Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores

Science.gov (United States)

Bell, Nicholas A. W.; Keyser, Ulrich F.

2016-07-01

The simultaneous detection of a large number of different analytes is important in bionanotechnology research and in diagnostic applications. Nanopore sensing is an attractive method in this regard as the approach can be integrated into small, portable device architectures, and there is significant potential for detecting multiple sub-populations in a sample. Here, we show that highly multiplexed sensing of single molecules can be achieved with solid-state nanopores by using digitally encoded DNA nanostructures. Based on the principles of DNA origami, we designed a library of DNA nanostructures in which each member contains a unique barcode; each bit in the barcode is signalled by the presence or absence of multiple DNA dumbbell hairpins. We show that a 3-bit barcode can be assigned with 94% accuracy by electrophoretically driving the DNA structures through a solid-state nanopore. Select members of the library were then functionalized to detect a single, specific antibody through antigen presentation at designed positions on the DNA. This allows us to simultaneously detect four different antibodies of the same isotype at nanomolar concentration levels.

Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids

Science.gov (United States)

Aramesh, M.; Shimoni, O.; Fox, K.; Karle, T. J.; Lohrmann, A.; Ostrikov, K.; Prawer, S.; Cervenka, J.

2015-03-01

Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 1015 molecules per cm2 down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers.Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated

DNA base-calling from a nanopore using a Viterbi algorithm.

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Timp, Winston; Comer, Jeffrey; Aksimentiev, Aleksei

2012-05-16

Nanopore-based DNA sequencing is the most promising third-generation sequencing method. It has superior read length, speed, and sample requirements compared with state-of-the-art second-generation methods. However, base-calling still presents substantial difficulty because the resolution of the technique is limited compared with the measured signal/noise ratio. Here we demonstrate a method to decode 3-bp-resolution nanopore electrical measurements into a DNA sequence using a Hidden Markov model. This method shows tremendous potential for accuracy (~98%), even with a poor signal/noise ratio. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Controllable Shrinking of Glass Capillary Nanopores Down to sub-10 nm by Wet-Chemical Silanization for Signal-Enhanced DNA Translocation.

Science.gov (United States)

Xu, Xiaolong; Li, Chuanping; Zhou, Ya; Jin, Yongdong

2017-10-27

Diameter is a major concern for nanopore based sensing. However, directly pulling glass capillary nanopore with diameter down to sub-10 nm is very difficult. So, post treatment is sometimes necessary. Herein, we demonstrate a facile and effective wet-chemical method to shrink the diameter of glass capillary nanopore from several tens of nanometers to sub-10 nm by disodium silicate hydrolysis. Its benefits for DNA translocation are investigated. The shrinking of glass capillary nanopore not only slows down DNA translocation, but also enhances DNA translocation signal and signal-to-noise ratio significantly (102.9 for 6.4 nm glass nanopore, superior than 15 for a 3 nm silicon nitride nanopore). It also affects DNA translocation behaviors, making the approach and glass capillary nanopore platform promising for DNA translocation studies.

Dynamic translocation of ligand-complexed DNA through solid-state nanopores with optical tweezers

International Nuclear Information System (INIS)

Sischka, Andy; Spiering, Andre; Anselmetti, Dario; Khaksar, Maryam; Laxa, Miriam; Koenig, Janine; Dietz, Karl-Josef

2010-01-01

We investigated the threading and controlled translocation of individual lambda-DNA (λ-DNA) molecules through solid-state nanopores with piconewton force sensitivity, millisecond time resolution and picoampere ionic current sensitivity with a set-up combining quantitative 3D optical tweezers (OT) with electrophysiology. With our virtually interference-free OT set-up the binding of RecA and single peroxiredoxin protein molecules to λ-DNA was quantitatively investigated during dynamic translocation experiments where effective forces and respective ionic currents of the threaded DNA molecule through the nanopore were measured during inward and outward sliding. Membrane voltage-dependent experiments of reversible single protein/DNA translocation scans yield hysteresis-free, asymmetric single-molecule fingerprints in the measured force and conductance signals that can be attributed to the interplay of optical trap and electrostatic nanopore potentials. These experiments allow an exact localization of the bound protein along the DNA strand and open fascinating applications for label-free detection of DNA-binding ligands, where structural and positional binding phenomena can be investigated at a single-molecule level.

Nanoporous metal/oxide hybrid electrodes for electrochemical supercapacitors

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Lang, Xingyou; Hirata, Akihiko; Fujita, Takeshi; Chen, Mingwei

2011-04-01

Electrochemical supercapacitors can deliver high levels of electrical power and offer long operating lifetimes, but their energy storage density is too low for many important applications. Pseudocapacitive transition-metal oxides such as MnO2 could be used to make electrodes in such supercapacitors, because they are predicted to have a high capacitance for storing electrical charge while also being inexpensive and not harmful to the environment. However, the poor conductivity of MnO2 (10-5-10-6 S cm-1) limits the charge/discharge rate for high-power applications. Here, we show that hybrid structures made of nanoporous gold and nanocrystalline MnO2 have enhanced conductivity, resulting in a specific capacitance of the constituent MnO2 (~1,145 F g-1) that is close to the theoretical value. The nanoporous gold allows electron transport through the MnO2, and facilitates fast ion diffusion between the MnO2 and the electrolytes while also acting as a double-layer capacitor. The high specific capacitances and charge/discharge rates offered by such hybrid structures make them promising candidates as electrodes in supercapacitors, combining high-energy storage densities with high levels of power delivery.

Concentration Polarization in Translocation of DNA through Nanopores and Nanochannels

NARCIS (Netherlands)

Das, S.; Dubsky, P.; van den Berg, Albert; Eijkel, Jan C.T.

2012-01-01

In this Letter we provide a theory to show that high-field electrokinetic translocation of DNA through nanopores or nanochannels causes large transient variations of the ionic concentrations in front and at the back of the DNA due to concentration polarization (CP). The CP causes strong local

Detecting a single molecule using a micropore-nanopore hybrid chip.

Science.gov (United States)

Liu, Lei; Zhu, Lizhong; Ni, Zhonghua; Chen, Yunfei

2013-11-21

Nanopore-based DNA sequencing and biomolecule sensing have attracted more and more attention. In this work, novel sensing devices were built on the basis of the chips containing nanopore arrays in polycarbonate (PC) membranes and micropores in Si3N4 films. Using the integrated chips, the transmembrane ionic current induced by biomolecule's translocation was recorded and analyzed, which suggested that the detected current did not change linearly as commonly expected with increasing biomolecule concentration. On the other hand, detailed translocation information (such as translocation gesture) was also extracted from the discrete current blockages in basic current curves. These results indicated that the nanofluidic device based on the chips integrated by micropores and nanopores possessed comparative potentials in biomolecule sensing.

Design of Hydrogen Storage Alloys/Nanoporous Metals Hybrid Electrodes for Nickel-Metal Hydride Batteries

Science.gov (United States)

Li, M. M.; Yang, C. C.; Wang, C. C.; Wen, Z.; Zhu, Y. F.; Zhao, M.; Li, J. C.; Zheng, W. T.; Lian, J. S.; Jiang, Q.

2016-06-01

Nickel metal hydride (Ni-MH) batteries have demonstrated key technology advantages for applications in new-energy vehicles, which play an important role in reducing greenhouse gas emissions and the world’s dependence on fossil fuels. However, the poor high-rate dischargeability of the negative electrode materials—hydrogen storage alloys (HSAs) limits applications of Ni-MH batteries in high-power fields due to large polarization. Here we design a hybrid electrode by integrating HSAs with a current collector of three-dimensional bicontinuous nanoporous Ni. The electrode shows enhanced high-rate dischargeability with the capacity retention rate reaching 44.6% at a discharge current density of 3000 mA g-1, which is 2.4 times that of bare HSAs (18.8%). Such a unique hybrid architecture not only enhances charge transfer between nanoporous Ni and HSAs, but also facilitates rapid diffusion of hydrogen atoms in HSAs. The developed HSAs/nanoporous metals hybrid structures exhibit great potential to be candidates as electrodes in high-performance Ni-MH batteries towards applications in new-energy vehicles.

Conformational Thermodynamics of DNA Strands in Hydrophilic Nanopores.

Science.gov (United States)

Cruz, Fernando J A L; Mota, Jose P B

2016-08-18

Enhanced sampling techniques spanning a sub-microsecond timescale reveal that a double-stranded DNA dodecamer can be spontaneously encapsulated into (51,0) and (40,0) single-walled carbon nanotubes under the influence of an electric field, leading to hybrids with a 40 kJ/mol enhanced free-energy. The confinement mechanism allows the nucleic acid to retain its mobility, diffusing anisotropically along the endohedral volume, visiting regions of space determined by entropic factors (diameter, free-volume) and linked by a thermodynamical highway. In spite of the energetic similarities between both topologies (4.1× 103 kJ/mol), the biomolecule favours positioning either parallel to the nanopore central axis, (40,0), or in close contact with the solid walls, (51,0), in the latter encasing a hollow cylindrical domain of diameter 1 - 1.5 nm. Precise physiological conditions allow the extrapolation of results to in vivo systems and constitute a novel and thorough contribution to nanotube technology in the areas of nucleic acid encapsulation/delivery and personalized therapeutics.

Nanofluidic Device with Embedded Nanopore

Science.gov (United States)

Zhang, Yuning; Reisner, Walter

2014-03-01

Nanofluidic based devices are robust methods for biomolecular sensing and single DNA manipulation. Nanopore-based DNA sensing has attractive features that make it a leading candidate as a single-molecule DNA sequencing technology. Nanochannel based extension of DNA, combined with enzymatic or denaturation-based barcoding schemes, is already a powerful approach for genome analysis. We believe that there is revolutionary potential in devices that combine nanochannels with nanpore detectors. In particular, due to the fast translocation of a DNA molecule through a standard nanopore configuration, there is an unfavorable trade-off between signal and sequence resolution. With a combined nanochannel-nanopore device, based on embedding a nanopore inside a nanochannel, we can in principle gain independent control over both DNA translocation speed and sensing signal, solving the key draw-back of the standard nanopore configuration. We demonstrate that we can detect - using fluorescent microscopy - successful translocation of DNA from the nanochannel out through the nanopore, a possible method to 'select' a given barcode for further analysis. We also show that in equilibrium DNA will not escape through an embedded sub-persistence length nanopore until a certain voltage bias is added.

Ion transport by gating voltage to nanopores produced via metal-assisted chemical etching method

Science.gov (United States)

Van Toan, Nguyen; Inomata, Naoki; Toda, Masaya; Ono, Takahito

2018-05-01

In this work, we report a simple and low-cost way to create nanopores that can be employed for various applications in nanofluidics. Nano sized Ag particles in the range from 1 to 20 nm are formed on a silicon substrate with a de-wetting method. Then the silicon nanopores with an approximate 15 nm average diameter and 200 μm height are successfully produced by the metal-assisted chemical etching method. In addition, electrically driven ion transport in the nanopores is demonstrated for nanofluidic applications. Ion transport through the nanopores is observed and could be controlled by an application of a gating voltage to the nanopores.

Ultrasensitive electrochemical detection of DNA based on Zn²⁺ assistant DNA recycling followed with hybridization chain reaction dual amplification.

Science.gov (United States)

Qian, Yong; Wang, Chunyan; Gao, Fenglei

2015-01-15

A new strategy to combine Zn(2+) assistant DNA recycling followed with hybridization chain reaction dual amplification was designed for highly sensitive electrochemical detection of target DNA. A gold electrode was used to immobilize molecular beacon (MB) as the recognition probe and perform the amplification procedure. In the presence of the target DNA, the hairpin probe 1 was opened, and the DNAzyme was liberated from the caged structure. The activated DNAzyme hybridized with the MB and catalyzed its cleavage in the presence of Zn(2+) cofactor and resulting in a free DNAzyme strand. Finally, each target-induced activated DNAzyme underwent many cycles triggering the cleavage of MB, thus forming numerous MB fragments. The MB fragments triggered the HCR and formed a long double-helix DNA structure. Because both H1 and H2 were labeled by biotin, a lot of SA-ALP was captured on the electrode surface, thus catalyzing a silver deposition process for electrochemical stripping analysis. This novel cascade signal amplification strategy can detect target DNA down to the attomolar level with a dynamic range spanning 6 orders of magnitude. This highly sensitive and specific assay has a great potential to become a promising DNA quantification method in biomedical research and clinical diagnosis. Copyright © 2014 Elsevier B.V. All rights reserved.

Fabrication of Low Noise Borosilicate Glass Nanopores for Single Molecule Sensing.

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Jayesh A Bafna

Full Text Available We show low-cost fabrication and characterization of borosilicate glass nanopores for single molecule sensing. Nanopores with diameters of ~100 nm were fabricated in borosilicate glass capillaries using laser assisted glass puller. We further achieve controlled reduction and nanometer-size control in pore diameter by sculpting them under constant electron beam exposure. We successfully fabricate pore diameters down to 6 nm. We next show electrical characterization and low-noise behavior of these borosilicate nanopores and compare their taper geometries. We show, for the first time, a comprehensive characterization of glass nanopore conductance across six-orders of magnitude (1M-1μM of salt conditions, highlighting the role of buffer conditions. Finally, we demonstrate single molecule sensing capabilities of these devices with real-time translocation experiments of individual λ-DNA molecules. We observe distinct current blockage signatures of linear as well as folded DNA molecules as they undergo voltage-driven translocation through the glass nanopores. We find increased signal to noise for single molecule detection for higher trans-nanopore driving voltages. We propose these nanopores will expand the realm of applications for nanopore platform.

Selective detection and quantification of modified DNA with solid-state nanopores.

Science.gov (United States)

Carlsen, Autumn T; Zahid, Osama K; Ruzicka, Jan A; Taylor, Ethan W; Hall, Adam R

2014-10-08

We demonstrate a solid-state nanopore assay for the unambiguous discrimination and quantification of modified DNA. Individual streptavidin proteins are employed as high-affinity tags for DNA containing a single biotin moiety. We establish that the rate of translocation events corresponds directly to relative concentration of protein-DNA complexes and use the selectivity of our approach to quantify modified oligonucleotides from among a background of unmodified DNA in solution.

DNA damage due to perfluorooctane sulfonate based on nano-gold embedded in nano-porous poly-pyrrole film

Energy Technology Data Exchange (ETDEWEB)

Lu, Liping, E-mail: lipinglu@bjut.edu.cn; Xu, Laihui; Kang, Tianfang; Cheng, Shuiyuan

2013-11-01

DNA damage induced from perfluorooctane sulfonate (PFOS) was further developed on a nano-porous bionic interface. The interface was formed by assembling DNA on nano-gold particles which were embedded in a nano-porous overoxidized polypyrrole film (OPPy). Atomic force microscopy, scanning electron microscope and electrochemical investigations indicate that OPPy can be treated to form nano-pore structures. DNA damage due to PFOS was proved using electrochemistry and X-ray photoelectron spectroscopy (XPS) and was investigated by detecting differential pulse voltammetry (DPV) response of methylene blue (MB) which was used as electro-active indicator in the system. The current of MB attenuates obviously after incubation of DNA in PFOS. Moreover, electrochemical impedance spectroscopy (EIS) demonstrates that PFOS weakens DNA charge transport. The tentative binding ratio of PFOS: DNA base pair was obtained by analyzing XPS data of this system.

Probing DNA in nanopores via tunneling: from sequencing to ``quantum'' analogies

Science.gov (United States)

di Ventra, Massimiliano

2012-02-01

Fast and low-cost DNA sequencing methods would revolutionize medicine: a person could have his/her full genome sequenced so that drugs could be tailored to his/her specific illnesses; doctors could know in advance patients' likelihood to develop a given ailment; cures to major diseases could be found faster [1]. However, this goal of ``personalized medicine'' is hampered today by the high cost and slow speed of DNA sequencing methods. In this talk, I will discuss the sequencing protocol we suggest which requires the measurement of the distributions of transverse currents during the translocation of single-stranded DNA into nanopores [2-5]. I will support our conclusions with a combination of molecular dynamics simulations coupled to quantum mechanical calculations of electrical current in experimentally realizable systems [2-5]. I will also discuss recent experiments that support these theoretical predictions. In addition, I will show how this relatively unexplored area of research at the interface between solids, liquids, and biomolecules at the nanometer length scale is a fertile ground to study quantum phenomena that have a classical counterpart, such as ionic quasi-particles, ionic ``quantized'' conductance [6,7] and Coulomb blockade [8]. Work supported in part by NIH. [4pt] [1] M. Zwolak, M. Di Ventra, Physical Approaches to DNA Sequencing and Detection, Rev. Mod. Phys. 80, 141 (2008).[0pt] [2] M. Zwolak and M. Di Ventra, Electronic signature of DNA nucleotides via transverse transport, Nano Lett. 5, 421 (2005).[0pt] [3] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Fast DNA sequencing via transverse electronic transport, Nano Lett. 6, 779 (2006).[0pt] [4] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport, Biophys. J. 93, 2384 (2007).[0pt] [5] M. Krems, M. Zwolak, Y.V. Pershin, and M. Di Ventra, Effect of noise on DNA sequencing via transverse electronic transport

Conversion of Isoprenoid Oil by Catalytic Cracking and Hydrocracking over Nanoporous Hybrid Catalysts

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Toshiyuki Kimura

2012-01-01

Full Text Available In order to produce petroleum alternatives from biomass, a significant amount of research has been focused on oils from microalgae due to their origin, which would not affect food availability. Nanoporous hybrid catalysts composed of ns Al2O3 and zeolites have been proven to be very useful compared to traditional catalysts in hydrotreating (HT, hydrocracking (HC, and catalytic cracking (CC of large molecules. To evaluate the reaction scheme and products from model isoprenoid compounds of microalgae oil, nanoporous hybrid catalyst technologies (CC: ns Al2O3/H-USY and ns Al2O3/H-GaAlMFI; HC: [Ni-Mo/γ-Al2O3]/ns Al2O3/H-beta were studied. The major product from CC on ns Al2O3/H-USY was highly aromatic gasoline, while the product from HC was half-isoparaffinic/olefinic kerosene. Although more than 50 wt% of the products from HT/CC on the USY catalyst was liquefied petroleum gas due to overcracking, the product from HT/CC on the MFI catalyst was high-octane-number gasoline. Delightfully, the product from HT/HC was kerosene and its average number was 11, with more than 80 wt% being isoparaffinic. As a result, it was demonstrated that hydrotreating may convert isoprenoid oil from microalgae over nanoporous hybrid catalysts into a variety of products.

Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing.

Science.gov (United States)

Hargreaves, Adam D; Mulley, John F

2015-01-01

Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper, Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0-2% with hybrid error correction and 3% with de novo error correction. Our corrected data provides full coding sequences and 5' and 3' UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species.

Origin of the electrophoretic force on DNA in solid-state nanopores

Science.gov (United States)

van Dorp, Stijn; Keyser, Ulrich F.; Dekker, Nynke H.; Dekker, Cees; Lemay, Serge G.

2009-05-01

Despite gel electrophoresis being one of the main workhorses of molecular biology, the physics of polyelectrolyte electrophoresis in a strongly confined environment remains poorly understood. Theory indicates that forces in electrophoresis result from interplay between ionic screening and hydrodynamics, but these ideas could so far be addressed only indirectly by experiments based on macroscopic porous gels. Here, we provide a first direct experimental test by measuring the electrophoretic force on a single DNA molecule threading through a solid-state nanopore as a function of pore size. The stall force gradually decreases on increasing the nanopore diameter from 6 to 90nm, inconsistent with expectations from simple electrostatics and strikingly demonstrating the influence of the hydrodynamic environment. We model this process by applying the coupled Poisson-Boltzmann and Stokes equations in the nanopore geometry and find good agreement with the experimental results.

Detecting single-abasic residues within a DNA strand immobilized in a biological nanopore using an integrated CMOS sensor.

