIV ds-DNA sequences.

    Science.gov (United States)

    Zhao, Hai-Qing; Yang, Shui-Ping; Ding, Ni-Ni; Qin, Liang; Qiu, Gui-Hua; Chen, Jin-Xiang; Zhang, Wen-Hua; Chen, Wen-Hua; Hor, T S Andy

    2016-03-15

    Polymorphic compounds {[Cu(dcbb)2(H2O)2]·10H2O}n (, 1D chain), [Cu(dcbb)2]n (, 2D layer) and their co-crystal {[Cu(dcbb)2(H2O)][Cu(dcbb)2]2}n () have been prepared from the coordination reaction of a 2D polymer [Na(dcbb)(H2O)]n (, H2dcbbBr = 1-(3,5-dicarboxybenzyl)-4,4'-bipyridinium bromide) with Cu(NO3)2·3H2O at different temperatures in water. Compounds have an identical metal-to-ligand stoichiometric ratio of 1 : 2, but absolutely differ in structure. Compound features a 2D layer structure with aromatic rings, positively charged pyridinium and free carboxylates on its surface, promoting electrostatic, π-stacking and/or hydrogen-bonding interactions with the carboxyfluorescein (FAM) labeled probe single-stranded DNA (probe ss-DNA, delineates as P-DNA). The resultant P-DNA@ system facilitated fluorescence quenching of FAM via a photoinduced electron transfer process. The P-DNA@ system functions as an efficient fluorescent sensor selective for HIV double-stranded DNA (HIV ds-DNA) due to the formation of a rigid triplex structure with the recovery of FAM fluorescence. The system reported herein also distinguishes complementary HIV ds-DNA from mismatched target DNA sequences with the detection limit of 1.42 nM. PMID:26883749

  1. Time-resolved FRET and PCT in cationic conjugated polymer/dye-labeled DNA complex

    Science.gov (United States)

    Kim, Inhong; Kim, Jihoon; Kim, Bumjin; Kang, Mijeong; Woo, Han Young; Kyhm, Kwangseuk

    2011-12-01

    The energy transfer mechanism between cationic conjugated polyelectrolytes and a single stranded DNA labeled with fluorescein was investigated in terms of Förster resonance energy transfer (FRET) and photo-induced charge transfer (PCT) by time-resolved fluorescence. Both FRET and PCT rate efficiencies were obtained by phenomenological coupled rate equations, which are in excellent agreement with experiments. We found the total energy transfer in the complex is maximized as a consequence of FRET and PCT at an optimum distance 32.7Å.

  2. A novel strategy for highly efficient isolation and analysis of circulating tumor-specific cell-free DNA from lung cancer patients using a reusable conducting polymer nanostructure.

    Science.gov (United States)

    Lee, HyungJae; Jeon, SeungHyun; Seo, Jin-Suck; Goh, Sung-Ho; Han, Ji-Youn; Cho, Youngnam

    2016-09-01

    We have developed a reusable nanostructured polypyrrole nanochip and demonstrated its use in the electric field-mediated recovery of circulating cell-free DNA (cfDNA) from the plasma of lung cancer patients. Although cfDNA has been recognized and widely studied as a versatile and promising biomarker for the diagnosis and prognosis of cancers, the lack of efficient strategies to directly isolate cfDNA from the plasma has become a great hindrance to its potential clinical use. As a proof-of-concept study, we demonstrated a technique for the rapid and efficient isolation of cfDNA with high yield and purity. In particular, the synergistic effects of the electro-activity and the nanostructured features of the polypyrrole polymer enabled repeated retrieval of cfDNA using a single platform. Moreover, polypyrrole nanochip facilitated the amplification of tumor-specific DNA fragments from the plasma samples of patients with lung cancer characterized by mutations in exons 21 of the epidermal growth factor receptor gene (EGFR). Overall, the proposed polypyrrole nanochip has enormous potential for industrial and clinical applications with significantly enhanced efficiency in the recovery of tumor-associated circulating cfDNA. This may ultimately contribute to more robust and reliable evaluation of gene mutations in peripheral blood. PMID:27294542

  3. Recyclable magnetite nanoparticle coated with cationic polymers for adsorption of DNA.

    Science.gov (United States)

    Rutnakornpituk, B; Theppaleak, T; Rutnakornpituk, M; Vilaivan, T

    2016-08-01

    Magnetite nanoparticle (MNP) grafted with a cationic copolymer between poly(2-(N,N-diethylamino) ethyl methacrylate) and poly(poly(ethylene glycol) methyl ether methacrylate)) for efficient and recyclable adsorption of 5'-fluorescein-tagged DNA (FAM-dT9) was prepared. MNP having highest degree of positive charge (+32.1 ± 1.9 mV) retained 100% adsorption of FAM-dT9 during eight adsorption-separation-desorption cycles. The MNP having lower degree of positive charge showed a slight decrease in adsorption percentages (94-98% adsorption) after multiple recycling processes. This biocompatible hybrid material with charged surface and magnetic-responsive properties might be applicable for use as a nanosolid support for efficient and facile separation of various bioentities. PMID:27206488

  4. Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds.

    Science.gov (United States)

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

    2016-03-01

    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. PMID:26978374

  5. Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds

    Directory of Open Access Journals (Sweden)

    Marion Navarri

    2016-03-01

    Full Text Available 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.

  6. Evidence for the extramembranous location of the putative amphipathic helix of acetylcholine receptor

    International Nuclear Information System (INIS)

    Evidence has been obtained demonstrating that the peptides GVKYIAE and AIKYIAE found in the potential amphipathic helices of the α and β subunits, respectively, of acetylcholine receptor are not buried in the membrane. The peptide KYIAE was synthesized, and polyclonal antibodies were prepared against a conjugate of bovine serum albumin and synthetic peptide. An immunoadsorbent capable of binding and subsequently releasing peptides ending with the sequence-YIAE was produced by attaching these specific antibodies to agarose. Native acetylcholine receptor was labeled with pyridoxal phosphate and Na[3H]BH4. The labeled protein was stripped of phospholipid and digested with the protease from Staphylococcus aureus strain V8. The digest was submitted to immunoadsorption to isolate the labeled indigenous peptides. As a control, α and β polypeptides prepared by gel filtration of a solution of acetylcholine receptor in detergent were stripped of detergent and labeled with pyridoxal phosphate and Na[3H]BH4 in the presence of 8 M urea. The labeled α and β polypeptides were digested and submitted to immunoadsorption. The specific radioactivities of the indigenous peptides from the α and β subunits labeled under native and denaturing conditions were nearly equal. In similar experiments using isethionyl (2',4'-dinitrophenyl)-3-aminopropionimidate as the labeling agent, the indigenous peptides from native and denatured receptor were also labeled to the same extent. Since these peptides are labeled to the same extent whether or not the protein is denatured, they cannot be buried in the membrane

  7. Conserved Amphipathic Helices Mediate Lipid Droplet Targeting of Perilipins 1-3.

    Science.gov (United States)

    Rowe, Emily R; Mimmack, Michael L; Barbosa, Antonio D; Haider, Afreen; Isaac, Iona; Ouberai, Myriam M; Thiam, Abdou Rachid; Patel, Satish; Saudek, Vladimir; Siniossoglou, Symeon; Savage, David B

    2016-03-25

    Perilipins (PLINs) play a key role in energy storage by orchestrating the activity of lipases on the surface of lipid droplets. Failure of this activity results in severe metabolic disease in humans. Unlike all other lipid droplet-associated proteins, PLINs localize almost exclusively to the phospholipid monolayer surrounding the droplet. To understand how they sense and associate with the unique topology of the droplet surface, we studied the localization of human PLINs inSaccharomyces cerevisiae,demonstrating that the targeting mechanism is highly conserved and that 11-mer repeat regions are sufficient for droplet targeting. Mutations designed to disrupt folding of this region into amphipathic helices (AHs) significantly decreased lipid droplet targetingin vivoandin vitro Finally, we demonstrated a substantial increase in the helicity of this region in the presence of detergent micelles, which was prevented by an AH-disrupting missense mutation. We conclude that highly conserved 11-mer repeat regions of PLINs target lipid droplets by folding into AHs on the droplet surface, thus enabling PLINs to regulate the interface between the hydrophobic lipid core and its surrounding hydrophilic environment. PMID:26742848

  8. DNA structure

    OpenAIRE

    Bowater, R

    2003-01-01

    Deoxyribonucleic acid (DNA) is a polymer of nucleotides. In the cell, DNA usually adopts a double-stranded helical form, with complementary base-pairing holding the two strands together. The most stable conformation is called B-form DNA, although other structures can occur under specific conditions.

  9. Mitochondria-dependent apoptosis induced by a novel amphipathic photochemotherapeutic agent ZnPcS2P2 in HL60 cells

    Institute of Scientific and Technical Information of China (English)

    Hui-fang HUANG; Yuan-zhong CHEN; Yong WU

    2005-01-01

    Aim: To investigate the mechanism underlying the killing effects of a novel amphipathic photosensitizer, disulfonated diphthalimidomethyl phthalocyanine zinc (ZnPcS2P2), mediated photodynamic therapy (ZnPc-PDT) in human myelogenous leukemia HL60 cells. Methods: After incubation for 5 h with 0.5 μmol/L ZnPcS2P2, the HL60 cells were exposed to a light source of 670 nm wavelength.Thereafter, the cells were detected at different time intervals after PDT. The characteristics of apoptosis were detected by observation of ultrastructure assay,DNA fragmentation assay and terminal deoxynucleotidyl transferase deoxyuridine nick-end labeling method (TUNEL). Mitochondria-dependent apoptosis was determined by the detection of mitochondrial membrane potential (Δψm), activities of caspase family protease and of caspase-3, cytosol cytochrome c. Proteins Bcl-2and Bax were detected by immunoblot analysis. Results: Evident characteristics of apoptosis were observed post-ZnPc-PDT with ultrastructure assay, DNA fragmentation assay and TUNEL staining. TUNEL assay showed that apoptotic rates in the cells collected from 6 h, 12 h and 24 h after PDT were 9.6%, 24.4%, and 33.0%,respectively. HL60 cells underwent mitochondria-dependent apoptosis as a result of cytochrome c release from mitochondria into cytosol accompanied by a reduction of Δψm. The activities of caspase family protease and of caspase-3were elevated. Furthermore, ZnPc-PDT could remarkably down-regulate the Bcl-2pro-apoptotic protein and up-regulate the anti-apoptotic Bax protein. Conclusion:ZnPc-PDT could induce mitochondria-dependent apoptosis in HL60 cells.

  10. Effects of increasing hydrophobicity on the physical-chemical and biological properties of a class A amphipathic helical peptide.

    Science.gov (United States)

    Datta, G; Chaddha, M; Hama, S; Navab, M; Fogelman, A M; Garber, D W; Mishra, V K; Epand, R M; Epand, R F; Lund-Katz, S; Phillips, M C; Segrest, J P; Anantharamaiah, G M

    2001-07-01

    We have recently shown that a class A amphipathic peptide 5F with increased amphipathicity protected mice from diet-induced atherosclerosis (Garber et al. J. Lipid Res. 2001. 42: 545-552). We have now examined the effects of increasing the hydrophobicity of a series of homologous class A amphipathic peptides, including 5F, on physical and functional properties related to atherosclerosis inhibition by systematically replacing existing nonpolar amino acids with phenylalanine. The peptides, based on the sequence Ac-D-W-L-K-A-F-Y-D-K-V-A-E-K-L-K-E-A-F-NH(2) (Ac-18A-NH(2) or 2F) were: 3F(3)(Ac-F(3)18A-NH(2)), 3F(14)(Ac-F(14)18A-NH(2)), 4F(Ac-F(3,14)18A-NH(2)), 5F(Ac-F(11,14,17) 18A-NH(2)), 6F(Ac-F(10,11,14,17)18A-NH(2)), and 7F(Ac-F(3,10,11,14,17) 18A-NH(2)). Measurements of aqueous solubility, HPLC retention time, exclusion pressure for penetration into an egg phosphatidylcholine (EPC) monolayer, and rates of EPC solubilization revealed an abrupt increase in the hydrophobicity between peptides 4F and 5F; this was accompanied by increased ability to associate with phospholipids. The peptides 6F and 7F were less effective, indicating a limit to increased hydrophobicity for promoting lipid interaction in these peptides. Despite this marked increase in lipid affinity, these peptides were less effective than apoA-I in activating the plasma enzyme, lecithin:cholesterol acyltransferase, with 5F activating LCAT the best (80% of apoA-I). Peptides 4F, 5F, and 6F were equally potent in inhibiting LDL-induced monocyte chemotactic activity. These studies suggest that an appropriate balance between peptide-peptide and peptide-lipid interactions is required for optimal biological activity of amphipathic peptides. These studies provide a rationale for the design of small apoA-I-mimetics with increased potency for atherosclerosis inhibition. PMID:11441137

  11. Osmotically induced membrane tension modulates membrane permeabilization by class L amphipathic helical peptides: nucleation model of defect formation.

    OpenAIRE

    Polozov, I V; Anantharamaiah, G.M.; Segrest, J P; Epand, R M

    2001-01-01

    The mechanism of action of lytic peptides on membranes is widely studied and is important in view of potential medical applications. Previously (I. V. Polozov, A. I. Polozova, E. M. Tytler, G. M. Anantharamaiah, J. P. Segrest, G. A. Woolley, and R. M., Biochemistry, 36:9237--9245) we analyzed the mechanism of membrane permeabilization by 18L, the archetype lytic peptide featuring the class L amphipathic alpha-helix, according to the classification of Segrest et al. (J. P. Segrest, G. de Loof,...

  12. Effect of Pendant Group on pDNA Delivery by Cationic-β-Cyclodextrin:Alkyl-PVA-PEG Pendant Polymer Complexes

    OpenAIRE

    Kulkarni, Aditya; Badwaik, Vivek; DeFrees, Kyle; Schuldt, Ryan A.; Gunasekera, Dinara S.; Powers, Cory; Vlahu, Alexander; VerHeul, Ross; Thompson, David H.

    2013-01-01

    We have previously shown that cationic-β-CD:R-poly(vinyl alcohol)-poly(ethylene glycol) pendant polymer host:guest complexes are safe and efficient vehicles for nucleic acid delivery, where R = benzylidene-linked adamantyl or cholesteryl esters. Herein, we report the synthesis and biological performance of a family of PVA-PEG pendant polymers whose pendant groups have a wide range of different affinities for the β-CD cavity. Cytotoxicity studies revealed that all of the cationic-β-CD:pendant ...

  13. DNA barcoding via counterstaining with AT/GC sensitive ligands in injection-molded all-polymer nanochannel devices

    DEFF Research Database (Denmark)

    Østergaard, Peter Friis; Matteucci, Marco; Reisner, Walter;

    2013-01-01

    /or requirement of specialized facilities/skill-sets. In this article we show that nanochannel-based mapping can be performed in all polymer chips fabricated via injection molding: a fabrication process so inexpensive that the devices can be considered disposable. Fluorescent intensity variations can be obtained...

  14. The role of MscL amphipathic N terminus indicates a blueprint for bilayer-mediated gating of mechanosensitive channels.

    Science.gov (United States)

    Bavi, Navid; Cortes, D Marien; Cox, Charles D; Rohde, Paul R; Liu, Weihong; Deitmer, Joachim W; Bavi, Omid; Strop, Pavel; Hill, Adam P; Rees, Douglas; Corry, Ben; Perozo, Eduardo; Martinac, Boris

    2016-01-01

    The bacterial mechanosensitive channel MscL gates in response to membrane tension as a result of mechanical force transmitted directly to the channel from the lipid bilayer. MscL represents an excellent model system to study the basic biophysical principles of mechanosensory transduction. However, understanding of the essential structural components that transduce bilayer tension into channel gating remains incomplete. Here using multiple experimental and computational approaches, we demonstrate that the amphipathic N-terminal helix of MscL acts as a crucial structural element during tension-induced gating, both stabilizing the closed state and coupling the channel to the membrane. We propose that this may also represent a common principle in the gating cycle of unrelated mechanosensitive ion channels, allowing the coupling of channel conformation to membrane dynamics. PMID:27329693

  15. 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

    2010-01-01

    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.......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...... 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...

  16. Structural and dynamic evolution of the amphipathic N-terminus diversifies enzyme thermostability in the glycoside hydrolase family 12.

    Science.gov (United States)

    Jiang, Xukai; Chen, Guanjun; Wang, Lushan

    2016-08-21

    Understanding the molecular mechanism underlying protein thermostability is central to the process of efficiently engineering thermostable cellulases, which can provide potential advantages in accelerating the conversion of biomass into clean biofuels. Here, we explored the general factors that diversify enzyme thermostability in the glycoside hydrolase family 12 (GH12) using comparative molecular dynamics (MD) simulations coupled to a bioinformatics approach. The results indicated that protein stability is not equally distributed over the whole structure: the N-terminus is the most thermal-sensitive region of the enzymes with a β-sandwich architecture and it tends to lose its secondary structure during the course of protein unfolding. Furthermore, we found that the total interaction energy within the N-terminus is appreciably correlated with enzyme thermostability. Interestingly, the internal interactions within the N-terminus are organized in a special amphipathic pattern in which a hydrophobic packing cluster and a hydrogen bonding cluster lie at the two ends of the N-terminus. Finally, bioinformatics analysis demonstrated that the amphipathic pattern is highly conserved in GH12 and besides that, the evolution of the amino acids in the N-terminal region is an inherent mechanism underlying the diversity of enzyme thermostability. Taken together, our results demonstrate that the N-terminus is generally the structure that determines enzyme thermostability in GH12, and thereby it is also an ideal engineering target. The dynameomics study of a protein family can give a general view of protein functions, which will offer a wide range of applications in future protein engineering. PMID:27425569

  17. Direct-write femtosecond laser ablation and DNA combing and imprinting for fabrication of a micro/nanofluidic device on an ethylene glycol dimethacrylate polymer

    International Nuclear Information System (INIS)

    Arrays of microwells connected by nanoscale channels with sizes on the order of 10 nm can be created in an ethylene glycol dimethacrylate (EGMDA) polymer using the DNA combing and imprinting technique. Larger micro-scale channels which lead into the microwell/nanochannel arrays are needed to allow the arrays to be externally filled with desired reagents, molecules and cells. In this work, direct-write femtosecond laser ablation was employed as a post process to fabricate these microscale filling channels. Single pulse and multiple pulses overlap ablation was first conducted on an EGMDA polymer using a focused femtosecond laser beam. Scanning electron microscopy was employed to measure the ablated channel width. Single pulse ablation threshold fluence and incubation coefficient were found and were used to predict microchannel width. Finally, femtosecond laser ablation was used to fabricate filling channels on microwell/nanochannel arrays. Fluorescent flow testing was performed to verify fluid connectivity between the laser-ablated filling channels and the microwell/nanochannel array.

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

    Directory of Open Access Journals (Sweden)

    Aubin eMoutal

    2015-01-01

    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.

  19. The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix

    Science.gov (United States)

    Barneda, David; Planas-Iglesias, Joan; Gaspar, Maria L; Mohammadyani, Dariush; Prasannan, Sunil; Dormann, Dirk; Han, Gil-Soo; Jesch, Stephen A; Carman, George M; Kagan, Valerian; Parker, Malcolm G; Ktistakis, Nicholas T; Klein-Seetharaman, Judith; Dixon, Ann M; Henry, Susan A; Christian, Mark

    2015-01-01

    Maintenance of energy homeostasis depends on the highly regulated storage and release of triacylglycerol primarily in adipose tissue, and excessive storage is a feature of common metabolic disorders. CIDEA is a lipid droplet (LD)-protein enriched in brown adipocytes promoting the enlargement of LDs, which are dynamic, ubiquitous organelles specialized for storing neutral lipids. We demonstrate an essential role in this process for an amphipathic helix in CIDEA, which facilitates embedding in the LD phospholipid monolayer and binds phosphatidic acid (PA). LD pairs are docked by CIDEA trans-complexes through contributions of the N-terminal domain and a C-terminal dimerization region. These complexes, enriched at the LD–LD contact site, interact with the cone-shaped phospholipid PA and likely increase phospholipid barrier permeability, promoting LD fusion by transference of lipids. This physiological process is essential in adipocyte differentiation as well as serving to facilitate the tight coupling of lipolysis and lipogenesis in activated brown fat. DOI: http://dx.doi.org/10.7554/eLife.07485.001 PMID:26609809

  20. Polymer films

    Science.gov (United States)

    Granick, Steve; Sukhishvili, Svetlana A.

    2008-12-30

    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.

  1. Mixed α/β-Peptides as a Class of Short Amphipathic Peptide Hydrogelators with Enhanced Proteolytic Stability.

    Science.gov (United States)

    Mangelschots, Jeroen; Bibian, Mathieu; Gardiner, James; Waddington, Lynne; Van Wanseele, Yannick; Van Eeckhaut, Ann; Acevedo, Maria M Diaz; Van Mele, Bruno; Madder, Annemieke; Hoogenboom, Richard; Ballet, Steven

    2016-02-01

    Peptide hydrogels are a highly promising class of materials for biomedical application, albeit facing many challenges with regard to stability and tunability. Here, we report a new class of amphipathic peptide hydrogelators, namely mixed α/β-peptide hydrogelators. These mixed α/β-gelators possess good rheological properties (high storage moduli) and form transparent self-supporting gels with shear-thinning behavior. Infrared spectroscopy indicates the presence of β-sheets as the underlying secondary structure. Interestingly, self-assembled nanofibers of the mixed α/β-peptides display unique structural morphologies with alteration of the C-terminus (acid vs amide) playing a key role in the fiber formation and gelation properties of the resulting hydrogels. The incorporation of β3-homoamino acid residues within the mixed α/β-peptide gelators led to an increase in proteolytic stability of the peptides under nongelating conditions (in solution) as well as gelating conditions (as hydrogel). Under diluted conditions, degradation of mixed α/β-peptides in the presence of elastase was slowed down 120-fold compared to that of an α-peptide, thereby demonstrating beneficial enzymatic resistance for hydrogel applications in vivo. In addition, increased half-life values were obtained for the mixed α/β-peptides in human blood plasma, as compared to corresponding α-peptides. It was also found that the mixed α/β-peptides were amenable to injection via needles used for subcutaneous administrations. The preformed peptide gels could be sheared upon injection and were found to quickly reform to a state close to that of the original hydrogel. The shown properties of enhanced proteolytic stability and injectability hold great promise for the use of these novel mixed α/β-peptide hydrogels for applications in the areas of tissue engineering and drug delivery. PMID:26741458

  2. Efficient Capture and Isolation of Tumor-Related Circulating Cell-Free DNA from Cancer Patients Using Electroactive Conducting Polymer Nanowire Platforms

    OpenAIRE

    Jeon, SeungHyun; Lee, HyungJae; Bae, Kieun; Yoon, Kyong-Ah; Lee, Eun Sook; Cho, Youngnam

    2016-01-01

    Circulating cell-free DNA (cfDNA) is currently recognized as a key non-invasive biomarker for cancer diagnosis and progression and therapeutic efficacy monitoring. Because cfDNA has been detected in patients with diverse types of cancers, the use of efficient strategies to isolate cfDNA not only provides valuable insights into tumour biology, but also offers the potential for developing new cancer-specific targets. However, the challenges associated with conventional cfDNA extraction methods ...

  3. Towards understanding the Tat translocation mechanism through structural and biophysical studies of the amphipathic region of TatA from Escherichia coli

    OpenAIRE

    Chan, Catherine S.; Evan F. Haney; Hans J Vogel; Turner, Raymond J.

    2011-01-01

    The twin-arginine translocase (Tat) system is used by many bacteria and plants to move folded proteins across the cytoplasmic or thylakoid membrane. In most bacteria, the TatA protein is believed to form a defined pore in the membrane through homo-oligomerization with other TatA protomers. The predicted secondary structure of TatA includes a transmembrane helix, an amphipathic helix, and an unstructured C-terminal region. Here biophysical and structural investigations were performed on a synt...

  4. Biodegradable Polymers

    OpenAIRE

    Isabelle Vroman; Lan Tighzert

    2013-01-01

    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. ...

  5. 三元复合驱采油污水对水丝蚓DNA损伤的影响%DNA Damage of Limnodrilu hoffmeisteri Somatopiasm by Oily Sewage of Alkali-surfactant-polymer Flooding

    Institute of Scientific and Technical Information of China (English)

    尹伟平; 徐长君; 殷亚杰; 秦姝冕; 李铭; 聂春雨

    2013-01-01

    [目的]研究三元复合驱采油污水对水生动物基因的毒性效应.[方法]以霍甫水丝蚓(Limnodrilu hoffmeisteri)为受试生物,以浓度分别为12%、36%、24%和44%的采油污水稀释液为供试污染物,采用碱性单细胞凝胶电泳实验,以尾长(TL)、头部DNA含量(Head DNA)和尾部DNA含量(Tail DNA)为指标检测不同浓度采油污水对水丝蚓DNA的损伤程度.[结果]三元复合驱采油污水会引起水丝蚓体细胞DNA损失,暴露组中受试生物的头部DNA含量与对照组相比均显著减少(P<0.05),尾长和尾部DNA含量均显著升高(P<0.05),随着采油污水浓度的增加,DNA损伤表现出明显的“剂量-效应”关系.[结论]该研究表明三元复合驱采油污水对水丝蚓具有基因毒性效应,可能对油田生态环境产生严重影响.%[Objective] The aim was to study the genotoxicity effects of oily sewage of alkali-surfactant-polymer flooding on aquatic animals. [Method] Limnodrilu hoffmeisteri exposed to oily sewage with concentrations of 12% ,36% ,24% and 44% ( V/V) respectively. Then the lysed cells were detected by single cell gel electrophoresis under alkaline conditions and the DNA damage of limnodnlu hoffmeisteri cells was detected by using the tail length (TL) ,Head DNA content and tail DNA content as the indexes. [Result] The oily sewage of alkali-surfactant-polymer flooding could cause the damage of Limnodrilu hoffmeisteri somatopiasm DNA. The tail length and tail DNA content of all the treated groups increased significantly compared with those of control (P <0.05) ,and the head DNA content were decreased significantly (P <0.05). The DNA damage showed obvious "dose-effect" relationship along with the concentration increased of oily sewage. [ Conclusion] This study showed that the oily sewage of alkali-surfactant-polymer flooding has genotoxicity effect on Limnodrilu hoffmeisteri,and may have a serious impact on the ecological environment of oil field.

  6. Intracellular segment between transmembrane helices S0 and S1 of BK channel α subunit contains two amphipathic helices connected by a flexible loop

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Pan [Hefei National Laboratory of Microscale Physical Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027 (China); High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031 (China); Li, Dong; Lai, Chaohua [Hefei National Laboratory of Microscale Physical Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027 (China); Zhang, Longhua, E-mail: zlhustc@ustc.edu.cn [Hefei National Laboratory of Microscale Physical Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [Hefei National Laboratory of Microscale Physical Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027 (China); High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031 (China)

    2013-08-02

    Highlights: •The loop between S0 and S1 of BK channel was overexpressed and purified in DPC. •NMR studies indicated BK-IS1 contained two helices connected by a flexible loop. •Mg{sup 2+} titration of BK-IS1 indicated two possible binding sites of divalent ions. -- Abstract: 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{sup 2+} and Mg{sup 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{sup 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 {sup 1}H–{sup 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{sup 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.

  7. Effects of chain length of an amphipathic polypeptide carrying the repeated amino acid sequence (LETLAKA)(n) on α-helix and fibrous assembly formation.