Science.gov (United States)

Kim, Jungsuk; Maitra, Raj D; Pedrotti, Ken; Dunbar, William B

2013-02-01

In this paper, we demonstrate the application of a novel current-measuring sensor (CMS) customized for nanopore applications. The low-noise CMS is fabricated in a 0.35μm CMOS process and is implemented in experiments involving DNA captured in an α-hemolysin (α-HL) nanopore. Specifically, the CMS is used to build a current amplitude map as a function of varying positions of a single-abasic residue within a homopolymer cytosine single-stranded DNA (ssDNA) that is captured and held in the pore. Each ssDNA is immobilized using a biotin-streptavidin linkage. Five different DNA templates are measured and compared: one all-cytosine ssDNA, and four with a single-abasic residue substitution that resides in or near the ~1.5nm aperture of the α-HL channel when the strand is immobilized. The CMOS CMS is shown to resolves the ~5Å displacements of the abasic residue within the varying templates. The demonstration represents an advance in application-specific circuitry that is optimized for small-footprint nanopore applications, including genomic sequencing.

Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing

Directory of Open Access Journals (Sweden)

Adam D. Hargreaves

2015-11-01

Full Text Available Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper, Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0–2% with hybrid error correction and 3% with de novo error correction. Our corrected data provides full coding sequences and 5′ and 3′ UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete and Sanger-based ESTs (15/29. We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species.

Expanding the functionality and applications of nanopore sensors

Science.gov (United States)

Venta, Kimberly E.

Nanopore sensors have developed into powerful tools for single-molecule studies since their inception two decades ago. Nanopore sensors function as nanoscale Coulter counters, by monitoring ionic current modulations as particles pass through a nanopore. While nanopore sensors can be used to study any nanoscale particle, their most notable application is as a low cost, fast alternative to current DNA sequencing technologies. In recent years, signifcant progress has been made toward the goal of nanopore-based DNA sequencing, which requires an ambitious combination of a low-noise and high-bandwidth nanopore measurement system and spatial resolution. In this dissertation, nanopore sensors in thin membranes are developed to improve dimensional resolution, and these membranes are used in parallel with a high-bandwidth amplfier. Using this nanopore sensor system, the signals of three DNA homopolymers are differentiated for the first time in solid-state nanopores. The nanopore noise is also reduced through the addition of a layer of SU8, a spin-on polymer, to the supporting chip structure. By increasing the temporal and spatial resolution of nanopore sensors, studies of shorter molecules are now possible. Nanopore sensors are beginning to be used for the study and characterization of nanoparticles. Nanoparticles have found many uses from biomedical imaging to next-generation solar cells. However, further insights into the formation and characterization of nanoparticles would aid in developing improved synthesis methods leading to more effective and customizable nanoparticles. This dissertation presents two methods of employing nanopore sensors to benet nanoparticle characterization and fabrication. Nanopores were used to study the formation of individual nanoparticles and serve as nanoparticle growth templates that could be exploited to create custom nanoparticle arrays. Additionally, nanopore sensors were used to characterize the surface charge density of anisotropic

Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

Science.gov (United States)

Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

2013-01-01

Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry. PMID:23435052

Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

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Yuji Miyahara

2013-02-01

Full Text Available Peptide nucleic acid (PNA has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

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Shan Wei

2018-05-01

Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

Direct Detection of Unnatural DNA Nucleotides dNaM and d5SICS using the MspA Nanopore.

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Jonathan M Craig

Full Text Available Malyshev et al. showed that the four-letter genetic code within a living organism could be expanded to include the unnatural DNA bases dNaM and d5SICS. However, verification and detection of these unnatural bases in DNA requires new sequencing techniques. Here we provide proof of concept detection of dNaM and d5SICS in DNA oligomers via nanopore sequencing using the nanopore MspA. We find that both phi29 DNA polymerase and Hel308 helicase are capable of controlling the motion of DNA containing dNaM and d5SICS through the pore and that single reads are sufficient to detect the presence and location of dNaM and d5SICS within single molecules.

DNA Physical Mapping via the Controlled Translocation of Single Molecules through a 5-10nm Silicon Nitride Nanopore

Science.gov (United States)

Stein, Derek; Reisner, Walter; Jiang, Zhijun; Hagerty, Nick; Wood, Charles; Chan, Jason

2009-03-01

The ability to map the binding position of sequence-specific markers, including transcription-factors, protein-nucleic acids (PNAs) or deactivated restriction enzymes, along a single DNA molecule in a nanofluidic device would be of key importance for the life-sciences. Such markers could give an indication of the active genes at particular stage in a cell's transcriptional cycle, pinpoint the location of mutations or even provide a DNA barcode that could aid in genomics applications. We have developed a setup consisting of a 5-10 nm nanopore in a 20nm thick silicon nitride film coupled to an optical tweezer setup. The translocation of DNA across the nanopore can be detected via blockades in the electrical current through the pore. By anchoring one end of the translocating DNA to an optically trapped microsphere, we hope to stretch out the molecule in the nanopore and control the translocation speed, enabling us to slowly scan across the genome and detect changes in the baseline current due to the presence of bound markers.

DNA-assisted binding of microspheres on glass substrates and their laser-induced release

International Nuclear Information System (INIS)

Kim, Sejong; Geiss, Erik; Yu, Phillip; Papadimitrakopoulos, Fotios; Marcus, Harris L.

2006-01-01

DNA hybridization has been increasingly adopted in materials sciences due to its complementary nature of single stranded DNAs. This unique property could be potentially used in the realization of 2 dimensional (2D) arrays of colloidal microspheres as a precursor to further build more complicated superstructures. In order to precisely understand this DNA-assisted assembly of colloidal particles, we quantitatively assessed the surface density of grafted and hybridizing accessible DNA oligomers on both substrate and colloidal particles. The DNA grafting densities were determined by UV-Vis of dye-functionalized complementary DNA oligomers, in conjunction with theoretical models. The variations of the concentration of hybridized DNA as a function of parameters such as the number of DNA base pairs (bp), the length of spacer and the size of sphere were also investigated to determine the immobilization strength of colloidal microspheres on the substrate. Dehybridization of the particle was conducted by utilizing a focused laser beam. These results were also compared with the particle hybridization energies and modeled according to the sum of DNA bindings as a function of the number of hybridized bases

On site DNA barcoding by nanopore sequencing.

Directory of Open Access Journals (Sweden)

Michele Menegon

Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

Side-gated ultrathin-channel nanopore FET sensors

International Nuclear Information System (INIS)

Yanagi, Itaru; Haga, Takanobu; Ando, Masahiko; Yamamoto, Jiro; Mine, Toshiyuki; Ishida, Takeshi; Hatano, Toshiyuki; Akahori, Rena; Yokoi, Takahide; Anazawa, Takashi; Oura, Takeshi

2016-01-01

A side-gated, ultrathin-channel nanopore FET (SGNAFET) is proposed for fast and label-free DNA sequencing. The concept of the SGNAFET comprises the detection of changes in the channel current during DNA translocation through a nanopore and identifying the four types of nucleotides as a result of these changes. To achieve this goal, both p- and n-type SGNAFETs with a channel thicknesses of 2 or 4 nm were fabricated, and the stable transistor operation of both SGNAFETs in air, water, and a KCl buffer solution were confirmed. In addition, synchronized current changes were observed between the ionic current through the nanopore and the SGNAFET’s drain current during DNA translocation through the nanopore. (paper)

Nanostructured ZnO-based biosensor: DNA immobilization and hybridization

Directory of Open Access Journals (Sweden)

Ahmed Mishaal Mohammed

2017-09-01

Full Text Available An electrochemical DNA biosensor was successfully fabricated by using (3-aminopropyl triethoxysilane (APTES with zinc oxide (ZnO nanorods synthesized using microwave-assisted chemical bath deposition method on thermally oxidized SiO2 thin films. The structural quality and morphology of the ZnO nanorods were determined by employing scanning electron microscopy (SEM and X-ray diffraction (XRD, which show a hexagonal wurtzite structure with a preferred orientation along the (101 direction. The surface of the SiO2 thin films was chemically modified with ZnO. Label-free detection DNA immobilization and hybridization were performed using potassium hexacyanoferrate with cyclic voltammetry (CV measurements. The capacitance, permittivity, and conductivity profiles of the fabricated sensor clearly indicate DNA immobilization and hybridization. Results show that the capacitance values of bare, ZnO- modified surface immobilization, and target DNA hybridization were 46×10−12F, 47×10−8F, 27μF, and 17μF, respectively, at 1Hz. The permittivity measurement increased from 3.94×103 to 251×103 and 165×103 at the frequency range of approximately 200 to 1Hz for bare and DNA immobilization and hybridization, respectively. The measured conductivity values for the bare, ZnO, immobilized, and hybridization device were 2.4×10−9, 10×10−8, 1.6×10−7, and 1.3×10−7Scm−1, respectively. Keywords: Zinc oxide, Biosensor, Capacitance, Permittivity, Conductivity

DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA

DEFF Research Database (Denmark)

Christensen, H.; Angen, Øystein; Mutters, R.

2000-01-01

The present study was aimed at reducing the time and labour used to perform DNA-DNA hybridizations for classification of bacteria at the species level. A micro-well-format DNA hybridization method was developed and validated. DNA extractions were performed by a small-scale method and DNA...... was sheared mechanically into fragments of between 400 and 700 bases. The hybridization conditions were calibrated according to DNA similarities obtained by the spectrophotometric method using strains within the family Pasteurellaceae, Optimal conditions were obtained with 300 ng DNA added per well and bound...... by covalent attachment to NucleoLink. Hybridization was performed with 500 ng DNA, 5% (w/w) of which was labelled with photo-activatable biotin (competitive hybridization) for 2.5 h at 65 degrees C in 2 x SSC followed by stringent washing with 2 x SSC at the same temperature. The criteria for acceptance...

Nanopore sensors : From hybrid to abiotic systems

NARCIS (Netherlands)

Kocer, Armagan; Tauk, Lara; Dejardin, Philippe

2012-01-01

The use of nanopores of well controlled geometry for sensing molecules in solution is reviewed. Focus is concentrated especially on synthetic track-etch pores in polymer foils and on biological nanopores, i.e. ion channels. After a brief section about multipore sensors, specific attention is

Translocation of DNA Molecules through Nanopores with Salt Gradients: The Role of Osmotic Flow

Science.gov (United States)

Hatlo, Marius M.; Panja, Debabrata; van Roij, René

2011-08-01

Recent experiments of translocation of double-stranded DNA through nanopores [M. Wanunu , Nature Nanotech. 5, 160 (2009)NNAABX1748-338710.1038/nnano.2009.379] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the pore. We show that osmotic flow combined with electrophoretic effects can quantitatively explain the experimental data on the salt-gradient dependence of the capture rate.

Effect of sample storage time on detection of hybridization signals in Checkerboard DNA-DNA hybridization.

Science.gov (United States)

do Nascimento, Cássio; Muller, Katia; Sato, Sandra; Albuquerque Junior, Rubens Ferreira

2012-04-01

Long-term sample storage can affect the intensity of the hybridization signals provided by molecular diagnostic methods that use chemiluminescent detection. The aim of this study was to evaluate the effect of different storage times on the hybridization signals of 13 bacterial species detected by the Checkerboard DNA-DNA hybridization method using whole-genomic DNA probes. Ninety-six subgingival biofilm samples were collected from 36 healthy subjects, and the intensity of hybridization signals was evaluated at 4 different time periods: (1) immediately after collecting (n = 24) and (2) after storage at -20 °C for 6 months (n = 24), (3) for 12 months (n = 24), and (4) for 24 months (n = 24). The intensity of hybridization signals obtained from groups 1 and 2 were significantly higher than in the other groups (p  0.05). The Checkerboard DNA-DNA hybridization method was suitable to detect hybridization signals from all groups evaluated, and the intensity of signals decreased significantly after long periods of sample storage.

Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building.

Science.gov (United States)

Pomerantz, Aaron; Peñafiel, Nicolás; Arteaga, Alejandro; Bustamante, Lucas; Pichardo, Frank; Coloma, Luis A; Barrio-Amorós, César L; Salazar-Valenzuela, David; Prost, Stefan

2018-04-01

Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here, we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack in one of the world's most imperiled biodiversity hotspots, the Ecuadorian Chocó rainforest. We used portable equipment, including the MinION nanopore sequencer (Oxford Nanopore Technologies) and the miniPCR (miniPCR), to perform DNA extraction, polymerase chain reaction amplification, and real-time DNA barcoding of reptile specimens in the field. We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. The flexibility of our mobile laboratory further allowed us to generate sequence information at the Universidad Tecnológica Indoamérica in Quito for rare, endangered, and undescribed species. This includes the recently rediscovered Jambato toad, which was thought to be extinct for 28 years. Sequences generated on the MinION required as few as 30 reads to achieve high accuracy relative to Sanger sequencing, and with further multiplexing of samples, nanopore sequencing can become a cost-effective approach for rapid and portable DNA barcoding. Overall, we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas to aid in conservation efforts and be applied to research facilities in developing countries. This opens up possibilities for biodiversity studies by promoting local research capacity building, teaching nonspecialists and students about the environment, tackling wildlife crime, and promoting conservation via research-focused ecotourism.

Optical detection of two-color-fluorophore barcode for nanopore DNA sensing

Science.gov (United States)

Zhang, M.; Sychugov, I.; Schmidt, T.; Linnros, J.

2015-06-01

A simple schematic on parallel optical detection of two-fluorophore barcode for single-molecule nanopore sensing is presented. The chosen two fluorophores, ATTO-532 and DY-521-XL, emitting in well-separated spectrum range can be excited at the same wavelength. A beam splitter was employed to separate signals from the two fluorophores and guide them to the same CCD camera. Based on a conventional microscope, sources of background in the nanopore sensing system, including membranes, compounds in buffer solution, and a detection cell was characterized. By photoluminescence excitation measurements, it turned out that silicon membrane has a negligible photoluminescence under the examined excitation from 440 nm to 560 nm, in comparison with a silicon nitrite membrane. Further, background signals from the detection cell were suppressed. Brownian motion of 450 bps DNA labelled with single ATTO-532 or DY-521-XL was successfully recorded by our optical system.

The effect of the shape of single, sub-ms voltage pulses on the rates of surface immobilization and hybridization of DNA

International Nuclear Information System (INIS)

Cabeca, R; Rodrigues, M; Chu, V; Conde, J P; Prazeres, D M F

2009-01-01

Electric fields generated by single square and sinusoidal voltage pulses with amplitudes below 2 V were used to assist the covalent immobilization of single-stranded, thiolated DNA probes, onto a chemically functionalized SiO 2 surface and to assist the specific hybridization of single-stranded DNA targets with immobilized complementary probes. The single-stranded immobilized DNA probes were either covalently immobilized (chemisorption) or electrostatically adsorbed (physisorption) to a chemically functionalized surface. Comparing the speed of electric field assisted immobilization and hybridization with the corresponding control reactions (without electric field), an increase of several orders of magnitude is observed, with the reaction timescaled down from 1 to 2 h to a range between 100 ns and 1 ms. The influence of the shape of the voltage pulse (square versus sinusoidal) and its duration were studied for both immobilization and hybridization reactions. The results show that pulsed electric fields are a useful tool to achieve temporal and spatial control of surface immobilization and hybridization reactions of DNA.

Impedimetric DNA Biosensor Based on a Nanoporous Alumina Membrane for the Detection of the Specific Oligonucleotide Sequence of Dengue Virus

Directory of Open Access Journals (Sweden)

Chee-Seng Toh

2013-06-01

Full Text Available A novel and integrated membrane sensing platform for DNA detection is developed based on an anodic aluminum oxide (AAO membrane. Platinum electrodes (~50–100 nm thick are coated directly on both sides of the alumina membrane to eliminate the solution resistance outside the nanopores. The electrochemical impedance technique is employed to monitor the impedance changes within the nanopores upon DNA binding. Pore resistance (Rp linearly increases in response towards the increasing concentration of the target DNA in the range of 1 × 10−12 to 1 × 10−6 M. Moreover, the biosensor selectively differentiates the complementary sequence from single base mismatched (MM-1 strands and non-complementary strands. This study reveals a simple, selective and sensitive method to fabricate a label-free DNA biosensor.

Impedimetric DNA biosensor based on a nanoporous alumina membrane for the detection of the specific oligonucleotide sequence of dengue virus.

Science.gov (United States)

Deng, Jiajia; Toh, Chee-Seng

2013-06-17

A novel and integrated membrane sensing platform for DNA detection is developed based on an anodic aluminum oxide (AAO) membrane. Platinum electrodes (~50-100 nm thick) are coated directly on both sides of the alumina membrane to eliminate the solution resistance outside the nanopores. The electrochemical impedance technique is employed to monitor the impedance changes within the nanopores upon DNA binding. Pore resistance (Rp) linearly increases in response towards the increasing concentration of the target DNA in the range of 1 × 10⁻¹² to 1 × 10⁻⁶ M. Moreover, the biosensor selectively differentiates the complementary sequence from single base mismatched (MM-1) strands and non-complementary strands. This study reveals a simple, selective and sensitive method to fabricate a label-free DNA biosensor.

Nanoporous Hybrid Electrolytes for High-Energy Batteries Based on Reactive Metal Anodes

Energy Technology Data Exchange (ETDEWEB)

Tu, Zhengyuan [Department of Materials Science and Engineering, Cornell University, Ithaca NY 14850 USA; Zachman, Michael J. [School of Applied and Engineering Physics, Cornell University, Ithaca NY 14850 USA; Choudhury, Snehashis [School of Chemical Engineering and Biomolecular Engineering, Cornell University, Ithaca NY 14850 USA; Wei, Shuya [School of Chemical Engineering and Biomolecular Engineering, Cornell University, Ithaca NY 14850 USA; Ma, Lin [Department of Materials Science and Engineering, Cornell University, Ithaca NY 14850 USA; Yang, Yuan [Department of Chemistry and Geochemistry, Colorado School of Mines, Golden CO 80401 USA; Kourkoutis, Lena F. [School of Applied and Engineering Physics, Cornell University, Ithaca NY 14850 USA; Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca NY 14853 USA; Archer, Lynden A. [Department of Materials Science and Engineering, Cornell University, Ithaca NY 14850 USA; School of Chemical Engineering and Biomolecular Engineering, Cornell University, Ithaca NY 14850 USA

2017-01-06

Successful strategies for stabilizing electrodeposition of reactive metals, including lithium, sodium, and aluminum are a requirement for safe, high-energy electrochemical storage technologies that utilize these metals as anodes. Unstable deposition produces high-surface area dendritic structures at the anode/electrolyte interface, which causes premature cell failure by complex physical and chemical processes that have presented formidable barriers to progress. Here, it is reported that hybrid electrolytes created by infusing conventional liquid electrolytes into nanoporous membranes provide exceptional ability to stabilize Li. Electrochemical cells based on γ-Al2O3 ceramics with pore diameters below a cut-off value above 200 nm exhibit long-term stability even at a current density of 3 mA cm-2. The effect is not limited to ceramics; similar large enhancements in stability are observed for polypropylene membranes with less monodisperse pores below 450 nm. These findings are critically assessed using theories for ion rectification and electrodeposition reactions in porous solids and show that the source of stable electrodeposition in nanoporous electrolytes is fundamental.

Nanoporous Hybrid Electrolytes for High-Energy Batteries Based on Reactive Metal Anodes

KAUST Repository

Tu, Zhengyuan

2017-01-06

Successful strategies for stabilizing electrodeposition of reactive metals, including lithium, sodium, and aluminum are a requirement for safe, high-energy electrochemical storage technologies that utilize these metals as anodes. Unstable deposition produces high-surface area dendritic structures at the anode/electrolyte interface, which causes premature cell failure by complex physical and chemical processes that have presented formidable barriers to progress. Here, it is reported that hybrid electrolytes created by infusing conventional liquid electrolytes into nanoporous membranes provide exceptional ability to stabilize Li. Electrochemical cells based on γ-Al2O3 ceramics with pore diameters below a cut-off value above 200 nm exhibit long-term stability even at a current density of 3 mA cm−2. The effect is not limited to ceramics; similar large enhancements in stability are observed for polypropylene membranes with less monodisperse pores below 450 nm. These findings are critically assessed using theories for ion rectification and electrodeposition reactions in porous solids and show that the source of stable electrodeposition in nanoporous electrolytes is fundamental.