    Science.gov (United States)

    Takei, Toshiaki; Hasegawa, Kazuya; Imada, Katsumi; Namba, Keiichi; Tsumoto, Kouhei; Kuriki, Yukino; Yoshino, Masakuni; Yazaki, Kazumori; Kojima, Shuichi; Takei, Tsunetomo; Ueda, Takuya; Miura, Kin-ichiro

    2013-04-23

    Polypeptide α3 (21 residues), with three repeats of a seven-amino-acid sequence (LETLAKA)(3), forms an amphipathic α-helix and a long fibrous assembly. Here, we investigated the ability of α3-series polypeptides (with 14-42 residues) of various chain lengths to form α-helices and fibrous assemblies. Polypeptide α2 (14 residues), with two same-sequence repeats, did not form an α-helix, but polypeptide α2L (15 residues; α2 with one additional leucine residue on its carboxyl terminal) did form an α-helix and fibrous assembly. Fibrous assembly formation was associated with polypeptides at least as long as polypeptide α2L and with five leucine residues, indicating that the C-terminal leucine has a critical element for stabilization of α-helix and fibril formation. In contrast, polypeptides α5 (35 residues) and α6 (42 residues) aggregated easily, although they formed α-helices. A 15-35-residue chain was required for fibrous assembly formation. Electron microscopy and X-ray fiber diffraction showed that the thinnest fibrous assemblies of polypeptides were about 20 Å and had periodicities coincident with the length of the α-helix in a longitudinal direction. These results indicated that the α-helix structures were orientated along the fibrous axis and assembled into a bundle. Furthermore, the width and length of fibrous assemblies changed with changes in the pH value, resulting in variations in the charged states of the residues. Our results suggest that the formation of fibrous assemblies of amphipathic α-helices is due to the assembly of bundles via the hydrophobic faces of the helices and extension with hydrophobic noncovalent bonds containing a leucine. PMID:23530905

  8. Label-Free DNA Detection through Energy Transfer of Conjugated Polymer Complexes%基于共轭高分子复合物能量转移的非标记DNA检测

    Institute of Scientific and Technical Information of China (English)

    邓洪平; 王国建; 朱邦尚; 朱利娟; 王大力; 庄园园; 朱新远

    2012-01-01

    Label-free DNA detection is a highly sensitive and selective method with great scientific and social significance. Water-soluble cationic conjugated polymer (CCP), poly(9,9-bis(6'-N,N,N-trimethylammonium)-hexyl)-fluorene phenylene) (PFP), was synthesized by cross coupling reaction under the catalysis of palladium, and water-soluble anionic conjugated polymer (ACP), poly(3-thiophene sodium acetate) (P3TSA), was prepared through oxidative addition polymerization with anhydrous ferric chloride as the catalyst. Both PFP and P3TSA were well characterized by 1H nuclear magnetic resonance (1H NMR) and Fourier transform infrared (FTIR) tests. Owing to the existence of opposite ionic side-chains, PFP and P3TSA were both water-soluble and could form polymer complexes through electrostatic interactions. The transmittance measurements of the polymer complex solution with wavelength ranging from 600 to 750 nm were performed. The results showed that the transmittance was almost unchanged for all samples, confirming the high solubility and stability of polymer complexes. The ultraviolet-visible (UV-vis) and photoluminescence emission measurements showed that the emission spectrum of PFP overlapped a lot with the absorption spectrum of P3TSA, proving the energy transfer from PFP (donor) to P3TSA (acceptor). By fixing the donor concentration, energy transfer efficiency (ETEF) of the polymer complexes increased with the concentration of P3TSA. With the enhancement of P3TSA concentration, the ETEF increased slowly at first and then relatively fast at a high P3TSA concentration. A sample with a high ETEF was selected to investigate the effect of DNA probe (X1) concentration on ETEF. It was observed that ETEF decreased with the increase of X1 concentration, owing to the repulsion of P3TSA by negative charged DNA probes. DNA hybridization was conducted by using 0.2 nmol of X1 as a probe. The experimental results showed that the perfectly matched, double mismatched and non-matched target

  9. Development of Targeted Recombinant Polymers that can deliver siRNA to the Cytoplasm and Plasmid DNA to the Cell Nucleus

    OpenAIRE

    Canine, Brenda F.; Wang, Yuhua; Ouyang, Wenyun; Hatefi, Arash

    2010-01-01

    One of the major limitations to effective siRNA delivery is the lack of a siRNA-specific delivery system. Currently, the same delivery systems that are used for plasmid DNA (pDNA) delivery to the cell nucleus are used for siRNA delivery to the cytoplasm. To fill this gap, the objective of this study was to design a biopolymer that can be programmed via its amino acid sequence to deliver siRNA specifically to cytoplasm. For pDNA delivery, a nuclear localization signal (NLS) was added to the bi...

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

    Science.gov (United States)

    Lim, Wei Kang; Denton, Alan R.

    2014-09-01

    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.

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

    International Nuclear Information System (INIS)

    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

  12. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

    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.

  13. Routing of individual polymers in designed patterns

    DEFF Research Database (Denmark)

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

    2015-01-01

    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...

  14. Polymer Chemistry

    Science.gov (United States)

    Williams, Martha; Roberson, Luke; Caraccio, Anne

    2010-01-01

    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.

  15. Star Polymers.

    Science.gov (United States)

    Ren, Jing M; McKenzie, Thomas G; Fu, Qiang; Wong, Edgar H H; Xu, Jiangtao; An, Zesheng; Shanmugam, Sivaprakash; Davis, Thomas P; Boyer, Cyrille; Qiao, Greg G

    2016-06-22

    Recent advances in controlled/living polymerization techniques and highly efficient coupling chemistries have enabled the facile synthesis of complex polymer architectures with controlled dimensions and functionality. As an example, star polymers consist of many linear polymers fused at a central point with a large number of chain end functionalities. Owing to this exclusive structure, star polymers exhibit some remarkable characteristics and properties unattainable by simple linear polymers. Hence, they constitute a unique class of technologically important nanomaterials that have been utilized or are currently under audition for many applications in life sciences and nanotechnologies. This article first provides a comprehensive summary of synthetic strategies towards star polymers, then reviews the latest developments in the synthesis and characterization methods of star macromolecules, and lastly outlines emerging applications and current commercial use of star-shaped polymers. The aim of this work is to promote star polymer research, generate new avenues of scientific investigation, and provide contemporary perspectives on chemical innovation that may expedite the commercialization of new star nanomaterials. We envision in the not-too-distant future star polymers will play an increasingly important role in materials science and nanotechnology in both academic and industrial settings. PMID:27299693

  16. Polymer Informatics

    Science.gov (United States)

    Adams, Nico

    Polymers are arguably the most important set of materials in common use. The increasing adoption of both combinatorial as well as high-throughput approaches, coupled with an increasing amount of interdisciplinarity, has wrought tremendous change in the field of polymer science. Yet the informatics tools required to support and further enhance these changes are almost completely absent. In the first part of the chapter, a critical analysis of the challenges facing modern polymer informatics is provided. It is argued, that most of the problems facing the field today are rooted in the current scholarly communication process and the way in which chemists and polymer scientists handle and publish data. Furthermore, the chapter reviews existing modes of representing and communicating polymer information and discusses the impact, which the emergence of semantic technologies will have on the way in which scientific and polymer data is published and transmitted. In the second part, a review of the use of informatics tools for the prediction of polymer properties and in silico design of polymers is offered.

  17. Controlled Release from Recombinant Polymers

    OpenAIRE

    Price, Robert; Poursaid, Azadeh; Ghandehari, Hamidreza

    2014-01-01

    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 tempor...

  18. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

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

  19. The Transition from Closed to Open Conformation of Treponema pallidum Outer Membrane-associated Lipoprotein TP0453 Involves Membrane Sensing and Integration by Two Amphipathic Helices*

    Science.gov (United States)

    Luthra, Amit; Zhu, Guangyu; Desrosiers, Daniel C.; Eggers, Christian H.; Mulay, Vishwaroop; Anand, Arvind; McArthur, Fiona A.; Romano, Fabian B.; Caimano, Melissa J.; Heuck, Alejandro P.; Malkowski, Michael G.; Radolf, Justin D.

    2011-01-01

    The molecular architecture and composition of the outer membrane (OM) of Treponema pallidum (Tp), the noncultivable agent of venereal syphilis, differ considerably from those of typical Gram-negative bacteria. Several years ago we described TP0453, the only lipoprotein associated with the inner leaflet of the Tp OM. Whereas polypeptides of other treponemal lipoproteins are hydrophilic, non-lipidated TP0453 can integrate into membranes, a property attributed to its multiple amphipathic helices (AHs). Furthermore, membrane integration of the TP0453 polypeptide was found to increase membrane permeability, suggesting the molecule functions in a porin-like manner. To better understand the mechanism of membrane integration of TP0453 and its physiological role in Tp OM biogenesis, we solved its crystal structure and used mutagenesis to identify membrane insertion elements. The crystal structure of TP0453 consists of an α/β/α-fold and includes five stably folded AHs. In high concentrations of detergent, TP0453 transitions from a closed to open conformation by lateral movement of two groups of AHs, exposing a large hydrophobic cavity. Triton X-114 phase partitioning, liposome floatation assay, and bis-1-anilino-8-naphthalenesulfonate binding revealed that two adjacent AHs are critical for membrane sensing/integration. Using terbium-dipicolinic acid complex-loaded large unilamellar vesicles, we found that TP0453 increased efflux of fluorophore only at acidic pH. Gel filtration and cross-linking experiments demonstrated that one AH critical for membrane sensing/insertion also forms a dimeric interface. Based on structural dynamics and comparison with Mycobacterium tuberculosis lipoproteins LprG and LppX, we propose that TP0453 functions as a carrier of lipids, glycolipids, and/or derivatives during OM biogenesis. PMID:21965687

  20. Organometallic Polymers.

    Science.gov (United States)

    Carraher, Charles E., Jr.

    1981-01-01

    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)

  1. Coloured Polymers

    OpenAIRE

    Pesando, I.

    1993-01-01

    We show that non-oriented coloured polymers (self--avoiding walks with different types of links) are in the same universality class of the ordinary self--avoiding walks, while the oriented coloured are not.

  2. Polymer electrolytes

    Czech Academy of Sciences Publication Activity Database

    Abbrent, Sabina; Greenbaum, S.; Peled, E.; Golodnitsky, D.

    Singapore: World Scientific Publishing, 2015 - (Dudney, N.; West, W.; Nanda, J.), s. 523-589 ISBN 978-981-4651-89-9 Institutional support: RVO:61389013 Keywords : polymer electrolytes * applications * mesuring techniques Subject RIV: CD - Macromolecular Chemistry

  3. DNA ELECTROPHORESIS AT SURFACES

    Energy Technology Data Exchange (ETDEWEB)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

    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.

  4. Engineering Polymer Informatics

    OpenAIRE

    Adams, Nico; Ryder, Jennifer; Jessop, David M; Corbett, Peter; Murray-Rust, Peter

    2007-01-01

    The poster describes a strategy of for the development of polymer informatics. In particular, the development of polymer markup language, a polymer ontology and natural language processing tools for polymer literature.

  5. Antimocrobial Polymer

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-09-06

    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.

  6. Polymer electronics

    CERN Document Server

    Geoghegan, Mark

    2013-01-01

    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

  7. Polymer Materials

    Institute of Scientific and Technical Information of China (English)

    Charles C. Han; DONG Jinyong; NIU Hui; CHENG He; HUANG Ye; ZHENG Jianfen; XU Shanshan

    2011-01-01

    @@ Since the second half of the 20th century, polymer materials have already become an essential part of our daily life.The use of polymeric materials has already exceeded that of metals and ceramics in terms of volume and is intimately connected to our clothing, food, household use, transportation, and medical needs.Meanwhile it also brought some recycle and environmental problems.In the 21 st century, human beings are facing ever increasing challenges on environmental protection, energy shortage, and health-medical problems, which have made even higher demand on polymer materials due to its light weight, flexibility and high functionality.

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

    Science.gov (United States)

    Meller, Stephan; Domizio, Jeremy Di; Voo, Kui S; Friedrich, Heike C; Chamilos, Georgios; Ganguly, Dipyaman; Conrad, Curdin; Gregorio, Josh; Roy, Didier Le; Roger, Thierry; Ladbury, John E; Homey, Bernhard; Watowich, Stanley; Modlin, Robert L; Kontoyiannis, Dimitrios P; Liu, Yong-Jun; Arold, Stefan T; Gilliet, Michel

    2016-01-01

    Interleukin 17–producing helper T cells (TH17 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. PMID:26168081

  9. Effects of the Incorporation of a Hydrophobic Middle Block into a PEG-Polycation Diblock Copolymer on the Physicochemical and Cell Interaction Properties of the Polymer-DNA Complexes

    OpenAIRE

    Sharma, Rahul; Lee, Jae-Sung; Bettencourt, Ryan C.; Xiao, Chuan; Konieczny, Stephen F.; Won, You-Yeon

    2008-01-01

    One-component homopolymers of cationic monomers (polycations) and diblock copolymers comprising poly(ethylene glycol) (PEG) and a polycation block have been the most widely used types of polymers for formulation of polymer-based gene delivery systems. In this study, we incorporate a hydrophobic middle block into the conventional PEG-polycation architecture, and investigate the effects of this hydrophobic modification on the physicochemical and cell-level biological properties of the polymer-D...

  10. Polymer physics

    CERN Document Server

    Gedde, Ulf W

    1999-01-01

    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...

  11. Polymer Science.

    Science.gov (United States)

    Frank, Curtis W.

    1979-01-01

    Described is a series of four graduate level courses in polymer science, offered or currently in preparation, at Stanford University. Course descriptions and a list of required and recommended texts are included. Detailed course outlines for two of the courses are presented. (BT)

  12. Fabricating Nanoscale DNA Patterns with Gold Nanowires

    OpenAIRE

    Chen, Yulin; Kung, Sheng-Chin; Taggart, David K.; Halpern, Aaron R.; Penner, Reginald M.; Corn, Robert M.

    2010-01-01

    Surface patterns of single-stranded DNA (ssDNA) consisting of nanoscale lines as thin as 40 nm were fabricated on polymer substrates for nanotechnology and bioaffinity sensing applications. Large scale arrays (with areas up to 4 cm2) of ssDNA “nanolines” were created on streptavidin-coated polymer (PDMS) surfaces by transferring biotinylated ssDNA from a master pattern of gold nanowires attached to a glass substrate. The gold nanowires were first formed on the glass substrate by the process o...

  13. Molecular electronics : A DNA that conducts

    OpenAIRE

    Scheer, Elke

    2014-01-01

    Experiments with conducting atomic force microscopy provide a clear demonstration of long-range charge transport in G-quadruplex DNA molecules, and allow a hopping transport model to be developed that could also be applied to other conductive polymers.

  14. Molecular electronics: A DNA that conducts

    Science.gov (United States)

    Scheer, Elke

    2014-12-01

    Experiments with conducting atomic force microscopy provide a clear demonstration of long-range charge transport in G-quadruplex DNA molecules, and allow a hopping transport model to be developed that could also be applied to other conductive polymers.

  15. Sustained Release of Antibacterial Lipopeptides from Biodegradable Polymers against Oral Pathogens.

    Science.gov (United States)

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

    2016-01-01

    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

  16. Tops and Writhing DNA

    Science.gov (United States)

    Samuel, Joseph; Sinha, Supurna

    2011-04-01

    The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's "local writhe expression" which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations.

  17. Tops and Writhing DNA

    OpenAIRE

    Samuel, Joseph; Sinha, Supurna

    2010-01-01

    The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops...

  18. When DNA Collides With Itself

    Science.gov (United States)

    Azad, Zubair; Riehn, Robert

    2015-03-01

    Long range interactions in large DNA molecules are typically modeled as self-avoiding random walks. While this is useful for understanding equilibrium configurations, dynamic behavior may include more complex polymer-polymer coupling. Here we explore the possibility of internal friction within hernias of DNA under nano-confinement and fluid flow. We study the rates at which DNA hernias form and recoil at various flow speeds and hernia sizes. The formation and recoil behaviors point to possible entanglement between two genetically distant regions of DNA as they flow in the same direction. To explore internal friction between two strands moving in opposite directions, we scan the two strands comprising the hernia as well as two independent molecules against each other. From these studies, we address the drag or friction forces on two molecules under confinement and compare to the analogous system of one nano-confined molecule.

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

    CERN Document Server

    Rapaport, D C

    2016-01-01

    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.

  20. Fabricating nanoscale DNA patterns with gold nanowires.

    Science.gov (United States)

    Chen, Yulin; Kung, Sheng-Chin; Taggart, David K; Halpern, Aaron R; Penner, Reginald M; Corn, Robert M

    2010-04-15

    Surface patterns of single-stranded DNA (ssDNA) consisting of nanoscale lines as thin as 40 nm were fabricated on polymer substrates for nanotechnology and bioaffinity sensing applications. Large scale arrays (with areas up to 4 cm(2)) of ssDNA "nanolines" were created on streptavidin-coated polymer (PDMS) surfaces by transferring biotinylated ssDNA from a master pattern of gold nanowires attached to a glass substrate. The gold nano-wires were first formed on the glass substrate by the process of lithographically patterned nanowire electrodeposition (LPNE), and then "inked" with biotinylated ssDNA by hybridization adsorption to a thiol-modified ssDNA monolayer attached to the gold nanowires. The transferred ssDNA nanolines were capable of hybridizing with ssDNA from solution to form double-stranded DNA (dsDNA) patterns; a combination of fluorescence and atomic force microscopy (AFM) measurements were used to characterize the dsDNA nanoline arrays. To demonstrate the utility of these surfaces for biosensing, optical diffraction measurements of the hybridization adsorption of DNA-coated gold nanoparticles onto the ssDNA nanoline arrays were used to detect a specific target sequence of unlabeled ssDNA in solution. PMID:20337428

  1. Development of Recombinant Cationic Polymers for Gene Therapy Research

    OpenAIRE

    Canine, Brenda F.; Hatefi, Arash

    2010-01-01

    Cationic polymers created through recombinant DNA technology have the potential to fill a void in the area of gene delivery. The recombinant cationic polymers to be discussed here are amino acid based polymers synthesized in E.coli with the purpose to not only address the major barriers to efficient gene delivery but offer safety, biodegradability, targetability and cost-effectiveness. This review helps the readers to get a better understanding about the evolution of recombinant cationic poly...

  2. Advanced Developments in Cyclic Polymers: Synthesis, Applications, and Perspectives

    OpenAIRE

    Zhu, Yinghuai; Narayan S. Hosmane

    2015-01-01

    Due to the topological effect, cyclic polymers demonstrate different and unique physical and biological properties in comparison with linear counterparts having the same molecular-weight range. With advanced synthetic and analytic technologies, cyclic polymers with different topologies, e.g. multicyclic polymers, have been reported and well characterized. For example, various cyclic DNA and related structures, such as cyclic duplexes, have been prepared conveniently by click chemistry. These ...

  3. Graft polymer conjugates for passive targeting to the solid tumors

    Czech Academy of Sciences Publication Activity Database

    Etrych, Tomáš; Chytil, Petr; Mrkvan, Tomáš; Říhová, Blanka; Ulbrich, Karel

    Gargnano : European Polymer Federation, 2006. [European Polymer Conference EUPOC. Branched Macromolecular Structures. 07.05.2006-12.05.2006, Gargnano] R&D Projects: GA MŠk 1M0505; GA AV ČR IAA4050201 Keywords : poly(L- lysine ) * DNA * polyelectrolyte complex Subject RIV: CD - Macromolecular Chemistry

  4. DNA Book

    OpenAIRE

    Kawai, Jun; Hayashizaki, Yoshihide

    2003-01-01

    We propose herein a new method of DNA distribution, whereby DNA clones or PCR products are printed directly onto the pages of books and delivered to users along with relevant scientific information. DNA sheets, comprising water-soluble paper onto which DNA is spotted, can be bound into books. Readers can easily extract the DNA fragments from DNA sheets and amplify them using PCR. We show that DNA sheets can withstand various conditions that may be experienced during bookbinding and deli...

  5. Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase beta and the XRCC1 protein.

    OpenAIRE

    Kubota, Y; Nash, R. A.; Klungland, A; Schär, P; Barnes, D E.; Lindahl, T

    1996-01-01

    Repair of a uracil-guanine base pair in DNA has been reconstituted with the recombinant human proteins uracil-DNA glycosylase, apurinic/apyrimidinic endonuclease, DNA polymerase beta and DNA ligase III. The XRCC1 protein, which is known to bind DNA ligase III, is not absolutely required for the reaction but suppresses strand displacement by DNA polymerase beta, allowing for more efficient ligation after filling of a single nucleotide patch. We show that XRCC1 interacts directly with DNA polym...

  6. Cleaving DNA with DNA

    Science.gov (United States)

    Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.

    1998-03-01

    A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This ``deoxyribozyme'' can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min-1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domains can be altered, making possible the targeted cleavage of single-stranded DNAs with different nucleotide sequences. Several small synthetic DNAs were made to function as simple ``restriction enzymes'' for the site-specific cleavage of single-stranded DNA.

  7. Modeling of Polymer Erosion

    OpenAIRE

    Göpferich, Achim; Langer, Robert S.

    1993-01-01

    The erosion of bioerodible polymers depends on many factors including the polymer chain length, bond cleavage velocity, swellability, crystallinity, and water diffusivity in the polymer matrix. This multitude of parameters makes modeling of erosion difficult. Only a few models exist that describe morphological changes of polymers during erosion qualitatively. In the present approach the polymer matrix was represented as the sum of small individual polymer matrix parts. The factors that determ...

  8. Premeltons in DNA.

    Science.gov (United States)

    Sobell, Henry M

    2016-03-01

    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. PMID

  9. From Commodity Polymers to Functional Polymers

    OpenAIRE

    Tao Xiang; Ling-Ren Wang; Lang Ma; Zhi-Yuan Han; Rui Wang; Chong Cheng; Yi Xia; Hui Qin; Chang-Sheng Zhao

    2014-01-01

    Functional polymers bear specified chemical groups, and have specified physical, chemical, biological, pharmacological, or other uses. To adjust the properties while keeping material usage low, a method for direct synthesis of functional polymers is indispensable. Here we show that various functional polymers can be synthesized by in situ cross-linked polymerization/copolymerization. We demonstrate that the polymers synthesized by the facile method using different functional monomers own outs...

  10. DNA Partitioning in Confining Nanofluidic Slits

    Science.gov (United States)

    Greenier, Madeline; Levy, Stephen

    We measure the partitioning of double stranded DNA molecules in moderately and strongly confining nanofluidic slit-like structures. Using fluorescent microscopy, the free energy penalty of confinement is inferred by comparing the concentration of DNA molecules in adjoining slits of different depths. These depths range in size from several persistence lengths to the DNA molecule's radius of gyration. The partition coefficient is determined as a function of the slit depth, DNA contour length, and DNA topology. We compare our results to theory and Monte Carlo simulations that predict the loss of free energy for ideal and semiflexible excluded volume polymers confined between parallel plates.

  11. DNA supercoiling inhibits DNA knotting.

    OpenAIRE

    Burnier Y.; Dorier J.; Stasiak A.

    2008-01-01

    Despite the fact that in living cells DNA molecules are long and highly crowded, they are rarely knotted. DNA knotting interferes with the normal functioning of the DNA and, therefore, molecular mechanisms evolved that maintain the knotting and catenation level below that which would be achieved if the DNA segments could pass randomly through each other. Biochemical experiments with torsionally relaxed DNA demonstrated earlier that type II DNA topoisomerases that permit inter- and intramolecu...

  12. Polymer bank notes

    OpenAIRE

    Brian Lang

    2002-01-01

    In May 1999 the Reserve Bank issued its first polymer bank notes into circulation. By March 2000 all denominations had been converted from paper to polymer. By the end of 2001 approximately 110 million polymer notes had been issued into circulation. This article assesses the performance of polymer notes compared with our expectations at the time they were introduced.

  13. Shape memory polymers

    Science.gov (United States)

    Wilson, Thomas S.; Bearinger, Jane P.

    2015-06-09

    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.

  14. Bio-Polymer Hairpin Loops Sustained by Polarons

    CERN Document Server

    Chakrabarti, B; Zakrzewski, W J

    2012-01-01

    We show that polarons can sustain loop-like configurations in flexible bio-polymers and that the size of the loops depend on both the flexural rigidity of the polymer and the electron-phonon coupling constant. In particular we show that for single stranded DNA (ssDNA) such loops can have as little as 10 base pairs. For polyacetylene the shortest loop must have at least 12 nodes. We also show that these configurations are very stable under thermal fluctuations and can facilitate the formation of hairpin-loops of ssDNA.

  15. Synthesis of cholic-acid-carrying polymer and in-vitro evaluation of hepatoma-targeting nanoparticles decorated with the polymer.

    Science.gov (United States)

    Zhang, Jiantao; Yu, Changjun; Jiang, Guoqiang

    2016-06-01

    The specific interaction between bile acids and the bile acids transporters provides a promising way for hepatoma-targeted drug delivery. We synthesized an amphipathic polymer containing cholic acid (CA), the main bile acids in body, and prepared CA-functionalized nanoparticles to target hepatoma cells. Poly-[3-(4-vinylbenzonate)-7, 12-dihydroxy-5-cholan-24-oic acid] (PVBCA) was synthesized by introducing methyl cholate onto polyvinyl benzoate polymer backbone, and was characterized by (1)H-NMR, FT-IR, and GFC. PVBCA can be incorporated onto PLGA nanoparticles surface via the emulsion-solvent evaporation procedure, resulting in the nanoparticles carrying CA moieties on their surface. The binding of CA moieties to the bile acids' transporters on the cell membrane enhances the cellular uptake of the nanoparticles significantly. The SMMC-7721 cell uptake of PVBCA-decorated nanoparticles increases with amount of incorporated PVBCA and is 2- to 2.8-fold higher than that of the normal PLGA nanoparticles. By exclusion of specific endocytosis pathways using chemical inhibitors, we found that the uptake mechanism of PVBCA-decorated nanoparticles was mainly attributed to clathrin-and-caveolae-independent endocytosis, which was distinct from that of PLGA nanoparticles. The present study provides a simple and versatile method for hepatoma-targeted delivery of nanoparticles. PMID:27045998

  16. Polymer friction Molecular Dynamics

    OpenAIRE

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

    2010-01-01

    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 ...

  17. Friction between Polymer Brushes

    OpenAIRE

    Sokoloff, J. B.

    2006-01-01

    By solving the equilibrium equations for a polymer in a neutral polymer brush, the degree of interpenetration of two polymer brushes in contact and near contact is calculated. These results are used to calculate values of the force of static friction in agreement with recent friction measurements for polymer brush lubricated surfaces. It is shown that at sufficiently light loads polymer brush coated surfaces can slide, with the load supported entirely by osmotic pressure, at a sufficiently la...

  18. DNA vaccines

    OpenAIRE

    Coban, Cevayir; Kobiyama, Kouji; Jounai, Nao; Tozuka, Miyuki; Ishii, Ken J.

    2013-01-01

    Since the introduction of DNA vaccines two decades ago, this attractive strategy has been hampered by its low immunogenicity in humans. Studies conducted to improve the immunogenicity of DNA vaccines have shown that understanding the mechanism of action of DNA vaccines might be the key to successfully improving their immunogenicity. Our current understanding is that DNA vaccines induce innate and adaptive immune responses in two ways: (1) encoded protein (or polypeptide) antigen(s) by the DNA...

  19. Polymer nanocomposites: polymer and particle dynamics

    KAUST Repository

    Kim, Daniel

    2012-01-01

    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.

  20. Loop polymer brushes from polymer single crystals

    Science.gov (United States)

    Zhou, Tian; Li, Christopher

    2014-03-01

    Loop polymer brushes represent a category of polymer brushes with both chain ends being tethered to a surface or interface with sufficiently high density. Due to this morphological difference, loop brushes exhibit distinct properties compared with traditional polymer brushes with single chain end being tethered. In our study, α, ω-functionalized polycaprolactone (PCL) single crystals were prepared as templates for polymer brush synthesis. By carefully controlling crystallization condition and immobilization, looped polymer brushes were successfully prepared. Comprehensive studies on the morphology and physical properties of these polymer brushes were carried out using Atomic Force Microscopy and FTIR. Advantages of using this method include exclusive loop morphology, high grafting density, controlled tethering sites and tunable loop size.