Recent advances in nanopore-based nucleic acid analysis and sequencing

International Nuclear Information System (INIS)

Shi, Jidong; Fang, Ying; Hou, Junfeng

2016-01-01

Nanopore-based sequencing platforms are transforming the field of genomic science. This review (containing 116 references) highlights some recent progress on nanopore-based nucleic acid analysis and sequencing. These studies are classified into three categories, biological, solid-state, and hybrid nanopores, according to their nanoporous materials. We begin with a brief description of the translocation-based detection mechanism of nanopores. Next, specific examples are given in nanopore-based nucleic acid analysis and sequencing, with an emphasis on identifying strategies that can improve the resolution of nanopores. This review concludes with a discussion of future research directions that will advance the practical applications of nanopore technology. (author)

DNA and ion transport through solid-state nanopores

NARCIS (Netherlands)

Smeets, R.M.M.

2008-01-01

This thesis describes experimental work on a novel type of devices capable of detecting single-(bio)molecules; nanometer-sized pores, or nanopores. Individual nanopores are placed in between two electrolyte-filled liquid compartments and (bio)molecules are electrophoretically driven through them.

Electrokinetic acceleration of DNA hybridization in microsystems.

Science.gov (United States)

Lei, Kin Fong; Wang, Yun-Hsiang; Chen, Huai-Yi; Sun, Jia-Hong; Cheng, Ji-Yen

2015-06-01

In this work, electrokinetic acceleration of DNA hybridization was investigated by different combinations of frequencies and amplitudes of actuating electric signals. Because the frequencies from low to high can induce different kinds of electrokinetic forces, i.e., electroosmotic to electrothermal forces, this work provides an in-depth investigation of electrokinetic enhanced hybridization. Concentric circular Cr/Au microelectrodes of 350 µm in diameter were fabricated on a glass substrate and probe DNA was immobilized on the electrode surface. Target DNA labeled with fluorescent dyes suspending in solution was then applied to the electrode. Different electrokinetic forces were induced by the application of different electric signals to the circular microelectrodes. Local microfluidic vortexes were generated to increase the collision efficiency between the target DNA suspending in solution and probe DNA immobilized on the electrode surface. DNA hybridization on the electrode surface could be accelerated by the electrokinetic forces. The level of hybridization was represented by the fluorescent signal intensity ratio. Results revealed that such 5-min dynamic hybridization increased 4.5 fold of signal intensity ratio as compared to a 1-h static hybridization. Moreover, dynamic hybridization was found to have better differentiation ability between specific and non-specific target DNA. This study provides a strategy to accelerate DNA hybridization in microsystems. Copyright © 2015 Elsevier B.V. All rights reserved.

Nanopore Analysis of the 5-Guanidinohydantoin to Iminoallantoin Isomerization in Duplex DNA.

Science.gov (United States)

Zeng, Tao; Fleming, Aaron M; Ding, Yun; Ren, Hang; White, Henry S; Burrows, Cynthia J

2018-04-06

In DNA, guanine oxidation yields diastereomers of 5-guanidinohydantoin (Gh) as one of the major products. In nucleosides and single-stranded DNA, Gh is in a pH-dependent equilibrium with its constitutional isomer iminoallantoin (Ia). Herein, the isomerization reaction between Gh and Ia was monitored in duplex DNA using a protein nanopore by measuring the ionic current when duplex DNA interacts with the pore under an electrophoretic force. Monitoring current levels in this single-molecule method proved to be superior for analysis of population distributions in an equilibrating mixture of four isomers in duplex DNA as a function of pH. The results identified Gh as a major isomer observed when base paired with A, C, or G at pH 6.4-8.4, and Ia was a minor isomer of the reaction mixture that was only observed when the pH was >7.4 in the duplex DNA context. The present results suggest that Gh will be the dominant isomer in duplex DNA under physiological conditions regardless of the base-pairing partner in the duplex.

Theoretical and experimental studies on ionic currents in nanopore-based biosensors.

Science.gov (United States)

Liu, Lei; Li, Chu; Ma, Jian; Wu, Yingdong; Ni, Zhonghua; Chen, Yunfei

2014-12-01

Novel generation of analytical technology based on nanopores has provided possibilities to fabricate nanofluidic devices for low-cost DNA sequencing or rapid biosensing. In this paper, a simplified model was suggested to describe DNA molecule's translocation through a nanopore, and the internal potential, ion concentration, ionic flowing speed and ionic current in nanopores with different sizes were theoretically calculated and discussed on the basis of Poisson-Boltzmann equation, Navier-Stokes equation and Nernst-Planck equation by considering several important parameters, such as the applied voltage, the thickness and the electric potential distributions in nanopores. In this way, the basic ionic currents, the modulated ionic currents and the current drops induced by translocation were obtained, and the size effects of the nanopores were carefully compared and discussed based on the calculated results and experimental data, which indicated that nanopores with a size of 10 nm or so are more advantageous to achieve high quality ionic current signals in DNA sensing.

DNA:DNA hybridization studies on the pink-pigmented facultative methylotrophs.

Science.gov (United States)

Hood, D W; Dow, C S; Green, P N

1987-03-01

The genomic relatedness among 36 strains of pink-pigmented facultatively methylotrophic bacteria (PPFMs) was estimated by determination of DNA base composition and by DNA:DNA hybridization studies. A reproducible hybridization system was developed for the rapid analysis of multiple DNA samples. Results indicated that the PPFMs comprise four major and several minor homology groups, and that they should remain grouped in a single genus, Methylobacterium.

Control of DNA hybridization by photoswitchable molecular glue.

Science.gov (United States)

Dohno, Chikara; Nakatani, Kazuhiko

2011-12-01

Hybridization of DNA is one of the most intriguing events in molecular recognition and is essential for living matter to inherit life beyond generations. In addition to the function of DNA as genetic material, DNA hybridization is a key to control the function of DNA-based materials in nanoscience. Since the hybridization of two single stranded DNAs is a thermodynamically favorable process, dissociation of the once formed DNA duplex is normally unattainable under isothermal conditions. As the progress of DNA-based nanoscience, methodology to control the DNA hybridization process has become increasingly important. Besides many reports using the chemically modified DNA for the regulation of hybridization, we focused our attention on the use of a small ligand as the molecular glue for the DNA. In 2001, we reported the first designed molecule that strongly and specifically bound to the mismatched base pairs in double stranded DNA. Further studies on the mismatch binding molecules provided us a key discovery of a novel mode of the binding of a mismatch binding ligand that induced the base flipping. With these findings we proposed the concept of molecular glue for DNA for the unidirectional control of DNA hybridization and, eventually photoswitchable molecular glue for DNA, which enabled the bidirectional control of hybridization under photoirradiation. In this tutorial review, we describe in detail how we integrated the mismatch binding ligand into photoswitchable molecular glue for DNA, and the application and perspective in DNA-based nanoscience.

An efficient enzyme-powered micromotor device fabricated by cyclic alternate hybridization assembly for DNA detection.

Science.gov (United States)

Fu, Shizhe; Zhang, Xueqing; Xie, Yuzhe; Wu, Jie; Ju, Huangxian

2017-07-06

An efficient enzyme-powered micromotor device was fabricated by assembling multiple layers of catalase on the inner surface of a poly(3,4-ethylenedioxythiophene and sodium 4-styrenesulfonate)/Au microtube (PEDOT-PSS/Au). The catalase assembly was achieved by programmed DNA hybridization, which was performed by immobilizing a designed sandwich DNA structure as the sensing unit on the PEDOT-PSS/Au, and then alternately hybridizing with two assisting DNA to bind the enzyme for efficient motor motion. The micromotor device showed unique features of good reproducibility, stability and motion performance. Under optimal conditions, it showed a speed of 420 μm s -1 in 2% H 2 O 2 and even 51 μm s -1 in 0.25% H 2 O 2 . In the presence of target DNA, the sensing unit hybridized with target DNA to release the multi-layer DNA as well as the multi-catalase, resulting in a decrease of the motion speed. By using the speed as a signal, the micromotor device could detect DNA from 10 nM to 1 μM. The proposed micromotor device along with the cyclic alternate DNA hybridization assembly technique provided a new path to fabricate efficient and versatile micromotors, which would be an exceptional tool for rapid and simple detection of biomolecules.

Solid-State Nanopore

Directory of Open Access Journals (Sweden)

Zhishan Yuan

2018-02-01

Full Text Available Abstract Solid-state nanopore has captured the attention of many researchers due to its characteristic of nanoscale. Now, different fabrication methods have been reported, which can be summarized into two broad categories: “top-down” etching technology and “bottom-up” shrinkage technology. Ion track etching method, mask etching method chemical solution etching method, and high-energy particle etching and shrinkage method are exhibited in this report. Besides, we also discussed applications of solid-state nanopore fabrication technology in DNA sequencing, protein detection, and energy conversion.

Effect of Pore Geometry on Resistive-Pulse Sensing of DNA Using Track-Etched PET Nanopore Membrane

International Nuclear Information System (INIS)

Kaya, Dila; Dinler, Ali; San, Nevim; Kececi, Kaan

2016-01-01

We have investigated the effect of nanopore geometry on translocation properties of poly(ethylene terephthalate) (PET) membranes. In order to vary the cone angles of the conically shaped nanopores, which were obtained by track-etch method, we have added different volume fractions of methanol to the alkali etching solution. We have confirmed through the characterization of PET membranes that methanol has a promoting effect on cone angle. Additionally, we have reported the positive influence of a higher cone angle for resistive pulse sensing of 50-bp DNA. We have also shown the change in electric field as a function of cone angle by using finite element simulations and confirmed a higher electric field with increasing cone angle.

DNA hybridization sensing for cytogenetic analysis

DEFF Research Database (Denmark)

Kwasny, Dorota; Dapra, Johannes; Brøgger, Anna Line

2013-01-01

are rearrangements between two chromosome arms that results in two derivative chromosomes having a mixed DNA sequence. The current detection method is a Fluorescent In situ Hybridization, which requires a use of expensive, fluorescently labeled probes that target the DNA sequences of two chromosomes involved...... in the translocation (Kwasny et al., 2012). We have developed a new double hybridization assay that allows for sorting of the DNA chromosomal fragments into separate compartment, moreover allowing for detection of the translocation. To detect the translocation it is necessary to determine that the two DNA sequences...... forming a derivative chromosome are connected, which is achieved by two subsequent hybridization steps. The first example of the translocation detection was presented on lab-on-a-disc using fluorescently labeled DNA fragments, representing the derivative chromosome (Brøgger et al., 2012). To allow...

Localized surface plasmon resonance (LSPR) study of DNA hybridization at single nanoparticle transducers

International Nuclear Information System (INIS)

Schneider, T.; Jahr, N.; Jatschka, J.; Csaki, A.; Stranik, O.; Fritzsche, W.

2013-01-01

The effect of DNA–DNA interaction on the localized surface plasmon resonance of single 80 nm gold nanoparticles is studied. Therefore, both the attachment of the capture DNA strands at the particle surface and the sequence-specific DNA binding (hybridization) of analyte DNA to the immobilized capture DNA is subject of investigations. The influence of substrate attachment chemistry, the packing density of DNA as controlled by an assisting layer of smaller molecules, and the distance as increased by a linker on the LSPR efficiency is investigated. The resulting changes in signal can be related to a higher hybridization efficiency of the analyte DNA to the immobilized capture DNA. The subsequent attachment of additional DNA strands to this system is studied, which allows for a multiple step detection of binding and an elucidation of the resulting resonance shifts. The detection limit was determined for the utilized DNA system by incubation with various concentration of analyte DNA. Although the method allows for a marker-free detection, we show that additional markers such as 20 nm gold particle labels increase the signal and thereby the sensitivity significantly. The study of resonance shift for various DNA lengths revealed that the resonance shift per base is stronger for shorter DNA molecules (20 bases) as compared to longer ones (46 bases).

DNA hybridization sensor based on pentacene thin film transistor.

Science.gov (United States)

Kim, Jung-Min; Jha, Sandeep Kumar; Chand, Rohit; Lee, Dong-Hoon; Kim, Yong-Sang

2011-01-15

A DNA hybridization sensor using pentacene thin film transistors (TFTs) is an excellent candidate for disposable sensor applications due to their low-cost fabrication process and fast detection. We fabricated pentacene TFTs on glass substrate for the sensing of DNA hybridization. The ss-DNA (polyA/polyT) or ds-DNA (polyA/polyT hybrid) were immobilized directly on the surface of the pentacene, producing a dramatic change in the electrical properties of the devices. The electrical characteristics of devices were studied as a function of DNA immobilization, single-stranded vs. double-stranded DNA, DNA length and concentration. The TFT device was further tested for detection of λ-phage genomic DNA using probe hybridization. Based on these results, we propose that a "label-free" detection technique for DNA hybridization is possible through direct measurement of electrical properties of DNA-immobilized pentacene TFTs. Copyright © 2010 Elsevier B.V. All rights reserved.

Mechanisms of Surface-Mediated DNA Hybridization

Science.gov (United States)

2015-01-01

Single-molecule total internal reflection fluorescence microscopy was employed in conjunction with resonance energy transfer (RET) to observe the dynamic behavior of donor-labeled ssDNA at the interface between aqueous solution and a solid surface decorated with complementary acceptor-labeled ssDNA. At least 100 000 molecular trajectories were determined for both complementary strands and negative control ssDNA. RET was used to identify trajectory segments corresponding to the hybridized state. The vast majority of molecules from solution adsorbed nonspecifically to the surface, where a brief two-dimensional search was performed with a 7% chance of hybridization. Successful hybridization events occurred with a characteristic search time of ∼0.1 s, and unsuccessful searches resulted in desorption from the surface, ultimately repeating the adsorption and search process. Hybridization was reversible, and two distinct modes of melting (i.e., dehybridization) were observed, corresponding to long-lived (∼15 s) and short-lived (∼1.4 s) hybridized time intervals. A strand that melted back onto the surface could rehybridize after a brief search or desorb from the interface. These mechanistic observations provide guidance for technologies that involve DNA interactions in the near-surface region, suggesting a need to design surfaces that both enhance the complex multidimensional search process and stabilize the hybridized state. PMID:24708278

Soft matter in hard confinement: phase transition thermodynamics, structure, texture, diffusion and flow in nanoporous media

Science.gov (United States)

Huber, Patrick

2015-03-01

Spatial confinement in nanoporous media affects the structure, thermodynamics and mobility of molecular soft matter often markedly. This article reviews thermodynamic equilibrium phenomena, such as physisorption, capillary condensation, crystallisation, self-diffusion, and structural phase transitions as well as selected aspects of the emerging field of spatially confined, non-equilibrium physics, i.e. the rheology of liquids, capillarity-driven flow phenomena, and imbibition front broadening in nanoporous materials. The observations in the nanoscale systems are related to the corresponding bulk phenomenologies. The complexity of the confined molecular species is varied from simple building blocks, like noble gas atoms, normal alkanes and alcohols to liquid crystals, polymers, ionic liquids, proteins and water. Mostly, experiments with mesoporous solids of alumina, gold, carbon, silica, and silicon with pore diameters ranging from a few up to 50 nm are presented. The observed peculiarities of nanopore-confined condensed matter are also discussed with regard to applications. A particular emphasis is put on texture formation upon crystallisation in nanoporous media, a topic both of high fundamental interest and of increasing nanotechnological importance, e.g. for the synthesis of organic/inorganic hybrid materials by melt infiltration, the usage of nanoporous solids in crystal nucleation or in template-assisted electrochemical deposition of nano structures.

Hybridization thermodynamics of DNA bound to gold nanoparticles

International Nuclear Information System (INIS)

Lang, Brian

2010-01-01

Isothermal Titration Calorimetry (ITC) was used to study the thermodynamics of hybridization on DNA-functionalized colloidal gold nanoparticles. When compared to the thermodynamics of hybridization of DNA that is free in solution, the differences in the values of the Gibbs free energy of reaction, Δ r G o , the enthalpy, Δ r H o , and entropy, Δ r S o , were small. The change in Δ r G o between the free and bound states was always positive but with statistical significance outside the 95% confidence interval, implying the free DNA is slightly more stable than when in the bound state. Additionally, ITC was also able to reveal information about the binding stoichiometry of the hybridization reactions on the DNA-functionalized gold nanoparticles, and indicates that there is a significant fraction of the DNA on gold nanoparticle surface that is unavailable for DNA hybridization. Furthermore, the fraction of available DNA is dependent on the spacer group on the DNA that is used to span the gold surface from that to the probe DNA.

Highly transparent and durable superhydrophobic hybrid nanoporous coatings fabricated from polysiloxane.

Science.gov (United States)

Wang, Ding; Zhang, Zongbo; Li, Yongming; Xu, Caihong

2014-07-09

Highly transparent and durable superhydrophobic hybrid nanoporous coatings with different surface roughnesses were fabricated via a simple solidification-induced phase-separation method using a liquid polysiloxane (PSO) containing SiH and SiCH═CH2 groups as precursors and methyl-terminated poly(dimethylsiloxane)s (PDMS) as porogens. Owing to the existence of SiCHn units, the hybrid material is intrinsically hydrophobic without modification with expensive fluorinated reagents. The roughness of the coating can be easily controlled at the nanometer scale by changing the viscosity of PDMS to achieve both superhydrophobicity and high transparency. The influence of surface roughness on the transparency and hydrophobicity of the coatings was investigated. The enhancement from hydrophobic to superhydrophobic with increasing surface roughness can be explained by the transition from the Wenzel state to the Cassie state. The optimum performance coating has an average transmittance higher than 85% in the visible-light range (400-780 nm), a water contact angle of 155°, and a slide angle lower than 1°. The coatings also exhibit good thermal and mechanical stability and durable superhydrophobicity, which paves the way for real applications of highly transparent superhydrophobic coatings.

Hybrid male sterility is caused by mitochondrial DNA deletion.

Science.gov (United States)

Hayashida, Kenji; Kohno, Shigeru

2009-07-01

Although it is known that the hybrid male mouse is sterile just like any other animal's heterogametic sex, the reason why only the male germ cells are impaired has yet to be discovered. TdT-mediated dUTP nick end labeling assay using a confocal fluorescence microscope and DNA fragmentation assay of hybrid testis indicated destruction of the mitochondrial DNA (mtDNA) rather than the nuclear DNA. Previously we reported that maternal mtDNA inheritance is through selective sperm mtDNA elimination based on the sperm factor and two egg factors, and expression of these three factors was recognized in the hybrid testis. It was thereby assumed that mtDNA destruction caused by the expression of maternal mtDNA inheritance system in male germ cells is implicated in the hybrid male sterility of mice.

Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy

International Nuclear Information System (INIS)

Renner, Stephan; Bessonov, Andrey; Simmel, Friedrich C; Gerland, Ulrich

2010-01-01

Nanopore force spectroscopy is used to study the unzipping kinetics of two DNA hairpin molecules with a 12 base pair long stem containing two contiguous stretches of six GC and six AT base pairs in interchanged order. Even though the thermodynamic stabilities of the two structures are nearly the same, they differ greatly in their unzipping kinetics. When the GC segment has to be broken before the AT segment, the unfolding rate is orders of magnitude smaller than in the opposite case. We also investigated hairpins with stem regions consisting only of AT or GC base pairs. The pure AT hairpins translocate much faster than the other hairpins, whereas the pure GC hairpins translocate on similar timescales to the hairpins with only an initial GC segment. For each hairpin, nanopore force spectroscopy is performed for different loading rates and the resulting unzipping distributions are mathematically transformed to a master curve that yields the unfolding rate as a function of applied voltage. This is compared with a stochastic model of the unfolding process for the two sequences for different voltages. The results can be rationalized in terms of the different natures of the free energy landscapes for the unfolding process.

Digital quantification of rolling circle amplified single DNA molecules in a resistive pulse sensing nanopore.

Science.gov (United States)

Kühnemund, M; Nilsson, M

2015-05-15

Novel portable, sensitive and selective DNA sensor methods for bio-sensing applications are required that can rival conventionally used non-portable and expensive fluorescence-based sensors. In this paper, rolling circle amplification (RCA) products are detected in solution and on magnetic particles using a resistive pulse sensing (RPS) nanopore. Low amounts of DNA molecules are detected by padlock probes which are circularized in a strictly target dependent ligation reaction. The DNA-padlock probe-complex is captured on magnetic particles by sequence specific capture oligonucleotides and amplified by a short RCA. Subsequent RPS analysis is used to identify individual particles with single attached RCA products from blank particles. This proof of concept opens up for a novel non-fluorescent digital DNA quantification method that can have many applications in bio-sensing and diagnostic approaches. Copyright © 2014 Elsevier B.V. All rights reserved.

Tungsten disulfide nanosheet and exonuclease III co-assisted amplification strategy for highly sensitive fluorescence polarization detection of DNA glycosylase activity

International Nuclear Information System (INIS)

Zhao, Jingjin; Ma, Yefei; Kong, Rongmei; Zhang, Liangliang; Yang, Wen; Zhao, Shulin

2015-01-01

Herein, we introduced a tungsten disulfide (WS 2 ) nanosheet and exonuclease III (Exo III) co-assisted signal amplification strategy for highly sensitive fluorescent polarization (FP) assay of DNA glycosylase activity. Two DNA glycosylases, uracil-DNA glycosylase (UDG) and human 8-oxoG DNA glycosylase 1 (hOGG1), were tested. A hairpin-structured probe (HP) which contained damaged bases in the stem was used as the substrate. The removal of damaged bases from substrate by DNA glycosylase would lower the melting temperature of HP. The HP was then opened and hybridized with a FAM dye-labeled single strand DNA (DP), generating a duplex with a recessed 3′-terminal of DP. This design facilitated the Exo III-assisted amplification by repeating the hybridization and digestion of DP, liberating numerous FAM fluorophores which could not be adsorbed on WS 2 nanosheet. Thus, the final system exhibited a small FP signal. However, in the absence of DNA glycosylases, no hybridization between DP and HP was occurred, hampering the hydrolysis of DP by Exo III. The intact DP was then adsorbed on the surface of WS 2 nanosheet that greatly amplified the mass of the labeled-FAM fluorophore, resulting in a large FP value. With the co-assisted amplification strategy, the sensitivity was substantially improved. In addition, this method was applied to detect UDG activity in cell extracts. The study of the inhibition of UDG was also performed. Furthermore, this method is simple in design, easy in implementation, and selective, which holds potential applications in the DNA glycosylase related mechanism research and molecular diagnostics. - Highlights: • A fluorescence polarization strategy for DNA glycosylase activity detection was developed. • The present method was based on WS 2 nanosheet and exonuclease III co-assisted signal amplification. • A high sensitivity and desirable selectivity were achieved. • This method provides a promising universal platform for DNA glycosylase

Tungsten disulfide nanosheet and exonuclease III co-assisted amplification strategy for highly sensitive fluorescence polarization detection of DNA glycosylase activity

Energy Technology Data Exchange (ETDEWEB)

Zhao, Jingjin; Ma, Yefei [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin, 541004 (China); Kong, Rongmei [The Key Laboratory of Life-Organic Analysis, College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165 (China); Zhang, Liangliang, E-mail: liangzhang319@163.com [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin, 541004 (China); Yang, Wen; Zhao, Shulin [Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin, 541004 (China)

2015-08-05

Herein, we introduced a tungsten disulfide (WS{sub 2}) nanosheet and exonuclease III (Exo III) co-assisted signal amplification strategy for highly sensitive fluorescent polarization (FP) assay of DNA glycosylase activity. Two DNA glycosylases, uracil-DNA glycosylase (UDG) and human 8-oxoG DNA glycosylase 1 (hOGG1), were tested. A hairpin-structured probe (HP) which contained damaged bases in the stem was used as the substrate. The removal of damaged bases from substrate by DNA glycosylase would lower the melting temperature of HP. The HP was then opened and hybridized with a FAM dye-labeled single strand DNA (DP), generating a duplex with a recessed 3′-terminal of DP. This design facilitated the Exo III-assisted amplification by repeating the hybridization and digestion of DP, liberating numerous FAM fluorophores which could not be adsorbed on WS{sub 2} nanosheet. Thus, the final system exhibited a small FP signal. However, in the absence of DNA glycosylases, no hybridization between DP and HP was occurred, hampering the hydrolysis of DP by Exo III. The intact DP was then adsorbed on the surface of WS{sub 2} nanosheet that greatly amplified the mass of the labeled-FAM fluorophore, resulting in a large FP value. With the co-assisted amplification strategy, the sensitivity was substantially improved. In addition, this method was applied to detect UDG activity in cell extracts. The study of the inhibition of UDG was also performed. Furthermore, this method is simple in design, easy in implementation, and selective, which holds potential applications in the DNA glycosylase related mechanism research and molecular diagnostics. - Highlights: • A fluorescence polarization strategy for DNA glycosylase activity detection was developed. • The present method was based on WS{sub 2} nanosheet and exonuclease III co-assisted signal amplification. • A high sensitivity and desirable selectivity were achieved. • This method provides a promising universal platform for DNA

Biomimetic glass nanopores employing aptamer gates responsive to a small molecule†

Science.gov (United States)

Abelow, Alexis E.; Schepelina, Olga; White, Ryan J.; Vallée-Bélisle, Alexis

2011-01-01

We report the preparation of 20 and 65 nm radii glass nanopores whose surface is modified with DNA aptamers controlling the molecular transport through the nanopores in response to small molecule binding. PMID:20865192

Carbon Nanofiber/3D Nanoporous Silicon Hybrids as High Capacity Lithium Storage Materials.

Science.gov (United States)

Park, Hyeong-Il; Sohn, Myungbeom; Kim, Dae Sik; Park, Cheolho; Choi, Jeong-Hee; Kim, Hansu

2016-04-21

Carbon nanofiber (CNF)/3D nanoporous (3DNP) Si hybrid materials were prepared by chemical etching of melt-spun Si/Al-Cu-Fe alloy nanocomposites, followed by carbonization using a pitch. CNFs were successfully grown on the surface of 3DNP Si particles using residual Fe impurities after acidic etching, which acted as a catalyst for the growth of CNFs. The resulting CNF/3DNP Si hybrid materials showed an enhanced cycle performance up to 100 cycles compared to that of the pristine Si/Al-Cu-Fe alloy nanocomposite as well as that of bare 3DNP Si particles. These results indicate that CNFs and the carbon coating layer have a beneficial effect on the capacity retention characteristics of 3DNP Si particles by providing continuous electron-conduction pathways in the electrode during cycling. The approach presented here provides another way to improve the electrochemical performances of porous Si-based high capacity anode materials for lithium-ion batteries. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DNA/RNA hybrid substrates modulate the catalytic activity of purified AID.

Science.gov (United States)

Abdouni, Hala S; King, Justin J; Ghorbani, Atefeh; Fifield, Heather; Berghuis, Lesley; Larijani, Mani

2018-01-01

Activation-induced cytidine deaminase (AID) converts cytidine to uridine at Immunoglobulin (Ig) loci, initiating somatic hypermutation and class switching of antibodies. In vitro, AID acts on single stranded DNA (ssDNA), but neither double-stranded DNA (dsDNA) oligonucleotides nor RNA, and it is believed that transcription is the in vivo generator of ssDNA targeted by AID. It is also known that the Ig loci, particularly the switch (S) regions targeted by AID are rich in transcription-generated DNA/RNA hybrids. Here, we examined the binding and catalytic behavior of purified AID on DNA/RNA hybrid substrates bearing either random sequences or GC-rich sequences simulating Ig S regions. If substrates were made up of a random sequence, AID preferred substrates composed entirely of DNA over DNA/RNA hybrids. In contrast, if substrates were composed of S region sequences, AID preferred to mutate DNA/RNA hybrids over substrates composed entirely of DNA. Accordingly, AID exhibited a significantly higher affinity for binding DNA/RNA hybrid substrates composed specifically of S region sequences, than any other substrates composed of DNA. Thus, in the absence of any other cellular processes or factors, AID itself favors binding and mutating DNA/RNA hybrids composed of S region sequences. AID:DNA/RNA complex formation and supporting mutational analyses suggest that recognition of DNA/RNA hybrids is an inherent structural property of AID. Copyright © 2017 Elsevier Ltd. All rights reserved.

DNA Electronic Fingerprints by Local Spectroscopy on Graphene

Science.gov (United States)

Balatsky, Alexander

2013-03-01

Working and scalable alternatives to the conventional chemical methods of DNA sequencing that are based on electronic/ionic signatures would revolutionize the field of sequencing. The approach of a single molecule imaging and spectroscopy with unprecedented resolution, achieved by Scanning Tunneling Spectroscopy (STS) and nanopore electronics could enable this revolution. We use the data from our group and others in applying this local scanning tunneling microscopy and illustrate possibilities of electronic sequencing of freeze dried deposits on graphene. We will present two types of calculated fingerprints: first in Local Density of States (LDOS) of DNA nucleotide bases (A,C,G,T) deposited on graphene. Significant base-dependent features in the LDOS in an energy range within few eV of the Fermi level were found in our calculations. These features can serve as electronic fingerprints for the identification of individual bases in STS. In the second approach we present calculated base dependent electronic transverse conductance as DNA translocates through the graphene nanopore. Thus we argue that the fingerprints of DNA-graphene hybrid structures may provide an alternative route to DNA sequencing using STS. Work supported by US DOE, NORDITA.

Solid-state nanopores for scanning single molecules and mimicking biology

NARCIS (Netherlands)

Kowalczyk, S.W.

2011-01-01

Solid-state nanopores, nanometer-size holes in a thin synthetic membrane, are a versatile tool for the detection and manipulation of charged biomolecules. This thesis describes mostly experimental work on DNA translocation through solid-state nanopores, which we study at the single-molecule level.

Electronic conductance model in constricted MoS{sub 2} with nanopores

Energy Technology Data Exchange (ETDEWEB)

Sarathy, Aditya [Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801 (United States); Department of Electrical and Computer Engineering, University of Illinois, Urbana, Illinois 61801 (United States); Leburton, Jean-Pierre, E-mail: jleburto@illinois.edu [Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801 (United States); Department of Electrical and Computer Engineering, University of Illinois, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois, Urbana, Illinois 61801 (United States)

2016-02-01

We describe a self-consistent model for electronic transport in a molybdenum di-sulphide (MoS{sub 2}) layer containing a nanopore in a constricted geometry. Our approach is based on a semi-classical thermionic Poisson-Boltzmann technique using a two-valley model within the effective mass approximation to investigate perturbations caused by the nanopore on the electronic current. In particular, we show that the effect of the nanopore on the conductance is reduced as the nanopore is moved from the center to the layer edges. Our model is applied to the detection of DNA translocating through the nanopore, which reveals current features similar to those as predicted in nanopore graphene layers.

Synthesis and characterization of ruthenium-decorated nanoporous platinum materials

International Nuclear Information System (INIS)

Peng Xinsheng; Koczkur, Kallum; Chen, Aicheng

2007-01-01

We report on the synthesis of novel three-dimensional nanoporous Pt-Ru bimetallic networks by decorating nanoporous Pt networks with Ru using a hydrothermally assisted precipitating process. Scanning electron microscopy (SEM) and energy dispersive x-ray spectroscopy (EDS) were used to characterize the morphology and the composition of the nanoporous Pt-Ru networks formed. X-ray diffraction analysis confirmed that, after protected annealing treatment, Pt-Ru bimetallic material was formed. The electrocatalytic activity of the synthesized nanoporous Pt-Ru networks was characterized using electrochemical oxidation of methanol as a probe. The electrocatalytic activity of the nanoporous Pt networks significantly increases with the increments of decorated Ru and reaches the highest value with 41% of Ru. The peak current of methanol oxidation on the nanoporous Pt-Ru(41%) bimetallic networks is over 180% higher than that on the nanoporous Pt networks without Ru decoration. This is very desirable for fuel cell development and electrochemical sensor design

Microcantilver-based DNA hybridization sensors for Salmonella identification

Directory of Open Access Journals (Sweden)

Carlo Ricciardi

2012-02-01

Full Text Available The detection of pathogenic microorganisms in foods remains a challenging since the safety of foodstuffs has to be ensured by the food producing companies. Conventional methods for the detection and identification of bacteria mainly rely on specific microbiological and biochemical identification. Biomolecular methods, are commonly used as a support for traditional techniques, thanks to their high sensitivity, specificity and not excessive costs. However, new methods like biosensors for example, can be an exciting alternative to the more traditional tecniques for the detection of pathogens in food. In this study we report Salmonella enterica serotype Enteritidis DNA detection through a novel class of label-free biosensors: microcantilevers (MCs. In general, MCs can operate as a microbalance and is used to detect the mass of the entities anchored to the cantilever surface using the decrease in the resonant frequency. We use DNA hybridization as model reaction system and for this reason, specific single stranded probe DNA of the pathogen and three different DNA targets (single-stranded complementary DNA, PCR product and serial dilutions of DNA extracted from S. Enteritidis strains were applied. Two protocols were reported in order to allow the probe immobilization on cantilever surface: i MC surface was functionalized with 3-aminopropyltriethoxysilane and glutaraldehyde and an amino-modified DNA probe was used; ii gold-coated sensors and thiolated DNA probes were used in order to generate a covalent bonding (Th-Au. For the first one, measures after hybridization with the PCR product showed related frequency shift 10 times higher than hybridization with complementary probe and detectable signals were obtained at the concentrations of 103 and 106 cfu/mL after hybridization with bacterial DNA. There are currently optimizations of the second protocol, where preliminary results have shown to be more uniform and therefore more precise within each of the

Nanopore arrays in a silicon membrane for parallel single-molecule detection: fabrication

Science.gov (United States)

Schmidt, Torsten; Zhang, Miao; Sychugov, Ilya; Roxhed, Niclas; Linnros, Jan

2015-08-01

Solid state nanopores enable translocation and detection of single bio-molecules such as DNA in buffer solutions. Here, sub-10 nm nanopore arrays in silicon membranes were fabricated by using electron-beam lithography to define etch pits and by using a subsequent electrochemical etching step. This approach effectively decouples positioning of the pores and the control of their size, where the pore size essentially results from the anodizing current and time in the etching cell. Nanopores with diameters as small as 7 nm, fully penetrating 300 nm thick membranes, were obtained. The presented fabrication scheme to form large arrays of nanopores is attractive for parallel bio-molecule sensing and DNA sequencing using optical techniques. In particular the signal-to-noise ratio is improved compared to other alternatives such as nitride membranes suffering from a high-luminescence background.

Ultrasensitive FRET-based DNA sensor using PNA/DNA hybridization.

Science.gov (United States)

Yang, Lan-Hee; Ahn, Dong June; Koo, Eunhae

2016-12-01

In the diagnosis of genetic diseases, rapid and highly sensitive DNA detection is crucial. Therefore, many strategies for detecting target DNA have been developed, including electrical, optical, and mechanical methods. Herein, a highly sensitive FRET based sensor was developed by using PNA (Peptide Nucleic Acid) probe and QD, in which red color QDs are hybridized with capture probes, reporter probes and target DNAs by EDC-NHS coupling. The hybridized probe with target DNA gives off fluorescent signal due to the energy transfer from QD to Cy5 dye in the reporter probe. Compared to the conventional DNA sensor using DNA probes, the DNA sensor using PNA probes shows higher FRET factor and efficiency due to the higher reactivity between PNA and target DNA. In addition, to elicit the effect of the distance between the donor and the acceptor, we have investigated two types of the reporter probes having Cy5 dyes attached at the different positions of the reporter probes. Results show that the shorter the distance between QDs and Cy5s, the stronger the signal intensity. Furthermore, based on the fluorescence microscopy images using microcapillary chips, the FRET signal is enhanced to be up to 276% times stronger than the signal obtained using the cuvette by the fluorescence spectrometer. These results suggest that the PNA probe system conjugated with QDs can be used as ultrasensitive DNA nanosensors. Copyright © 2016. Published by Elsevier B.V.

1/f noise in graphene nanopores

International Nuclear Information System (INIS)

Heerema, S J; Schneider, G F; Rozemuller, M; Vicarelli, L; Zandbergen, H W; Dekker, C

2015-01-01

Graphene nanopores are receiving great attention due to their atomically thin membranes and intrinsic electrical properties that appear greatly beneficial for biosensing and DNA sequencing. Here, we present an extensive study of the low-frequency 1/f noise in the ionic current through graphene nanopores and compare it to noise levels in silicon nitride pore currents. We find that the 1/f noise magnitude is very high for graphene nanopores: typically two orders of magnitude higher than for silicon nitride pores. This is a drawback as it significantly lowers the signal-to-noise ratio in DNA translocation experiments. We evaluate possible explanations for these exceptionally high noise levels in graphene pores. From examining the noise for pores of different diameters and at various salt concentrations, we find that in contrast to silicon nitride pores, the 1/f noise in graphene pores does not follow Hooge’s relation. In addition, from studying the dependence on the buffer pH, we show that the increased noise cannot be explained by charge fluctuations of chemical groups on the pore rim. Finally, we compare single and bilayer graphene to few-layer and multi-layer graphene and boron nitride (h-BN), and we find that the noise reduces with layer thickness for both materials, which suggests that mechanical fluctuations may be the underlying cause of the high 1/f noise levels in monolayer graphene nanopore devices. (paper)

Information Dynamics of a Nonlinear Stochastic Nanopore System

Directory of Open Access Journals (Sweden)

Claire Gilpin

2018-03-01

Full Text Available Nanopores have become a subject of interest in the scientific community due to their potential uses in nanometer-scale laboratory and research applications, including infectious disease diagnostics and DNA sequencing. Additionally, they display behavioral similarity to molecular and cellular scale physiological processes. Recent advances in information theory have made it possible to probe the information dynamics of nonlinear stochastic dynamical systems, such as autonomously fluctuating nanopore systems, which has enhanced our understanding of the physical systems they model. We present the results of local (LER and specific entropy rate (SER computations from a simulation study of an autonomously fluctuating nanopore system. We learn that both metrics show increases that correspond to fluctuations in the nanopore current, indicating fundamental changes in information generation surrounding these fluctuations.

Fabrication and characterization of a solid-state nanopore with self-aligned carbon nanoelectrodes for molecular detection

International Nuclear Information System (INIS)

Spinney, Patrick S; Collins, Scott D; Smith, Rosemary L; Howitt, David G

2012-01-01

Stochastic molecular sensors based on resistive pulse nanopore modalities are envisioned as facile DNA sequencers. However, recent advances in nanotechnology fabrication have highlighted promising alternative detection mechanisms with higher sensitivity and potential single-base resolution. In this paper we present the novel self-aligned fabrication of a solid-state nanopore device with integrated transverse graphene-like carbon nanoelectrodes for polyelectrolyte molecular detection. The electrochemical transduction mechanism is characterized and found to result primarily from thermionic emission between the two transverse electrodes. Response of the nanopore to Lambda dsDNA and short (16-mer) ssDNA is demonstrated and distinguished. (paper)

Electrochemical DNA Hybridization Sensors Based on Conducting Polymers

Science.gov (United States)

Rahman, Md. Mahbubur; Li, Xiao-Bo; Lopa, Nasrin Siraj; Ahn, Sang Jung; Lee, Jae-Joon

2015-01-01

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. PMID:25664436

Electrochemical DNA Hybridization Sensors Based on Conducting Polymers

Directory of Open Access Journals (Sweden)

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.

Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparisons with Other Methods

International Nuclear Information System (INIS)

Wu, Liyou; Yi, T.Y.; Van Nostrand, Joy; Zhou, Jizhong

2010-01-01

Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site (Hanford Reach of the Columbia River (HRCR), 11 strains), Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.

Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

Energy Technology Data Exchange (ETDEWEB)

Wu, Liyou; Yi, T. Y.; Van Nostrand, Joy; Zhou, Jizhong

2010-05-17

Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.

The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage

DEFF Research Database (Denmark)

Lafuente-Barquero, Juan; Luke-Glaser, Sarah; Graf, Marco

2017-01-01

of Fanconi anemia protein M (FANCM), is required for cell viability in the absence of RNase H enzymes. The integrity of the Mph1 helicase domain is crucial to prevent the accumulation of RNA-DNA hybrids and RNA-DNA hybrid-dependent DNA damage, as determined by Rad52 foci. Mph1 forms foci when RNA-DNA hybrids...