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

    CERN Document Server

    Lu, Bing-Sui; Podgornik, Rudolf

    2016-01-01

    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...

  2. Wet Organic Field Effect Transistor as DNA sensor

    OpenAIRE

    Chiu, Yu-Jui

    2008-01-01

    Label-free detection of DNA has been successfully demonstrated on field effect transistor (FET) based devices. Since conducting organic materials was discovered and have attracted more and more research efforts by their profound advantages, this work will focus on utilizing an organic field effect transistor (OFET) as DNA sensor. An OFET constructed with a transporting fluidic channel, WetOFET, forms a fluid-polymer (active layer) interface where the probe DNA can be introduced. DNA hybridiza...

  3. Biophysics of protein-DNA interactions and chromosome organization

    OpenAIRE

    Marko, John F.

    2015-01-01

    The function of DNA in cells depends on its interactions with protein molecules, which recognize and act on base sequence patterns along the double helix. These notes aim to introduce basic polymer physics of DNA molecules, biophysics of protein-DNA interactions and their study in single-DNA experiments, and some aspects of large-scale chromosome structure. Mechanisms for control of chromosome topology will also be discussed.

  4. Polymer segregation under confinement: Influences of macromolecular crowding and the interaction between the polymer and crowders

    Science.gov (United States)

    Chen, Yuhao; Yu, Wancheng; Wang, Jiajun; Luo, Kaifu

    2015-10-01

    Entropy driven polymer segregation in confinements as a model for chromosome separation in bacteria has attracted wide attention; however, the effects of macromolecular crowding and the interaction between the binding protein and the newly replicated DNA on the segregation dynamics are not clear. Using Langevin dynamics simulations, we investigate the influences of crowders and the attractive interaction between the polymer and a small number of crowders on segregation of two overlapping polymers under a cylindrical confinement. We find that the segregation time increases with increasing the volume fraction of crowders due to the slower chain diffusion in crowded environments. For a fixed volume fraction of crowders, the segregation time decreases with increasing the size of crowders. Moreover, the attractive interaction between the polymer and a small number of crowders can significantly facilitate the chain segregation. These results are important for understanding the chromosome segregation in living cells.

  5. DNA Methylation

    OpenAIRE

    Alokail, Majed S.; Alenad, Amal M

    2015-01-01

    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...

  6. DNA looping.

    OpenAIRE

    Matthews, K S

    1992-01-01

    DNA-looping mechanisms are part of networks that regulate all aspects of DNA metabolism, including transcription, replication, and recombination. DNA looping is involved in regulation of transcriptional initiation in prokaryotic operons, including ara, gal, lac, and deo, and in phage systems. Similarly, in eukaryotic organisms, the effects of enhancers appear to be mediated at least in part by loop formation, and examples of DNA looping by hormone receptor proteins and developmental regulator...

  7. Polymer Fluid Dynamics.

    Science.gov (United States)

    Bird, R. Byron

    1980-01-01

    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)

  8. 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;

    2011-01-01

    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....

  9. Platinated DNA oligonucleotides: new probes forming ultrastable conjugates with graphene oxide

    Science.gov (United States)

    Wang, Feng; Liu, Juewen

    2014-05-01

    Metal containing polymers have expanded the property of polymers by involving covalently associated metal complexes. DNA is a special block copolymer. While metal ions are known to influence DNA, little is explored on its polymer property when strong metal complexes are associated. In this work, we study cisplatin modified DNA as a new polymer and probe. Out of the complexes formed between cisplatin-A15, HAuCl4-A15, Hg2+-T15 and Ag+-C15, only the cisplatin adduct is stable under the denaturing gel electrophoresis condition. Each Pt-nucleobase bond gives a positive charge and thus makes DNA a zwitterionic polymer. This allows ultrafast adsorption of DNA by graphene oxide (GO) and the adsorbed complex is highly stable. Non-specific DNA, protein, surfactants and thiolated compounds cannot displace platinated DNA from GO, while non-modified DNA is easily displaced in most cases. The stable GO/DNA conjugate is further tested for surface hybridization. This is the first demonstration of using metallated DNA as a polymeric material for interfacing with nanoscale materials.Metal containing polymers have expanded the property of polymers by involving covalently associated metal complexes. DNA is a special block copolymer. While metal ions are known to influence DNA, little is explored on its polymer property when strong metal complexes are associated. In this work, we study cisplatin modified DNA as a new polymer and probe. Out of the complexes formed between cisplatin-A15, HAuCl4-A15, Hg2+-T15 and Ag+-C15, only the cisplatin adduct is stable under the denaturing gel electrophoresis condition. Each Pt-nucleobase bond gives a positive charge and thus makes DNA a zwitterionic polymer. This allows ultrafast adsorption of DNA by graphene oxide (GO) and the adsorbed complex is highly stable. Non-specific DNA, protein, surfactants and thiolated compounds cannot displace platinated DNA from GO, while non-modified DNA is easily displaced in most cases. The stable GO/DNA conjugate

  10. Polymer Based Biosensors for Medical Applications

    DEFF Research Database (Denmark)

    Cherré, Solène; Rozlosnik, Noemi

    2015-01-01

    , 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......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...... 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. The...

  11. Enhanced luminescence in metal/ (conducting polymer) nanocomposites

    International Nuclear Information System (INIS)

    Full text: We will discuss the ELINOR effect, the Enhanced Luminescence of INorganic and ORganic origin, which we recently identified in different (noble metal)/(conducting polymer) nanocomposites. The intense fluorescence of these composites can be pinned down to a synergic interaction between the plasmonic response of the nanostructured metallic aggregate and the electronic relaxation offered by the conducting polymer chains. We have shown that by careful control of the preparation conditions we can tune both the intensity and the wavelength of the emission maximum. We will discuss possible applications of these nanocomposites as molecular biomarkers (where we exploit the electrical affinity between conducting polymer chains and DNA molecules) and in the increase of efficiency of photovoltaic devices and solid state displays. Preliminary results of the ELINOR effect as a tool for rapid diagnosis of viral diseases and genetic polymorphisms will be also presented

  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. Nanoporous polymer electrolyte

    Science.gov (United States)

    Elliott, Brian; Nguyen, Vinh

    2012-04-24

    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 25.degree. 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.

  14. The Borrelia burgdorferi telomere resolvase, ResT, anneals ssDNA complexed with its cognate ssDNA-binding protein.

    Science.gov (United States)

    Huang, Shu Hui; Kobryn, Kerri

    2016-06-20

    Spirochetes of the genus Borrelia possess unusual genomes that consist in a linear chromosome and multiple linear and circular plasmids. The linear replicons are terminated by covalently closed hairpin ends, referred to as hairpin telomeres. The hairpin telomeres represent a simple solution to the end-replication problem. Deoxyribonucleic acid replication initiates internally and proceeds bidirectionally toward the hairpin telomeres. The telomere resolvase, ResT, forms the hairpin telomeres from replicated telomere intermediates in a reaction with similarities to those promoted by type IB topoisomerases and tyrosine recombinases. ResT has also been shown to possess DNA single-strand annealing activity. We report here that ResT promotes single-strand annealing of both free DNA strands and ssDNA complexed with single-stranded DNA binding protein (SSB). The annealing of complementary strands bound by SSB requires a ResT-SSB interaction that is mediated by the conserved amphipathic C-terminal tail of SSB. These properties of ResT are similar to those demonstrated for the recombination mediator protein, RecO, of the RecF pathway. Borrelia burgdorferi is unusual in lacking identifiable homologs of the RecFOR proteins. We propose that ResT may provide missing RecFOR functions. PMID:27131360

  15. The structural diversity of artificial genetic polymers

    OpenAIRE

    Anosova, Irina; Kowal, Ewa A.; Dunn, Matthew R.; Chaput, John C.; Van Horn, Wade D.; Egli, Martin

    2015-01-01

    Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeg...

  16. Ni2+ doping DNA: a semiconducting biopolymer

    International Nuclear Information System (INIS)

    DNA is a one-dimensional nanowire in nature, and it may not be used in nanodevices due to its low conductivity. In order to improve the conducting property of DNA, divalent Ni2+ are incorporated into the base pairs of DNA at pH≥8.5 and nickel DNA (Ni-DNA) is formed. Conducting scanning probe microscopy (SPM) analysis reveals that the Ni-DNA is a semiconducting biopolymer and the Schottky barrier of Ni-DNA reduces to 2 eV. Meanwhile, electrochemical analysis by cyclic voltammetry and AC impedance shows that the conductance of Ni-DNA is better than that of native DNA by a factor of approximately 20-fold. UV spectroscopy and DNA base pair mismatch analyses show that the conducting mechanism of Ni-DNA is due to electrons hopping through the π-π stacking of DNA base pairs. This biomaterial is a designable one-dimensional semiconducting polymer for usage in nanodevices

  17. Use of Polymer Micro-Structures for Drug & Gene Delivery

    Science.gov (United States)

    Chu, Ben

    2005-03-01

    The design of polymer microstructures, including polyelectrolyte-surfactant complex formation, plays an important role in the protection and controlled release of drugs & DNA fragments. Two examples are presented: one for drug release and one for gene delivery. Non-viral gene therapy is a challenging problem that has not yet met much success even though numerous attempts have been made. The gene delivery illustration aims to present one specific approach on how DNA fragments can be delivered to a cell by using an electro-spun scaffold as a carrier, i.e., to consider how DNA fragments can be trapped into a scaffold for subsequent release and transfection. Our scheme is to capture the DNA fragments by taking advantage of the DNA coil-to-globule transition and to encapsulate the condensed DNA globule by using block copolymers. The supra-molecular capsule can then be incorporated into a nano-structured biodegradable polymer scaffold by means of electro-spinning. Subsequent DNA release to cells that adhere to the scaffolds was measured by using fluorescence microscopy.AcknowledgementsFinancial Support:National Science Foundation, Polymers Program (DMR9984102 & Creativity Extension Award), Center for Biotechnology at Stony Brook, ITG Grant, and NIH SBIR Grant to STAR.Main contributors include Professors Benjamin S. Hsiao and Michael Hadjiargyrou, Drs. Dufei Fang, Dehai Liang and Kwangsok Kim, Ms. K. Luu and Mr. J. Chiu.

  18. Reducible poly(amido ethylenimine)-based gene delivery system for improved nucleus trafficking of plasmid DNA

    OpenAIRE

    Jeong, Ji Hoon; Kim, Sun Hwa; Christensen, Lane V.; Feijen, Jan; Kim, Sung Wan

    2010-01-01

    In a non-viral gene delivery system, localization of a plasmid DNA in the nucleus is a prerequisite for expression of a desired therapeutic protein encoded in the plasmid DNA. In this study, a reducible polymer-based gene delivery system for improved intracellular trafficking and nuclear translocation of plasmid DNA is introduced. The system is consisted of two components, a plasmid DNA having repeated biding sequence for a karyophilic protein, NFκB, and a reducible polymer. A reducible poly(...

  19. Bio-Polymer Hairpin Loops Sustained by Polarons

    OpenAIRE

    Chakrabarti, B.; Piette, B.; Zakrzewski, W.J.Z.

    2012-01-01

    We show that polarons can sustain loop-like configurations in flexible bio-polymers and that the size of the loops depend on both the flexural rigidity of the polymer and the electron-phonon coupling constant. In particular we show that for single stranded DNA (ssDNA) such loops can have as little as 10 base pairs. For polyacetylene the shortest loop must have at least 12 nodes. We also show that these configurations are very stable under thermal fluctuations and can facilitate the formation ...

  20. DNA-Assisted β-phase Nucleation and Alignment of Molecular Dipoles in PVDF Film: A Realization of Self-Poled Bioinspired Flexible Polymer Nanogenerator for Portable Electronic Devices.

    Science.gov (United States)

    Tamang, Abiral; Ghosh, Sujoy Kumar; Garain, Samiran; Alam, Md Mehebub; Haeberle, Jörg; Henkel, Karsten; Schmeisser, Dieter; Mandal, Dipankar

    2015-08-01

    A flexible nanogenerator (NG) is fabricated with a poly(vinylidene fluoride) (PVDF) film, where deoxyribonucleic acid (DNA) is the agent for the electroactive β-phase nucleation. Denatured DNA is co-operating to align the molecular -CH2/-CF2 dipoles of PVDF causing piezoelectricity without electrical poling. The NG is capable of harvesting energy from a variety of easily accessible mechanical stress such as human touch, machine vibration, football juggling, and walking. The NG exhibits high piezoelectric energy conversion efficiency facilitating the instant turn-on of several green or blue light-emitting diodes. The generated energy can be used to charge capacitors providing a wide scope for the design of self-powered portable devices. PMID:26189605

  1. DNA Immunization

    OpenAIRE

    Wang, Shixia; Lu, Shan

    2013-01-01

    DNA immunization was discovered in early 1990s and its use has been expanded from vaccine studies to a broader range of biomedical research, such as the generation of high quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation and gene gun. In addition, several common considerations related to DNA immunization are discussed.

  2. DNA deoxyribophosphodiesterase.

    OpenAIRE

    Franklin, W A; Lindahl, T

    1988-01-01

    A previously unrecognized enzyme acting on damaged termini in DNA is present in Escherichia coli. The enzyme catalyses the hydrolytic release of 2-deoxyribose-5-phosphate from single-strand interruptions in DNA with a base-free residue on the 5' side. The partly purified protein appears to be free from endonuclease activity for apurinic/apyrimidinic sites, exonuclease activity and DNA 5'-phosphatase activity. The enzyme has a mol. wt of approximately 50,000-55,000 and has been termed DNA deox...

  3. Polymer dynamics from synthetic polymers to proteins

    Indian Academy of Sciences (India)

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

    2008-10-01

    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.

  4. Effect of anchor positioning on binding and diffusion of elongated 3D DNA nanostructures on lipid membranes

    Science.gov (United States)

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

    2016-05-01

    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.

  5. Cleaving DNA with DNA

    OpenAIRE

    Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.

    1998-01-01

    A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This “deoxyribozyme” can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min−1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domai...

  6. Artificial Informational Polymers and Nanomaterials from Ring-Opening Metathesis Polymerization

    OpenAIRE

    James, Carrie Rae

    2015-01-01

    Inspired by naturally occurring polymers (DNA, polypeptides, polysaccharides, etc.) that can self- assemble on the nanoscale into complex, information-rich architectures, we have synthesized nucleic acid based polymers using ROMP. These polymers were synthesized using a graft-through strategy, whereby nucleic acids bearing a strained cyclic olefin were directly polymerized. This is the first example of the graft-through polymerization of nucleic acids. Our approach takes advantage of non-char...

  7. DNA glue

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...

  8. Polymer radiation chemistry

    International Nuclear Information System (INIS)

    This article reviews some of the work carried out in the Polymer and Radiation Group at the University of Queensland over the past ten years. The objective of the work has been to investigate the relationships between polymer structure and sensitivity towards high energy radiation, including 60Co gamma radiation, electron beams and UV radiation. A range of synthetic polymers containing carboxyl groups, acrylate groups, sulfone groups, amide linkages and aromatic residues have been investigated. (author). 18 refs, 2 figs, 4 tabs

  9. Degradation effects in polymers

    International Nuclear Information System (INIS)

    The extremely long molecular chains of polymers can be broken easily by the absorption of a quantum of energy above the energy of the covalent bond of the main carbon chain, which typically is in the range of 5-10 eV. The energy of beta and gamma photons of 1 to 10 MeV surpasses by many orders of magnitude this minimum value, representing a high risk of degradation to all kind of polymers, naturals and synthetics alike. The protection of polymers against high doses (20 - 1000 kGy) requires efficient additives preventing and/or stopping chain reaction type oxidative degradation. Primary and secondary antioxidants work well here in synergy. Commercial raw materials are available for radiation-sterilizable medical devices made out of polyolefins and other thermoplastics. Similarly, polymer compounds of suitable formulae are offered commercially for high-dose applications of polymers in nuclear installations. The controlled degradation of polymers of large molecular mass - or even of cross-linked molecular structures - is a promising field of radiation application. One area here is related to recycling non-accessible polymers such as fluorinated plastics of cross-linked rubber products. Another large possible area is the controlled radiation degradation of natural polymer systems. Radiation may facilitate the access to cross-linked natural polymer systems, such as wood, plant cellulose and biomass in general, decreasing to use of aggressive chemicals. The result is energetically favorable, environmentally friendly new procedures and raw materials of natural origin. A limited dose applied to polymers - although may cause some degradation - however may initiate new bonds on the 'wounded' chain. The popular graft-copolymerization technique can be applied in new, up-coming polymer processing technologies such as alloying, composite processing and reconstitutive recycling. By this way, even those polymers described earlier as radiation-degrading types, can be cross

  10. Nanostructured polymers for photonics

    OpenAIRE

    Chantal Paquet; Eugenia Kumacheva

    2008-01-01

    We review recent progress in the development of polymer nanostructured materials with periodic structures and compositions having applications in photonics and optical data storage. This review provides a brief description of the microfabrication and self-assembly methods used for the production of polymer materials with periodic structures, and highlights the properties and applications of photonic materials derived from block copolymers, colloid crystals, and microfabricated polymers. We co...

  11. Multilayer polymer microspot targets

    International Nuclear Information System (INIS)

    Last year the authors reported on the development of a seeded microspot x-ray diagnostic target. This target consisted of a 300-μm-diam, 2-μm-thick disk of silicon or sulfur-seeded hydrocarbon polymer nested tightly in a hole in a 2-μm-thick film of pure hydrocarbon polymer. This year they extended our work on the microspot target, fully encapsulating the microspot in what they call the multilayer polymer microspot target

  12. BSA Hybrid Synthesized Polymer

    Institute of Scientific and Technical Information of China (English)

    Zong Bin LIU; Xiao Pei DENG; Chang Sheng ZHAO

    2006-01-01

    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.

  13. All Polymer Micropump

    OpenAIRE

    Hansen, Thomas Steen; Larsen, Niels Bent; Hassager, Ole

    2008-01-01

    In this thesis an all polymer micropump, and the fabrication method required to fabricate this, are examined. Polymer microfluidic. devices are of major scientific interest because they can combine complicated chemical and biological analys~s in cheap and disposable devices. The electrode system in the micropump is based on the conducting polymer poly(3,4 ethylenedioxythiophene) (PEDOT). The majority of the work conducted was therefore aimed at developing methods for patterning and processing...

  14. Triclosan antimicrobial polymers

    OpenAIRE

    Petersen, Richard C.

    2016-01-01

    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 ...

  15. Thermally conductive polymers

    Science.gov (United States)

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

    1971-01-01

    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.

  16. Characterisation of polymers, 1

    CERN Document Server

    Crompton, Roy

    2008-01-01

    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

  17. Antioxidant Stabilisation of Polymers

    Science.gov (United States)

    Shlyapnikov, Yurii A.

    1981-06-01

    Physicochemical aspects of the stabilisation of polymers are discussed. Attention is paid mainly to the aging and stabilisation of polymers under processing conditions. Topics considered are the kinetics and mechanism of the high-temperature oxidation of polymers, critical phenomena in the inhibited oxidation of polymers, the theory of synergism and antagonism among antioxidants, the reasons for differences in efficiency of antioxidants, and certain aspects of the relation between the efficiency of antioxidants and their molecular structure. A list of 132 references is included.

  18. Nanostructured polymers for photonics

    Directory of Open Access Journals (Sweden)

    Chantal Paquet

    2008-04-01

    Full Text Available We review recent progress in the development of polymer nanostructured materials with periodic structures and compositions having applications in photonics and optical data storage. This review provides a brief description of the microfabrication and self-assembly methods used for the production of polymer materials with periodic structures, and highlights the properties and applications of photonic materials derived from block copolymers, colloid crystals, and microfabricated polymers. We conclude with a summary of current and future research efforts and opportunities in the development of polymer materials for photonic applications.

  19. Wireframe and tensegrity DNA nanostructures.

    Science.gov (United States)

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

    2014-06-17

    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

  20. Enzymatic Ligation of Large Biomolecules to DNA

    DEFF Research Database (Denmark)

    Sørensen, Rasmus Schøler; Okholm, Anders Hauge; Schaffert, David Henning; Kodal, Anne Louise Bank; Gothelf, Kurt Vesterager; Kjems, Jørgen

    2013-01-01

    application. However, conjugation of DNA to large molecular components using classical chemistries often suffers from suboptimal yields. Here, we report the use of terminal deoxynucleotidyl transferase (TdT) for direct enzymatic ligation of native DNA to nucleotide triphosphates coupled to proteins and other...... self-assembled structures, antisense therapeutics, microarray diagnostics, and biosensors. Such applications frequently require DNA to be modified and conjugated to other macromolecules, including proteins, polymers, or fatty acids, in order to equip the system with properties required for a particular...

  1. DNA probes

    International Nuclear Information System (INIS)

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  2. [DNA computing].

    Science.gov (United States)

    Błasiak, Janusz; Krasiński, Tadeusz; Popławski, Tomasz; Sakowski, Sebastian

    2011-01-01

    Biocomputers can be an alternative for traditional "silicon-based" computers, which continuous development may be limited due to further miniaturization (imposed by the Heisenberg Uncertainty Principle) and increasing the amount of information between the central processing unit and the main memory (von Neuman bottleneck). The idea of DNA computing came true for the first time in 1994, when Adleman solved the Hamiltonian Path Problem using short DNA oligomers and DNA ligase. In the early 2000s a series of biocomputer models was presented with a seminal work of Shapiro and his colleguas who presented molecular 2 state finite automaton, in which the restriction enzyme, FokI, constituted hardware and short DNA oligomers were software as well as input/output signals. DNA molecules provided also energy for this machine. DNA computing can be exploited in many applications, from study on the gene expression pattern to diagnosis and therapy of cancer. The idea of DNA computing is still in progress in research both in vitro and in vivo and at least promising results of these research allow to have a hope for a breakthrough in the computer science. PMID:21735816

  3. Triclosan antimicrobial polymers

    Directory of Open Access Journals (Sweden)

    Richard C. Petersen

    2016-03-01

    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

  4. Liquid crystalline phases in concentrated aqueous solutions of Na+ DNA.

    OpenAIRE

    Rill, R L

    1986-01-01

    Concentrated aqueous saline solutions of short (146-base-pair) DNA fragments suddenly become turbid and iridescent when the DNA concentration is slightly increased or the temperature is decreased. Microscopic examination through crossed polarizing filters shows that turbidity and iridescence is due to formation of a liquid crystalline DNA phase similar to cholesteric liquid crystals formed by other semirigid, but nonelectrolyte, chiral polymers. Several distinct textures of the liquid crystal...

  5. Self-Assembly of Emulsion Droplets into Polymer Chains

    Science.gov (United States)

    Bargteil, Dylan; McMullen, Angus; Brujic, Jasna

    We experimentally investigate `beads-on-a-string' models of polymers using the spontaneous assembly of emulsion droplets into linear chains. Droplets functionalized with surface-mobile DNA allow for programmable 'monomers' through which we can influence the three-dimensional structure of the assembled 'polymer'. Such model polymers can be used to study conformational changes of polypeptides and the principles governing protein folding. In our system, we find that droplets bind via complementary DNA strands that are recruited into adhesion patches. Recruitment is driven by the DNA hybridization energy, and is limited by the energy cost of surface deformation and the entropy loss of the mobile linkers, yielding adhesion patches of a characteristic size with a given number of linkers. By tuning the initial surface coverage of linkers, we control valency between the droplets to create linear or branched polymer chains. We additionally control the flexibility of the model polymers by varying the salt concentration and study their dynamics between extended and collapsed states. This system opens the possibility of programming stable three-dimensional structures, such as those found within folded proteins.

  6. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    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

  7. Formation of globules and aggregates of DNA chains in DNA/polyethylene glycol/monovalent salt aqueous solutions

    OpenAIRE

    Kawakita, H.; Uneyama, T.; Kojima, M; Morishima, K.; Masubuchi, Y.; Watanabe, H.(Max-Planck-Institut für Kernphysik, 69117, Heidelberg, Germany)

    2009-01-01

    It has been known that giant DNA shows structural transitions in aqueous solutions under the existence of counterions and other polymers. However, the mechanism of these transitions has not been fully understood. In this study, we directly observed structures of probed (dye-labeled), dilute DNA chains in unprobed DNA/polyethylene glycol (PEG)/monovalent salt (NaCl) aqueous solutions with fluorescent microscopy to examine this mechanism. Specifically, we varied the PEG molecular weight and sal...

  8. Mechanically Invisible Polymer Coatings

    DEFF Research Database (Denmark)

    2014-01-01

    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....

  9. Polymer light emitting diodes

    International Nuclear Information System (INIS)

    We study sandwich type semiconducting polymer light emitting diodes; anode/polymer/cathode. ITO is selected as anode, this polymer is a blend of a commercially available polymer with a high hole transport ability: polyvinyl-carbazole and a laser dye: coumarin-515. Magnesium covered with silver is chosen for the anode. We study the influence of polymer thickness and coumarin doping ratio on electroluminescence spectrum, electric characteristics and quantum efficiency. An important drawback is that diodes lifetime remains low. In the second part of our study we determine degradations causes with X-Ray reflectivity experiments. It may be due to ITO very high roughness. We realize a new type of planar electroluminescent device: a channel type electroluminescent device in which polymer layer is inserted into an aluminium channel. Such a device is by far more stable than using classical sandwich structures with the same polymer composition: indeed, charges are generated by internal-field ionization and there is no injection from the electrode to the polymer. This avoids electrochemical reactions at electrodes, thus reducing degradations routes. (author)

  10. Polymer bank notes

    OpenAIRE

    Brian Lang; John Barry

    1999-01-01

    On 3 May 1999 the Bank issued a new $20 bank note into circulation that had been printed on a polymer substrate. This article traces the history of polymer, briefly describes the process of production, and highlights the benefits of the substrate and the implications for the future of bank note handling within the country.

  11. Polymers in Waveguide Packaging

    Institute of Scientific and Technical Information of China (English)

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

    2003-01-01

    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.

  12. Stiff Quantum Polymers

    OpenAIRE

    Kleinert, H

    2007-01-01

    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.

  13. Doped Chiral Polymer Metamaterials Project

    Data.gov (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...

  14. Polymer wear evaluation

    DEFF Research Database (Denmark)

    Lagerbon, Mikkel; Sivebæk, Ion Marius

    2012-01-01

    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 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. 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...

  15. Theory of polymer blends

    International Nuclear Information System (INIS)

    We have recently developed a new theoretical approach to the study of polymer liquids. The theory is based on the ''reference interaction site model'' (RISM theory) of Chandler and Andersen, which has been successful in describing the structure of small molecule liquids. We have recently extended our polymer RISM theory to the case of polymer blends. In the present investigation we have applied this theory to two special binary blends: (1) the athermal mixture where we isolate structural effects, and (2) the isotopic mixture in which structurally identical polymer chains interact with dissimilar attractive interactions. By studying these two special cases we are able to obtain insights into the molecular factors which control the miscibility in polymer mixtures. 18 refs., 2 figs

  16. Semiconducting polymer LEDs

    Directory of Open Access Journals (Sweden)

    David Braun

    2002-06-01

    The field of semiconducting polymers has its root in the 1977 discovery of the semiconducting properties of polyacetylene1. This breakthrough earned Alan Heeger, Alan MacDiarmid, and Hideki Shirakawa the 2000 Nobel Prize in Chemistry for ‘the discovery and development of conductive polymers’2–5. Other review articles capture how more than two decades of developments in the physical and chemical understanding of these novel materials has led to new device applications as active and passive electronic and optoelectronic devices ranging from diodes and transistors to polymer LEDs, photodiodes, lasers, and solar cells6–11. Much interest in plastic devices derives from the opportunities to use clever control of polymer structure combined with relatively economical polymer synthesis and processing techniques to obtain simultaneous control over electronic, optical, chemical, and mechanical features5. This article focuses on the advances leading to polymer LEDs12–14.

  17. Electroactive polymers for sensing.

    Science.gov (United States)

    Wang, Tiesheng; Farajollahi, Meisam; Choi, Yeon Sik; Lin, I-Ting; Marshall, Jean E; Thompson, Noel M; Kar-Narayan, Sohini; Madden, John D W; Smoukov, Stoyan K

    2016-08-01

    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

  18. Ion Implantation of Polymers

    DEFF Research Database (Denmark)

    Popok, Vladimir

    2012-01-01

    The current paper presents a state-of-the-art review in the field of ion implantation of polymers. Numerous published studies of polymers modified by ion beams are analysed. General aspects of ion stopping, latent track formation and changes of structure and composition of organic materials...... 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...... is put on the low-energy implantation of metal ions causing the nucleation and growth of nanoparticles in the shallow polymer layers. Electrical, optical and magnetic properties of metal/polymer composites are under the discussion and the approaches towards practical applications are overviewed....

  19. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    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...

  20. DNA data

    Data.gov (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.,...

  1. Ancient DNA

    OpenAIRE

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of t...

  2. DNA Photolyasen

    OpenAIRE

    Maul, Melanie

    2009-01-01

    Neben der fehlerfreien Weitergabe der genetischen Information während der Zellteilung durch einen intakten Replikationsapparat, ist auch die Aufrechterhaltung der genetischen Integrität der DNA durch Reparaturenzyme entscheidend für das Überleben der Zellen, sowie für einen gesunden Organismus. Um die genomische Integrität zu wahren, entwickelten sich im Laufe der Evolution verschiedene Mechanismen, u.a. die Exzisionreparatur von geschädigter DNA oder die direkte chemische R...

  3. DNA damage

    OpenAIRE

    Kumari, Sunita; Rastogi, Rajesh P.; Singh, Kanchan L.; Singh, Shailendra P; Sinha, Rajeshwar P.

    2008-01-01

    Even under the best of circumstances, DNA is constantly subjected to chemical modifications. Several types of DNA damage such as SSB (single strand break), DSB (double strand break), CPDs (cyclobutane pyrimidine dimers), 6-4PPs (6-4 photoproducts) and their Dewar valence isomers have been identified that result from alkylating agents, hydrolytic deamination, free radicals and reactive oxygen species formed by various photochemical processes including UV radiation. There are a n...

  4. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    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

  5. What Is Mitochondrial DNA?

    Science.gov (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 ...

  6. DNA and RNA sensor

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

    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.

  7. Polymer-Polymer Miscibility and Enthalpy Relaxations

    NARCIS (Netherlands)

    Bosma, Martin; Brinke, Gerrit ten; Ellis, Thomas S.

    1988-01-01

    Annealing of polymers below the glass transition temperature results in a decrease in enthalpy that is recovered during heating. The enthalpy recovery is visible as an endothermic peak in a differential scanning calorimetry (DSC) scan. The position of this peak depends on the thermal treatment given

  8. Self reinforced polymer-polymer composites

    Directory of Open Access Journals (Sweden)

    M. Bilewicz

    2007-10-01

    Full Text Available Purpose: Purpose of this paper is the applying of new technology in injection moulding technique and investigation of reinforcement of PC as dispersed phase inside PP matrix (Table 1. Second aim of work is enrichment of those composites by nanoclay and analyzing mechanical behaviour of nanocomposites.Design/methodology/approach: According to design of experiments (DOE specimens were injection moulded in the shape of rectangular bars. Additionally advanced technology of melt manipulation inside mold cavity after injection was used. To achieve this purpose Ferromatik Milacron injection moulding machine, equipped with externally controlled mold was used.Findings: Addition of nanoclay clearly presents highly reinforced system, especially for neat matrix. Evenly dispersed PC particles within PP majority show reinforcement as well. Inducement of shear rate in injection moulding radically improved absorption of energy in nanocomposite.Research limitations/implications: Different variation of material composition, such combination with other polymers and use of different reinforcements (flexible or either rigid is required to be checked in the further work.Practical implications: Reinforcement obtained thanks to dispersed phase and nanofillers creates composites with improved mechanical properties.Originality/value: Morphology development reflects on mechanical behaviour. Its manipulation may affect and improve mechanical properties. Use of advanced technologies opens wide range of possibilities in processing of polymer based systems. At present there is limited number of research of processing-structure-properties relationships of polymer-polymer composites and nanocomposites.

  9. 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.

    Science.gov (United States)

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

    2016-09-01

    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. PMID:27187187

  10. Neutron studies of polymers

    International Nuclear Information System (INIS)

    The possibility to contrast given fractions of a polymer system at a cost of a low enthalpy difference is responsible for the success of the neutron method. This approach is especially useful for polymers as compared to colloids or simple liquids, because of the significative intra- and inter-molecular correlations. In this respect, the pseudo diblock copolymer constitutes one of the best test molecule of homogeneous polymer system. A review is given of main results: polymer size in melts, true backbone conformation and universal constants related to polymer structures. Effects of mechanical stress, of mesogenic order have been revealed. Neutron spin-echo experiments have given characteristic dispersion relations of intra- and inter-polymer diffusive motions. The labelling method is however more powerful than first realized. The amplitude associated with a polymer structure at an interface has been obtained directly (as in ellipsometry) with the use of contrast variation. Such structures are currently investigated by neutron reflectivity. Latest developments are found in the use of spin polarized targets, from which important cross correlations are derived

  11. Influence of Polymer Molecular Weight on Drug-Polymer Solubility

    DEFF Research Database (Denmark)

    Knopp, Matthias Manne; Olesen, Niels Erik; Holm, Per;

    2015-01-01

    In this study, the influence of polymer molecular weight on drug-polymer solubility was investigated using binary systems containing indomethacin (IMC) and polyvinylpyrrolidone (PVP) of different molecular weights. The experimental solubility in PVP, measured using a differential scanning...... the solubility in the polymer. Hence, if a drug is soluble in an analogue of the polymer, it is most likely also soluble in the polymer. In conclusion, the solubility of a given drug-polymer system is determined by the strength of the drug-polymer interactions rather than the molecular weight of the...... polymer. Therefore, during the first screenings for drug solubility in polymers, only one representative molecular weight per polymer is needed....

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

    KAUST Repository

    Meller, Stephan

    2015-07-13

    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.

  13. Biomedical applications of polymers

    CERN Document Server

    Gebelein, C G

    1991-01-01

    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

  14. Polymer artificial muscles

    Directory of Open Access Journals (Sweden)

    Tissaphern Mirfakhrai

    2007-04-01

    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.

  15. SANS studies of polymers

    International Nuclear Information System (INIS)

    Before small-angle neutron scattering (SANS), chain conformation studies were limited to light and small angle x-ray scattering techniques, usually in dilute solution. SANS from blends of normal and labeled molecules could give direct information on chain conformation in bulk polymers. Water-soluble polymers may be examined in H2O/D2O mixtures using contrast variation methods to provide further information on polymer structure. This paper reviews some of the information provided by this technique using examples of experiments performed at the National Center for Small-Angle Scattering Research (NCSASR)

  16. Relaxation in polymers

    CERN Document Server

    Kobayashi, T

    1993-01-01

    Conjugated polymers are attractive from the viewpoint of possible applications as novel nonlinear optical materials and conductive materials. They are also very important as a group of materials of one dimensionality. The progress of research in this field is very rapid. At the present stage it is extremely useful to have review articles giving information on the most recent progress.Relaxation in Polymers contains state-of-the-art reviews on: ultrafast responses in various conjugated polymers with large optical nonlinearity; ultrafast relaxation in polysilanes; electronic properties of polysi

  17. Soluble porphyrin polymers

    Science.gov (United States)

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

    2015-07-07

    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. 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...

  19. DNA nanotechnology

    Directory of Open Access Journals (Sweden)

    Nadrian C Seeman

    2003-01-01

    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.

  20. 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

    2004-12-01

    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

  1. Microrheology of concentrated DNA solutions using optical tweezers

    Indian Academy of Sciences (India)

    Arun S Rajkumar; B M Jaffar Ali

    2008-06-01

    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.

  2. Enzyme-catalysed assembly of DNA hydrogel

    Science.gov (United States)

    Um, Soong Ho; Lee, Jong Bum; Park, Nokyoung; Kwon, Sang Yeon; Umbach, Christopher C.; Luo, Dan

    2006-10-01

    DNA is a remarkable polymer that can be manipulated by a large number of molecular tools including enzymes. A variety of geometric objects, periodic arrays and nanoscale devices have been constructed. Previously we synthesized dendrimer-like DNA and DNA nanobarcodes from branched DNA via ligases. Here we report the construction of a hydrogel entirely from branched DNA that are three-dimensional and can be crosslinked in nature. These DNA hydrogels were biocompatible, biodegradable, inexpensive to fabricate and easily moulded into desired shapes and sizes. The distinct difference of the DNA hydrogel to other bio-inspired hydrogels (including peptide-based, alginate-based and DNA (linear)-polyacrylamide hydrogels) is that the crosslinking is realized via efficient, ligase-mediated reactions. The advantage is that the gelling processes are achieved under physiological conditions and the encapsulations are accomplished in situ-drugs including proteins and even live mammalian cells can be encapsulated in the liquid phase eliminating the drug-loading step and also avoiding denaturing conditions. Fine tuning of these hydrogels is easily accomplished by adjusting the initial concentrations and types of branched DNA monomers, thus allowing the hydrogels to be tailored for specific applications such as controlled drug delivery, tissue engineering, 3D cell culture, cell transplant therapy and other biomedical applications.

  3. A Review of Monte Carlo Simulations of Polymers with PERM

    Science.gov (United States)

    Hsu, Hsiao-Ping; Grassberger, Peter

    2011-08-01

    In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the Θ point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally—as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.

  4. Designing new strategy for controlling DNA orientation in biosensors.

    Science.gov (United States)

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

    2015-01-01

    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

  5. DNA nanotechnology

    OpenAIRE

    Seeman, Nadrian C.

    2003-01-01

    Since Watson and Crick’s determination of its structure nearly 50 years ago, DNA has come to fill our lives in many areas, from genetic counseling to forensics, from genomics to gene therapy. These, and other ways in which DNA affects human activities, are related to its function as genetic material, not just our genetic material, but the genetic material of all living organisms. Here, we will ignore DNA’s biological role; rather, we will discuss how the properties that make it so successful ...

  6. Polymers for Protein Conjugation

    Directory of Open Access Journals (Sweden)

    Gianfranco Pasut

    2014-01-01

    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.

  7. Dendritic Polymers for Theranostics

    Science.gov (United States)

    Ma, Yuan; Mou, Quanbing; Wang, Dali; Zhu, Xinyuan; Yan, Deyue

    2016-01-01

    Dendritic polymers are highly branched polymers with controllable structures, which possess a large population of terminal functional groups, low solution or melt viscosity, and good solubility. Their size, degree of branching and functionality can be adjusted and controlled through the synthetic procedures. These tunable structures correspond to application-related properties, such as biodegradability, biocompatibility, stimuli-responsiveness and self-assembly ability, which are the key points for theranostic applications, including chemotherapeutic theranostics, biotherapeutic theranostics, phototherapeutic theranostics, radiotherapeutic theranostics and combined therapeutic theranostics. Up to now, significant progress has been made for the dendritic polymers in solving some of the fundamental and technical questions toward their theranostic applications. In this review, we briefly summarize how to control the structures of dendritic polymers, the theranostics-related properties derived from their structures and their theranostics-related applications.

  8. Polymer semiconductor crystals

    Directory of Open Access Journals (Sweden)

    Jung Ah Lim

    2010-05-01

    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

    Science.gov (United States)

    2016-01-01

    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. Conducting polymers: polyaniline

    Czech Academy of Sciences Publication Activity Database

    Stejskal, Jaroslav; Trchová, Miroslava; Bober, Patrycja; Humpolíček, P.; Kašpárková, V.; Sapurina, I.; Shishov, M. A.; Varga, M.

    Hoboken: John Wiley & Sons, 2015, s. 1-44. ISBN 9780471440260 Institutional support: RVO:61389013 Keywords : conducting polymers * polyaniline Subject RIV: CD - Macromolecular Chemistry http://onlinelibrary.wiley.com/book/10.1002/0471440264/

  11. THERMOCHROMIC POLYMER MATERIALS

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

    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. Shape-memory polymers

    Directory of Open Access Journals (Sweden)

    Marc Behl

    2007-04-01

    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.

  13. Supramolecular polymers in inhomogeneous systems

    OpenAIRE

    Zweistra, H.J.A.

    2007-01-01

    This thesis describes theoretical results of supramolecular polymers in inhomogeneous systems. Supramolecular polymers are linear assemblies of which the monomers are joined by reversible bonds. Many types of supramolecular polymers have been synthesized in recent years. Moreover, there are numerous compounds in nature which exhibit similar behavior. Simulations of coarse-grained models of supramolecular polymers yielded new insights into the properties of supramolecular polymers in inhomogen...

  14. Edible Polymers: Challenges and Opportunities

    OpenAIRE

    Subhas C. Shit; Shah, Pathik M.

    2014-01-01

    Edible polymers have established substantial deliberation in modern eons because of their benefits comprising use as edible materials over synthetic polymers. This could contribute to the reduction of environmental contamination. Edible polymers can practically diminish the complexity and thus improve the recyclability of materials, compared to the more traditional non-environmentally friendly materials and may be able to substitute such synthetic polymers. A synthetic hydrogel polymer unlock...

  15. Polymer optical motherboard technology

    Science.gov (United States)

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

    2008-02-01

    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.

  16. Polymer semiconductor crystals

    OpenAIRE

    Jung Ah Lim; Feng Liu; Sunzida Ferdous; Murugappan Muthukumar; Briseno, Alejandro L.

    2010-01-01

    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. Understa...

  17. Cellulose based conductive polymers

    OpenAIRE

    Lin, Haishu

    2015-01-01

    Conductive fibers show potential applications in different areas. In this thesis, cellulose and its derivatives, including carboxymethyl cellulose, cellulose acetate as well as methyl cellulose were used to produce fibers via wet spinning. Different conductive materials were also introduced in an attempt to obtain cellulose-derived conductive fibers. Different conductive fillers (Zelec, carbon black, conductive polymers) were evaluated. Among them, PEDOT and PPy conductive polymers showed...

  18. Voltammetry of conducting polymers

    OpenAIRE

    Gulaboski, Rubin

    2014-01-01

    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 ...

  19. MOLECULARLY IMPRINTED POLYMERS

    OpenAIRE

    Hall, Andrew J.

    2014-01-01

    The present invention refers to new classes of polymerisable monomers targeting biotin, a biotin derivative, a biotin analogue or a biotinylated molecule and related structures, as well as molecularly imprinted polymers obtainable by polymerisation of at least one of these monomers and at least one cross-linking monomer in the presence of a suitable template molecule. The obtained polymers may be used for separation of biotin and related small molecules, together with larger biotinylated mole...

  20. Dielectric Actuation of Polymers

    OpenAIRE

    Niu, Xiaofan

    2013-01-01

    Dielectric polymers are widely used in a plurality of applications, such as electrical insulation, dielectric capacitors, and electromechanical actuators. Dielectric polymers with large strain deformations under an electric field are named dielectric elastomers (DE), because of their relative low modulus, high elongation at break, and outstanding resilience. Dielectric elastomer actuators (DEA) are superior to traditional transducers as a muscle-like technology: large strains, high energy den...

  1. Toxicology of Biomedical Polymers

    OpenAIRE

    P. V. Vedanarayanan; A. C. Fernandez

    1987-01-01

    This paper deals with the various types of polymers, used in the fabrication of medical devices, their diversity of applications and toxic hazards which may arise out of their application. The potential toxicity of monomers and the various additives used in the manufacture of biomedical polymers have been discussed along with hazards which may arise out of processing of devices such as sterilization. The importance of quality control and stringent toxicity evaluation methods have been emphasi...

  2. Radiation treated propylene polymers

    International Nuclear Information System (INIS)

    A method is provided for imparting improved strength and discoloration resistance to a stabilized propylene polymer that is to be exposed to a sterilizing dose of radiation. From 200 to 400 ppm of a phenolic antioxidant containing an isocyanurate group in its molecular structure, and a thiosynergist in an amount at least 6 times the weight of the antioxidant, are incorporated into the polymer before irradiation

  3. Polymer Protected Gold Nanoparticles

    OpenAIRE

    Shan, Jun

    2006-01-01

    Polymer protected gold nanoparticles have successfully been synthesized by both "grafting-from" and "grafting-to" techniques. The synthesis methods of the gold particles were systematically studied. Two chemically different homopolymers were used to protect gold particles: thermo-responsive poly(N-isopropylacrylamide), PNIPAM, and polystyrene, PS. Both polymers were synthesized by using a controlled/living radical polymerization process, reversible addition-fragmentation chain transfer (RAFT)...

  4. Liquid crystalline polymers

    CERN Document Server

    Wang, Xin-Jiu

    2004-01-01

    This textbook consists of six chapters. The first chapter highlightsthe concept of liquid crystals, including chemical structure, phaseclassification, defect and texture, and continuum theory. It has beencarefully written to meet the needs of readers who do not specializein liquid crystals. The second chapter is related to the theoreticaldescription of liquid crystalline polymers, networks, and gels, whichdeals with subjects such as the formation of liquid crystallinity inthe polymer system, the phase transition and phase diagram, themolecular weight effect, chain conformation, physics proper

  5. Rapid Polymer Sequencer

    Science.gov (United States)

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

    2013-01-01

    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.

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

    Indian Academy of Sciences (India)

    S S Sekhon

    2003-04-01

    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.

  7. DNA Confined in Nanochannels and Nanoslits

    Science.gov (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

  8. Synthetic DNA

    OpenAIRE

    O’ Driscoll, Aisling; Sleator, Roy D.

    2013-01-01

    With world wide data predicted to exceed 40 trillion gigabytes by 2020, big data storage is a very real and escalating problem. Herein, we discuss the utility of synthetic DNA as a robust and eco-friendly archival data storage solution of the future.

  9. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  10. TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence

    OpenAIRE

    Fortin, Connor H.; Schulze, Katharina V.; Babbitt, Gregory A.

    2015-01-01

    Background It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence lo...

  11. Controlling polymer translocation and ion transport via charge correlations.

    Science.gov (United States)

    Buyukdagli, Sahin; Ala-Nissila, T

    2014-11-01

    We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores under physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl conductivity of open α-hemolysin pores is quantitatively explained by the presence of surface polarization effects. Upon the penetration of a DNA molecule into the pore, these polarization forces combined with the electroneutrality of DNA sets a lower boundary for the ionic current, explaining the weak salt dependence of blocked pore conductivities at dilute ion concentrations. The addition of multivalent counterions to the solution results in the reversal of the polymer charge and the direction of the electroosmotic flow. With trivalent spermidine or quadrivalent spermine molecules, the charge inversion is strong enough to stop the translocation of the polymer and to reverse its motion. This mechanism can be used efficiently in translocation experiments in order to improve the accuracy of DNA sequencing by minimizing the translocation velocity of the polymer. PMID:25310861

  12. Multilevel description of the DNA molecule translocation in solid-state synthetic nanopores

    Science.gov (United States)

    Nosik, V. L.; Rudakova, E. B.

    2016-07-01

    Interest of researchers in micro- and nanofluidics of polymer solutions and, in particular, DNA ionic solutions is constantly increasing. The use of DNA translocation with a controlled velocity through solid-state nanopores and pulsed X-ray beams in new sequencing schemes opens up new possibilities for studying the structure of DNA and other biopolymers. The problems related to the description of DNA molecular motion in a limited volume of nanopore are considered.

  13. Modeling of particle interactions in DNA-laden flows at the microscale.

    Science.gov (United States)

    Trebotichy, D; Millerz, G H; Bybee, M D

    2006-01-01

    We present a method for simulation of DNA-laden flows in complex microscale geometries. In this method an incompressible Newtonian fluid is discretized with a finite difference method in the interior of the domain and a Cartesian grid embedded boundary/volume-of-fluid method is used near the boundary. The DNA is represented by a bead-rod polymer model. The fluid and polymer are fully coupled through a body force representing hydrodynamic drag. The main objective in this work is to implement short range forces to properly model polymer-polymer and polymer-surface interactions. We will discuss two methods for these interactions: (1) a new rigid constraint algorithm whereby rods elastically bounce off one another, and (2) a classical (smooth) potential acting between rods. In addition, a smooth potential for the polymer-surface interactions is also implemented for comparison to the same interactions currently modeled by elastic collision. PMID:17959482

  14. Precursor polymer compositions comprising polybenzimidazole

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-14

    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.

  15. 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

    2016-01-01

    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....

  16. Ethanol Induced Shortening of DNA in Nanochannels

    Science.gov (United States)

    Gemmen, Greg; Reisner, Walter; Tegenfeldt, Jonas; Linke, Heiner

    2010-03-01

    The confinement of DNA in nanochannels has greatly facilitated the study of DNA polymer physics and holds promise as a powerful tool for genomic sequencing. Ethanol precipitation of DNA is a common tool in molecular biology, typically in >70% [EtOH]. Even at lower ethanol concentrations, however, DNA transforms from B-form to A-form, a shorter yet slightly less twisted conformation. Accordingly, we isolated individual YOYO-1 labeled λ-DNA molecules in 100nmx100nm channels in 0, 20, 40 and 60% [EtOH]. We observed a dramatic shortening in the mean measured lengths with increasing [EtOH] and a broadening of the distribution of measured lengths at the intermediate concentrations. These observed lengths are less than those expected from fully A-form λ-DNA, suggesting that poor solvency effects are involved. Also, substantial spatial variations in intensity in a small number of molecules at the higher [EtOH] suggest the presence of higher order DNA conformations, in accord with the observation that the effective persistence length of DNA has been greatly reduced.

  17. DNA Repair by Reversal of DNA Damage

    OpenAIRE

    Yi, Chengqi; He, Chuan

    2013-01-01

    Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-,...

  18. Spatially Varying Nanoconfinement as a Probe of Polymer Physics

    Science.gov (United States)

    Klotz, Alexander; Reisner, Walter

    2012-02-01

    Complex nanofluidic systems have the capability to unveil a rich landscape of new polymer physics. One-dimensional channels and two-dimensional slits have been used for precise measurements of persistence length and to verify scaling laws. Recently, devices with spatially varying confinement have been used to gain further control over single molecule polymer conformation. We use a system consisting of a nanofluidic slit embedded with a lattice of pits acting as entropic traps. Single DNA polymers in this system self-organize into discrete conformational states. We have shown that this system can be used to define stable DNA configurations at equilibrium and to fine-tune diffusion to a local minimum corresponding to stable conformational states. Measurements of mean occupancy with varying device parameters can be fit to theory, giving information about the confinement free energy of DNA in a nanoslit (a subject of controversy) and the strength of excluded volume interactions. Measurements of the excluded volume interaction provide information about the strength of intersegmental repulsive electrostatic interactions, quantified by the notion of effective width. The scaling of width with respect to salt concentration is observed in single DNA molecules for the first time.

  19. DNA Methylation

    OpenAIRE

    İzmirli, Müzeyyen; Tufan, Turan; Alptekin, Davut

    2012-01-01

    Methylation is a chemical reaction in biological systems for normal genome regulation and development. It is a well known type of epigenetic mechanism. Methylation which regulates gene expression via epigenetic events like gene activation, repression, and chromatin remodelling, consists of two methylation systems. One of these systems is DNA methylation whereas the other is protein (histone) methylation. These systems are associated with some fundamental abnormalities and diseases. This revi...

  20. DNA Nanorobotics

    OpenAIRE

    Hamdi M; Ferreira A

    2006-01-01

    This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics simulation the behavior of bionanorobotic components and structures through 3-D visualization. The main novelty of the proposed simulations is based on the mechanical characterization of passive/active robotic devices based on double stranded DNA molecules. Their ...

  1. DNA Methylation

    OpenAIRE

    Muzeyyen Izmirli; Turan Tufan; Davut Alptekin

    2012-01-01

    Methylation is a chemical reaction in biological systems for normal genome regulation and development. It is a well known type of epigenetic mechanism. Methylation which regulates gene expression via epigenetic events like gene activation, repression, and chromatin remodelling, consists of two methylation systems. One of these systems is DNA methylation whereas the other is protein (histone) methylation. These systems are associated with some fundamental abnormalities and diseases. This revie...

  2. 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; de la Rosa, Mario A. Díaz; Doniach, Sebastian; Shapiro, Lucy; Spakowitz, Andrew J.; McAdams, Harley H.

    2013-01-01

    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......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 is...... scaling 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...

  3. Optimization of Polymer Separation by Gradient Polymer Elution Chromatography

    OpenAIRE

    Liem, Gideon R; Wang, Linda Nien-Hwa

    2013-01-01

    High Performance Liquid Chromatography (HPLC) has been a versatile separation method for polymers for many years. Analysis of different polymers by HPLC is typically done by utilizing the differential solubility of the polymers by mixing a good solvent and an anti-solvent in various compositions. This method is called Gradient Polymer Elution Chromatography (GPEC). While GPEC has been used extensively, it commonly uses a linear gradient to separate components. Linear solvent gradients consume...

  4. Design of polymer motifs for nucleic acid recognition and assembly stabilization

    Science.gov (United States)

    Zhou, Zhun

    This dissertation describes the synthesis and assembly of bio-functional polymers and the applications of these polymers to drug encapsulation, delivery, and multivalent biomimetic macromolecular recognition between synthetic polymer and nucleic acids. The main content is divided into three parts: (1) polyacidic domains as strongly stabilizing design elements for aqueous phase polyacrylate diblock assembly; (2) small molecule/polymer recognition triggered macromolecular assembly and drug encapsulation; (3) trizaine derivatized polymer as a novel class of "bifacial polymer nucleic acid" (bPoNA) and applications of bPoNA to nanoparticle loading of DNA/RNA, silencing delivery as well as control of aptamer function. Through the studies in part (1) and part (2), it was demonstrated that well-designed polymer motifs are not only able to enhance assemblies driven by non-specific hydrophobic effect, but are also able to direct assemblies based on specific recognitions. In part (3) of this dissertation, this concept was further extended by the design of polyacrylate polymers that are capable of discrete and robust hybridization with nucleic acids. This surprising finding demonstrated both fundamental and practical applications. Overall, these studies provided insights into the rational design elements for improving the bio-functions of synthetic polymers, and significantly expanded the scope of biological applications in which polymers synthesized via controlled radical polymerization may play a role.

  5. A multi-field approach to DNA condensation

    Science.gov (United States)

    Ran, Shi-Yong; Jia, Jun-Li

    2015-12-01

    DNA condensation is an important process in many fields including life sciences, polymer physics, and applied technology. In the nucleus, DNA is condensed into chromosomes. In polymer physics, DNA is treated as a semi-flexible molecule and a polyelectrolyte. Many agents, including multi-valent cations, surfactants, and neutral poor solvents, can cause DNA condensation, also referred to as coil-globule transition. Moreover, DNA condensation has been used for extraction and gene delivery in applied technology. Many physical theories have been presented to elucidate the mechanism underlying DNA condensation, including the counterion correlation theory, the electrostatic zipper theory, and the hydration force theory. Recently several single-molecule studies have focused on DNA condensation, shedding new light on old concepts. In this document, the multi-field concepts and theories related to DNA condensation are introduced and clarified as well as the advances and considerations of single-molecule DNA condensation experiments are introduced. Project supported by the National Natural Science Foundation of China (Grant Nos. 21204065 and 20934004) and the Natural Science Foundation of Zhejiang Province, China (Grant No. Y4110357).

  6. The dynamics of the DNA denaturation transition

    CERN Document Server

    van Erp, Titus S

    2012-01-01

    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.

  7. Polymers in disordered environments

    Directory of Open Access Journals (Sweden)

    V. Blavatska

    2014-09-01

    Full Text Available A brief review of our recent studies aiming at a better understanding of the scaling behaviour of polymers in disordered environments is given. The main emphasis is on a simple generic model where the polymers are represented by (interacting self-avoiding walks and the disordered environment by critical percolation clusters. The scaling behaviour of the number of conformations and their average spatial extent as a function of the number of monomers and the associated critical exponents γ and ν are examined with two complementary approaches: numerical chain-growth computer simulations using the PERM algorithm and complete enumerations of all possible polymer conformations employing a recently developed very efficient exact counting method.