Techniques of DNA hybridization detect small numbers of mycobacteria with no cross-hybridization with non-mycobacterial respiratory organisms

International Nuclear Information System (INIS)

Shoemaker, S.A.; Fisher, J.H.; Scoggin, C.H.

1985-01-01

The traditional methods used in identifying mycobacteria, such as acid-fast bacillus stains and culture, are often time-consuming, insensitive, and nonspecific. As part of an ongoing program to improve diagnosis and characterization of mycobacteria, the authors have found that deoxyribonucleic acid (DNA) hybridization techniques using isotopically labeled, single-stranded, total DNA can be used to detect as little as 10(-4) micrograms of Mycobacterium tuberculosis (MTb) DNA. This amount of DNA represents approximately 2 X 10(4) genomes. They have also shown the MTb DNA is sufficiently different from the DNA of non-mycobacterial microorganisms such that cross-hybridization with MTb DNA does not occur under the hybridization conditions employed. The authors speculate that DNA hybridization techniques may allow the rapid, sensitive, and specific identification of mycobacteria

An exonuclease-assisted amplification electrochemical aptasensor for Hg(2+) detection based on hybridization chain reaction.

Science.gov (United States)

Bao, Ting; Wen, Wei; Zhang, Xiuhua; Xia, Qinghua; Wang, Shengfu

2015-08-15

In this work, a novel electrochemical aptasensor was developed for Hg(2+) detection based on exonuclease-assisted target recycling and hybridization chain reaction (HCR) dual signal amplification strategy. The presence of Hg(2+) induced the T-rich DNA partly folded into duplex-like structure via the Hg(2+) mediated T-Hg(2+)-T base pairs, which triggered the activity of exonuclease III (Exo III). Exo III selectively digested the double-strand DNA containing multiple T-Hg(2+)-T base pairs from its 3'-end, the released Hg(2+) participated analyte recycle. With each digestion cycle, a digestion product named as help DNA was obtained, which acted as a linkage between the capture DNA and auxiliary DNA. The presence of help DNA and two auxiliary DNA collectively facilitated successful HCR process and formed long double-stranded DNA. [Ru(NH3)6](3+) was used as redox indicator, which electrostatically bound to the double strands and produced an electrochemical signal. Exo III-assisted target recycling and HCR dual amplification significantly improved the sensitivity for Hg(2+) with a detection limit of 0.12 pM (S/N=3). Furthermore, the proposed aptasensor had a promising potential for the application of Hg(2+) detection in real aquatic sample analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Ion transport in sub-5-nm graphene nanopores

International Nuclear Information System (INIS)

Suk, Myung E.; Aluru, N. R.

2014-01-01

Graphene nanopore is a promising device for single molecule sensing, including DNA bases, as its single atom thickness provides high spatial resolution. To attain high sensitivity, the size of the molecule should be comparable to the pore diameter. However, when the pore diameter approaches the size of the molecule, ion properties and dynamics may deviate from the bulk values and continuum analysis may not be accurate. In this paper, we investigate the static and dynamic properties of ions with and without an external voltage drop in sub-5-nm graphene nanopores using molecular dynamics simulations. Ion concentration in graphene nanopores sharply drops from the bulk concentration when the pore radius is smaller than 0.9 nm. Ion mobility in the pore is also smaller than bulk ion mobility due to the layered liquid structure in the pore-axial direction. Our results show that a continuum analysis can be appropriate when the pore radius is larger than 0.9 nm if pore conductivity is properly defined. Since many applications of graphene nanopores, such as DNA and protein sensing, involve ion transport, the results presented here will be useful not only in understanding the behavior of ion transport but also in designing bio-molecular sensors

Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor

International Nuclear Information System (INIS)

Gracheva, Maria E; Aksimentiev, Aleksei; Leburton, Jean-Pierre

2006-01-01

In this paper, we evaluate the magnitude of the electrical signals produced by DNA translocation through a 1 nm diameter nanopore in a capacitor membrane with a numerical multi-scale approach, and assess the possibility of resolving individual nucleotides as well as their types in the absence of conformational disorder. We show that the maximum recorded voltage caused by the DNA translocation is about 35 mV, while the maximum voltage signal due to the DNA backbone is about 30 mV, and the maximum voltage of a DNA base is about 8 mV. Signals from individual nucleotides can be identified in the recorded voltage traces, suggesting a 1 nm diameter pore in a capacitor can be used to accurately count the number of nucleotides in a DNA strand. Furthermore, we study the effect of a single base substitution on the voltage trace, and calculate the differences among the voltage traces due to a single base mutation for the sequences C 3 AC 7 , C 3 CC 7 , C 3 GC 7 and C 3 TC 7 . The calculated voltage differences are in the 5-10 mV range. The calculated maximum voltage caused by the translocation of individual bases varies from 2 to 9 mV, which is experimentally detectable

X-ray scattering study of thermal nanopore templating in hybrid films of organosilicate precursor and reactive four-armed porogen

International Nuclear Information System (INIS)

Yoon, Jinhwan; Heo, Kyuyoung; Oh, Weontae; Jin, Kyeong Sik; Jin, Sangwoo; Kim, Jehan; Kim, Kwang-Woo; Chang, Taihyun; Ree, Moonhor

2006-01-01

The miscibility and the mechanism for thermal nanopore templating in films prepared from spin-coating and subsequent drying of homogenous solutions of curable polymethylsilsesquioxane dielectric precursor and thermally labile, reactive triethoxysilyl-terminated four-armed poly(ε-caprolactone) porogen were investigated in detail by in situ two-dimensional grazing incidence small-angle x-ray scattering analysis. The dielectric precursor and porogen components in the film were fully miscible. On heating, limited aggregations of the porogen, however, took place in only a small temperature range of 100-140 deg. C as a result of phase separation induced by the competition of the curing and hybridization reactions of the dielectric precursor and porogen; higher porogen loading resulted in relatively large porogen aggregates and a greater size distribution. The developed porogen aggregates underwent thermal firing above 300 deg. C without further growth and movement, and ultimately left their individual footprints in the film as spherical nanopores

Applications of Synthetic Microchannel and Nanopore Systems

Science.gov (United States)

Hinkle, Thomas Preston

This thesis describes research conducted on the physics and applications of micro- and nanoscale ion-conducting channels. Making use of the nanoscale physics that takes place in the vicinity of charged surfaces, there is the possibility that nanopores, holes on the order of 1 nm in size, could be used to make complex integrated ionic circuits. For inspiration on what such circuits could achieve we only need to look to biology systems, immensely complex machines that at their most basic level require precise control of ions and intercellular electric potentials to function. In order to contribute to the ever expanding field of nanopore research, we engineered novel hybrid insulator-conductor nanopores that behave analagously to ionic diodes, which allow passage of current flow in one direction but severely limit the current in the opposite direction. The experiments revealed that surface polarization of the conducting material can induce the formation of an electrical double layer in the same way static surface charges can. Furthermore, we showed that the hybrid device behaved similar to an ionic diode, and could see potential use as a standard rectifying element in ionic circuits. Another application based on ion conducting channels is resistive pulse sensing, a single particle detection and characterization method. We present three main experiments that expand the capacity of resistive pulse sensing for particle characterization. First, we demonstrate how resistive pulse sensing in pores with longitudinal irregularities can be used to measure the lengths of individual nanoparticles. Then, we describe an entirely new hybrid approach to resistive pulse sensing, whereby the electrical measurements are combined with simultaneous optical imaging. The hybrid method allows for validation of the resistive pulse signals and will greatly contribute to their interpretability. We present experiments that explore some of the possibilities of the hybrid method. Then, building

Self-assembly of multiferroic core-shell particulate nanocomposites through DNA-DNA hybridization and magnetic field directed assembly of superstructures

Energy Technology Data Exchange (ETDEWEB)

Sreenivasulu, Gollapudi; Srinivasan, Gopalan, E-mail: srinivas@oakland.edu, E-mail: chavez@oakland.edu [Department of Physics, Oakland University, Rochester, MI 48309-4401 (United States); Lochbiler, Thomas A.; Panda, Manashi; Chavez, Ferman A., E-mail: srinivas@oakland.edu, E-mail: chavez@oakland.edu [Department of Chemistry, Oakland University, Rochester, MI 48309-4401 (United States)

2016-04-15

Multiferroic composites of ferromagnetic and ferroelectric phases are of importance for studies on mechanical strain mediated coupling between the magnetic and electric subsystems. This work is on DNA-assisted self-assembly of superstructures of such composites with nanometer periodicity. The synthesis involved oligomeric DNA-functionalized ferroelectric and ferromagnetic nanoparticles, 600 nm BaTiO{sub 3} (BTO) and 200 nm NiFe{sub 2}O{sub 4} (NFO), respectively. Mixing BTO and NFO particles, possessing complementary DNA sequences, resulted in the formation of ordered core-shell heteronanocomposites held together by DNA hybridization. The composites were imaged by scanning electron microscopy and scanning microwave microscopy. The presence of heteroassemblies along with core-shell architecture is clearly observed. The reversible nature of the DNA hybridization allows for restructuring the composites into mm-long linear chains and 2D-arrays in the presence of a static magnetic field and ring-like structures in a rotating-magnetic field. Strong magneto-electric (ME) coupling in as-assembled composites is evident from static magnetic field H induced polarization and low-frequency magnetoelectric voltage coefficient measurements. Upon annealing the nanocomposites at high temperatures, evidence for the formation of bulk composites with excellent cross-coupling between the electric and magnetic subsystems is obtained by H-induced polarization and low-frequency ME voltage coefficient. The ME coupling strength in the self-assembled composites is measured to be much stronger than in bulk composites with randomly distributed NFO and BTO prepared by direct mixing and sintering.

Effects of humic substances on fluorometric DNA quantification and DNA hybridization

NARCIS (Netherlands)

Bachoon, DS; Otero, E; Hodson, RE

2001-01-01

DNA extracts from sediment and water samples are often contaminated with coextracted humic-like impurities, Estuarine humic substances and vascular plant extract were used to evaluate the effect of the presence of such impurities on DNA hybridization and quantification. The presence of humic

Application of DNA-DNA colony hybridization to the detection of catabolic genotypes in environmental samples

International Nuclear Information System (INIS)

Sayler, G.S.; Shields, M.S.; Tedford, E.T.; Breen, A.; Hooper, S.W.; Sirotkin, K.M.; Davis, J.W.

1985-01-01

The application of preexisting DNA hybridization techniques was investigated for potential in determining populations of specific gene sequences in environmental samples. Cross-hybridizations among two degradative plasmids, TOL and NAH, and two cloning vehicles, pLAFR1 and RSF1010, were determined. The detection limits for the TOL plasmid against a nonhomologous plasmid-bearing bacterial background was ascertained. The colony hybridization technique allowed detection of one colony containing TOL plasmid among 10(6) Escherichia coli colonies of nonhomologous DNA. Comparisons between population estimates derived from growth on selective substrates and from hybridizations were examined. Findings indicated that standard sole carbon source enumeration procedures for degradative populations lead to overestimations due to nonspecific growth of other bacteria on the microcontaminant carbon sources present in the media. Population estimates based on the selective growth of a microcosm population on two aromatic substrates (toluene and naphthalene) and estimates derived from DNA-DNA colony hybridizations, using the TOL or NAH plasmid as a probe, corresponded with estimates of substrate mineralization rates and past exposure to environmental contaminants. The applications of such techniques are hoped to eventually allow enumeration of any specific gene sequences in the environment, including both anabolic and catabolic genes. In addition, this procedure should prove useful in monitoring recombinant DNA clones released into environmental situations

DNA-dispersed graphene/NiO hybrid materials for highly sensitive non-enzymatic glucose sensor

International Nuclear Information System (INIS)

Lv Wei; Jin Fengmin; Guo Quangui; Yang Quanhong; Kang Feiyu

2012-01-01

Highlights: ► We investigated the potential of GNS/NiO/DNA hybrid used as a nonenzymatic sensor. ► DNA is a highly efficient disperse agent for GNS/NiO hybrid than ionic surfactants. ► GNS/NiO/DNA hybrid shows fast electron transfer in the electrochemical reaction. ► GNS/NiO/DNA hybrid shows good detection performance towards glucose. - Abstract: We demonstrate graphene nanosheet/NiO hybrids (GNS/NiO) as the active material for high-performance non-enzymatic glucose sensors. Such sensors are fabricated by DNA-dispersed GNS/NiO suspension deposited on glassy carbon electrodes. ss-DNA shows strong dispersing ability for the GNS/NiO hybrid materials resulting in stable water-dispersible GNS/NiO/DNA hybrids with fully separated layers. The GNS/NiO/DNA hybrids show enhanced electron transfer in the electrocatalytic reaction process, and accordingly, such hybrids modified electrodes show good sensing performance towards glucose and are characterized by large detection ranges, short response periods, low detection limit and high sensitivity and stability.

Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.

Science.gov (United States)

Cao, Chan; Long, Yi-Tao

2018-02-20

Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis

Electrokinetically-controlled RNA-DNA hybridization assay for foodborne pathogens

International Nuclear Information System (INIS)

Weng, X.; Jiang, H.; Li, D.

2012-01-01

We have developed a microfluidic chip for use in an RNA-DNA hybridization assay for foodborne pathogens. Automatic sequential reagent dispensing and washing was realized with a programmable DC voltage sequencer. Signal detection was achieved with a miniaturized optical detection module. Salmonella and Listeria monocytogenes bacteria in different concentrations were quantitatively determined by this RNA-DNA hybridization assay in the microfluidic chip. The detection limit for the Salmonella and Listeria monocytogenes bacteria is 10 3 to 10 4 CFU mL -1 . The method excels by a significant reduction in the consumption of sample and reagent, and a short assay time. This automatic-operating microfluidic RNA-DNA hybridization assay is promising for on-site pathogen detection. (author)

Streaming current magnetic fields in a charged nanopore

Science.gov (United States)

Mansouri, Abraham; Taheri, Peyman; Kostiuk, Larry W.

2016-01-01

Magnetic fields induced by currents created in pressure driven flows inside a solid-state charged nanopore were modeled by numerically solving a system of steady state continuum partial differential equations, i.e., Poisson, Nernst-Planck, Ampere and Navier-Stokes equations (PNPANS). This analysis was based on non-dimensional transport governing equations that were scaled using Debye length as the characteristic length scale, and applied to a finite length cylindrical nano-channel. The comparison of numerical and analytical studies shows an excellent agreement and verified the magnetic fields density both inside and outside the nanopore. The radially non-uniform currents resulted in highly non-uniform magnetic fields within the nanopore that decay as 1/r outside the nanopore. It is worth noting that for either streaming currents or streaming potential cases, the maximum magnetic field occurred inside the pore in the vicinity of nanopore wall, as opposed to a cylindrical conductor that carries a steady electric current where the maximum magnetic fields occur at the perimeter of conductor. Based on these results, it is suggested and envisaged that non-invasive external magnetic fields readouts generated by streaming/ionic currents may be viewed as secondary electronic signatures of biomolecules to complement and enhance current DNA nanopore sequencing techniques. PMID:27833119

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Full Text Available Oth.Unc.05.DNA-RNA_hybrids.AllCell sacCer3 TFs and others DNA-RNA hybrids Unclassif...ied http://dbarchive.biosciencedbc.jp/kyushu-u/sacCer3/assembled/Oth.Unc.05.DNA-RNA_hybrids.AllCell.bed ...

Nanolock-Nanopore Facilitated Digital Diagnostics of Cancer Driver Mutation in Tumor Tissue.

Science.gov (United States)

Wang, Yong; Tian, Kai; Shi, Ruicheng; Gu, Amy; Pennella, Michael; Alberts, Lindsey; Gates, Kent S; Li, Guangfu; Fan, Hongxin; Wang, Michael X; Gu, Li-Qun

2017-07-28

Cancer driver mutations are clinically significant biomarkers. In precision medicine, accurate detection of these oncogenic changes in patients would enable early diagnostics of cancer, individually tailored targeted therapy, and precise monitoring of treatment response. Here we investigated a novel nanolock-nanopore method for single-molecule detection of a serine/threonine protein kinase gene BRAF V600E mutation in tumor tissues of thyroid cancer patients. The method lies in a noncovalent, mutation sequence-specific nanolock. We found that the nanolock formed on the mutant allele/probe duplex can separate the duplex dehybridization procedure into two sequential steps in the nanopore. Remarkably, this stepwise unzipping kinetics can produce a unique nanopore electric marker, with which a single DNA molecule of the cancer mutant allele can be unmistakably identified in various backgrounds of the normal wild-type allele. The single-molecule sensitivity for mutant allele enables both binary diagnostics and quantitative analysis of mutation occurrence. In the current configuration, the method can detect the BRAF V600E mutant DNA lower than 1% in the tumor tissues. The nanolock-nanopore method can be adapted to detect a broad spectrum of both transversion and transition DNA mutations, with applications from diagnostics to targeted therapy.

Non-sticky translocation of bio-molecules through Tween 20-coated solid-state nanopores in a wide pH range

Science.gov (United States)

Li, Xiaoqing; Hu, Rui; Li, Ji; Tong, Xin; Diao, J. J.; Yu, Dapeng; Zhao, Qing

2016-10-01

Nanopore-based sensing technology is considered high-throughput and low-cost for single molecule detection, but solid-state nanopores have suffered from pore clogging issues. A simple Tween 20 coating method is applied to ensure long-term (several hours) non-sticky translocation of various types of bio-molecules through SiN nanopores in a wide pH range (4.0-13.0). We also emphasize the importance of choosing appropriate concentration of Tween 20 coating buffer for desired effect. By coating nanopores with a Tween 20 layer, we are able to differentiate between single-stranded DNA and double-stranded DNA, to identify drift-dominated domain for single-stranded DNA, to estimate BSA volume and to observe the shape of individual nucleosome translocation event without non-specific adsorption. The wide pH endurance from 4.0 to 13.0 and the broad types of detection analytes including nucleic acids, proteins, and biological complexes highlight the great application potential of Tween 20-coated solid-state nanopores.

Stability and Catalytic Kinetics of Horseradish Peroxidase Confined in Nanoporous SBA-15

DEFF Research Database (Denmark)

Ikemoto, Hediki; Chi, Qijin; Ulstrup, Jens

2010-01-01

We have synthesized nanoporous silica, SBA-15 in the 1 m size range with the pore diameter of 7.6 nm. The redox enzyme horseradish peroxidase (HRP) was entrapped in the pores to form nanostructured hybrid materials. The catalytic activity of free and immobilized enzyme was first compared at room...... likely due to different hydrogen bonding of water and increased hydration strength of the protein inside the nanopores....

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Single-molecule analysis of lead(II)-binding aptamer conformational changes in an α-hemolysin nanopore, and sensitive detection of lead(II)

International Nuclear Information System (INIS)

Wang, Hai-Yan; Song, Ze-Yang; Zhang, Hui-Sheng; Chen, Si-Ping

2016-01-01

The α-hemolysin (αHL) nanopore is capable of analyzing DNA duplex and DNA aptamer as they can be electrophoretically driven into the vestibule from the cis entrance. The current study describes the competitive interaction induced by Pb 2+ that changes the secondary structure of DNA duplex in asymmetrical electrolyte solution. DNA duplex formed by the partial complementary DNA and DNA aptamer sequence produced unzipping blockages with the dwell unzipping time lasting 2.84 ± 0.7 ms. By cation-DNA interaction with Pb 2+ , the DNA duplex will unwind and then form Pb 2+ -stabilized-DNA aptamer, which will be captured and unfolded in vestibule. The pore conductance were reduced to 54 % and 94 % with mean dwell unfolding times of 165 ± 12 ms. The competitive behavior between Pb 2+ and single-strand DNA was further utilized to detect Pb 2+ in solution with a detection limit of 0.5 nM. This nanopore platform also provides a powerful tool for studying the cation-DNA interactions in DNA aptamer conformational changes. Thus, the results drawn from these studies provide insights into the applications of α-hemolysin nanopore as a molecular sieve to different DNA secondary structure in future application of nanopore analysis. (author)

Solid-state nanopores for probing DNA and protein

NARCIS (Netherlands)

Plesa, C.