  8. Toxicology of Biomedical Polymers

    Directory of Open Access Journals (Sweden)

    P. V. Vedanarayanan

    1987-04-01

    Full Text Available This paper deals with the various types of polymers, used in the fabrication of medical devices, their diversity of applications and toxic hazards which may arise out of their application. The potential toxicity of monomers and the various additives used in the manufacture of biomedical polymers have been discussed along with hazards which may arise out of processing of devices such as sterilization. The importance of quality control and stringent toxicity evaluation methods have been emphasised since in our country, at present, there are no regulations covering the manufacturing and marketing of medical devices. Finally the question of the general and subtle long term systemic toxicity of biomedical polymers have been brought to attention with the suggestion that this question needs to be resolved permanently by appropriate studies.

  9. Protein Polymers and Amyloids

    DEFF Research Database (Denmark)

    Risør, Michael Wulff

    2014-01-01

    that inhibits its target protease through a large conformational change but mutations compromise this function and cause premature structural collapse into hyperstable polymers. Understanding the conformational disorders at a molecular level is not only important for our general knowledge on protein folding...... 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...... constructed and used to show how polymerogenic seeding and polymer propagation might happen inside the body. The locking of central structural elements during α1AT folding or in the native state represents a therapeutic strategy to prevent polymerization. Using Molecular Dynamics simulations, we identified...

  10. 'Stuffed' conducting polymers

    DEFF Research Database (Denmark)

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

    2005-01-01

    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....

  11. Semi-metallic polymers

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...... 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....

  12. Nanostructured silicate polymer concrete

    Directory of Open Access Journals (Sweden)

    Figovskiy Oleg L'vovich

    2014-03-01

    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.

  13. Flame spraying of polymers

    International Nuclear Information System (INIS)

    Statistical design-of-experiment studies of the thermal spraying of polymer powders are presented. Studies of the subsonic combustion (i.e., Flame) process were conducted in order to determine the quality and economics of polyester and urethane coatings. Thermally sprayed polymer coatings are of interest to several industries for anticorrosion applications, including the chemical, automotive, and aircraft industries. In this study, the coating design has been optimized for a site-specific application using Taguchi-type fractional-factorial experiments. Optimized coating designs are presented for the two powder systems. A substantial range of thermal processing conditions and their effect on the resultant polymer coatings is presented. The coatings were characterized by optical metallography, hardness testing, tensile testing, and compositional analysis. Characterization of the coatings yielded the thickness, bond strength, Knoop microhardness, roughness, deposition efficiency, and porosity. Confirmation testing was accomplished to verify the coating designs

  14. The structural diversity of artificial genetic polymers.

    Science.gov (United States)

    Anosova, Irina; Kowal, Ewa A; Dunn, Matthew R; Chaput, John C; Van Horn, Wade D; Egli, Martin

    2016-02-18

    Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space. PMID:26673703

  15. The relationship between periodic dinucleotides and the nucleosomal DNA deformation revealed by normal mode analysis

    International Nuclear Information System (INIS)

    Nucleosomes, which contain DNA and proteins, are the basic unit of eukaryotic chromatins. Polymers such as DNA and proteins are dynamic, and their conformational changes can lead to functional changes. Periodic dinucleotide patterns exist in nucleosomal DNA chains and play an important role in the nucleosome structure. In this paper, we use normal mode analysis to detect significant structural deformations of nucleosomal DNA and investigate the relationship between periodic dinucleotides and DNA motions. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing that they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently

  16. Polymer containing functional end groups is base for new polymers

    Science.gov (United States)

    Hirshfield, S. M.

    1971-01-01

    Butadiene is polymerized with lithium-p-lithiophenoxide to produce linear polymer containing oxy-lithium group at one end and active carbon-lithium group at other end. Living polymers represent new approach to preparation of difunctional polymers in which structural features, molecular weight, type and number of end groups are controlled.

  17. DNA binding fluorescent proteins for the direct visualization of large DNA molecules.

    Science.gov (United States)

    Lee, Seonghyun; Oh, Yeeun; Lee, Jungyoon; Choe, Sojeong; Lim, Sangyong; Lee, Hyun Soo; Jo, Kyubong; Schwartz, David C

    2016-01-01

    Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely 'paints' entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 μM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells. PMID:26264666

  18. Fabrication of a deoxyribonucleic acid polymer ridge waveguide electro-optic modulator by nanoimprint lithography

    Science.gov (United States)

    Fehrman Cory, Emily Marie

    The purpose of this dissertation is to develop the nanoimprint lithography (NIL) technique for direct patterning of the deoxyribonucleic acid biopolymer DNA-CTMA. The Mach Zehnder modulator was chosen as the test device to demonstrate the NIL patterning technique for DNA-CTMA as well as the unique optical and electrical properties of the DNA-CTMA as a cladding material for poled electro-optic polymers. Towards this goal, a DNA-CTMA clad inverted ridge waveguide is demonstrated at 633 nm and 1550 nm, the structure of which is patterned directly in the DNA-CTMA cladding by NIL. Additionally, EO modulation is demonstrated in a slab waveguide structure with DNA-CTMA cladding and SEO110 EO polymer core. Marine-derived deoxyribonucleic acid biopolymer (DNA-CTMA) is a green, nontoxic, low cost optical polymer material derived from waste products of the salmon fishing industry. It exhibits low optical loss at 1550 nm, forms a thin flexible film, is compatible with existing poled polymer technologies, increases the poling efficiency when used as a low resistivity cladding layer, and is thermally stable to 200 oC. Due to chemical incompatibility with the photoresists and the associated solvents, NIL has been developed for patterning the DNA biopolymer cladding to form an inverted ridge waveguide for the basis of the Mach Zehnder modulator. While DNA-CTMA presents significant advantages over other commonly used cladding materials for the 1550 nm wavelength range, one of the commonly used bands for optical communications, the mechanical properties and environmental susceptibility of the material poses significant fabrication challenges. A study of the effects of optical and mechanical effects of environmental humidity exposure are presented for the DNA-CTMA and SEO110 polymers used in the inverted ridge waveguide. While the soft, flexible nature of the DNA-CTMA is desirable for certain applications, this presents a challenge in producing a clean polished window for optical

  19. Antiviral Polymer Therapeutics

    DEFF Research Database (Denmark)

    Smith, Anton Allen Abbotsford

    2014-01-01

    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...

  20. Delocalization in polymer models

    CERN Document Server

    Jitomirskaya, S Yu; Stolz, G

    2003-01-01

    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.

  1. Polymers at cryogenic temperatures

    CERN Document Server

    Fu, Shao-Yun

    2013-01-01

    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.

  2. Antibacterial polymer coatings.

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-09-01

    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.

  3. Polymers and colloids

    International Nuclear Information System (INIS)

    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

  4. Nanoparticles from Renewable Polymers

    Directory of Open Access Journals (Sweden)

    Frederik Roman Wurm

    2014-07-01

    Full Text Available 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.

  5. Shape memory polymer foams

    Science.gov (United States)

    Santo, Loredana

    2016-02-01

    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.

  6. Polymers and colloids

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-11-01

    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.

  7. 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)

    2001-06-19

    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.

  8. Synthetic Metal-Containing Polymers

    Science.gov (United States)

    Manners, Ian

    2004-04-01

    The development of the field of synthetic metal-containing polymers - where metal atoms form an integral part of the main chain or side group structure of a polymer - aims to create new materials which combine the processability of organic polymers with the physical or chemical characteristics associated with the metallic element or complex. This book covers the major developments in the synthesis, properties, and applications of synthetic metal-containing macromolecules, and includes chapters on the preparation and characterization of metal-containing polymers, metallocene-based polymers, rigid-rod organometallic polymers, coordination polymers, polymers containing main group metals, and also covers dendritic and supramolecular systems. The book describes both polymeric materials with metals in the main chain or side group structure and covers the literature up to the end of 2002.

  9. Edible Polymers: Challenges and Opportunities

    Directory of Open Access Journals (Sweden)

    Subhas C. Shit

    2014-01-01

    Full Text Available Edible polymers have established substantial deliberation in modern eons because of their benefits comprising use as edible materials over synthetic polymers. This could contribute to the reduction of environmental contamination. Edible polymers can practically diminish the complexity and thus improve the recyclability of materials, compared to the more traditional non-environmentally friendly materials and may be able to substitute such synthetic polymers. A synthetic hydrogel polymer unlocked a new possibility for development of films, coatings, extrudable pellets, and synthetic nanopolymers, particularly designed for medical, agricultural, and industrial fields. Edible polymers offer many advantages for delivering drugs and tissue engineering. Edible polymer technology helps food industries to make their products more attractive and safe to use. Novel edible materials have been derived from many natural sources that have conventionally been regarded as discarded materials. The objective of this review is to provide a comprehensive introduction to edible polymers by providing descriptions in terms of their origin, properties, and potential uses.

  10. Conducting polymer 3D microelectrodes

    DEFF Research Database (Denmark)

    Sasso, Luigi; Vazquez, Patricia; Vedarethinam, Indumathi;

    2010-01-01

    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...

  11. Polymer-solvent molecular compounds

    CERN Document Server

    Guenet, Jean-Michel

    2010-01-01

    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

  12. Directed Polymer -- Directed Percolation Transition

    OpenAIRE

    Perlsman, Ehud; Havlin, Shlomo

    1999-01-01

    We study the relation between the directed polymer and the directed percolation models, for the case of a disordered energy landscape where the energies are taken from bimodal distribution. We find that at the critical concentration of the directed percolation, the directed polymer undergoes a transition from the directed polymer universality class to the directed percolation universality class. We also find that directed percolation clusters affect the characterisrics of the directed polymer...

  13. Scaling exponents of star polymers

    OpenAIRE

    von Ferber, Christian; Holovatch, Yurij

    2002-01-01

    We review recent results of the field theoretical renormalization group analysis on the scaling properties of star polymers. We give a brief account of how the numerical values of the exponents governing the scaling of star polymers were obtained as well as provide some examples of the phenomena governed by these exponents. In particular we treat the interaction between star polymers in a good solvent, the Brownian motion near absorbing polymers, and diffusion-controlled reactions involving p...

  14. Shape memory polymer medical device

    Science.gov (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.

    2010-06-29

    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.

  15. DNA Compaction by Yeast Mitochondrial Protein ABF2p

    Energy Technology Data Exchange (ETDEWEB)

    Friddle, R W; Klare, J E; Noy, A; Corzett, M; Balhorn, R; Baskin, R J; Martin, S S; Baldwin, E P

    2003-05-09

    We used high resolution Atomic Force Microscopy (AFM) to image compaction of linear and circular DNA by the yeast mitochondrial protein ABF2p , which plays a major role in maintaining mitochondrial DNA. AFM images show that protein binding induces drastic bends in the DNA backbone for both linear and circular DNA. At high concentration of ABF2p DNA collapses into a tight globular structure. We quantified the compaction of linear DNA by measuring the end-to-end distance of the DNA molecule at increasing concentrations of ABF2p. We also derived a polymer statistical mechanics model that gives quantitative description of compaction observed in our experiments. This model shows that a number of sharp bends in the DNA backbone is often sufficient to cause DNA compaction. Comparison of our model with the experimental data showed excellent quantitative correlation and allowed us to determine binding characteristics for ABF2. Our studies indicate that ABF2 compacts DNA through a novel mechanism that involves bending of DNA backbone. We discuss the implications of such a mechanism for mitochondrial DNA maintenance.

  16. Polymer Thermoelectric Generators: Device Considerations

    Science.gov (United States)

    Yee, Shannon

    2014-03-01

    Recent control of the transport properties in polymers has encouraged the development of polymer thermoelectric (TE) devices. Polymer TEs are thought to be less expensive and more scalable than their inorganic counterparts. The cost of the raw material is less and polymer TEs can leverage the large areal manufacturing technique established by the plastics industry. Additionally, while the overall ZT of polymer TEs appears attractive, individual polymer properties have a very different scale than their inorganic counterparts (i.e., the thermal conductivity and electrical conductivity are approximately one and two orders of magnitude smaller, respectively). Furthermore, the majority of TE measurements on polymers have been limited to thin-films where traditional TE materials are measured in bulk. So why should it be expected that polymer TE devices resemble traditional TE devices? Given the uniqueness of polymers, different device architectures are proposed that can leverage the unique strengths of polymer films. It will be shown that by logically considering device requirements, new polymer TE devices have non-linear features that are more attractive than linear inorganic TE devices. This leads to very different device optimizations that favor polymer TEs.

  17. Polymer modification via. cluster formation

    International Nuclear Information System (INIS)

    Ion beam treatment studies have been carried out to investigate the potential for improvements in conductivity properties of the polymers. Change in polymer stoichiometry were characterised by investigating into the carbon clusters formed along the latent tracks of energetic ions in polymers. Here we present some new results which have been derived from UV-Vis spectroscopic examinations. (author)

  18. Aerogel/polymer composite materials

    Science.gov (United States)

    Williams, Martha K. (Inventor); Smith, Trent M. (Inventor); Fesmire, James E. (Inventor); Roberson, Luke B. (Inventor); Clayton, LaNetra M. (Inventor)

    2010-01-01

    The invention provides new composite materials containing aerogels blended with thermoplastic polymer materials at a weight ratio of aerogel to thermoplastic polymer of less than 20:100. The composite materials have improved thermal insulation ability. The composite materials also have better flexibility and less brittleness at low temperatures than the parent thermoplastic polymer materials.

  19. Viscoelastic Properties of Polymer Blends

    Science.gov (United States)

    Hong, S. D.; Moacanin, J.; Soong, D.

    1982-01-01

    Viscosity, shear modulus and other viscoelastic properties of multicomponent polymer blends are predicted from behavior of individual components, using a mathematical model. Model is extension of two-component-blend model based on Rouse-Bueche-Zimm theory of polymer viscoelasticity. Extension assumes that probabilities of forming various possible intracomponent and intercomponent entanglements among polymer molecules are proportional to relative abundances of components.

  20. Agarose Gel Electrophoresis for the Separation of DNA Fragments

    OpenAIRE

    Lee, Pei Yun; Costumbrado, John; Hsu, Chih-Yuan; Kim, Yong Hoon

    2012-01-01

    Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb1. Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits2. During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel's molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA....

  1. DNA repair

    International Nuclear Information System (INIS)

    In this chapter a series of DNA repair pathways are discussed which are available to the cell to cope with the problem of DNA damaged by chemical or physical agents. In the case of microorganisms our knowledge about the precise mechanism of each DNA repair pathway and the regulation of it has been improved considerably when mutants deficient in these repair mechanisms became available. In the case of mammalian cells in culture, until recently there were very little repair deficient mutants available, because in almost all mammalian cells in culture at least the diploid number of chromosomes is present. Therefore the frequency of repair deficient mutants in such populations is very low. Nevertheless because replica plating techniques are improving some mutants from Chinese hamsters ovary cells and L5178Y mouse lymphoma cells are now available. In the case of human cells, cultures obtained from patients with certain genetic diseases are available. A number of cells appear to be sensitive to some chemical or physical mutagens. These include cells from patients suffering from xeroderma pigmentosum, Ataxia telangiectasia, Fanconi's anemia, Cockayne's syndrome. However, only in the case of xeroderma pigmentosum cells, has the sensitivity to ultraviolet light been clearly correlated with a deficiency in excision repair of pyrimidine dimers. Furthermore the work with strains obtained from biopsies from man is difficult because these cells generally have low cloning efficiencies and also have a limited lifespan in vitro. It is therefore very important that more repair deficient mutants will become available from established cell lines from human or animal origin

  2. Wrinkled DNA.

    OpenAIRE

    Arnott, S.; Chandrasekaran, R.; Puigjaner, L C; Walker, J K; Hall, I H; Birdsall, D L; Ratliff, R L

    1983-01-01

    The B form of poly d(GC):poly d(GC) in orthorhombic microcrystallites in oriented fibers has a secondary structure in which a dinucleotide is the repeated motif rather than a mononucleotide as in standard, smooth B DNA. One set of nucleotides (probably GpC) has the same conformations as the smooth form but the alternate (CpG) nucleotides have a different conformation at C3'-O3'. This leads to a distinctive change in the orientation of the phosphate groups. Similar perturbations can be detecte...

  3. A chloroplast DNA deletion located in RNA polymerase gene rpoC2 in CMS lines of sorghum.

    Science.gov (United States)

    Chen, Z; Muthukrishnan, S; Liang, G H; Schertz, K F; Hart, G E

    1993-01-01

    Fertile lines of sorghum (Sorghum bicolor) were shown to differ from cytoplasmic male sterile (CMS) lines by the presence of a 3.8 kb HindIII chloroplast DNA fragment in the former and a smaller (3.7 kb) fragment in the latter. DNA/DNA hybridization studies showed that these two fragments are homologous. Fertile plants from S. versicolor, S. almum, S. halepense, and Sorghastrum nutans (Yellow Indiangrass) also have the 3.8 kb fragment, and CMS lines studied containing A1, A2 and A3 cytoplasms have the 3.7 kb fragment. The size difference between the two fragments was localized to a 1.0 kb SacI-HindIII fragment by restriction mapping. A 165 bp deletion, which is flanked by a 51 bp tandem repeat, was identified in the CMS lines by sequencing the clones. Comparison of the two sequences with those from maize, rice, tobacco, spinach, pea, and liverwort revealed that the deleted sequence is located in the middle of the RNA polymerase beta" subunit encoded by the gene rpoC2. The amino acid sequence deleted in the CMS lines is in a monocot-specific region which contains two protein motifs that are characteristic of several transcriptional activation factors, namely, a leucine zipper motif and an acidic domain capable of forming an amphipathic alpha-helix. Further studies designed to determine whether or not the deletion is involved in CMS of sorghum are underway. PMID:8437572

  4. Active DNA Demethylation Mediated by DNA Glycosylases

    OpenAIRE

    Zhu, Jian-Kang

    2009-01-01

    Active DNA demethylation is involved in many vital developmental and physiological processes of plants and animals. Recent genetic and biochemical studies in Arabidopsis have demonstrated that a subfamily of DNA glycosylases function to promote DNA demethylation through a base excision-repair pathway. These specialized bifunctional DNA glycosylases remove the 5-methylcytosine base and then cleave the DNA backbone at the abasic site, resulting in a gap that is then filled with an unmethylated ...

  5. Molecular imaging of shear-induced polymer migration near a surface in dilute and semidilute solutions

    Science.gov (United States)

    Fang, Lin

    The goal of our research is to optically visualize shear-induced polymer migration near a surface on the single molecular level, and to enhance current understanding of interactions between flowing polymer solutions with surfaces. By using epi-fluorescence microscopy, we measured the mean fractional stretch and concentrations of lambda-phage DNA molecules above a glass surface in shear flows in a microchannel and a torsional shear cell. We find that DNA molecules are driven away to create a depletion layer near the surface. The shear-induced migration is enhanced with a larger depletion layer at high Weissenberg number (Wi), in qualitative agreement with theories. We proposed a simple mechanism for this shear-induced migration based on hydrodynamic interaction (HI) between the surface and polymer chains. We find that the thickness of depletion layer of lambda-phage DNA molecules is about 10mum at Wi = 10.3, which is thinner than in the predictions for the FENE-P dumbbell model [Ma and Graham (2005)] and in Brownian dynamics simulations. The discrepancies suggest that current theoretical models of the polymer migration phenomenon are incomplete. We find that the time scale of DNA migration is on the order of the diffusion time over the distance of depletion layer, and that the mean fractional stretch of DNA molecules decreases near the surface over this same time scale. Experiments with deliberately fragmented DNA indicate that the decrease in mean fractional stretch near the surface might be caused by the selective retention of fragments in the DNA solution owing to weaker HI effects between the surface and shorter polymer chains. The shear-induced migration of DNA molecules exists in diminished form up to 3.0 c* (c* is the overlap concentration), implying that: in the traditionally defined dilute regime (c c*); while the chains are overlapping, they do not screen out HI completely up to 3.0 c*.

  6. Polymer dye lasers

    DEFF Research Database (Denmark)

    Balslev, Søren

    2006-01-01

    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...... enkelt optisk ”mode”. Laserne er baseret på en mængde forskellige optiske egenskaber af polymer tyndfilm og vædsker. De praktiske muligheder for at integrere polymer farvestoflaserne demonstreres ved at integrere en mængde optiske og væske- komponenter på en enkelt chip sammen med en miniaturiseret...

  7. Cyclic polymers from alkynes

    Science.gov (United States)

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

    2016-08-01

    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.

  8. Segmented conjugated polymers

    Indian Academy of Sciences (India)

    G Padmanaban; S Ramakrishnan

    2003-08-01

    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.

  9. Rippling of polymer nanofibers.

    Science.gov (United States)

    Wu, Xiang-Fa; Kostogorova-Beller, Yulia Y; Goponenko, Alexander V; Hou, Haoqing; Dzenis, Yuris A

    2008-12-01

    This paper studies the evolution mechanism of surface rippling in polymer nanofibers under axial stretching. This rippling phenomenon has been detected in as-electrospun polyacrylonitrile in recent single-fiber tension tests, and in electrospun polyimide nanofibers after imidization. We herein propose a one-dimensional nonlinear elastic model that takes into account the combined effect of surface tension and nonlinear elasticity during the rippling initiation and its evolution in compliant polymer nanofibers. The polymer nanofiber is modeled as an incompressible, isotropically hyperelastic Mooney-Rivlin solid. The fiber geometry prior to rippling is considered as a long circular cylinder. The governing equation of surface rippling is established through linear perturbation of the static equilibrium state of the nanofiber subjected to finite axial prestretching. The critical stretch and ripple wavelength are determined in terms of surface tension, elastic property, and fiber radius. Numerical examples are demonstrated to examine these dependencies. In addition, a critical fiber radius is determined, below which the polymer nanofibers are intrinsically unstable. The present model, therefore, is capable of predicting the rippling condition in compliant nanofibers, and can be further used as a continuum mechanics approach for the study of surface instability and nonlinear wave propagation in compliant fibers and wires at the nanoscale. PMID:19256861

  10. Metal-Polymer Nanocomposites

    Science.gov (United States)

    Nicolais, Luigi; Carotenuto, Gianfranco

    2004-09-01

    A unique guide to an essential area of nanoscience Interest in nano-sized metals has increased greatly due to their special characteristics and suitability for a number of advanced applications. As technology becomes more refined-including the ability to effectively manipulate and stabilize metals at the nanoscale-these materials present ever-more workable solutions to a growing range of problems. Metal-Polymer Nanocomposites provides the first guide solely devoted to the unique properties and applications of this essential area of nanoscience. It offers a truly multidisciplinary approach, making the text accessible to readers in physical, chemical, and materials science as well as areas such as engineering and topology. The thorough coverage includes: * The chemical and physical properties of nano-sized metals * Different approaches to the synthesis of metal-polymer nanocomposites (MPN) * Advanced characterization techniques and methods for study of MPN * Real-world applications, including color filters, polarizers, optical sensors, nonlinear optical devices, and more * An extensive list of references on the topics covered A unique, cutting-edge resource for a vital area of nanoscience development, Metal-Polymer Nanocomposites is an invaluable text for students and practitioners of materials science, engineering, polymer science, chemical engineering, electrical engineering, and optics.

  11. Polymers of phenylenediamines

    Czech Academy of Sciences Publication Activity Database

    Stejskal, Jaroslav

    2015-01-01

    Roč. 41, February (2015), s. 1-31. ISSN 0079-6700 R&D Projects: GA ČR(CZ) GA13-00270S Institutional support: RVO:61389013 Keywords : polyphenylenediamine * phenylenediamine * conducting polymers Subject RIV: CD - Macromolecular Chemistry Impact factor: 26.932, year: 2014

  12. Self-sterilizing polymers

    Science.gov (United States)

    Tulis, J. J.; Daley, D. J.; Phillips, G. B.

    1973-01-01

    Addition of approximately 1% paraformaldehyde to room-temperature-vulcanizing potting polymer results in effective, controllable germicide. When heated above ambient temperatures, paraformaldehyde releases dry formaldehyde, which can penetrate enclosed areas and packages, will not damage material, and leaves no permanent residue.

  13. Transferases in Polymer Chemistry

    NARCIS (Netherlands)

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

    2010-01-01

    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

  14. Conformational properties of polymers

    Indian Academy of Sciences (India)

    A R Singh; D Giri; S Kumar

    2008-08-01

    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.

  15. Radiation curing of polymers

    International Nuclear Information System (INIS)

    Papers are presented on the surface coating applications, techniques and chemistry of radiation curing of polymers using ultraviolet, electron beam and laser radiation sources. Areas covered include printing, lacquers, wood finishes, adhesives and plastics. New work on photoinitiators is reported. (U.K.)

  16. Phosphazene Polymers Containing Carborane

    Science.gov (United States)

    Fewell, L. L.; Parker, J. A.; Basi, R. J.

    1986-01-01

    Addition of carborane increases thermal stability. Carborane-substituted polyphosphazenes prepared by thermal polymerization of phenylcarbonyl-pentachlorocyclotriphosphazene followed by reaction with sodium trifluoroethoxide to replace remaining chlorine atoms with trifluoroethoxy groups. Improved polymers offer high char yields and resistance to hydrolysis.

  17. Multichannel arrays on polymer substrates: toward a disposable proteomics chip

    Science.gov (United States)

    Becker, Holger; Ehrfeld, Wolfgang; Pommersheim, Rainer

    1999-03-01

    Miniaturization is dramatically changing the shape of biotechnology. After the first wave of discoveries inventions in the field of analytical methods and DNA-probes on silicon chips, the trend in recent years has been to more complex and integrated systems in terms of microfabrication for production purposes mainly focused on polymer substrates. Additionally, an increased complexity in the biochemical functionality for tasks like cell handling, cell lysis, polymerase chain reaction, DNA-sequencing and recently in the field of proteomics research can be observed. In this paper we describe the practical approach to a polymer substrate based, microfabricated chip-based multichannel array for 2D capillary electrophoresis. This chip can be fabricated by classical mass production techniques like hot embossing or injection modeling, and has the potential for on-chip-integration of electrodes and detection system.

  18. BEAM applications to polymer materials

    International Nuclear Information System (INIS)

    Recently papers about beam applications to polymers have been increasing rapidly both in the fundamental and applied fields. Fairly large number of papers have been published in the fundamental aspects of radiation effects of beam applications to polymers such as pulse radiolysis and high density electronic excitation effects. A number of papers have been published in the more applied aspects of beam applications to polymers such as radiation processing and curing. The present paper describes recent beam applications to polymers. 1. Radiation Effects on Polymers; Radiation effects on polymers have been studied for more than 40 years. Most of work on radiation effects on polymers has been carried out by using high energy photon (gamma-ray) and electron beams, since polymers are sensitive to any kinds of ionizing radiation. Even non-ionizing radiation such as ultraviolet and visible light excites electronic excited states of polymers and then photo-chemical reactions of polymers are induced from the electronic excited states. Studies on radiation effects of other ionizing radiation on polymers have not been so popular for a long time. Recently application of new radiation such as ion beams to polymers have been worthy of remark in fields of advanced science and technology, since new radiation beams induce different radiation effects from those induced by high energy gamma-rays and electrons. 2. Beam Applications of Polymers; Recent progress in beam applications to polymers such as radiation processing and curing, x-ray and electron beam microlithography, and applications of new beams such as ion beams to polymers has been reviewed. (author)

  19. φ29 DNA polymerase

    OpenAIRE

    Blanco, Luis; Bernad, Antonio; Salas, Margarita

    1996-01-01

    An improved method for determining the nucleotide base sequence of a DNA molecule employs a φ-29 type DNA polymerase modified to have reduced or no exonuclease activity. The method includes annealing the DNA molecule with a primer molecule able to hybridize to the DNA molecule; incubating the annealed mixture in a vessel containing four different deoxynucleoside triphosphates, a DNA polymerase, and one or more DNA synthesis terminating agents which terminate DNA synthesis at a specific nucleo...

  20. Self-diffusion in binary blends of cyclic and linear polymers

    OpenAIRE

    Shanbhag, Sachin

    2008-01-01

    A lattice model is used to estimate the self-diffusivity of entangled cyclic and linear polymers in blends of varying compositions. To interpret simulation results, we suggest a minimal model based on the physical idea that constraints imposed on a cyclic polymer by infiltrating linear chains have to be released, before it can diffuse beyond a radius of gyration. Both, the simulation, and recently reported experimental data on entangled DNA solutions support the simple model over a wide range...

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

    Directory of Open Access Journals (Sweden)

    Manohar Mahato

    2014-01-01

    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.

  2. Conducting Polymers for Neutron Detection

    International Nuclear Information System (INIS)

    Conjugated polymers have emerged as an attractive technology for large-area electronic applications. As organic semiconductors, they can be used to make large-area arrays of diodes or transistors using fabrication techniques developed for polymer coatings, such as spraying and screen-printing. We have demonstrated both neutron and alpha detection using diodes made from conjugated polymers and have done preliminary work to integrate a boron carbide layer into the conventional polymer device structure to capture thermal neutrons. The polymer devices appear to be insensitive to gamma rays, due to their small physical thickness and low atomic number

  3. Conducting Polymers for Neutron Detection

    Energy Technology Data Exchange (ETDEWEB)

    Kimblin, Clare; Miller, Kirk; Vogel, Bob; Quam, Bill; McHugh, Harry; Anthony, Glen; Mike, Grover

    2007-12-01

    Conjugated polymers have emerged as an attractive technology for large-area electronic applications. As organic semiconductors, they can be used to make large-area arrays of diodes or transistors using fabrication techniques developed for polymer coatings, such as spraying and screen-printing. We have demonstrated both neutron and alpha detection using diodes made from conjugated polymers and have done preliminary work to integrate a boron carbide layer into the conventional polymer device structure to capture thermal neutrons. The polymer devices appear to be insensitive to gamma rays, due to their small physical thickness and low atomic number.

  4. Frictional properties of confined polymers

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...

  5. Conjugated Polymer Surfaces and Interfaces

    Science.gov (United States)

    Salaneck, W. R.; Stafstrom, S.; Brédas, J. L.

    2003-10-01

    The authors illustrate the basic physics and materials science of conjugated polymers and their interfaces, particularly, but not exclusively, as they are applied to polymer-based light emitting diodes. The approach is to describe the basic physical and associated chemical principles that apply to these materials, which in many instances are different from those that apply to their inorganic counterparts. The main aim of the authors is to highlight specific issues and properties of polymer surfaces and interfaces that are relevant in the context of the emerging field of polymer-based electronics in general, and polymer-based light emitting diodes in particular. Both theoretical and experimental methods used in the study of these systems are discussed. This book will be of interest to graduate students and research workers in departments of physics, chemistry, electrical engineering and materials sciences studying polymer surfaces and interfaces and their application in polymer-based electronics.

  6. POLYMER ELECTROLYTE MEMBRANE FUEL CELLS

    DEFF Research Database (Denmark)

    2001-01-01

    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. With the...... thermally resistant polymer, e.g., polybenzimidazole or a mixture of polybenzimidazole and other thermoplastics as binder, the carbon-supported noble metal catalyst is tape-cast onto a hydrophobic supporting substrate. When doped with an acid mixture, electrodes are assembled with an acid doped solid...

  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

    2012-01-01

    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. Sequence-specific and general transcriptional activation by the bovine papillomavirus-1 E2 trans-activator require an N-terminal amphipathic helix-containing E2 domain.

    OpenAIRE

    Haugen, T H; Turek, L P; Mercurio, F M; Cripe, T P; Olson, B J; Anderson, R D; D. Seidl; Karin, M; Schiller, J.

    1988-01-01

    The sequence-specific trans-activator protein of bovine papillomavirus (BPV)-1, E2, strongly increases transcription at promoters containing papillomaviral ACCG(N)4CGGT (E2P) cis motifs, but can also activate a wide range of co-transfected promoters without E2P cores to a lower extent. Analysis of multiple E2 mutants in transfected cells revealed that the C-terminal DNA binding E2 domain binds to the E2P cis sequences in the form of pre-existing nuclear dimers. The DNA binding function of E2 ...

  9. SMS-5 Polymers and surfaces

    International Nuclear Information System (INIS)

    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 prevention of protein adsorption and anti-fouling activity. However, the characterization of polymer brush is still not straightforward since the brush layer is embedded between solid and water interface. One of limited number of analytical methods to reveal solid/water interface structures is neutron reflectivity (NR). We have been applying NR to reveal the problems related to polymer brush at solid/water interfaces and here present two subjects related to polymer brush. The first subject will be dynamic polymer brush which utilizes the surface segregation phenomena of copolymers with surface-active blocks for preparing polymer brush in spontaneous process. We have reported hydrophilic polymer brushes formed at the interface between water and hydrophobic elastomer by the segregation of amphiphilic diblock copolymers blended in the elastomer. In this system, while the hydrophilic block with high surface energy avoids air surface, upon contact with water the hydrophilic block segregates to cover the interface between hydrophobic elastomer and water. Surprisingly high density dynamic polymer brush at D2O/polymer interfaces was observed by NR. The second subject will be evaluating inclusion kinetics of polyrotaxane formation using NR. A polyrotaxane is composed of a polymer chain and cyclic molecules such as polyethylene glycol (PEG) and cyclodextrin (CD). Inclusion complex formation of a polymer chain with cyclic molecules is an important step to synthesize polyrotaxanes. However, inclusion complex formation induces gelation or precipitation of the complex, and hence makes detailed observation of the reaction difficult. We fixed polymer chains on a substrate, which is polymer brush, and conducted in-situ time slice NR measurement. NR results showed that brush layer thickness gradually increases and reaches its plateau by inclusion

  10. Effect of introduction of chondroitin sulfate into polymer-peptide conjugate responding to intracellular signals

    Science.gov (United States)

    Tomiyama, Tetsuro; Toita, Riki; Kang, Jeong-Hun; Koga, Haruka; Shiosaki, Shujiro; Mori, Takeshi; Niidome, Takuro; Katayama, Yoshiki

    2011-09-01

    We recently developed a novel tumor-targeted gene delivery system responding to hyperactivated intracellular signals. Polymeric carrier for gene delivery consists of hydrophilic neutral polymer as main chains and cationic peptide substrate for target enzyme as side chains, and was named polymer-peptide conjugate (PPC). Introduction of chondroitin sulfate (CS), which induces receptor-medicated endocytosis, into polymers mainly with a high cationic charge density such as polyethylenimine can increase tumor-targeted gene delivery. In the present study, we examined whether introduction of CS into PPC containing five cationic amino acids can increase gene expression in tumor cells. Size and zeta potential of plasmid DNA (pDNA)/PPC/CS complex were stability and gene regulation, compared with that of pDNA/PPC. Moreover, no difference in gene expression was identified between positive and negative polymer. These results were caused by fast disintegration of pDNA/PPC/CS complexes in the presence of serum. Thus, we suggest that introduction of negatively charged CS into polymers with a low charge density may lead to low stability and gene regulation of complexes.

  11. DNA ligase I, the replicative DNA ligase

    OpenAIRE

    Howes, Timothy R.L.; Tomkinson, Alan E.

    2012-01-01

    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...

  12. Interaction of fragmented double-stranded DNA with carbon nanotubes in aqueous solution

    Science.gov (United States)

    Gladchenko, G. O.; Karachevtsev, M. V.; Leontiev, V. S.; Valeev, V. A.; Glamazda, A. Yu.; Plokhotnichenko, A. M.; Stepanian, S. G.

    Aqueous suspensions of ultrasonically fragmented double-stranded (fds-) DNA and single-walled carbon nanotubes (SWNTs) have been investigated by UV- and IR-absorption, NIR-emission and Raman spectroscopy. According to gel-electrophoresis, the lengths of the polymer fragments were 100-500 base pairs. Analysis of IR and UV data indicates the presence of both double-stranded (ds) and single-stranded (ss)-regions in the fragments. SWNT complex with DNA was revealed by NIR-emission and Raman spectroscopy. It turned out that fds-DNA is less efficient in holding nanotubes in the aqueous solution than ss-DNA. From the UV-data, the character of the helix-coil transition is seen to be like that for fds-DNA off and on nanotube, however, DNA thermostability increased in this latter case. The effective charge density on the DNA sugar-phosphate backbone of the fds-DNA:SWNT hybrid was less than that of DNA alone. Spectroscopic data can be explained by a model in which the formation of hybrids starts due to the interaction between untwisted ss-regions of DNA and the nanotube: the strands wrap on the tube and thus create an 'anchor' for the whole polymer. The ds-part of the polymer is located close to the nanotube.

  13. CONTROL OF POLYMER PARTICLE SIZE USING POROUS GLASS MEMBRANE EMULSIFICATION A REVIEW

    Institute of Scientific and Technical Information of China (English)

    Guanghui Ma

    2003-01-01

    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. Dimensional reduction of duplex DNA under confinement to nanofluidic slits.

    Science.gov (United States)

    Vargas-Lara, Fernando; Stavis, Samuel M; Strychalski, Elizabeth A; Nablo, Brian J; Geist, Jon; Starr, Francis W; Douglas, Jack F

    2015-11-14

    There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency. Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations. PMID

  15. Antiviral Activity of Metal-Containing Polymers—Organotin and Cisplatin-Like Polymers

    Directory of Open Access Journals (Sweden)

    Girish Barot

    2011-05-01

    Full Text Available Polymers containing platinum and to a lesser extent tin, have repeatedly demonstrated antitumor activity in vitro and in vivo against a variety of cell and tumor types. The mechanisms responsible for the antitumor activity include inducing a delay in cell proliferation and sister chromatid exchanges blocking tumor growth. As most DNA and some RNA viruses require, and even induce, infected cells to initiate DNA replication and subsequent cell division, compounds with antitumor activity will very likely also possess antiviral activity. This article examines the use of metal-containing polymers as a novel class of antivirals.

  16. Coarse-graining polymers as soft colloids

    OpenAIRE

    Louis, A. A.; Bolhuis, P. G.; Finken, R.; Krakoviack, V.; Meijer, E. J.; Hansen, J. P.

    2001-01-01

    We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the polymers. We also show how to extend these methods to polymers in poor solvents and mixtures of polymers. Treating polymers as soft colloids can greatly speed up the simulation of complex many-polymer systems, including polymer-colloid mixtures.

  17. Polymer multilayer tattooing for enhanced DNA vaccination.

    Science.gov (United States)

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

    2013-04-01

    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. PMID:23353628

  18. Solid polymer membrane program

    Science.gov (United States)

    1971-01-01

    The results are presented for a solid polymer electrolyte fuel cell development program. Failure mechanism was identified and resolution of the mechanism experienced in small stack testing was demonstrated. The effect included laboratory analysis and evaluation of a matrix of configurations and operational variables for effects on the degree of hydrogen fluoride released from the cell and on the degree of blistering/delamination occurring in the reactant inlet areas of the cell and to correlate these conditions with cell life capabilities. The laboratory evaluation tests were run at conditions intended to accelerate the degradation of the solid polymer electrolyte in order to obtain relative evaluations as quick as possible. Evaluation of the resolutions for the identified failure mechanism in space shuttle configuration cell assemblies was achieved with the fabrication and life testing of two small stack buildups of four cell assemblies and eight cells each.

  19. All Polymer Micropump

    DEFF Research Database (Denmark)

    Hansen, Thomas Steen

    2008-01-01

    In this thesis an all polymer micropump, and the fabrication method required to fabricate this, are examined. Polymer microfluidic. devices are of major scientific interest because they can combine complicated chemical and biological analys~s in cheap and disposable devices. The electrode system...... room techniques. The conductive blend was coated with a layer of photoresist, exposed and developed. The resulting pattern was etched in a reactive ion etcher, yielding a well defined patterned with a resolution of approximately 2 J..lm. This technique was utilised to fabricate an ac electroosmotic...... 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...

  20. Photogenerating work from polymers

    Directory of Open Access Journals (Sweden)

    Hilmar Koerner

    2008-07-01

    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.

  1. Dielectric Actuation of Polymers

    Science.gov (United States)

    Niu, Xiaofan

    Dielectric polymers are widely used in a plurality of applications, such as electrical insulation, dielectric capacitors, and electromechanical actuators. Dielectric polymers with large strain deformations under an electric field are named dielectric elastomers (DE), because of their relative low modulus, high elongation at break, and outstanding resilience. Dielectric elastomer actuators (DEA) are superior to traditional transducers as a muscle-like technology: large strains, high energy densities, high coupling efficiency, quiet operation, and light weight. One focus of this dissertation is on the design of DE materials with high performance and easy processing. UV radiation curing of reactive species is studied as a generic synthesis methodology to provide a platform for material scientists to customize their own DE materials. Oligomers/monomers, crosslinkers, and other additives are mixed and cured at appropriate ratios to control the stress-strain response, suppress electromechanical instability of the resulting polymers, and provide stable actuation strains larger than 100% and energy densities higher than 1 J/g. The processing is largely simplified in the new material system by removal of the prestretching step. Multilayer stack actuators with 11% linear strain are demonstrated in a procedure fully compatible with industrial production. A multifunctional DE derivative material, bistable electroactive polymer (BSEP), is invented enabling repeatable rigid-to-rigid deformation without bulky external structures. Bistable actuation allows the polymer actuator to have two distinct states that can support external load without device failure. Plasticizers are used to lower the glass transition temperature to 45 °C. Interpenetrating polymer network structure is established inside the BSEP to suppress electromechanical instability, providing a breakdown field of 194 MV/m and a stable bistable strain as large as 228% with a 97% strain fixity. The application of BSEP

  2. 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

    2015-01-01

    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.

  3. Knots in polymers

    Indian Academy of Sciences (India)

    Yacov Kantov

    2005-06-01

    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.

  4. Photoelectrically active polymer nanocomposites

    Czech Academy of Sciences Publication Activity Database

    Pfleger, Jiří; Pavlík, Martin; Plieth, W.; Vohlídal, J.

    Prague : Ústav chemických procesů AV ČR, 2004, O22/1-3. [International Conference on Polymers and Organic Chemistry /11./. Prague (CZ), 18.06.2004-23.06.2004] R&D Projects: GA AV ČR IAA4050406 Institutional research plan: CEZ:AV0Z4050913 Keywords : nanocomposites * core/shell nanoparticles Subject RIV: CF - Physical ; Theoretical Chemistry

  5. Dynamics of polymers

    International Nuclear Information System (INIS)

    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

  6. Polymers in Fractal Disorder

    OpenAIRE

    Fricke, Niklas

    2016-01-01

    This work presents a numerical investigation of self-avoiding walks (SAWs) on percolation clusters, a canonical model for polymers in disordered media. A new algorithm has been developed allowing exact enumeration of over ten thousand steps. This is an increase of several orders of magnitude compared to previously existing enumeration methods, which allow for barely more than forty steps. Such an increase is achieved by exploiting the fractal structure of critical percolation clusters: they a...

  7. Mass transport in polymers

    OpenAIRE

    Ferrari, Maria Chiara

    2009-01-01

    The study of mass transport in polymeric membranes has grown in importance due to its potential application in many processes such as separation of gases and vapors, packaging, controlled drug release. The diffusion of a low molecular weight species in a polymer is often accompanied by other phenomena like swelling, reactions, stresses, that have not been investigated in all their aspects yet. Furthermore, novel materials have been developed that include inorganic fillers, reactive functional...

  8. Absorbable and biodegradable polymers

    CERN Document Server

    Shalaby, Shalaby W

    2003-01-01

    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

  9. Electrochemical polymer electrolyte membranes

    CERN Document Server

    Fang, Jianhua; Wilkinson, David P

    2015-01-01

    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

  10. High performance polymer concrete

    OpenAIRE

    Frías, M.; San-José, J. T.

    2007-01-01

    This paper studies the performance of concrete whose chief components are natural aggregate and an organic binder —a thermosetting polyester resin— denominated polymer concrete or PC. The material was examined macro- and microscopically and its basic physical and mechanical properties were determined using mercury porosimetry, scanning electron microscopy (SEM-EDAX), X-ray diffraction (XRD) and strength tests (modulus of elasticity, stress-strain curves and ultimate strengths). A...

  11. Dynamics of polymers

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-11-01

    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.

  12. Conductive Polymer Composites

    OpenAIRE

    Pierini, Filippo

    2013-01-01

    In recent years, nanotechnologies have led to the production of materials with new and sometimes unexpected qualities through the manipulation of nanoscale components. This research aimed primarily to the study of the correlation between hierarchical structures of hybrid organic-inorganic materials such as conductive polymer composites (CPCs). Using a bottom-up methodology, we could synthesize a wide range of inorganic nanometric materials with a high degree of homogeneity and purity, ...

  13. Aprotic gel polymer electrolytes

    Czech Academy of Sciences Publication Activity Database

    Vondrák, Jiří; Sedlaříková, M.; Krejza, O.

    Brno : University of Technology Brno, 2008, s. 71-72. ISBN 978-80-214-3659-6. [International Conference Advanced Batteries and Accumulators /9./. Brno (CZ), 29.06.2008-03.07.2008] R&D Projects: GA ČR(CZ) GA104/06/1471; GA AV ČR(CZ) KJB208130604 Institutional research plan: CEZ:AV0Z40320502 Keywords : gel polymer electrolytes Subject RIV: CA - Inorganic Chemistry

  14. Nonequilibrium thermodynamics of dilute polymer solutions in flow

    International Nuclear Information System (INIS)

    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

  15. Lattice polymer automata

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, S. [Los Alamos National Lab., NM (United States)]|[Santa Fe Institute, NM (United States); Smith, J.R. [Santa Fe Institute, NM (United States)]|[Massachusetts Media Lab., Cambridge, MA (United States). Physics and Media Group

    1995-05-01

    We present a new style of molecular dynamics and self-assembly simulation, the Lattice Polymer Automaton (LPA). In the LPA all interactions, including electromagnetic forces, are decomposed and communicated via propagating particles, {open_quotes}photons.{close_quotes} The monomer-monomer bondforces, the molecular excluded volume forces, the longer range intermolecular forces, and the polymer-solvent interactions may all be modeled with propagating particles. The LPA approach differs significantly from both of the standard approaches, Monte Carlo lattice methods and Molecular Dynamics simulations. On the one hand, the LPA provides more realism than Monte Carlo methods, because it produces a time series of configurations of a single molecule, rather than a set of causally unrelated samples from a distribution of configurations. The LPA can therefore be used directly to study dynamical properties; one can in fact watch polymers move in real time. On the other hand, the LPA is fully discrete, and therefore much simpler than traditional Molecular Dynamics models, which are continuous and operate on much shorter time scales. Due to this simplicity it is possible to simulate longer real time periods, which should enable the study of molecular self-organization on workstations supercomputers are not needed.

  16. Polymer composites for aerospace

    International Nuclear Information System (INIS)

    Composites may be defined as macroscopic combinations of two or more distinct materials having a recognizable interface between the two. Polymer composites are defined as reinforcement fibers supported by a polymer binder known as a matrix. In structural polymer composites, the fiber is stiffer and stronger than the continuous matrix phase. Almost all high strength/high stiffness materials fail because of the propagation of flaws. A fiber of such material is inherently stronger than the bulk form because the size of a flaw is limited by the small diameter of the fiber. Even if a flaw does produce failure in a fiber, it does not propagate to fail the entire assemblage, which would happen in a bulk material. Fiber advantages can be converted to practical applications when the fibers are embedded in a matrix that binds them together, transfers load to and between the fibers, and protects them from hazardous environments and handling. The high strengths and moduli can be tailored to the high load direction, with little material wasted on needless reinforcement

  17. The passive polymer problem

    CERN Document Server

    Wiese, K J

    1999-01-01

    In this article, we introduce a generalization of the diffusive motion of point-particles in a turbulent convective flow with given correlations to a polymer or membrane. In analogy to the passive scalar problem we call this the passive polymer or membrane problem. We shall focus on the expansion about the marginal limit of velocity-velocity correlations which are uncorrelated in time and grow with the distance x as |x|^epsilon, and epsilon small. This relation gets modified for polymers and membranes (the marginal advecting flow has correlations which are shorter ranged.) The construction is done in three steps: First, we reconsider the treatment of the passive scalar problem using the most convenient treatment via field theory and renormalization group. We explicitly show why IR-divergences and thus the system-size appear in physical observables. In a second step, we reformulate the problem in terms of a Langevin equation. This is not only interesting in its own, but also gives an efficient algorithm to det...

  18. DNA modifications: Another stable base in DNA

    Science.gov (United States)

    Brazauskas, Pijus; Kriaucionis, Skirmantas

    2014-12-01

    Oxidation of 5-methylcytosine has been proposed to mediate active and passive DNA demethylation. Tracking the history of DNA modifications has now provided the first solid evidence that 5-hydroxymethylcytosine is a stable epigenetic modification.

  19. Hyperbranched Polymer-Based Electrolyte for Lithium Polymer Batteries

    Institute of Scientific and Technical Information of China (English)

    Takahito Itoh

    2005-01-01

    @@ 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].

  20. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    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.

  1. Sperm DNA oxidative damage and DNA adducts.

    Science.gov (United States)

    Jeng, Hueiwang Anna; Pan, Chih-Hong; Chao, Mu-Rong; Lin, Wen-Yi

    2015-12-01

    The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n=112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and sperm chromatin structure assay (SCSA). The PAH-exposed group had a significant increase in bulky DNA adducts and 8-oxo-dGuo compared to the control subjects (Ps=0.002 and 0.045, respectively). Coke oven workers' percentages of DNA fragmentation and denaturation from the PAH-exposed group were not significantly different from those of the control subjects (Ps=0.232 and 0.245, respectively). Routine semen parameters and DNA integrity endpoints were not correlated. Concentrations of 8-oxo-dGuo were positively correlated with percentages of DNA fragmentation measured by both TUNEL and SCSA (Ps=0.045 and 0.034, respectively). However, the concentrations of 8-oxo-dGuo and percentages of DNA fragmentation did not correlate with concentrations of bulky DNA adducts. In summary, coke oven workers with chronic exposure to PAHs experienced decreased sperm DNA integrity. Oxidative stress could contribute to the degree of DNA fragmentation. Bulky DNA adducts may be independent of the formation of DNA fragmentation and oxidative adducts in sperm. Monitoring sperm DNA integrity is recommended as a part of the process of assessing the impact of occupational and environmental toxins on sperm

  2. DNA glycosylases: in DNA repair and beyond

    OpenAIRE

    Jacobs, Angelika L.; Schär, Primo

    2011-01-01

    The base excision repair machinery protects DNA in cells from the damaging effects of oxidation, alkylation, and deamination; it is specialized to fix single-base damage in the form of small chemical modifications. Base modifications can be mutagenic and/or cytotoxic, depending on how they interfere with the template function of the DNA during replication and transcription. DNA glycosylases play a key role in the elimination of such DNA lesions; they recognize and excise damaged bases, thereb...

  3. DNA vaccines and bacterial DNA in immunity

    OpenAIRE

    Bandholtz, Lisa Charlotta

    2002-01-01

    This thesis describes DNA-based vaccination and the importance of bacterial DNA in different immunological perspectives. Intranasal (i.n.) DNA vaccination utilizing a plasmid encoding the chlamydial heat shock protein 60 (p-hsp-60) generated lower bacterial burden and reduced pathology in the lungs of mice after subsequent infection with C. pneumoniae. This DNA vaccine- induced protection was dependent on T cells and induction of IFN-gamma. Co-administration of a plasmid...

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

    CERN Document Server

    Bell, Nicholas A W

    2016-01-01

    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. Electrophoresis of a DNA Coil Near a Nanopore

    CERN Document Server

    Rowghanian, Payam

    2013-01-01

    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.

  6. DNA encoding a DNA repair protein

    Science.gov (United States)

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  7. Fabrication of PLGA polymer microspheres for U. S. mediated gene delivery

    Science.gov (United States)

    Williamson, Rene G.; Saltzman, William M.; Brandsma, Janet L.

    2001-05-01

    The promises of gene therapy remain unfulfilled because of the lack of a safe and efficient method for transfecting DNA into cells. PLGA has been used as a vehicle for protein, drug, and gene delivery applications because of its biocompatibility and sustained release properties. PLGA polymer microspheres offer advantages of safety and the possibility of sustained intracytoplasmic delivery. The PLGA also protects the plasmid from degradation. Using the double-emulsion microsphere fabrication technique, a new DNA delivery vehicle, comprising of plasmid DNA and octafluoropropane gas encapsulated in PLGA polymer and PVA stabilizer (Sonospheres) was made. The encapsulated gas offers acoustic activity to the microspheres, which enables them to undergo cavitation in an acoustic field. The goal is to lead to increased DNA transfection when these Sonospheres are subjected to an acoustic field in the MHz frequency range. A summary of the fabrication methods and some initial in vitro studies will be presented.

  8. Capillary electrophoresis as a technique to analyze sequence-induced anomalously migrating DNA fragments.

    OpenAIRE

    Wenz, H M

    1994-01-01

    Sequence-induced anomalous migration of double-stranded (ds) DNA in native gel electrophoresis is a well known phenomenon. The retardation of migration is more obvious in polyacrylamide compared with agarose gels, and is greatly affected by the concentration of the gel and the temperature. This anomalous migration results in a difference between calculated and actual sizes of the affected DNA fragments. A low viscosity polymer solution (DNA Fragment Analysis Reagent) under investigation for u...

  9. DNA-Templated Polymerization of Side-Chain-Functionalized Peptide Nucleic Acid Aldehydes

    OpenAIRE

    Kleiner, Ralph E.; Brudno, Yevgeny; Birnbaum, Michael E.; Liu, David R.

    2008-01-01

    The DNA-templated polymerization of synthetic building blocks provides a potential route to the laboratory evolution of sequence-defined polymers with structures and properties not necessarily limited to those of natural biopolymers. We previously reported the efficient and sequence-specific DNA-templated polymerization of peptide nucleic acid (PNA) aldehydes. Here, we report the enzyme-free, DNA-templated polymerization of side-chain-functionalized PNA tetramer and pentamer aldehydes. We obs...

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

    Directory of Open Access Journals (Sweden)

    Nikolay Korolev

    2014-05-01

    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.

  11. Processing polymers with cyclodextrins

    Science.gov (United States)

    Williamson, Brandon Robert

    Cyclodextrins (CDs) are cyclic starch molecules that have the unique ability to include a variety of small molecules and polymers inside their cavities, forming "Inclusion Complexes" (ICs). While much work has been done to understand the formation and behavior of these ICs, far less is known about the fundamental property changes that can occur when CD is used to alter polymer chain morphology. The goal of my graduate research has been to discover different ways to improve upon existing polymer properties through CD processing, as well as explore the possibility of creating a novel type of IC using non-traditional forms of cyclodextrin. Poly(ε-caprolactone) (PCL) was processed with alpha-CD to form an IC. The cyclodextrin was then stripped away to yield a PCL with elongated, unentangled, and constrained polymer chains, a process referred to as coalescence. The physical and rheological property changes resulting from this coalescence were then examined. It was found that reorganizing PCL in this manner resulted in an increase in the melt crystallization temperature of up to 25°C. Coalescence also decreased the tan delta of the material and increased the average hardness and Young's modulus by 33 and 53%, respectively. Non-stoichiometric ICs (NS-ICs), or ICs with at least parts of some polymer chains uncovered, were formed between poly (methyl methacrylate) (PMMA) and gamma-CD as well as a synthesized poly(ε-caprolactone)-poly(propylene glycol)-poly(ε-caprolactone) (PCL-PPG-PCL) triblock copolymer and beta-CD. The property changes of the non-complexed polymer chains were then studied. The PMMA/gamma-CD NS-IC samples were determined to be extremely heterogeneous, however glass transition temperature increases of up to 27°C above that of as-received PMMA were observed. Diffraction data for the PMMA NS-ICs suggests slight crystallinity at partial coverage, with a similar crystal structure to that of the fully covered IC. XRD, DSC and FTIR data revealed an almost

  12. Claisen thermally rearranged (CTR) polymers

    Science.gov (United States)

    Tena, Alberto; Rangou, Sofia; Shishatskiy, Sergey; Filiz, Volkan; Abetz, Volker

    2016-01-01

    Thermally rearranged (TR) polymers, which are considered the next-generation of membrane materials because of their excellent transport properties and high thermal and chemical stability, are proven to have significant drawbacks because of the high temperature required for the rearrangement and low degree of conversion during this process. We demonstrate that using a [3,3]-sigmatropic rearrangement, the temperature required for the rearrangement of a solid glassy polymer was reduced by 200°C. Conversions of functionalized polyimide to polybenzoxazole of more than 97% were achieved. These highly mechanically stable polymers were almost five times more permeable and had more than two times higher degrees of conversion than the reference polymer treated under the same conditions. Properties of these second-generation TR polymers provide the possibility of preparing efficient polymer membranes in a form of, for example, thin-film composite membranes for various gas and liquid membrane separation applications.