2015-01-01

Solid-state nanopores are small nanometer-scale holes in thin membranes. When used to separate two chambers containing salt solution, any biomolecule passing from one chamber to the other is forced to pass through the pore constriction. An electric field applied across the membrane is used to create

Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes

Science.gov (United States)

Verschueren, Daniel V.; Yang, Wayne; Dekker, Cees

2018-04-01

We report a simple and scalable technique for the fabrication of nanopore arrays on freestanding SiN and graphene membranes based on electron-beam lithography and reactive ion etching. By controlling the dose of the single-shot electron-beam exposure, circular nanopores of any size down to 16 nm in diameter can be fabricated in both materials at high accuracy and precision. We demonstrate the sensing capabilities of these nanopores by translocating dsDNA through pores fabricated using this method, and find signal-to-noise characteristics on par with transmission-electron-microscope-drilled nanopores. This versatile lithography-based approach allows for the high-throughput manufacturing of nanopores and can in principle be used on any substrate, in particular membranes made out of transferable two-dimensional materials.

Alumina plate containing photosystem I reaction center complex oriented inside plate-penetrating silica nanopores.

Science.gov (United States)

Kamidaki, Chihiro; Kondo, Toru; Noji, Tomoyasu; Itoh, Tetsuji; Yamaguchi, Akira; Itoh, Shigeru

2013-08-22

The photosynthetic photosystem I reaction center complex (PSI-RC), which has a molecular diameter of 21 nm with 100 pigments, was incorporated into silica nanopores with a 100-nm diameter that penetrates an alumina plate of 60-μm thickness to make up an inorganic-biological hybrid photocell. PSI-RCs, purified from a thermophilic cyanobacterium, were stable inside the nanopores and rapidly photoreduced a mediator dye methyl viologen. The reduced dye was more stable inside nanopores suggesting the decrease of dissolved oxygen. The analysis by a cryogenic electron spin paramagnetic resonance indicated the oriented arrangement of RCs inside the 100-nm nanopores, with their surface parallel to the silica wall and perpendicular to the plane of the alumina plate. PSI RC complex in the semicrystalline orientation inside silica nanopores can be a new type of light energy conversion unit to supply strong reducing power selectively to other molecules inside or outside nanopores.

Hollow nanoporous covalent triazine frameworks via acid vapor-assisted solid phase synthesis for enhanced visible light photoactivity

KAUST Repository

Huang, Wei

2016-04-11

Herein, we report a novel trifluoromethanesulfonic acid vapor-assisted solid phase synthetic method to construct nanoporous covalent triazine frameworks with highly ordered hollow interconnected pores under mild reaction conditions. This unique solid state synthetic route allows not only the avoidance of undesired side reactions caused by traditional high temperature synthesis, but also the maintaining of defined and precise optical and electronic properties of the nonporous triazine frameworks. Promising photocatalytic activity of the polytriazine networks was demonstrated in the photoreduction reaction of 4-nitrophenol into 4-aminophenol under visible light irradiation.

Hollow nanoporous covalent triazine frameworks via acid vapor-assisted solid phase synthesis for enhanced visible light photoactivity

KAUST Repository

Huang, Wei; Wang, Zi Jun; Ma, Beatriz Chiyin; Ghasimi, Saman; Gehrig, Dominik; Laquai, Fré dé ric; Landfester, Katharina; Zhang, Kai A. I.

2016-01-01

Herein, we report a novel trifluoromethanesulfonic acid vapor-assisted solid phase synthetic method to construct nanoporous covalent triazine frameworks with highly ordered hollow interconnected pores under mild reaction conditions. This unique solid state synthetic route allows not only the avoidance of undesired side reactions caused by traditional high temperature synthesis, but also the maintaining of defined and precise optical and electronic properties of the nonporous triazine frameworks. Promising photocatalytic activity of the polytriazine networks was demonstrated in the photoreduction reaction of 4-nitrophenol into 4-aminophenol under visible light irradiation.

Label-free detection of DNA hybridization using transistors based on CVD grown graphene.

Science.gov (United States)

Chen, Tzu-Yin; Loan, Phan Thi Kim; Hsu, Chang-Lung; Lee, Yi-Hsien; Tse-Wei Wang, Jacob; Wei, Kung-Hwa; Lin, Cheng-Te; Li, Lain-Jong

2013-03-15

The high transconductance and low noise of graphene-based field-effect transistors based on large-area monolayer graphene produced by chemical vapor deposition are used for label-free electrical detection of DNA hybridization. The gate materials, buffer concentration and surface condition of graphene have been optimized to achieve the DNA detection sensitivity as low as 1 pM (10(-12) M), which is more sensitive than the existing report based on few-layer graphene. The graphene films obtained using conventional PMMA-assisted transfer technique exhibits PMMA residues, which degrade the sensing performance of graphene. We have demonstrated that the sensing performance of the graphene samples prepared by gold-transfer is largely enhanced (by 125%). Copyright © 2012 Elsevier B.V. All rights reserved.

Measuring DNA hybridization using fluorescent DNA-stabilized silver clusters to investigate mismatch effects on therapeutic oligonucleotides.

Science.gov (United States)

de Bruin, Donny; Bossert, Nelli; Aartsma-Rus, Annemieke; Bouwmeester, Dirk

2018-04-06

Short nucleic acid oligomers have found a wide range of applications in experimental physics, biology and medicine, and show potential for the treatment of acquired and genetic diseases. These applications rely heavily on the predictability of hybridization through Watson-Crick base pairing to allow positioning on a nanometer scale, as well as binding to the target transcripts, but also off-target binding to transcripts with partial homology. These effects are of particular importance in the development of therapeutic oligonucleotides, where off-target effects caused by the binding of mismatched sequences need to be avoided. We employ a novel method of probing DNA hybridization using optically active DNA-stabilized silver clusters (Ag-DNA) to measure binding efficiencies through a change in fluorescence intensity. In this way we can determine their location-specific sensitivity to individual mismatches in the sequence. The results reveal a strong dependence of the hybridization on the location of the mismatch, whereby mismatches close to the edges and center show a relatively minor impact. In parallel, we propose a simple model for calculating the annealing ratios of mismatched DNA sequences, which supports our experimental results. The primary result shown in this work is a demonstration of a novel technique to measure DNA hybridization using fluorescent Ag-DNA. With this technique, we investigated the effect of mismatches on the hybridization efficiency, and found a significant dependence on the location of individual mismatches. These effects are strongly influenced by the length of the used oligonucleotides. The novel probe method based on fluorescent Ag-DNA functions as a reliable tool in measuring this behavior. As a secondary result, we formulated a simple model that is consistent with the experimental data.

Conformational Selection and Induced Fit for RNA Polymerase and RNA/DNA Hybrid Backtracked Recognition

Directory of Open Access Journals (Sweden)

Haifeng eChen

2015-11-01

Full Text Available RNA polymerase catalyzes transcription with a high fidelity. If DNA/RNA mismatch or DNA damage occurs downstream, a backtracked RNA polymerase can proofread this situation. However, the backtracked mechanism is still poorly understood. Here we have performed multiple explicit-solvent molecular dynamics (MD simulations on bound and apo DNA/RNA hybrid to study backtracked recognition. MD simulations at room temperature suggest that specific electrostatic interactions play key roles in the backtracked recognition between the polymerase and DNA/RNA hybrid. Kinetics analysis at high temperature shows that bound and apo DNA/RNA hybrid unfold via a two-state process. Both kinetics and free energy landscape analyses indicate that bound DNA/RNA hybrid folds in the order of DNA/RNA contracting, the tertiary folding and polymerase binding. The predicted Φ-values suggest that C7, G9, dC12, dC15 and dT16 are key bases for the backtracked recognition of DNA/RNA hybrid. The average RMSD values between the bound structures and the corresponding apo ones and Kolmogorov-Smirnov (KS P test analyses indicate that the recognition between DNA/RNA hybrid and polymerase might follow an induced fit mechanism for DNA/RNA hybrid and conformation selection for polymerase. Furthermore, this method could be used to relative studies of specific recognition between nucleic acid and protein.

Recent progress in molecular simulation of nanoporous graphene membranes for gas separation

Science.gov (United States)

Fatemi, S. Mahmood; Baniasadi, Aminreza; Moradi, Mahrokh

2017-07-01

If an ideal membrane for gas separation is to be obtained, the following three characteristics should be considered: the membrane should be as thin as possible, be mechanically robust, and have welldefined pore sizes. These features will maximize its solvent flux, preserve it from fracture, and guarantee its selectivity. Graphene is made up of a hexagonal honeycomb lattice of carbon atoms with sp 2 hybridization state forming a one-atom-thick sheet of graphite. Following conversion of the honeycomb lattices into nanopores with a specific geometry and size, a nanoporous graphene membrane that offers high efficiency as a separation membrane because of the ultrafast molecular permeation rate as a result of its one-atom thickness is obtained. Applications of nanoporous graphene membranes for gas separation have been receiving remarkably increasing attention because nanoporous graphene membranes show promising results in this area. This review focuses on the recent advances in nanoporous graphene membranes for applications in gas separation, with a major emphasis on theoretical works. The attractive properties of nanoporous graphene membranes introduce make them appropriate candidates for gas separation and gas molecular-sieving processes in nanoscale dimensions.

File list: Oth.NoD.50.DNA-RNA_hybrids.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Oth.NoD.50.DNA-RNA_hybrids.AllCell sacCer3 TFs and others DNA-RNA hybrids No descri...ption http://dbarchive.biosciencedbc.jp/kyushu-u/sacCer3/assembled/Oth.NoD.50.DNA-RNA_hybrids.AllCell.bed ...

File list: Oth.NoD.20.DNA-RNA_hybrids.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Oth.NoD.20.DNA-RNA_hybrids.AllCell sacCer3 TFs and others DNA-RNA hybrids No descri...ption http://dbarchive.biosciencedbc.jp/kyushu-u/sacCer3/assembled/Oth.NoD.20.DNA-RNA_hybrids.AllCell.bed ...

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Lifescience Database Archive (English)

Full Text Available Oth.NoD.10.DNA-RNA_hybrids.AllCell sacCer3 TFs and others DNA-RNA hybrids No descri...ption http://dbarchive.biosciencedbc.jp/kyushu-u/sacCer3/assembled/Oth.NoD.10.DNA-RNA_hybrids.AllCell.bed ...

File list: Oth.NoD.05.DNA-RNA_hybrids.AllCell [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available Oth.NoD.05.DNA-RNA_hybrids.AllCell sacCer3 TFs and others DNA-RNA hybrids No descri...ption http://dbarchive.biosciencedbc.jp/kyushu-u/sacCer3/assembled/Oth.NoD.05.DNA-RNA_hybrids.AllCell.bed ...

Probing of miniPEGγ-PNA-DNA Hybrid Duplex Stability with AFM Force Spectroscopy.

Science.gov (United States)

Dutta, Samrat; Armitage, Bruce A; Lyubchenko, Yuri L

2016-03-15

Peptide nucleic acids (PNA) are synthetic polymers, the neutral peptide backbone of which provides elevated stability to PNA-PNA and PNA-DNA hybrid duplexes. It was demonstrated that incorporation of diethylene glycol (miniPEG) at the γ position of the peptide backbone increased the thermal stability of the hybrid duplexes (Sahu, B. et al. J. Org. Chem. 2011, 76, 5614-5627). Here, we applied atomic force microscopy (AFM) based single molecule force spectroscopy and dynamic force spectroscopy (DFS) to test the strength and stability of the hybrid 10 bp duplex. This hybrid duplex consisted of miniPEGγ-PNA and DNA of the same length (γ(MP)PNA-DNA), which we compared to a DNA duplex with a homologous sequence. AFM force spectroscopy data obtained at the same conditions showed that the γ(MP)PNA-DNA hybrid is more stable than the DNA counterpart, 65 ± 15 pN vs 47 ± 15 pN, respectively. The DFS measurements performed in a range of pulling speeds analyzed in the framework of the Bell-Evans approach yielded a dissociation constant, koff ≈ 0.030 ± 0.01 s⁻¹ for γ(MP)PNA-DNA hybrid duplex vs 0.375 ± 0.18 s⁻¹ for the DNA-DNA duplex suggesting that the hybrid duplex is much more stable. Correlating the high affinity of γ(MP)PNA-DNA to slow dissociation kinetics is consistent with prior bulk characterization by surface plasmon resonance. Given the growing interest in γ(MP)PNA as well as other synthetic DNA analogues, the use of single molecule experiments along with computational analysis of force spectroscopy data will provide direct characterization of various modifications as well as higher order structures such as triplexes and quadruplexes.

Automated DNA electrophoresis, hybridization and detection

International Nuclear Information System (INIS)

Zapolski, E.J.; Gersten, D.M.; Golab, T.J.; Ledley, R.S.

1986-01-01

A fully automated, computer controlled system for nucleic acid hybridization analysis has been devised and constructed. In practice, DNA is digested with restriction endonuclease enzyme(s) and loaded into the system by pipette; 32 P-labelled nucleic acid probe(s) is loaded into the nine hybridization chambers. Instructions for all the steps in the automated process are specified by answering questions that appear on the computer screen at the start of the experiment. Subsequent steps are performed automatically. The system performs horizontal electrophoresis in agarose gel, fixed the fragments to a solid phase matrix, denatures, neutralizes, prehybridizes, hybridizes, washes, dries and detects the radioactivity according to the specifications given by the operator. The results, printed out at the end, give the positions on the matrix to which radioactivity remains hybridized following stringent washing

Slowing down and stretching DNA with an electrically tunable nanopore in a p–n semiconductor membrane

International Nuclear Information System (INIS)

Melnikov, Dmitriy V; Gracheva, Maria E; Leburton, Jean-Pierre

2012-01-01

We have studied single-stranded DNA translocation through a semiconductor membrane consisting of doped p and n layers of Si forming a p–n-junction. Using Brownian dynamics simulations of the biomolecule in the self-consistent membrane–electrolyte potential obtained from the Poisson–Nernst–Planck model, we show that while polymer length is extended more than when its motion is constricted only by the physical confinement of the nanopore. The biomolecule elongation is particularly dramatic on the n-side of the membrane where the lateral membrane electric field restricts (focuses) the biomolecule motion more than on the p-side. The latter effect makes our membrane a solid-state analog of the α-hemolysin biochannel. The results indicate that the tunable local electric field inside the membrane can effectively control dynamics of a DNA in the channel to either momentarily trap, slow down or allow the biomolecule to translocate at will. (paper)

Clinical strains of acinetobacter classified by DNA-DNA hybridization

International Nuclear Information System (INIS)

Tjernberg, I.; Ursing, J.

1989-01-01

A collection of Acinetobacter strains consisting of 168 consecutive clinical strains and 30 type and reference strains was studied by DNA-DNA hybridization and a few phenotypic tests. The field strains could be allotted to 13 DNA groups. By means of reference strains ten of these could be identified with groups described by Bouvet and Grimont (1986), while three groups were new; they were given the numbers 13-15. The type strain of A. radioresistens- recently described by Nishimura et al. (1988) - was shown to be a member of DNA group 12, which comprised 31 clinical isolates. Of the 19 strains of A. junii, eight showed hemolytic acitivity on sheep and human blood agar and an additional four strains on human blood agar only. Strains of this species have previously been regarded as non-hemolytic. Reciprocal DNA pairing data for the reference strains of the DNA gropus were treated by UPGMA clustering. The reference strains for A. calcoaceticus, A. baumannii and DNA groups 3 and 13 formed a cluster with about 70% relatedness within the cluster. Other DNA groups joined at levels below 60%. (author)

Clinical strains of acinetobacter classified by DNA-DNA hybridization

Energy Technology Data Exchange (ETDEWEB)

Tjernberg, I; Ursing, J [Department of Medical Microbiology, University of Lund, Malmoe General Hospital, Malmoe (Sweden)

1989-01-01

A collection of Acinetobacter strains consisting of 168 consecutive clinical strains and 30 type and reference strains was studied by DNA-DNA hybridization and a few phenotypic tests. The field strains could be allotted to 13 DNA groups. By means of reference strains ten of these could be identified with groups described by Bouvet and Grimont (1986), while three groups were new; they were given the numbers 13-15. The type strain of A. radioresistens- recently described by Nishimura et al. (1988) - was shown to be a member of DNA group 12, which comprised 31 clinical isolates. Of the 19 strains of A. junii, eight showed hemolytic acitivity on sheep and human blood agar and an additional four strains on human blood agar only. Strains of this species have previously been regarded as non-hemolytic. Reciprocal DNA pairing data for the reference strains of the DNA gropus were treated by UPGMA clustering. The reference strains for A. calcoaceticus, A. baumannii and DNA groups 3 and 13 formed a cluster with about 70% relatedness within the cluster. Other DNA groups joined at levels below 60%. (author).

Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics

Science.gov (United States)

Hata, Hiroaki; Kitajima, Tetsuro

2018-01-01

Abstract Nucleic acid secondary structure plays an important role in nucleic acid–nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant. PMID:29220504

DNA hybridization on membrane-modified carbon electrodes

Czech Academy of Sciences Publication Activity Database

Kouřilová, Alena; Babkina, S. S.; Cahová, Kateřina; Havran, Luděk; Jelen, František; Paleček, Emil; Fojta, Miroslav

2005-01-01

Roč. 38, - (2005), s. 2493-2507 ISSN 0003-2719 R&D Projects: GA MPO(CZ) 1H-PK/42; GA AV ČR(CZ) IAA4004402; GA AV ČR(CZ) IBS5004355 Institutional research plan: CEZ:AV0Z50040507 Keywords : DNA hybridization * electrochemical DNA sensor * nitrocellulose membrane Subject RIV: BO - Biophysics Impact factor: 1.036, year: 2005

Distribution of 45S rDNA in Modern Rose Cultivars (Rosa hybrida), Rosa rugosa, and Their Interspecific Hybrids Revealed by Fluorescence in situ Hybridization.

Science.gov (United States)

Ding, Xiao-Liu; Xu, Ting-Liang; Wang, Jing; Luo, Le; Yu, Chao; Dong, Gui-Min; Pan, Hui-Tang; Zhang, Qi-Xiang

2016-01-01

To elucidate the evolutionary dynamics of the location and number of rDNA loci in the process of polyploidization in the genus Rosa, we examined 45S rDNA sites in the chromosomes of 6 modern rose cultivars (R. hybrida), 5 R. rugosa cultivars, and 20 hybrid progenies by fluorescence in situ hybridization. Variation in the number of rDNA sites in parents and their interspecific hybrids was detected. As expected, 4 rDNA sites were observed in the genomes of 4 modern rose cultivars, while 3 hybridization sites were observed in the 2 others. Two expected rDNA sites were found in 2 R. rugosa cultivars, while in the other 3 R. rugosa cultivars 4 sites were present. Among the 20 R. hybrida × R. rugosa offspring, 13 carried the expected number of rDNA sites, and 1 had 6 hybridization sites, which exceeded the expected number by far. The other 6 offspring had either 2 or 3 hybridization sites, which was less than expected. Differences in the number of rDNA loci were observed in interspecific offspring, indicating that rDNA loci exhibit instability after distant hybridization events. Abnormal chromosome pairing may be the main factor explaining the variation in rDNA sites during polyploidization. © 2016 S. Karger AG, Basel.

Engineering of highly ordered TiO2 nanopore arrays by anodization

Science.gov (United States)

Wang, Huijie; Huang, Zhennan; Zhang, Li; Ding, Jie; Ma, Zhaoxia; Liu, Yong; Kou, Shengzhong; Yang, Hangsheng

2016-07-01

Finite element analysis was used to simulate the current density distributions in the TiO2 barrier layer formed at the initial stage of Ti anodization. The morphology modification of the barrier layer was found to induce current density distribution change. By starting the anodization with proper TiO2 barrier layer morphology, the current density distribution can be adjusted to favor the formation of either nanotube arrays or nanopore arrays of anodic TiO2. We also found that the addition of sodium acetate into the electrolyte suppressed both the field-assisted chemical dissolution of TiO2 and the TiF62- hydrolysis induced TiO2 deposition during anodization, and thus further favored the nanopore formation. Accordingly, highly ordered anodic TiO2 nanopore arrays, similar to anodic aluminum oxide nanopore arrays, were successfully prepared.