  13. Supramolecular control over thermoresponsive polymers

    Directory of Open Access Journals (Sweden)

    Victor R. de la Rosa

    2016-01-01

    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.

  14. Compaction of DNA with Lipid Modified Silica Nanoparticles

    Science.gov (United States)

    Savarala, Sushma; Wunder, Stephanie L.; Ilies, Marc

    2012-02-01

    There is an increasing interest in modified inorganic nanoparticles, polymers or hybrid polymer-inorganic nanoparticles for use in DNA transfection, rather than viral vectors or liposomes. Adsorption of the DNA to the nanoparticles prevents enzymatic degradation of the DNA, although the reason for this protection is not completely understood. In order to compact the negatively charged DNA, a positively charged surface is required, and for transfection applications, the nanosystems must remain stable in suspension. It is also useful to minimize the amount of cytotoxic cationic lipid needed for DNA compaction in delivery applications. Here we investigate the colloidal stability of supported lipid bilayers (SLBs) composed of mixtures of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC, 14:0 PC) and 1,2-dimyristoyl-3-trimethylammonium-propane (DMTAP, 14:0 TAP), and their ability to compact plasmid DNA. Ionic strengths and DMPC/DMTAP ratios that resulted in SLB formation, no excess small unilamellar vesicles (SUVs) in the suspensions, and colloidal stability, were determined. DNA/SLB/lipid ratios that resulted in compaction were then investigated.

  15. Terminology of Polymers Containing Ionizable or Ionic Groups and of Polymers Containing Ions, VII.3

    Directory of Open Access Journals (Sweden)

    Jarm, V.

    2009-10-01

    Full Text Available The class of ionic polymers has widespread application in many areas of everyday life, in industrial production, and in the processes of living matter. The properties of ionic polymers depend on the polymer structure, and the nature, content, and location of the ionic groups. To clear differences among various ionic polymers, the IUPAC recommendations present 34 definitionsfor the ionomer, polyacid, polybase, polyampholytic polymer, ion-exchange polymer, polybetaine, polyelectrolyte, intrinsically conducting polymer, solid polymer electrolyte, etc

  16. Method for bonding a thermoplastic polymer to a thermosetting polymer component

    OpenAIRE

    Van Tooren, M.J.L.

    2012-01-01

    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 polymer component comprising an implant of a thermoplastic polymer at least at the part of the thermosetting polymer component to be bonded, locating a thermoplastic polymer in contact with at least the...

  17. Investigations of functional electroactive polymers

    OpenAIRE

    Tiitu, Mari

    2006-01-01

    Conjugated polymers containing pi-conjugated backbones form a scientifically and technologically important class of polymers. In their undoped form they are semiconductors, but they can be doped for electrical conductivity, and allow redox-activity, which all can lead to functional materials. One of the most important conjugated polymers in large scale applications is polyaniline due to its economics and good stability. Polyaniline is used for applications requiring conductivity as well as co...

  18. Functional polymer blends and nanocomposites

    OpenAIRE

    Weder, Christoph

    2010-01-01

    The broad class of (multi)functional polymers with unusual combinations of optical, electronic, mechanical and other properties is attracting significant interest, because it conceptually combines the advantages of polymers - low cost, ease of processing and a range of attractive mechanical characteristics - with the specific, tailorable properties of functional organic molecules. The caveat is that the synthesis of functional polymers is frequently complex and involves many steps, which make...

  19. Friction between Ring Polymer Brushes

    OpenAIRE

    2015-01-01

    Friction between ring-polymer brushes at melt densities sliding past each other are studied using extensive course-grained molecular dynamics simulations and scaling arguments, and the results are compared to the friction between linear-polymer brushes. We show that for a velocity range spanning over three decades, the frictional forces measured for ring-polymer brushes are half the corresponding friction in case of linear brushes. In the linear-force regime, the weak inter-digitation of two ...

  20. Rice Husk Filled Polymer Composites

    OpenAIRE

    Reza Arjmandi; Azman Hassan; Khaliq Majeed; Zainoha Zakaria

    2015-01-01

    Natural fibers from agricultural wastes are finding their importance in the polymer industry due to the many advantages such as their light weight, low cost and being environmentally friendly. Rice husk (RH) is a natural sheath that forms around rice grains during their growth. As a type of natural fiber obtained from agroindustrial waste, RH can be used as filler in composites materials in various polymer matrices. This review paper is aimed at highlighting previous works of RH filled polyme...

  1. Purification of HIV RNA from serum using a polymer capture matrix in a microfluidic device

    OpenAIRE

    Root, Brian E.; Agarwal, Abhishek K.; Kelso, David M.; Barron, Annelise E.

    2011-01-01

    In this report, we demonstrate the purification of DNA and RNA from a 10% serum sample using an oligonucleotide capture matrix. This approach provides a one-stage, completely aqueous system capable of purifying both RNA and DNA for downstream PCR amplification. The advantages of utilizing the polymer capture matrix method in place of the solid-phase extraction method is that the capture matrix eliminates both guanidine and the isopropanol wash that can inhibit downstream PCR and competition w...

  2. Antiviral Activity of Metal-Containing Polymers—Organotin and Cisplatin-Like Polymers

    OpenAIRE

    Girish Barot; Roner, Michael R.; Charles E. Carraher Jr.; Kimberly Shahi

    2011-01-01

    Polymers containing platinum and to a lesser extent tin, have repeatedly demonstrated antitumor activity in vitro and in vivo against a variety of cell and tumor types. The mechanisms responsible for the antitumor activity include inducing a delay in cell proliferation and sister chromatid exchanges blocking tumor growth. As most DNA and some RNA viruses require, and even induce, infected cells to initiate DNA replication and subsequent cell division, compounds with antitumor activity will ve...

  3. Ionic current inversion in pressure-driven polymer translocation through nanopores

    OpenAIRE

    Buyukdagli, Sahin; Blossey, Ralf; Ala-Nissila, T.

    2014-01-01

    We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics. In the presence of multivalent counterions, electrostatic many-body effects result in the reversal of the DNA charge. The attraction of anions to the charge-inverted DNA molecule reverses the sign of the ionic current through the pore. Our theory allows fo...

  4. Small angle scattering and polymers

    International Nuclear Information System (INIS)

    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. 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)

    1996-12-31

    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.

  6. Wear of polymers and composites

    CERN Document Server

    Abdelbary, Ahmed

    2015-01-01

    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

  7. Human placental DNA methyltransferase: DNA substrate and DNA binding specificity.

    OpenAIRE

    Wang, R.Y.; Huang, L. H.; Ehrlich, M

    1984-01-01

    We have partially purified a DNA methyltransferase from human placenta using a novel substrate for a highly sensitive assay of methylation of hemimethylated DNA. This substrate was prepared by extensive nick translation of bacteriophage XP12 DNA, which normally has virtually all of its cytosine residues replaced by 5-methylcytosine (m5C). Micrococcus luteus DNA was just as good a substrate if it was first similarly nick translated with m5dCTP instead of dCTP in the polymerization mixture. At ...

  8. The elastic theory of a single DNA molecule

    Indian Academy of Sciences (India)

    Haijun Zhou; Yang Zhang; Zhang-Can Ou-Yang

    2003-08-01

    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.

  9. 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

    2005-01-01

    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.

  10. Radiation Synthesis of Superabsorbent Polymers Based on Natural Polymers

    International Nuclear Information System (INIS)

    The objectives of proposed research contract were first synthesize superabsorbent polymers based on natural polymers to be used as disposable diapers and soil conditioning materials in agriculture, horticulture and other super adsorbent using industries. We have planned to use the natural polymers; locust beam gum, tara gum, guar gum and sodium alginate on the preparation of natural superabsorbent polymers(SAP). The aqueous solution of natural polymers and their blends with trace amount of monomer and cross-linking agents will be irradiated in paste like conditions by gamma rays for the preparation of cross-linked superabsorbent systems. The water absorption and deswellling capacity of prepared super adsorbents and retention capacity, absorbency under load, suction power, swelling pressure and pet-rewet properties will be determined. Use of these materials instead of synthetic super absorbents will be examined by comparing the performance of finished products. The experimental studies achieved in the second year of project mainly on the effect of radiation on the chemistry of sodium alginate polymers in different irradiation conditions and structure-property relationship particularly with respect to radiation induced changes on the molecular weight of natural polymers and preliminary studies on the synthesis of natural-synthetic hydride super adsorbent polymers were given in details

  11. Thermoresponsive Polymers for Nuclear Medicine: Which Polymer Is the Best?

    Science.gov (United States)

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

    2016-06-21

    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. PMID:27238593

  12. Enhancement of Polymer Cytocompatibility by Nanostructuring of Polymer Surface

    Czech Academy of Sciences Publication Activity Database

    Slepička, P.; Kasálková-Slepičková, N.; Bačáková, Lucie; Kolská, Z.; Švorčík, V.

    2012-01-01

    Roč. 2012, č. 2012 (2012), ID527403. ISSN 1687-4110 R&D Projects: GA ČR(CZ) GBP108/12/G108 Institutional support: RVO:67985823 Keywords : polymer cytocompatibility * polymer surface * nanotechnology Subject RIV: EI - Biotechnology ; Bionics Impact factor: 1.547, year: 2012

  13. Thermochromic polymer opals

    Science.gov (United States)

    Sussman, Jason; Snoswell, David; Kontogeorgos, Andreas; Baumberg, Jeremy J.; Spahn, Peter

    2009-10-01

    Large-scale shear-ordered photonic crystals are shown to exhibit unusual thermochromic properties. By balancing the refractive index of the polymer core and composite shell components at room temperature, transparent films are created, which become colored on heating to 150 °C. Since this scattering-based structural color depends only on resonant Bragg scattering of the unpigmented components, it can be tuned to any wavelength. The observed color shifts with temperature are not simply accounted for by theory and are sensitive to the constituents.

  14. Polymer solidification national program

    International Nuclear Information System (INIS)

    Brookhaven National Laboratory (BNL) has developed several new and innovative polymer processes for the solidification of low-level radioactive, hazardous and mixed wastes streams. Polyethylene and modified sulfur cement solidification technologies have undergone steady, gradual development at BNL over the past nine years. During this time they have progressed through each of the stages necessary for logical technology maturation: from process conception, parameter optimization, waste form testing, evaluation of long-term durability, economic analysis, and scale-up feasibility. This technology development represents a significant investment which can potentially provide DOE with both short- and long-term savings

  15. Hyperscaling for polymer rings

    OpenAIRE

    Duplantier, Bertrand

    1994-01-01

    The statistics of a long closed self-avoiding walk (SAW) or polymer ring on a $ d $-dimensional lattice obeys hyperscaling. The combination $ p_N \\left\\langle R^2 \\right\\rangle^{ d/2}_N\\mu^{ -N}, $ (where $ p_N $ is the number of configurations of an oriented and rooted $ N $-step ring, $ \\left\\langle R^2 \\right\\rangle_ N $ a typical average size squared, and $ \\mu $ the SAW effective connectivity constant of the lattice) is equal for $ N \\longrightarrow \\infty $ to a lattice-dependent consta...

  16. Controlled Synthesis of Polymer Brushes via Polymer Single Crystal Templates

    Science.gov (United States)

    Zhou, Tian

    A novel synthetic method of polymer brushes using polymer single crystals (PSCs) as solid-state templates is introduced in this study. PSC has a quasi-2D lamellae structure with polymer chains fold back-and-forth perpendicular to the lamellae surfaces. During crystallization, the chain ends are excluded from the unit cell onto the lamellae surfaces, which makes the material extremely versatile in its functionality. Such structure holds the unique capability to harvest nanoparticles, or being immobilized onto macroscopic flat surfaces. After dissolving PSCs in good solvent, polymer brushes are chemically tethered on either nanoparticles or flat macroscopic surfaces. Because the chain-folding structure can be conveniently tailored by changing the molecular weight of polymer and the crystallization temperature, the thickness, grafting density and morphology of resulted polymer brushes can be precisely controlled. As a model system, poly(?-caprolactone) with thiol or alkoxysilane terminal groups was used, and polymer brushes were successfully prepared on both nanoparticles and glass/Au flat surfaces. The structure-property relationships of the as-prepared polymer brushes were studied in detail using multiple characterization techniques. First of all, when functionalizing nanoparticles, by engineering the chain-folding structure of the PSCs, interesting complex nanostructures can be formed by nanoparticles including Janus nanoparticles and nanoparticle dimers. These unique structures render hybrid nanoparticles very interesting responsive behavior which have been studied in detail in this dissertation. When grafted onto a flat surface on the other hand, not only the molecular weight and grafting density can be precisely controlled, the tethering points of a single polymer chain can also be conveniently tailored, resulting polymer brushes with either tail or loop structures. Such difference in brush structure can significantly alter the properties of functional surface

  17. Thermally Activated Processes in Polymer Glasses

    OpenAIRE

    V. Parihar; Drosdoff, D.; Widom, A.; Srivastava, Y. N.

    2005-01-01

    A derivation is given for the Vogel-Fulcher-Tammann thermal activation law for the glassy state of a bulk polymer. Our microscopic considerations involve the entropy of closed polymer molecular chains (i.e. polymer closed strings). For thin film polymer glasses, one obtains open polymer strings in that the boundary surfaces serve as possible string endpoint locations. The Vogel-Fulcher-Tammann thermal activation law thereby holds true for a bulk polymer glass but is modified in the neighborho...

  18. The energetics of tightly bent DNA: a composite elastica model including local melting

    Science.gov (United States)

    Evans, Arthur; Levine, Alex

    2012-02-01

    Melting transitions are well-known to be affected by the application of mechanical stress. Motivated by the experiments of Zocchi and collaborators (Qu and Zocchi 2011, EPL 94 18003), we explore the effect of the application of mechanical stress on DNA melting in a particular composite of a stiff double stranded piece of DNA (dsDNA), shorter than its own persistence length, whose ends are linked by a flexible single stranded piece of DNA (ssDNA). The flexible ssDNA acts as a Gaussian polymer coil bending the stiff dsDNA through an elastic force that is controllable by the length of the ssDNA chain. In this talk we present theoretical predictions for two experimentally accessible features: the degree of local dsDNA melting and the local elastic energy of the dsDNA/ssDNA construct both as a function of the length of the attached ssDNA. We also address the effect of introducing a nick (broken covalent bond) in the dsDNA backbone on these results and discuss the implications of such data on the relative importance of backbone elasticity versus base stacking and base pairing interactions in determining the elasticity of dsDNA. This work also addresses open questions in the nonlinear elasticity of DNA in tightly bent curves.

  19. The investigation of interaction of podophyllotoxin and etoposide with DNA by fluorescence method

    International Nuclear Information System (INIS)

    The interaction of podophyllotoxin (Ptox) and etoposide with DNA by fluorescent spectroscopy method has been investigated. It has been revealed, that Ptox is able to interact with DNA molecule directly. Preservation of fluorescent intensity at the constant level, with increase of of Ptox/DNA ratio, shows the existence of limited number of binding sites of Ptox to DNA molecule. Defect or/and end sites on DNA can serve as similar sites. It has been also shown, that in spite of Ptox, etoposide binds only to polymer DNA. Interaction with f-DNA practically is not observed. Possibly it is conditioned by mainly indirect interaction of etoposide with DNA, as far as it previously forms a complex with topoisomerase

  20. Facile preparation of a DNA sensor for rapid herpes virus detection

    Energy Technology Data Exchange (ETDEWEB)

    Tam, Phuong Dinh, E-mail: tampd-hast@mail.hut.edu.vn [Hanoi Advanced School of Science and Technology, Hanoi University of Technology (Viet Nam); Tuan, Mai Anh, E-mail: tuanma-itims@mail.hut.edu.vn [International Training Institute for Materials Science, Hanoi University of Technology (Viet Nam); Huy, Tran Quang [National Institute of Hygiene and Epidemiology (NIHE), 01 Yersin, Hai Ba Trung District, Hanoi (Viet Nam); Le, Anh-Tuan [Hanoi Advanced School of Science and Technology, Hanoi University of Technology (Viet Nam); Hieu, Nguyen Van, E-mail: hieu@itims.edu.vn [International Training Institute for Materials Science, Hanoi University of Technology (Viet Nam)

    2010-10-12

    In this paper, a simple DNA sensor platform was developed for rapid herpes virus detection in real samples. The deoxyribonucleic acid (DNA) sequences of the herpes simplex virus (DNA probe) were directly immobilized on the surface of interdigitated electrodes by electrochemical polymerization along with pyrrole monomers. The potential was scanned from - 0.7 to + 0.6 V, and the scanning rate was 100 mV/s. Fourier transform infrared spectroscopy was employed to verify specific DNA sequence binding and the conducting polymer. The morphology of the conducting polymer doped with DNA strands was characterized using a field emission scanning electron microscope. As-obtained DNA sensor was used to detect the herpes virus DNA in the real samples. The results show that the current DNA sensors detected the lowest DNA concentration of 2 nM. This sensitivity appears to be better than that of the DNA sensors prepared by immobilization of the DNA probe on the 3-aminopropyl-triethoxy-silance (APTS) membrane.

  1. Chitosan chip and application to evaluate DNA loading on the surface of the metal

    Energy Technology Data Exchange (ETDEWEB)

    Bao Junbo; Song Cunxian, E-mail: scxian@eyou.co [Key Laboratory of Biomedical Materials of Tianjin, Institute of Biomedical Engineering, Peking Union Med College, Chinese Academy of Medical Sciences, Tianjin 300192 (China)

    2009-02-15

    The plasmid DNA (pDNA) loading by cationic polymers or/and cationic lipids is essential for gene therapy, especially for metal implants such as stents and artificial joints. Polycations can condense with pDNA by self-assembly, forming polyplexes spontaneously as a result of electrostatic interactions to carry and transfer pDNA in vivo. Cationic polymers, such as chitosan, can also protect pDNA from degradation by DNase. In this study, a chitosan chip was prepared and loaded with pDNA layer-by-layer with polycation/cationic lipids. By real-time surface plasmon resonance (SPR) sensorgram, pDNA loading ability, layer stability and protective effect on pDNA from DNase degradation have been detected. Chitosan can increase the pDNA loading amount of N-(1-(2,3-dioleoyloxy)propyl)-N, N, N-trimethylammonium methyl sulphate (DOTAP) and Lipofectmine 2000 (Lipo) on the chip surface. Different flow rates can affect the pDNA loading on the chitosan chip, and it is not significant at a lower flow rate. The pDNA protection by chitosan with different molecular weights from DNase degradation was also tested. Polycationic chitosan with higher molecular weight (>=200 kDa) can fulfil the requirements for effective gene protection from DNase degradation. The results of this study present a platform for further optimization studies of polycation-based gene delivery systems. (communication)

  2. Facile preparation of a DNA sensor for rapid herpes virus detection

    International Nuclear Information System (INIS)

    In this paper, a simple DNA sensor platform was developed for rapid herpes virus detection in real samples. The deoxyribonucleic acid (DNA) sequences of the herpes simplex virus (DNA probe) were directly immobilized on the surface of interdigitated electrodes by electrochemical polymerization along with pyrrole monomers. The potential was scanned from - 0.7 to + 0.6 V, and the scanning rate was 100 mV/s. Fourier transform infrared spectroscopy was employed to verify specific DNA sequence binding and the conducting polymer. The morphology of the conducting polymer doped with DNA strands was characterized using a field emission scanning electron microscope. As-obtained DNA sensor was used to detect the herpes virus DNA in the real samples. The results show that the current DNA sensors detected the lowest DNA concentration of 2 nM. This sensitivity appears to be better than that of the DNA sensors prepared by immobilization of the DNA probe on the 3-aminopropyl-triethoxy-silance (APTS) membrane.

  3. DNA extraction by zinc.

    OpenAIRE

    Kejnovský, E; Kypr, J

    1997-01-01

    A fast, very simple and efficient method of DNA extraction is described which takes advantage of DNA sedimentation induced by millimolar concentrations of ZnCl2. The zinc-induced sedimentation is furthermore strongly promoted by submillimolar phosphate anion concentrations. Within 90% of DNA irrespective of whether a plasmid DNA or short oligonucleotides are the extracted material. The method works with plasmid DNA and oligonucleotide concentrations as low as 100 ng/ml and 10 microg/ml, respe...

  4. Wedging out DNA damage

    OpenAIRE

    Schärer, Orlando D.; Campbell, Arthur J

    2009-01-01

    The DNA-repair machinery is faced with the significant challenge of differentiating DNA lesions from unmodified DNA. Two recent publications, one in this issue of Nature Structural & Molecular Biology, uncover a new way of recognizing minimally distorting DNA lesions: insertion of a 3- or 4-amino-acid wedge into DNA to extrude the lesion into a shallow binding pocket that can accommodate various damaged bases.

  5. Graphene/Polymer Nanocomposites

    Science.gov (United States)

    Macosko, Chris

    2010-03-01

    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.

  6. Electroelasticity of polymer networks

    Science.gov (United States)

    Cohen, Noy; Dayal, Kaushik; deBotton, Gal

    2016-07-01

    A multiscale analysis of the electromechanical coupling in elastic dielectrics is conducted, starting from the discrete monomer level through the polymer chain and up to the macroscopic level. Three models for the local relations between the molecular dipoles and the electric field that can fit a variety of dipolar monomers are considered. The entropy of the network is accounted for within the framework of statistical mechanics with appropriate kinematic and energetic constraints. At the macroscopic level closed-form explicit expressions for the behaviors of amorphous dielectrics and isotropic polymer networks are determined, none of which admits the commonly assumed linear relation between the polarization and the electric field. The analysis reveals the dependence of the macroscopic coupled behavior on three primary microscopic parameters: the model assumed for the local behavior, the intensity of the local dipole, and the length of the chain. We show how these parameters influence the directional distributions of the monomers and the hence the resulting overall response of the network. In particular, the dependences of the polarization and the polarization induced stress on the deformation of the dielectric are illustrated. More surprisingly, we also reveal a dependence of the stress on the electric field which stems from the kinematic constraint imposed on the chains.

  7. Wood and concrete polymer composites

    International Nuclear Information System (INIS)

    There are several ways to prepare and use wood and concrete polymer composites. The most important improvements in the case of concrete polymer composites are obtained for compressive and tensile strengths. The progress in this field in United States and other countries is discussed in this rview. (M.S.)

  8. HIGH TEMPERATURE POLYMER FUEL CELLS

    DEFF Research Database (Denmark)

    Jensen, Jens Oluf; Qingfeng, Li; He, Ronghuan;

    2003-01-01

    This paper will report recent results from our group on polymer fuel cells (PEMFC) based on the temperature resistant polymer polybenzimidazole (PBI), which allow working temperatures up to 200°C. The membrane has a water drag number near zero and need no water management at all. The high working...

  9. Polymer highlights for September 1975

    Energy Technology Data Exchange (ETDEWEB)

    Hammon, H.G.; Althouse, L.P.; Buckner, A.T.; McKinley, B.; Walkup, C.M.; Rinde, J.; Lorensen, L.L.; Cady, W.E.; Caley, L.E.

    1988-12-15

    Research programs in polymer chemistry are briefly described. The following polymers are under investigation for use as adhesives, nozzles, insulators, or fluid cushions: urethanes, teflon, TFE, Tefzel, Ryton, H Resin, Imidite 2803, PPQ, KELF 800, and KELF 5500. Areas of research application include geothermal and solar energy fields. (CBS)

  10. Temperature-sensitive polymer vaccines

    Czech Academy of Sciences Publication Activity Database

    Laga, Richard; Lynn, G.; Pechar, Michal; Pola, Robert; Etrych, Tomáš; Seymour, L.; Seder, R.

    Salt Lake City: The University of Utah, 2015. P38. [International Symposium on Recent Advances in Drug Delivery Systems /17./. 14.06.2015-17.06.2015, Salt Lake City] R&D Projects: GA MŠk(CZ) EE2.3.30.0029 Institutional support: RVO:61389013 Keywords : polymer vaccines * thermo-sensitive polymers * recombinant antigens Subject RIV: CE - Biochemistry

  11. 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...

  12. Polymer-based photonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Edrington, A.C.; Urbas, A.M.; Fink, Y.; Thomas, E.L. [Massachusetts Inst. of Tech., Cambridge (United States). Dept. of Materials Science and Engineering; DeRege, P. [Firmenich, Inc., Port Newark, NJ (United States); Chen, C.X.; Swager, T.M. [Massachusetts Inst. of Tech., Cambridge, MA (United States). Dept. of Chemistry; Hadjichristidis, N. [Athens Univ. (Greece). Dept. of Chemistry; Xenidou, M.; Fetters, L.J. [ExxonMobil Research Corp., Annandale, NJ (United States); Joannopoulos, J.D. [Massachusetts Inst. of Tech., Cambridge, MA (United States). Dept. of Physics

    2001-03-16

    The development of polymers as photonic crystals is highlighted, placing special emphasis on self-assembled block copolymers. 1D self-assembled multilayers as well as 2D and 3D self-assembled structures are examined, then intricate block polymer structures such as that shown in the Figure are discussed as are birefringent multilayer and elastomeric films. (orig.)

  13. POLYMERS BEYOND THE YEAR 2000

    Institute of Scientific and Technical Information of China (English)

    Ingolf Buethe

    2000-01-01

    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.

  14. Bioreducible cross-linked polymers based on G1 peptide dendrimer as potential gene delivery vectors.

    Science.gov (United States)

    Li, Chun-Yan; Wang, Hai-Jiao; Cao, Jing-Ming; Zhang, Ji; Yu, Xiao-Qi

    2014-11-24

    A series of cationic polymers based on low generation (G1) peptide dendrimer were synthesized with disulfide-containing linkages. The DNA binding abilities of the target polymers were studied by gel electrophoresis and fluorescence quenching assay. The bioreducible property of the disulfide-containing polymers P2 and P3 was also investigated in the presence of dithiothreitol (DTT). Results from dynamic light scattering (DLS) and transmission electron microscopy (TEM) assays reveal that these materials may condense DNA into nanoparticles with proper sizes and zeta-potentials. In vitro cell experiments show that compared to branched 25 KDa PEI, P2 and P3 may exhibit much higher gene transfection efficiency and lower cytotoxicity in both HEK293 and U-2OS cells. Additionally, polymer prepared from Michael addition gives better gene transfection ability, while polymer prepared from ring-opening reaction has better serum tolerance. Results indicate that these polymers might be promising non-viral gene vectors for their easy preparation, very low cytotoxicity, and good transfection efficiency. PMID:25282264

  15. Fundamental studies of polymer filtration

    Energy Technology Data Exchange (ETDEWEB)

    Smith, B.F.; Lu, M.T.; Robison, T.W.; Rogers, Y.C.; Wilson, K.V.

    1998-12-31

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). The objectives of this project were (1) to develop an enhanced fundamental understanding of the coordination chemistry of hazardous-metal-ion complexation with water-soluble metal-binding polymers, and (2) to exploit this knowledge to develop improved separations for analytical methods, metals processing, and waste treatment. We investigated features of water-soluble metal-binding polymers that affect their binding constants and selectivity for selected transition metal ions. We evaluated backbone polymers using light scattering and ultrafiltration techniques to determine the effect of pH and ionic strength on the molecular volume of the polymers. The backbone polymers were incrementally functionalized with a metal-binding ligand. A procedure and analytical method to determine the absolute level of functionalization was developed and the results correlated with the elemental analysis, viscosity, and molecular size.

  16. Grafted polymer under shear flow

    Science.gov (United States)

    Kumar, Sanjiv; Foster, Damien P.; Giri, Debaprasad; Kumar, Sanjay

    2016-04-01

    A self-attracting-self-avoiding walk model of polymer chain on a square lattice has been used to gain an insight into the behaviour of a polymer chain under shear flow in a slit of width L. Using exact enumeration technique, we show that at high temperature, the polymer acquires the extended state continuously increasing with shear stress. However, at low temperature the polymer exhibits two transitions: a transition from the coiled to the globule state and a transition to a stem-flower like state. For a chain of finite length, we obtained the exact monomer density distributions across the layers at different temperatures. The change in density profile with shear stress suggests that the polymer under shear flow can be used as a molecular gate with potential application as a sensor.

  17. Neutron scattering in polymer physics

    Science.gov (United States)

    Richter, D.

    2000-03-01

    By example this short review presents recent scientific advances which were achieved by the application of neutron scattering to polymer systems, thereby, keeping in mind also practical applications. We first focus on experiments on the structure and morphology of polymer systems covering conformational studies, investigations on polymer-microemulsions systems and the observation of aggregation states in living polymerization. Thereafter, we present recent results in the field of polymer dynamics. We begin with local motions which are behind the classical relaxation processes in polymer melts. Then we relate to universal dynamics, we address the Rouse model and its limits, present new results on the dynamic miscibility in blends and display the latest investigations on entanglement dynamics. Finally, we report first observations of ripplon excitations of phase boundaries in diblock copolymer melts.

  18. Accelerated Characterization of Polymer Properties

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-07-30

    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.

  19. Polymer research by neutron scattering

    International Nuclear Information System (INIS)

    Polymer physics aims on an understanding of the macroscopic behavior of polymer systems on the basis of their molecular structure and dynamics. For this purpose neutrons serve as a unique probe, allowing a simultaneous investigation of polymer structure and dynamics on a molecular scale. Furthermore, hydrogen deuterium exchange facilitates molecular labeling and offers the possibility to observe selected chains or chain parts in dense systems. Neutron small angle scattering reveals information on the conformation and possible aggregation of polymer chains. Data on linear and star like molecules are shown as examples. High resolution neutron spin-echospectroscopy observes the molecular dynamics of long chain molecules. Results on the large scale motion of chins in polymer melts are presented. finally, experiments on chain relaxation close to the glass transition are displayed. Three distinctly different relaxation processes are revealed. (author)

  20. Polymers for Cardiovascular Stent Coatings

    Directory of Open Access Journals (Sweden)

    Anne Strohbach

    2015-01-01

    Full Text Available Polymers have found widespread applications in cardiology, in particular in coronary vascular intervention as stent platforms (scaffolds and coating matrices for drug-eluting stents. Apart from permanent polymers, current research is focussing on biodegradable polymers. Since they degrade once their function is fulfilled, their use might contribute to the reduction of adverse events like in-stent restenosis, late stent-thrombosis, and hypersensitivity reactions. After reviewing current literature concerning polymers used for cardiovascular applications, this review deals with parameters of tissue and blood cell functions which should be considered to evaluate biocompatibility of stent polymers in order to enhance physiological appropriate properties. The properties of the substrate on which vascular cells are placed can have a large impact on cell morphology, differentiation, motility, and fate. Finally, methods to assess these parameters under physiological conditions will be summarized.

  1. Polymer materials for fusion reactors

    International Nuclear Information System (INIS)

    The radiation-resistant polymer materials have recently drawn much attention from the viewpoint of components for fusion reactors. These are mainly applied to electrical insulators, thermal insulators and structural supports of superconducting magnets in fusion reactors. The polymer materials used for these purposes are required to withstand the synergetic effects of high mechanical loads, cryogenic temperatures and intense nuclear radiation. The objective of this review is to summarize the anticipated performance of candidate materials including polymer composites for fusion magnets. The cryogenic properties and the radiation effects of polymer materials are separately reviewed, because there is only limited investigation on the above-mentioned synergetic effects. Additional information on advanced polymer materials for fusion reactors is also introduced with emphasis on recent developments. (orig.)

  2. Review of polymer MEMS micromachining

    International Nuclear Information System (INIS)

    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. (topical review)

  3. Direct Photopatterning of Electrochromic Polymers

    DEFF Research Database (Denmark)

    Jensen, Jacob; Dyer, Aubrey L.; Shen, D. Eric;

    2013-01-01

    Propylenedioxythiophene (ProDOT) polymers are synthesized using an oxidative polymerization route that results in methacrylate substituted poly(ProDOTs) having a Mn of 10–20 kDa wherein the methacrylate functionality constitutes from 6 to 60% of the total monomer units. Solutions of these polymers...... show excellent film forming abilities, with thin films prepared using both spray‐casting and spin‐coating. These polymers are demonstrated to crosslink upon UV irradiation at 350 nm, in the presence of an appropriate photoinitiator, to render the films insoluble to common organic solvents....... Electrochemical, spectroelectrochemical, and colorimetric analyses of the crosslinked polymer films are performed to establish that they retain the same electrochromic qualities as the parent polymers with no detriment to the observed properties. To demonstrate applicability for multi‐film processing...

  4. Ligation-based mutation detection and RCA in surface un-modified OSTE+ polymer microfluidic chambers

    DEFF Research Database (Denmark)

    Saharil, Farizah; Ahlford, Annika; Kuhnemund, Malte; Skolimowski, Maciej; Conde, Alvaro; Dufva, Martin; Nilsson, Mats; Brivio, Monica; van der Wijngaart, Wouter; Haraldsson, Tommy

    2013-01-01

    For the first time, we demonstrate DNA mutation detection in surface un-modified polymeric microfluidic chambers without suffering from bubble trapping or bubble formation. Microfluidic devices were manufactured in off-stoichiometry thiol-ene epoxy (OSTE+) polymer using an uncomplicated and rapid...

  5. 3DNA: A Tool for DNA Sculpting

    OpenAIRE

    Gupta, Shikhar Kumar; Joshi, Foram; Limbachiya, Dixita; Gupta, Manish K.

    2014-01-01

    DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures. One such technique involves the implementation of DNA Bricks proposed by Ke et al., 2012 to create complex three-dimensional (3D) structures. Modeling these DNA nano structures can prove to be a cumbersome and tedious task. Exploiting the programmability of b...

  6. A Fast, Sensitive and Label Free Electrochemical DNA Sensor

    International Nuclear Information System (INIS)

    A label free and sensitive DNA/RNA silicon based electrochemical microsensor array was developed by using thin film of the conducting polymer polypyrrole doped with an oligonucleotide probe. The electrochemical potential pulse amperometry technique was used for a biowarfare pathogen target DNA detection. The electrical potential assistanted DNA hybridisation method was applied. The sensor signal was increased by increasing the electrical potential assistanted DNA hybridisation time. It was possible to detect 0.34pmol and 0.072fmol of complementary oligonucleotide target in 0.1ml in seconds by using unpolished and polished gold electrode respectively. The probe preparation was also in seconds time, comparing indirect electrochemical DNA sensor, it has a fast sensor preparation as well as sensor response and label free advantages. The silicon microfabrication technique was used for this sensor array fabrication, which holds the potential to integrate with sensor electrical circuits. The conducting polymer polypyrrole was electrochemically deposited on each electrode respectively which has a possibility to dope the different DNA probe into the individual electrode to form a sensor array

  7. Effect of temperature on DNA double helix: An insight from molecular dynamics simulation

    Indian Academy of Sciences (India)

    Sangeeta Kundu; Sanchita Mukherjee; Dhananjay Bhattacharyya

    2012-07-01

    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.

  8. Radiation-induced DNA breaks detected by immuno labelling of poly(ADP-ribose) in CHO cells. Standardization by pulsed-field gel electrophoresis

    International Nuclear Information System (INIS)

    The poly (ADP-ribose) polymerase is an ubiquitous nuclear protein capable of binding specifically to DNA strand breaks. It synthesizes ADP-ribose polymers proportionally to DNA breaks. The actual method of reference to determine DNA double strand breaks is pulsed-field gel electrophoresis, but this requires many cells. It thus appeared of interest to use poly (ADP-ribos)ylation to follow and estimate γ-ray-induced DNA fragmentation at the level of isolated cells after γ-irradiation in chinese hamster ovary cells (CHO-K1). The results obtained by the immuno-labelling technique of ADP-ribose polymers were compared to those obtained by pulsed-field gel electrophoresis. They show that poly (ADP-ribos)ylation reflects the occurrence of radiation-induced DNA strand breaks. A clear relationship exists between the amount of ADP-ribose polymers detected and DNA double strand breaks after γ-irradiation. (authors)

  9. DNA Polymerase-Catalyzed DNA Network Growth

    OpenAIRE

    Keller, Sascha; Wang, Jie; Chandra, Madhaviah; Berger, Rüdiger; Marx, Andreas

    2008-01-01

    The distinct base pairing property of DNA is an advantageous phenomenon that has been exploited in the usage of DNA as scaffold for directed self-organization to form nanometer-sized objects in a desirable fashion. Herein we report the construction of three-dimensional DNA-based networks that can be generated and amplified by the DNA polymerase chain reaction (PCR). The approach is flexible allowing tuning of the meshes of the network by variation of the size of the template. Additionally, fu...

  10. Recent developments in Inorganic polymers: A Review with focus on Si-Al based inorganic polymers

    OpenAIRE

    Shrray Srivastava; Ravindra Gadhave

    2015-01-01

    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...

  11. EDITORIAL: Electroactive polymer materials

    Science.gov (United States)

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

    2007-04-01

    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. Atomistic simulation of polymer/solid and polymer/polymer interfaces

    International Nuclear Information System (INIS)

    Atomistic simulation techniques have been used to provide a molecular level perspective on the phenomena which control adhesion at metal oxide/polymer and polymer/polymer interfaces relevant to steel coating systems. Two simulation methodologies illustrated by relevant examples will be discussed. The physisorption of an epoxy resin (widely used as the basis of primer paint systems for metallic structural materials) onto alumina and chromia surfaces was compared. Initial model conformations of an epoxy resin oligomer were generated using the Theodorou-Suter technique and the metal oxide surfaces were represented by the low index Miller planes of AlIII and CrIII oxides. The simulated complexes of a single oligomer and various metal oxide surfaces were compared both geometrically and energetically and revealed the basis for better adhesion to the chromia surface. In order to simulate adhesion at polymer/polymer interfaces fully periodic amorphous models of interfaces were constructed and submitted to molecular dynamics. The results of these studies are in general agreement with experimental observations and provide the basis for developing a better understanding of the factors controlling adhesion at metal oxide/polymer and polymer/polymer interfaces

  13. DNA polymerase δ and DNA repair: DNA repair synthesis in human fibroblasts requires DNA polymerase δ

    International Nuclear Information System (INIS)

    When UV-irradiated cultured diploid human fibroblasts were permeabilized with Brij-58 then separated from soluble material by centrifugation, conservative DNA repair synthesis could be restored by a soluble factor obtained from the supernate of similarly treated HeLa cells. Monoclonal antibody to KB cell DNA polymerase α, while binding to HeLa DNA polymerase α, did not bind to the HeLa DNA polymerase δ. Moreover, at micromolar concentrations N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate (BuPdGT) and 2(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate (BuAdATP) were potent inhibitors of DNA polymerase α, but did not inhibit the DNA polymerase δ. Neither purified DNA polymerase α nor β could promote repair DNA synthesis in the permeabilized cells. Furthermore, if monoclonal antibodies to DNA polymerase α BuPdGTP, or BuAdATP was added to the reconstituted system, there was no significant inhibition

  14. SULFUR POLYMER ENCAPSULATION

    International Nuclear Information System (INIS)

    Sulfur polymer cement (SPC) is a thermoplastic polymer consisting of 95 wt% elemental sulfur and 5 wt% organic modifiers to enhance long-term durability. SPC was originally developed by the U.S. Bureau of Mines as an alternative to hydraulic cement for construction applications. Previous attempts to use elemental sulfur as a construction material in the chemical industry failed due to premature degradation. These failures were caused by the internal stresses that result from changes in crystalline structure upon cooling of the material. By reacting elemental sulfur with organic polymers, the Bureau of Mines developed a product that successfully suppresses the solid phase transition and significantly improves the stability of the product. SPC, originally named modified sulfur cement, is produced from readily available, inexpensive waste sulfur derived from desulfurization of both flue gases and petroleum. The commercial production of SPC is licensed in the United States by Martin Resources (Odessa, Texas) and is marketed under the trade name Chement 2000. It is sold in granular form and is relatively inexpensive ((approx)$0.10 to 0.12/lb). Application of SPC for the treatment of radioactive, hazardous, and mixed wastes was initially developed and patented by Brookhaven National Laboratory (BNL) in the mid-1980s (Kalb and Colombo, 1985; Colombo et al., 1997). The process was subsequently investigated by the Commission of the European Communities (Van Dalen and Rijpkema, 1989), Idaho National Engineering Laboratory (Darnell, 1991), and Oak Ridge National Laboratory (Mattus and Mattus, 1994). SPC has been used primarily in microencapsulation applications but can also be used for macroencapsulation of waste. SPC microencapsulation has been demonstrated to be an effective treatment for a wide variety of wastes, including incinerator hearth and fly ash; aqueous concentrates such as sulfates, borates, and chlorides; blowdown solutions; soils; and sludges. It is not

  15. Nucleic Acid-Peptide Complex Phase Controlled by DNA Hybridization

    Science.gov (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.

  16. Ionic Current Inversion in Pressure-Driven Polymer Translocation through Nanopores

    Science.gov (United States)

    Buyukdagli, Sahin; Blossey, Ralf; Ala-Nissila, T.

    2015-02-01

    We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics. In the presence of multivalent counterions, electrostatic many-body effects result in the reversal of the DNA charge. The attraction of anions to the charge-inverted DNA molecule reverses the sign of the ionic current through the pore. Our theory allows for a comprehensive understanding of the complex features of the resulting streaming currents. The underlying mechanism is an efficient way to detect DNA charge reversal in pressure-driven translocation experiments with multivalent cations.

  17. Polymers and supramolecular polymer systems for radionuclide delivery

    Czech Academy of Sciences Publication Activity Database

    Hrubý, Martin; Kučka, Jan; Sedláček, Ondřej; Vetrík, Miroslav; Pospíšilová, Aneta; Švec, Pavel; Štěpánek, Petr

    Budapest : Polymer Chemistry Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2015 - (Kasza, G.). s. 9 ISBN 978-963-12-3161-8. [International Symposium on Amphiphilic Polymers, Networks, Gels and Membranes - APNGM15. 30.08.2015-02.09.2015, Budapest] R&D Projects: GA ČR(CZ) GA13-08336S; GA MPO(CZ) FR-TI4/625; GA MZd(CZ) NV15-25781A Grant ostatní: AV ČR(CZ) M200501201 Institutional support: RVO:61389013 Keywords : radiopharmaceutical * polymer * micelle Subject RIV: FR - Pharmacology ; Medidal Chemistry

  18. Confined polymers in the extended de Gennes regime

    Science.gov (United States)

    Mehlig, Bernhard

    In the ''extended de Gennes regime'' the problem of describing the conformations of a semiflexible polymer confined to a channel can be mapped onto the weakly self-avoiding random-walk model. For large contour lengths the asymptotically exact solution of this model predicts how the conformational fluctuations of the confined polymer depend upon the channel dimensions and upon the physical properties of the polymer, its effective width and persistence length. The extended de Gennes regime (where the polymer is neither weakly nor strongly confined) has recently been studied intensively experimentally and by means of computer simulations of worm-like chain models. In this talk I explain the mapping, summarise the predictions derived from the exact solution, and compare the predictions to results of computer simulations [Dorfman et al.] and experiments [Westerlund et al.] of DNA molecules confined to nanochannels. I conclude by summarising open questions. This talk is mainly based on joint work with E. Werner [Phys Rev. E 90 (2014) 062602].

  19. The Extraction and Partial Purification of Bacterial DNA as a Practical Exercise for GCE Advanced Level Students.

    Science.gov (United States)

    Falconer, A. C.; Hayes, L. J.

    1986-01-01

    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)

  20. Blending of polyethylenimine with a cationic polyurethane greatly enhances both DNA delivery efficacy and reduces the overall cytotoxicity.

    Science.gov (United States)

    Cherng, J Y; Hung, W C; Kao, H C

    2011-05-01

    Three blending methods were introduced to combine a biodegradable cationic- polyurethane (PUg3) and polyethylenimine (PEI) together with DNA by different mixing sequences. Results of gel electrophoresis assays and particle size measurements show that complexes prepared by method 1 and 3 bear an ability to condense DNA into small nanoparticles. On the contrary, the use of method 2 in making complexes produces significantly large particles because of the weaker interaction with DNA and lack of DNA condensation. Moreover, cell proliferation assays show that no cytotoxicity of the DNA/blended-polymers complexes (exhibited by method 1) was found and due to a result of the outer coating of PUg3, reducing cytotoxic PEI exposure outside the complexes. With a new technique in pharmaceutics, the complexes prepared for DNA delivery by mixing of PEI and PUg3 with DNA in a sequence (method 1) could achieve an even better transfection efficiency (reaching 40% higher) than using PEI alone as well as reduce the cytotoxicity substantially. In conclusion, a new class of complexes (non-viral combo-system) made by a skillful blending sequence (method 1) has been designed and demonstrated to obtain the beneficial properties from two useful and individual polymers for gene delivery. This method can be used in greatly improving the transfection efficiency of polymer-based gene vectors. The blended polymers with DNA also have a better biocompatibility and no cytotoxicity, which are the requirements and critical points for great success in performing gene therapy in vivo. PMID:21446905

  1. Polymers from renewable materials.

    Science.gov (United States)

    Rus, Anika Zafiah M

    2010-01-01

    With the world facing depletion of its oil reserves, attention is being focused on how the plastics industry will address shortages and price increases in its crucial raw materials. One renewable resource is that of vegetable oils and fats and about a dozen crop plants make up the main vegetable oil-seed market. The main constituents of these oils are saturated and unsaturated fatty acids that are unique to the plant in which they have been developed. Moreover, technological processes can produce more well-defined and pure oils, and the fatty acid contents in the vegetable oils can be altered with modern crop development techniques. This article describes recent advances in utilising such vegetable oils in sourcing new polymeric materials. It also gives the context for the development of polymers based on renewable materials in general. PMID:21047019

  2. Self-healing polymers

    Science.gov (United States)

    Klein, Daniel J. (Inventor)

    2011-01-01

    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 190.degree. 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 29.degree. 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.

  3. DNA fragmentation in apoptosis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    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.

  4. Electrochromic in conjugated polymers

    International Nuclear Information System (INIS)

    This revision considered object the description of one of the materials with the greatest potential in the field of electrochromic (mainly in the visible region): the conjugated polymers (CP), area of enormous potential both now and in a short time ahead. The CP are insulating materials and organic semiconductors in a state not doped. They can be doped positively or negatively being observed a significant increase in the conductivity and being generated a color change in these materials. The understanding of how optical properties vary based on the chemical structure of the polymer or its mixtures and more precisely of the alternatives that can be entered into the conjugated system or π system to obtain a material that besides to be flexible, environmentally stable, presents the colored states. The revision was centred chiefly in the polypyrrole (Ppy), the polythiophene (PTh) and their derivatives such as poly (3.4-ethylenedioxythiophene) (PEDOT). The advantage of using monomers with variable structure, to adjust the composition of the copolymer, or to blend with the PC, allows to obtain a variety of colored states that can be modulated through the visible spectrum and even with applications to wavelengths outside of this region. Because the PC presented at least two different colored states can be varied continuously as a function of the voltage applied. In some cases, they may submit multicoloured statements, which offers a range of possibilities for their application in flexible electronic devices type screens and windows. Applications include smart windows, camouflage clothing and data screens. This type of material is emerging as one of the substitutes of the traditional inorganic semiconductor, with the advantage of its low cost, high flexibility and the possibility to generate multiple colors through the handling of the monomers in the structure and control of energy of his band gap. (author)

  5. Monitoring of polymer melt processing

    International Nuclear Information System (INIS)

    The paper reviews the state-of-the-art of in-line and on-line monitoring during polymer melt processing by compounding, extrusion and injection moulding. Different spectroscopic and scattering techniques as well as conductivity and viscosity measurements are reviewed and compared concerning their potential for different process applications. In addition to information on chemical composition and state of the process, the in situ detection of morphology, which is of specific interest for multiphase polymer systems such as polymer composites and polymer blends, is described in detail. For these systems, the product properties strongly depend on the phase or filler morphology created during processing. Examples for optical (UV/vis, NIR) and ultrasonic attenuation spectra recorded during extrusion are given, which were found to be sensitive to the chemical composition as well as to size and degree of dispersion of micro or nanofillers in the polymer matrix. By small-angle light scattering experiments, process-induced structures were detected in blends of incompatible polymers during compounding. Using conductivity measurements during extrusion, the influence of processing conditions on the electrical conductivity of polymer melts with conductive fillers (carbon black or carbon nanotubes) was monitored. (topical review)

  6. Fragmentation pathways of polymer ions.

    Science.gov (United States)

    Wesdemiotis, Chrys; Solak, Nilüfer; Polce, Michael J; Dabney, David E; Chaicharoen, Kittisak; Katzenmeyer, Bryan C

    2011-01-01

    Tandem mass spectrometry (MS/MS) is increasingly applied to synthetic polymers to characterize chain-end or in-chain substituents, distinguish isobaric and isomeric species, and determine macromolecular connectivities and architectures. For confident structural assignments, the fragmentation mechanisms of polymer ions must be understood, as they provide guidelines on how to deduce the desired information from the fragments observed in MS/MS spectra. This article reviews the fragmentation pathways of synthetic polymer ions that have been energized to decompose via collisionally activated dissociation (CAD), the most widely used activation method in polymer analysis. The compounds discussed encompass polystyrenes, poly(2-vinyl pyridine), polyacrylates, poly(vinyl acetate), aliphatic polyester copolymers, polyethers, and poly(dimethylsiloxane). For a number of these polymers, several substitution patterns and architectures are considered, and questions regarding the ionization agent and internal energy of the dissociating precursor ions are also addressed. Competing and consecutive dissociations are evaluated in terms of the structural insight they provide about the macromolecular structure. The fragmentation pathways of the diverse array of polymer ions examined fall into three categories, viz. (1) charge-directed fragmentations, (2) charge-remote rearrangements, and (3) charge-remote fragmentations via radical intermediates. Charge-remote processes predominate. Depending on the ionizing agent and the functional groups in the polymer, the incipient fragments arising by pathways (1)-(3) may form ion-molecule complexes that survive long enough to permit inter-fragment hydrogen atom, proton, or hydride transfers. PMID:20623599

  7. Elastic Behavior of Polymer Chains

    Institute of Scientific and Technical Information of China (English)

    Teng Lu; Tao Chen; Hao-jun Liang

    2008-01-01

    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.

  8. Behavior of DNA under hydrothermal conditions with MgCl2 additive using an in situ UV-vis spectrophotometer

    International Nuclear Information System (INIS)

    The capillary flow hydrothermal reactor system for the UV-vis spectrophotometric detection system (CHUS) has been applied to inspect the behavior of DNA at temperatures up to 300 deg. C. Double-stranded DNA (dsDNA) was monitored with and without ethidium bromide in the presence of MgCl2. The ratio (A+DNA/A-DNA) of the absorbance of EB with DNA (A+DNA) to that without DNA (A-DNA) increased steeply over 1 at temperatures around 100 deg. C, which was not observed in the absence of MgCl2. This was found to be due to the decrease of solubility of DNA in hot water, where dsDNA is converted to single-stranded DNA and become insoluble. At temperatures over 175 deg. C, DNA becomes soluble again because of the degradation of long insoluble DNA polymers to short soluble DNA oligomers. This study points out the importance of solubility of DNA for life at extremely high temperatures as well as the stability of DNA

  9. Efimov-Like Behaviour in Low-Dimensional Polymer Models

    Science.gov (United States)

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

    2016-05-01

    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 (dintroduction 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.

  10. Metal-conductive polymer hybrid nanostructures: preparation and electrical properties of palladium-polyimidazole nanowires

    Science.gov (United States)

    Al-Hinai, Mariam; Hassanien, Reda; Watson, Scott M. D.; Wright, Nicholas G.; Houlton, Andrew; Horrocks, Benjamin R.

    2016-03-01

    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 {{{{PdCl}}}4}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.

  11. DNA damage and autophagy

    International Nuclear Information System (INIS)

    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.

  12. Statistical properties of curved polymer

    Indian Academy of Sciences (India)

    Surya Kanta Ghosh; Anirban Sain

    2008-08-01

    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.

  13. Metal-containing conducting polymers

    Energy Technology Data Exchange (ETDEWEB)

    Higgins, S. (Dept. of Chemistry, Univ. of St. Andrews, Fife (United Kingdom)); Crayston, J.A. (Dept. of Chemistry, Univ. of St. Andrews, Fife (United Kingdom))

    1993-03-22

    Poly-(2,6-di-(2-thienyl) pyridine) was investigated for its ability to complex to metals via the pyridine group. Ag[sup +], Cu[sup 2+] and Pd[sup 2+] were reducible in MeCN at the polymer coated electrode after it had been activated by cathodic potentials. The polymer was insulating in aqueous media but in MeCN the cation Ru[sub 3]O(OAc)[sub 6](py)[sub 2](MeOH)[sup +], py=pyridine, was adsorbed onto the polymer as a monolayer. (orig.)

  14. Multilayer Electroactive Polymer Composite Material

    Science.gov (United States)

    Ounaies, Zoubeida (Inventor); Park, Cheol (Inventor); Harrison, Joycelyn S. (Inventor); Holloway, Nancy M. (Inventor); Draughon, Gregory K. (Inventor)

    2011-01-01

    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.

  15. Radiation crosslinking of biocompatible polymers

    Czech Academy of Sciences Publication Activity Database

    Sedláček, Ondřej; Kučka, Jan; Monnery, B. D.; Hoogenboom, R.; Hrubý, Martin

    Bratislava : Young Scientists Council of Polymer Institute of Slovak Academy of Sciences, 2016. s. 89. ISBN 978-80-970923-8-2. [Bratislava Young Polymer Scientists workshop /6./ - BYPoS 2016. 14.03.2016-18.03.2016, Ždiar] R&D Projects: GA MŠk(CZ) LO1507; GA MŠk(CZ) LH14079; GA MZd(CZ) NV15-25781A; GA ČR(CZ) GA13-08336S Institutional support: RVO:61389013 Keywords : radiolysis * radiotherapeutics * biocompatible polymer s Subject RIV: CD - Macromolecular Chemistry

  16. Physics of photorefraction in polymers

    CERN Document Server

    West, Dave

    2004-01-01

    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.

  17. Thermoresponsive Polymers for Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Theoni K. Georgiou

    2011-08-01

    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.

  18. Physical properties of polymers handbook

    CERN Document Server

    2007-01-01

    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.

  19. Wetting of brushes by polymer melts

    NARCIS (Netherlands)

    Maas, J.

    2001-01-01

    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

  20. Carbon nanotube-polymer composite actuators

    Science.gov (United States)

    Gennett, Thomas; Raffaelle, Ryne P.; Landi, Brian J.; Heben, Michael J.

    2008-04-22

    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.