Organophosphonate functionalized silicon nanowires for DNA hybridization studies

Energy Technology Data Exchange (ETDEWEB)

Pedone, Daniel; Cattani Scholz, Anna; Birner, Stefan; Abstreiter, Gerhard [WSI, TU Muenchen (Germany); Dubey, Manish; Schwartz, Jeffrey [Princeton University, NJ (United States); Tornow, Marc [IHT, TU Braunschweig (Germany)

2007-07-01

Semiconductor nanowire field effect devices have great appeal for label-free sensing applications due to their sensitivity to surface potential changes that may originate from charged adsorbates. In addition to requiring high sensitivity, suitable passivation and functionalization of the semiconductor surface is obligatory. We have fabricated both freely suspended and oxide-supported silicon nanowires from Silicon-on-Insulator substrates using standard nanopatterning methods (EBL, RIE) and sacrificial oxide layer etching. Subsequent to nanofabrication, the devices were first coated with an hydroxyalkylphosphonate monolayer and then bound via bifunctional linker groups to single stranded DNA or PNA oligonucleotides, respectively. We investigated DNA hybridization on such functionalized nanowires using a difference resistance setup, where subtracting the reference signal from a second wire could be used to exclude most non-specific effects. A net change in surface potential on the order of a few mV could be detected upon addition of the complementary DNA strand. This surface potential change corresponds to the hybridization of about 10{sup 10}cm{sup -2} probe strands according to our model calculations that takes into account the entire hybrid system in electrolyte solution.

Influence of Nanopore Shapes on Thermal Conductivity of Two-Dimensional Nanoporous Material.

Science.gov (United States)

Huang, Cong-Liang; Huang, Zun; Lin, Zi-Zhen; Feng, Yan-Hui; Zhang, Xin-Xin; Wang, Ge

2016-12-01

The influence of nanopore shapes on the electronic thermal conductivity (ETC) was studied in this paper. It turns out that with same porosity, the ETC will be quite different for different nanopore shapes, caused by the different channel width for different nanopore shapes. With same channel width, the influence of different nanopore shapes can be approximately omitted if the nanopore is small enough (smaller than 0.5 times EMFP in this paper). The ETC anisotropy was discovered for triangle nanopores at a large porosity with a large nanopore size, while there is a similar ETC for small pore size. It confirmed that the structure difference for small pore size may not be seen by electrons in their moving.

Restriction endonuclease analysis of chloroplast DNA in interspecies somatic Hybrids of Petunia.

Science.gov (United States)

Kumar, A; Cocking, E C; Bovenberg, W A; Kool, A J

1982-12-01

Restriction endonuclease cleavage pattern analysis of chloroplast DNA (cpDNA) of three different interspecific somatic hybrid plants revealed that the cytoplasms of the hybrids contained only cpDNA of P. parodii. The somatic hybrid plants analysed were those between P. parodii (wild type) + P. hybrida (wild type); P. parodii (wild type)+P. inflata (cytoplasmic albino mutant); P. parodii (wild type) + P. parviflora (nuclear albino mutant). The presence of only P. parodii chloroplasts in the somatic hybrid of P. parodii + P. inflata is possibly due to the stringent selection used for somatic hybrid production. However, in the case of the two other somatic hybrids P. parodii + P. hybrida and P. parodii + P. parviflora it was not possible to determine whether the presence of only P. parodii chloroplasts in these somatic hybrid plants was due to the nature of the selection schemes used or simply occurred by chance. The relevance of such somatic hybrid material for the study of genomic-cytoplasmic interaction is discussed, as well as the use of restriction endonuclease fragment patterns for the analysis of taxonomic and evolutionary inter-relationships in the genus Petunia.

Spectroscopically forbidden infra-red emission in Au-vertical graphene hybrid nanostructures

Science.gov (United States)

Sivadasan, A. K.; Parida, Santanu; Ghosh, Subrata; Pandian, Ramanathaswamy; Dhara, Sandip

2017-11-01

Implementation of Au nanoparticles (NPs) is a subject for frontier plasmonic research due to its fascinating optical properties. Herein, the present study deals with plasmonic assisted emission properties of Au NPs-vertical graphene (VG) hybrid nanostructures. The influence of effective polarizability of Au NPs on the surface enhanced Raman scattering and luminescence properties is investigated. In addition, a remarkable infra-red emission in the hybrid nanostructures is observed and interpreted on the basis of intra-band transitions in Au NPs. The flake-like nanoporous VG structure is invoked for the generation of additional confined photons to impart additional momentum and a gradient of confined excitation energy towards initiating the intra-band transitions of Au NPs. Integrating Au plasmonic materials in three-dimensional VG nanostructures enhances the light-matter interactions. The present study provides a new adaptable plasmonic assisted pathway for optoelectronic and sensing applications.

Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: complex theoretical and experimental studies.

Science.gov (United States)

Kratochvílová, Irena; Vala, Martin; Weiter, Martin; Špérová, Miroslava; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

2013-01-01

Oligonucleotides conduct electric charge via various mechanisms and their characterization and understanding is a very important and complicated task. In this work, experimental (temperature dependent steady state fluorescence spectroscopy, time-resolved fluorescence spectroscopy) and theoretical (Density Functional Theory) approaches were combined to study charge transfer processes in short DNA/DNA and RNA/DNA duplexes with virtually equivalent sequences. The experimental results were consistent with the theoretical model - the delocalized nature of HOMO orbitals and holes, base stacking, electronic coupling and conformational flexibility formed the conditions for more effective short distance charge transfer processes in RNA/DNA hybrids. RNA/DNA and DNA/DNA charge transfer properties were strongly connected with temperature affected structural changes of molecular systems - charge transfer could be used as a probe of even tiny changes of molecular structures and settings. © 2013. Published by Elsevier B.V. All rights reserved.

Detection of DNA hybridization using graphene-coated black phosphorus surface plasmon resonance sensor

Science.gov (United States)

Pal, Sarika; Verma, Alka; Raikwar, S.; Prajapati, Y. K.; Saini, J. P.

2018-05-01

In this paper, graphene-coated black phosphorus at the metal surface for the detection of DNA hybridization event is numerically demonstrated. The strategy consists of placing the sensing medium on top of black phosphorus-graphene-coated SPR which interfaces with phosphate-buffered saline solution carrying single-stranded DNA. Upon hybridization with its complementary DNA, desorption of the nanostructures takes place and thus enables the sensitive detection of the DNA hybridization event. The proposed sensor exhibits a sensitivity (125 ο/RIU), detection accuracy (0.95) and quality factor (13.62 RIU-1) for complementary DNA. In comparison with other reported papers, our suggested sensor provides much better performance. Thus, this label-free DNA detection platform should spur off new interest towards the use of black phosphorus-graphene-coated SPR interfaces.

A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks.

Science.gov (United States)

Valero, Julián; Pal, Nibedita; Dhakal, Soma; Walter, Nils G; Famulok, Michael

2018-06-01

Biological motors are highly complex protein assemblies that generate linear or rotary motion, powered by chemical energy. Synthetic motors based on DNA nanostructures, bio-hybrid designs or synthetic organic chemistry have been assembled. However, unidirectionally rotating biomimetic wheel motors with rotor-stator units that consume chemical energy are elusive. Here, we report a bio-hybrid nanoengine consisting of a catalytic stator that unidirectionally rotates an interlocked DNA wheel, powered by NTP hydrolysis. The engine consists of an engineered T7 RNA polymerase (T7RNAP-ZIF) attached to a dsDNA nanoring that is catenated to a rigid rotating dsDNA wheel. The wheel motor produces long, repetitive RNA transcripts that remain attached to the engine and are used to guide its movement along predefined ssDNA tracks arranged on a DNA nanotube. The simplicity of the design renders this walking nanoengine adaptable to other biological nanoarchitectures, facilitating the construction of complex bio-hybrid structures that achieve NTP-driven locomotion.

Microfluidic Arrayed Lab-On-A-Chip for Electrochemical Capacitive Detection of DNA Hybridization Events.

Science.gov (United States)

Ben-Yoav, Hadar; Dykstra, Peter H; Bentley, William E; Ghodssi, Reza

2017-01-01

A microfluidic electrochemical lab-on-a-chip (LOC) device for DNA hybridization detection has been developed. The device comprises a 3 × 3 array of microelectrodes integrated with a dual layer microfluidic valved manipulation system that provides controlled and automated capabilities for high throughput analysis of microliter volume samples. The surface of the microelectrodes is functionalized with single-stranded DNA (ssDNA) probes which enable specific detection of complementary ssDNA targets. These targets are detected by a capacitive technique which measures dielectric variation at the microelectrode-electrolyte interface due to DNA hybridization events. A quantitative analysis of the hybridization events is carried out based on a sensing modeling that includes detailed analysis of energy storage and dissipation components. By calculating these components during hybridization events the device is able to demonstrate specific and dose response sensing characteristics. The developed microfluidic LOC for DNA hybridization detection offers a technology for real-time and label-free assessment of genetic markers outside of laboratory settings, such as at the point-of-care or in-field environmental monitoring.

Building a Phylogenetic Tree of the Human and Ape Superfamily Using DNA-DNA Hybridization Data

Science.gov (United States)

Maier, Caroline Alexander

2004-01-01

The study describes the process of DNA-DNA hybridization and the history of its use by Sibley and Alquist in simple, straightforward, and interesting language that students easily understand to create their own phylogenetic tree of the hominoid superfamily. They calibrate the DNA clock and use it to estimate the divergence dates of the various…

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations.

Science.gov (United States)

Oikonomopoulos, Spyros; Wang, Yu Chang; Djambazian, Haig; Badescu, Dunarel; Ragoussis, Jiannis

2016-08-24

To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length. The abundance of the ERCC cDNA molecules sequenced by MinION agreed with their expected concentration. No length or GC content bias was observed. The majority of cDNAs were sequenced as full length. Additionally, a complex cDNA population derived from a human HEK-293 cell line was sequenced on an Illumina HiSeq 2500, PacBio RS II and ONT MinION platforms. We observed that there was a good agreement in the measured cDNA abundance between PacBio RS II and ONT MinION (rpearson = 0.82, isoforms with length more than 700bp) and between Illumina HiSeq 2500 and ONT MinION (rpearson = 0.75). This indicates that the ONT MinION can sequence quantitatively both long and short full length cDNA molecules.

Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers

DEFF Research Database (Denmark)

Yao, Danfeng; Kim, Junyoung; Yu, Fang

2005-01-01

at an intermediate sodium concentration (approximately 100 mM). These effects were mainly ascribed to the electrostatic cross talk among the hybridized DNA molecules and the secondary structure of PCR amplicons. For the negatively charged DNA probes, the hybridization reaction was subjected additionally to the DNA....../DNA electrostatic barrier, particularly in lower ionic strength range (e.g., 10 approximately 150 mM Na(+)). The electrostatic cross talk was shown to be largely reduced if the PNA probe layer was sufficiently diluted by following a strategic templated immobilization method. As a consequence, a pseudo...

Colloidal Au-enhanced surface plasmon resonance imaging: application in a DNA hybridization process

International Nuclear Information System (INIS)

Manera, M G; Spadavecchia, J; Taurino, A; Rella, R

2010-01-01

The detection of the DNA hybridization mechanism using monodispersed gold nanoparticles as labels is an interesting alternative to increase the sensitivity of the SPR imaging technique. DNA-modified Au nanoparticles (DNA-Au NPs) containing single-stranded (ss) portions of DNA were prepared by monitoring their monolayer formation by UV–vis spectroscopy. The hybridization process between specific thio-oligonucleotides immobilized on the DNA–Au NPs and the corresponding complementary strands is reported and compared with the traditional hybridization process on properly self-assembled thin gold films deposited on glass substrates. A remarkable signal amplification is observed, following the incorporation of colloidal Au into a SPR biosensing experiment, resulting in an increased SPR response to DNA–DNA interactions. In particular Fusarium thiolated DNA (5'HS poly(T) 15 ATC CCT CAA AAA CTG CCG CT-3) and trichothecenes complementary DNA (5'-AGC GGC AGT TTT TGA GGG AT-3') sequences have been explored due to their possible application to agro-industry for the control of food quality

Interconnected V2O5 nanoporous network for high-performance supercapacitors.

Science.gov (United States)

Saravanakumar, B; Purushothaman, Kamatchi K; Muralidharan, G

2012-09-26

Vanadium pentoxide (V(2)O(5)) has attracted attention for supercapcitor applications because of its extensive multifunctional properties. In the present study, V(2)O(5) nanoporous network was synthesized via simple capping-agent-assisted precipitation technique and it is further annealed at different temperatures. The effect of annealing temperature on the morphology, electrochemical and structural properties, and stability upon oxidation-reduction cycling has been analyzed for supercapacitor application. We achieved highest specific capacitance of 316 F g(-1) for interconnected V(2)O(5) nanoporous network. This interconnected nanoporous network creates facile nanochannels for ion diffusion and facilitates the easy accessibility of ions. Moreover, after six hundred consecutive cycling processes the specific capacitance has changed only by 24%. A simple cost-effective preparation technique of V(2)O(5) nanoporous network with excellent capacitive behavior, energy density, and stability encourages its possible commercial exploitation for the development of high-performance supercapacitors.

Nanoporous ceramic hybrid materials synthesized by organically modified ceramic precursor with terminal amine group

Energy Technology Data Exchange (ETDEWEB)

Velikova, Nina E.; Vueva, Yuliya E.; Abdallah, Mohammed E.; Ivanova, Yordanka Y.; Dimitriev, Yanko B. [Department of Silicate Technology, University of Chemical Technology and Metallurgy, Sofia (Bulgaria); Salvado, Isabel M.; Fernandes, Maria H. [Ceramic and Glass Engineering Department CICECO, University of Aveiro, Aveiro, (Portugal)

2013-07-01

Nanoporous ceramic materials was functionalized by co-condensation of tetraethyl orthosilicate (TEOS) and different 3-aminopropyltriethoxysilane (APTES) amounts in the presence of amphiphilic triblock copolymer poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (EO{sub 20}PO{sub 70}EO{sub 20} ), who was previously dissolved in acid solution with different acid concentrations. Pluronic P123 was used as structure-directing agent and xylene as a swelling agent. Inorganic salt was introduced in order to improve structure ordering and to tailor framework porosity. The synthesized materials were characterized by scanning electron microscopy (SEM), X-ray diffraction, nuclear magnetic resonance ( {sup 29}Si MAS NMR and {sup 13}C CP MAS NMR), Fourier –transform infrared spectroscopy (FT-IR) and elemental analysis. The results from NMR and FT-IR show that the organic functional group is successfuly incorporated in the silica framework and P123 was successfully extracted. The results from all analyzes prove that the acid concentration has significant influence on the materials morphology and properties. Kay words: sol-gel, mesoporous materials, hybrid materials, as structure-directing agent.

CO_2 capture by amine-functionalized nanoporous materials: A review

International Nuclear Information System (INIS)

Chen, Chao; Kim, Jun; Ahn, Wha-Seung

2014-01-01

Amine-functionalized nanoporous materials can be prepared by the incorporation of diverse organic amine moieties into the pore structures of a range of support materials, such as mesoporous silica and alumina, zeolite, carbon and metal organic frameworks (MOFs), either by direct functionalization or post-synthesis through physical impregnation or grafting. These hybrid materials have great potential for practical applications, such as dry adsorbents for postcombustion CO_2 capture, owing to their high CO_2 capture capacity, high capture selectivity towards CO_2 compared to other gases, and excellent stability. This paper summarizes the preparation methods and CO_2 capture performance based on the equilibrium CO_2 uptake of a range of amine-functionalized nanoporous materials

An electrochemical impedance biosensor for Hg2+ detection based on DNA hydrogel by coupling with DNAzyme-assisted target recycling and hybridization chain reaction.

Science.gov (United States)

Cai, Wei; Xie, Shunbi; Zhang, Jin; Tang, Dianyong; Tang, Ying

2017-12-15

In this work, an electrochemical impedance biosensor for high sensitive detection of Hg 2+ was presented by coupling with Hg 2+ -induced activation of Mg 2+ -specific DNAzyme (Mg 2+ -DNAzyme) for target cycling and hybridization chain reaction (HCR) assembled DNA hydrogel for signal amplification. Firstly, we synthesized two different copolymer chains P1 and P2 by modifying hairpin DNA H3 and H4 with acrylamide polymer, respectively. Subsequently, Hg 2+ was served as trigger to activate the Mg 2+ -DNAzyme for selectively cleavage ribonucleobase-modified substrate in the presence of Mg 2+ . The partial substrate strand could dissociate from DNAzyme structure, and hybridize with capture probe H1 to expose its concealed sequence for further hybridization. With the help of the exposed sequence, the HCR between hairpin DNA H3 and H4 in P1 and P2 was initiated, and assembled a layer of DNA cross-linked hydrogel on the electrode surface. The formed non-conductive DNA hydrogel film could greatly hinder the interfacial electronic transfer which provided a possibility for us to construct a high sensitive impedance biosensor for Hg 2+ detection. Under the optimal conditions, the impedance biosensor showed an excellent sensitivity and selectivity toward Hg 2+ in a concentration range of 0.1pM - 10nM with a detection limit of 0.042pM Moreover, the real sample analysis reveal that the proposed biosensor is capable of discriminating Hg 2+ ions in reliable and quantitative manners, indicating this method has a promising potential for preliminary application in routine tests. Copyright © 2017 Elsevier B.V. All rights reserved.

A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses.

Science.gov (United States)

Yamamoto, F; Yamamoto, M

2004-07-01

We previously developed a PCR-based DNA fingerprinting technique named the Methylation Sensitive (MS)-AFLP method, which permits comparative genome-wide scanning of methylation status with a manageable number of fingerprinting experiments. The technique uses the methylation sensitive restriction enzyme NotI in the context of the existing Amplified Fragment Length Polymorphism (AFLP) method. Here we report the successful conversion of this gel electrophoresis-based DNA fingerprinting technique into a DNA microarray hybridization technique (DNA Microarray MS-AFLP). By performing a total of 30 (15 x 2 reciprocal labeling) DNA Microarray MS-AFLP hybridization experiments on genomic DNA from two breast and three prostate cancer cell lines in all pairwise combinations, and Southern hybridization experiments using more than 100 different probes, we have demonstrated that the DNA Microarray MS-AFLP is a reliable method for genetic and epigenetic analyses. No statistically significant differences were observed in the number of differences between the breast-prostate hybridization experiments and the breast-breast or prostate-prostate comparisons.

Oxford Nanopore MinION Sequencing and Genome Assembly

Directory of Open Access Journals (Sweden)

Hengyun Lu

2016-10-01

Full Text Available The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS technology. The third-generation sequencing (TGS technology, led by Pacific Biosciences (PacBio, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT. MinION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage.

Science.gov (United States)

Cristini, Agnese; Groh, Matthias; Kristiansen, Maiken S; Gromak, Natalia

2018-05-08

R-loops comprise an RNA/DNA hybrid and displaced single-stranded DNA. They play important biological roles and are implicated in pathology. Even so, proteins recognizing these structures are largely undefined. Using affinity purification with the S9.6 antibody coupled to mass spectrometry, we defined the RNA/DNA hybrid interactome in HeLa cells. This consists of known R-loop-associated factors SRSF1, FACT, and Top1, and yet uncharacterized interactors, including helicases, RNA processing, DNA repair, and chromatin factors. We validate specific examples of these interactors and characterize their involvement in R-loop biology. A top candidate DHX9 helicase promotes R-loop suppression and transcriptional termination. DHX9 interacts with PARP1, and both proteins prevent R-loop-associated DNA damage. DHX9 and other interactome helicases are overexpressed in cancer, linking R-loop-mediated DNA damage and disease. Our RNA/DNA hybrid interactome provides a powerful resource to study R-loop biology in health and disease. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Precise fabrication of a 5 nm graphene nanopore with a helium ion microscope for biomolecule detection

Science.gov (United States)

Deng, Yunsheng; Huang, Qimeng; Zhao, Yue; Zhou, Daming; Ying, Cuifeng; Wang, Deqiang

2017-01-01

We report a scalable method to fabricate high-quality graphene nanopores for biomolecule detection using a helium ion microscope (HIM). HIM milling shows promising capabilities for precisely controlling the size and shape, and may allow for the potential production of nanopores at wafer scale. Nanopores could be fabricated at different sizes ranging from 5 to 30 nm in diameter in few minutes. Compared with the current solid-state nanopore fabrication techniques, e.g. transmission electron microscopy, HIM is fast. Furthermore, we investigated the exposure-time dependence of graphene nanopore formation: the rate of pore expansion did not follow a simple linear relationship with exposure time, but a fast expansion rate at short exposure time and a slow rate at long exposure time. In addition, we performed biomolecule detection with our patterned graphene nanopore. The ionic current signals induced by 20-base single-stranded DNA homopolymers could be used as a basis for homopolymer differentiation. However, the charge interaction of homopolymer chains with graphene nanopores, and the conformations of homopolymer chains need to be further considered to improve the accuracy of discrimination.

The strategies of DNA immobilization and hybridization detection mechanism in the construction of electrochemical DNA sensor: A review

Directory of Open Access Journals (Sweden)

Jahwarhar Izuan Abdul Rashid

2017-11-01

Full Text Available In recent years, electrochemical deoxyribonucleic acid (DNA sensor has recently emerged as promising alternative clinical diagnostic devices especially for infectious disease by exploiting DNA recognition events and converting them into an electrochemical signal. This is because the existing DNA diagnostic method possesses certain drawbacks such as time-consuming, expensive, laborious, low selectivity and sensitivity. DNA immobilization strategies and mechanism of electrochemical detection are two the most important aspects that should be considered before developing highly selective and sensitive electrochemical DNA sensor. Here, we focus on some recent strategies for DNA probes immobilization on the surface of electrochemical transducer such as adsorption, covalent bonding and Avidin/Streptavidin-Biotin interaction on the electrode surface for specific interaction with its complementary DNA target. A numerous approach for DNA hybridization detection based electrochemical technique that frequently used including direct DNA electrochemical detection and label based electrochemical (redox-active indicator, enzyme label and nanoparticles were also discussed in aiming to provide general guide for the design of electrochemical DNA sensor. We also discussed the challenges and suggestions to improve the application of electrochemical DNA sensor at point-care setting. Keywords: Electrochemical DNA sensor, DNA immobilization, DNA hybridization, Electrochemical mechanism

A methodology for the preparation of nanoporous polyimide films with low dielectric constants

International Nuclear Information System (INIS)

Jiang Lizhong; Liu Jiugui; Wu Dezhen; Li Hangquan; Jin Riguang

2006-01-01

A method to generate nanoporous polyimide films with low dielectric constants was proposed. The preparation consisted of two steps. Firstly, a polyimide/silica hybrid film was prepared via sol-gel process. Secondly, the hybrid film was treated with hydrofluoric acid to remove the dispersed silica particles, leaving pores with diameters between 20 and 120 nm, depending on the size of silica particles. Both hybrid and porous films were subjected to a variety of characterizations including transmission electron microscopy observation, dielectric constant measurement and tensile strength measurement

Directed self-assembly of nanoporous metallic- and bimetallic nanoparticle thin films

Energy Technology Data Exchange (ETDEWEB)

Pietsch, Torsten [Fachbereich Physik, Universitaet Konstanz (Germany); Gindy, Nabil; Fahmi, Amir [Department of Mechanical, Materials and Manufacturing Engineering, University of Nottingham (United Kingdom)

2010-07-01

Nanoporous thin films attracted considerable interest due to potential applications in optical coatings, catalysis, sensors as well as electronic devices. Recently, such films were prepared by post deposition treatments. The present study is focused on the fabrication of nanoporous thin films via directed self-assembly of hybrid materials. Due to the nature of this process no additional treatments are necessary to develop the pores. Hierarchical nanoporous structures are fabricated directly via deposition of polymer templated Au-nanoparticles onto hydrophilic substrates. These films exhibit two different pore diameters and a total pore density of more than 10{sup 10} holes per cm{sup 2}. Control over the pore size is achieved by changing the molecular weight of the PS-b-P4VP diblock copolymer. Moreover, the porous morphology is used as a template to fabricate bimetallic nanostructured thin films. Such well-defined nanostructures, not only exhibit unique physical properties but also provide control over the hydrophobicity of the coated surfaces.

Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure.

Science.gov (United States)

Gade, Chandrasekhar Reddy; Sharma, Nagendra K

2017-12-15

This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC 5 ) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

The chromosomal constitution of fish hybrid lineage revealed by 5S rDNA FISH.

Science.gov (United States)

Zhang, Chun; Ye, Lihai; Chen, Yiyi; Xiao, Jun; Wu, Yanhong; Tao, Min; Xiao, Yamei; Liu, Shaojun

2015-12-03

The establishment of the bisexual fertile fish hybrid lineage including the allodiploid and allotetraploid hybrids, from interspecific hybridization of red crucian carp (Carassius auratus red var. 2n = 100, 2n = AA) (♀) × common carp (Cyprinus carpio L. 2n = 100, 2n = BB) (♂), provided a good platform to investigate genetic relationship between the parents and their hybrid progenies. The chromosomal inheritance of diploid and allotetraploid hybrid progenies in successive generations, was studied by applying 5S rDNA fluorescence in situ hybridization. Signals of 5S rDNA distinguished the chromosomal constitution of common carp (B-genome) from red crucian carp (A-genome), in which two strong signals were observed on the first submetacentric chromosome, while no major signal was found in common carp. After fish hybridization, one strong signal of 5S rDNA was detected in the same locus on the chromosome of diploid hybrids. As expected, two strong signals were observed in 4nF3 tetraploid hybrids offspring and it is worth mentioning that two strong signals were detected in a separating bivalent of a primary spermatocyte in 4nF3. Furthermore, the mitosis of heterozygous chromosomes was shown normal and stable with blastular tissue histological studies. We revealed that 5S rDNA signal can be applied to discern A-genome from B-genome, and that 5S rDNA bearing chromosomes can be stably passed down in successive generations. Our work provided a significant method in fish breeding and this is important for studies in fish evolutionary biology.

Direct immobilization and hybridization of DNA on group III nitride semiconductors

Energy Technology Data Exchange (ETDEWEB)

Xu Xiaobin; Jindal, Vibhu; Shahedipour-Sandvik, Fatemeh; Bergkvist, Magnus [College of Nanoscale Science and Engineering, University at Albany (SUNY), 255 Fuller Road, Albany, NY 12203 (United States); Cady, Nathaniel C. [College of Nanoscale Science and Engineering, University at Albany (SUNY), 255 Fuller Road, Albany, NY 12203 (United States)], E-mail: ncady@uamail.albany.edu

2009-03-15

A key concern for group III-nitride high electron mobility transistor (HEMT) biosensors is the anchoring of specific capture molecules onto the gate surface. To this end, a direct immobilization strategy was developed to attach single-stranded DNA (ssDNA) to AlGaN surfaces using simple printing techniques without the need for cross-linking agents or complex surface pre-functionalization procedures. Immobilized DNA molecules were stably attached to the AlGaN surfaces and were able to withstand a range of pH and ionic strength conditions. The biological activity of surface-immobilized probe DNA was also retained, as demonstrated by sequence-specific hybridization experiments. Probe hybridization with target ssDNA could be detected by PicoGreen fluorescent dye labeling with a minimum detection limit of 2 nM. These experiments demonstrate a simple and effective immobilization approach for attaching nucleic acids to AlGaN surfaces which can further be used for the development of HEMT-based DNA biosensors.

Immobilization/hybridization of amino-modified DNA on plasma-polymerized allyl chloride

International Nuclear Information System (INIS)

Zhang Zhihong; Feng Chuanliang

2007-01-01

The present work describes the fabrication and characterization of chloride-derivatized polymer coatings prepared by continuous wave (cw) plasma polymerization as adhesion layers in DNA immobilization/hybridization. The stability of plasma-polymerized allyl chloride (ppAC) in H 2 O was characterized by variation of the thickness of polymer films and its wettability was examined by water contact angle technique. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) were used to study polymer matrix properties and oligonucleotide/DNA binding interaction. With the same carrier gas rate and process pressure, plasma polymers deposited at different input powers show various comparable immobilization properties; nevertheless, low input power plasma-polymerized films gives a lower sensitivity toward DNA binding than that from high input power plasma-deposited films. The following DNA immobilization on chloride-functionalized surfaces was found dependence on the macromolecular architecture of the plasma films. The hybridization between probe DNA and total mismatch target DNA shows no non-specific adsorption between target and ppAC

Dendrimer-based biosensor for chemiluminescent detection of DNA hybridization

International Nuclear Information System (INIS)

Liu, P.; Hun, X.; Qing, H.

2011-01-01

We report on a highly sensitive chemiluminescent (CL) biosensor for the sequence-specific detection of DNA using a novel bio barcode DNA probe modified with gold nanoparticles that were covered with a dendrimer. The modified probe is composed of gold nanoparticles, a dendrimer, the CL reagent, and the DNA. The capture probe DNA was immobilized on magnetic beads covered with gold. It first hybridizes with the target DNA and then with one terminal end of the signal DNA on the barcoded DNA probe. CL was generated by adding H 2 O 2 and Co(II) ions as the catalyst. The immobilization of dendrimer onto the gold nanoparticles can significantly enhance sensitivity and gives a detection limit of 6 fmol L -1 of target DNA. (author)

One-step coelectrodeposition-assisted layer-by-layer assembly of gold nanoparticles and reduced graphene oxide and its self-healing three-dimensional nanohybrid for an ultrasensitive DNA sensor.

Science.gov (United States)

Kumarasamy, Jayakumar; Camarada, María Belén; Venkatraman, Dharuman; Ju, Huangxian; Dey, Ramendra Sundar; Wen, Yangping

2018-01-18

A layer-by-layer (LBL) assembly was employed for preparing multilayer thin films with a controlled architecture and composition. In this study, we report the one-step coelectrodeposition-assisted LBL assembly of both gold nanoparticles (AuNPs) and reduced graphene oxide (rGO) on the surface of a glassy carbon electrode (GCE) for the ultrasensitive electrochemical impedance sensing of DNA hybridization. A self-healable nanohybrid thin film with a three-dimensional (3D) alternate-layered nanoarchitecture was obtained by the one-step simultaneous electro-reduction of both graphene oxide and gold chloride in a high acidic medium of H 2 SO 4 using cyclic voltammetry and was confirmed by different characterization techniques. The DNA bioelectrode was prepared by immobilizing the capture DNA onto the surface of the as-obtained self-healable AuNP/rGO/AuNP/GCE with a 3D LBL nanoarchitecture via gold-thiol interactions, which then served as an impedance sensing platform for the label-free ultrasensitive electrochemical detection of DNA hybridization over a wide range from 1.0 × 10 -9 to 1.0 × 10 -13 g ml -1 , a low limit of detection of 3.9 × 10 -14 g ml -1 (S/N = 3), ultrahigh sensitivity, and excellent selectivity. This study presents a promising electrochemical sensing platform for the label-free ultrasensitive detection of DNA hybridization with potential application in cancer diagnostics and the preparation of a self-healable nanohybrid thin film with a 3D alternate-layered nanoarchitecture via a one-step coelectrodeposition-assisted LBL assembly.

Mechanisms of water infiltration into conical hydrophobic nanopores.

Science.gov (United States)

Liu, Ling; Zhao, Jianbing; Yin, Chun-Yang; Culligan, Patricia J; Chen, Xi

2009-08-14

Fluid channels with inclined solid walls (e.g. cone- and slit-shaped pores) have wide and promising applications in micro- and nano-engineering and science. In this paper, we use molecular dynamics (MD) simulations to investigate the mechanisms of water infiltration (adsorption) into cone-shaped nanopores made of a hydrophobic graphene sheet. When the apex angle is relatively small, an external pressure is required to initiate infiltration and the pressure should keep increasing in order to further advance the water front inside the nanopore. By enlarging the apex angle, the pressure required for sustaining infiltration can be effectively lowered. When the apex angle is sufficiently large, under ambient condition water can spontaneously infiltrate to a certain depth of the nanopore, after which an external pressure is still required to infiltrate more water molecules. The unusual involvement of both spontaneous and pressure-assisted infiltration mechanisms in the case of blunt nanocones, as well as other unique nanofluid characteristics, is explained by the Young's relation enriched with the size effects of surface tension and contact angle in the nanoscale confinement.

DNA hybridization kinetics: zippering, internal displacement and sequence dependence.

Science.gov (United States)

Ouldridge, Thomas E; Sulc, Petr; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A

2013-10-01

Although the thermodynamics of DNA hybridization is generally well established, the kinetics of this classic transition is less well understood. Providing such understanding has new urgency because DNA nanotechnology often depends critically on binding rates. Here, we explore DNA oligomer hybridization kinetics using a coarse-grained model. Strand association proceeds through a complex set of intermediate states, with successful binding events initiated by a few metastable base-pairing interactions, followed by zippering of the remaining bonds. But despite reasonably strong interstrand interactions, initial contacts frequently dissociate because typical configurations in which they form differ from typical states of similar enthalpy in the double-stranded equilibrium ensemble. Initial contacts must be stabilized by two or three base pairs before full zippering is likely, resulting in negative effective activation enthalpies. Non-Arrhenius behavior arises because the number of base pairs required for nucleation increases with temperature. In addition, we observe two alternative pathways-pseudoknot and inchworm internal displacement-through which misaligned duplexes can rearrange to form duplexes. These pathways accelerate hybridization. Our results explain why experimentally observed association rates of GC-rich oligomers are higher than rates of AT- rich equivalents, and more generally demonstrate how association rates can be modulated by sequence choice.

Molecular modeling of cationic porphyrin-anthraquinone hybrids as DNA topoisomerase IIβ inhibitors.

Science.gov (United States)

Arba, Muhammad; Ruslin; Ihsan, Sunandar; Tri Wahyudi, Setyanto; Tjahjono, Daryono H

2017-12-01

Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14. We found that the binding of porphyrin hybrids occured through intercalation and groove binding mode in addition interaction with the amino acid residues constituting the active cavity of Topo IIβ. Each porphyrin-Topo IIβ complex was stabilized during 20-ns dynamics simulations. The MM-PBSA free energy calculation shows that the binding affinities of porphyrin hybrids were modified with the number of meso substituent. Interestingly, the affinity of all porphyrin hybrids to Topo IIβ was stronger than that of native ligand (EVP), indicating the potential of the designed porphyrin to be considered in experimental research. Copyright © 2017 Elsevier Ltd. All rights reserved.

Managing the wastewater microbiome: Rapid microbial surveillance using Nanopore DNA sequencing

DEFF Research Database (Denmark)

Andersen, Martin Hjorth; Kirkegaard, Rasmus Hansen; Albertsen, Mads

and lead to process breakdown, leading to increased operational costs and potential environmental hazards[1,2]. With current methods, it is often impossible to predict a system crash before it is too late. Monitoring the microbial community for critical changes is tedious, as the process from sample...... to results generally take several days and requires expert knowledge as well as expensive lab facilities. A faster workflow is therefore necessary to ensure a more efficient wastewater management in the future. Experimental design Protocols were developed with focus on portability, ease-of-use and equipment...... (Oxford Nanopore Technologies, UK). The amplicon libraries were sequenced on a MinION (Oxford Nanopore Technologies, UK) and data for the first 10 minutes of sequencing was base-called on a local laptop, mapped to the MiDAS database using minimap2 and analysed in the R environment using the R package...

Nanoporous Hybrid Electrolytes for High-Energy Batteries Based on Reactive Metal Anodes

KAUST Repository

Tu, Zhengyuan; Zachman, Michael J.; Choudhury, Snehashis; Wei, Shuya; Ma, Lin; Yang, Yuan; Kourkoutis, Lena F.; Archer, Lynden A.

2017-01-01

electrolytes created by infusing conventional liquid electrolytes into nanoporous membranes provide exceptional ability to stabilize Li. Electrochemical cells based on γ-Al2O3 ceramics with pore diameters below a cut-off value above 200 nm exhibit long

Comparison of kDNA PCR-hybridization assay with three PCR methods for canines visceral Leishmaniasis diagnosis

Energy Technology Data Exchange (ETDEWEB)

Pilatti, Marcia M.; Andrade, Antero S.R. [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)], e-mail: marciapilatti@yahoo.com.br, e-mail: antero@cdtn.br; Ferreira, Sidney A. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Parasitologia], e-mail: saninoalmeida@gmail.com

2009-07-01

The sensitivity of the kDNA PCR-Hybridization assay, which uses radioactive DNA probes (labeled with {sup 32}P), was compared with three conventional PCR methods used for canine visceral leishmaniasis diagnosis. All PCR methods had two steps: a first amplification followed by hybridization or by a new amplification (nested or semi nested). Two methods (kDNA PCR-Hybridization and kDNA snPCR) used primers addressed to kinetoplast minicircles and the other two methods to the coding (LnPCR) and intergenic noncoding regions (ITS-1 nPCR) of the ribosomal rRNA genes. The comparison was accomplished in two groups of 23 infected dogs using samples collected by the conjunctival swab procedure. In the Group 1 the DNA was extracted from cotton swabs by phenol-chloroform and in Group 2 by boiling. The most efficient PCR methods in the Group 1 were those based on kDNA targets. The kDNA PCR-Hybridization was able to detect parasites in 22/23 dogs (95.6%) and in 40/46 samples (86.9%). The kDNA snPCR was positive for 21/23 dogs (91.3%) and for 40/46 samples (86.9%). The positivities of the kDNA based methods were significantly higher than the positivities verified for the methods based on ribosomal rRNA genes (p<0.05). In the Group 2 the kDNA PCR- Hybridization showed a better performance detecting parasites in 18/23 dogs (78.3%) and in 31/46 samples (67.4%), significantly higher than the other three methods (p<0.05). The higher sensitivity of the minicircle kDNA based assays reported by others was confirmed in this study and kDNA PCR-Hybridization showed the best sensitivity among the assays evaluated. (author)

Comparison of kDNA PCR-hybridization assay with three PCR methods for canines visceral Leishmaniasis diagnosis

International Nuclear Information System (INIS)

Pilatti, Marcia M.; Andrade, Antero S.R.; Ferreira, Sidney A.

2009-01-01

The sensitivity of the kDNA PCR-Hybridization assay, which uses radioactive DNA probes (labeled with 32 P), was compared with three conventional PCR methods used for canine visceral leishmaniasis diagnosis. All PCR methods had two steps: a first amplification followed by hybridization or by a new amplification (nested or semi nested). Two methods (kDNA PCR-Hybridization and kDNA snPCR) used primers addressed to kinetoplast minicircles and the other two methods to the coding (LnPCR) and intergenic noncoding regions (ITS-1 nPCR) of the ribosomal rRNA genes. The comparison was accomplished in two groups of 23 infected dogs using samples collected by the conjunctival swab procedure. In the Group 1 the DNA was extracted from cotton swabs by phenol-chloroform and in Group 2 by boiling. The most efficient PCR methods in the Group 1 were those based on kDNA targets. The kDNA PCR-Hybridization was able to detect parasites in 22/23 dogs (95.6%) and in 40/46 samples (86.9%). The kDNA snPCR was positive for 21/23 dogs (91.3%) and for 40/46 samples (86.9%). The positivities of the kDNA based methods were significantly higher than the positivities verified for the methods based on ribosomal rRNA genes (p<0.05). In the Group 2 the kDNA PCR- Hybridization showed a better performance detecting parasites in 18/23 dogs (78.3%) and in 31/46 samples (67.4%), significantly higher than the other three methods (p<0.05). The higher sensitivity of the minicircle kDNA based assays reported by others was confirmed in this study and kDNA PCR-Hybridization showed the best sensitivity among the assays evaluated. (author)

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

Science.gov (United States)

Munir, Ahsan; Waseem, Hassan; Williams, Maggie R.; Stedtfeld, Robert D.; Gulari, Erdogan; Tiedje, James M.; Hashsham, Syed A.

2017-01-01

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131). PMID:28555058

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

Directory of Open Access Journals (Sweden)

Ahsan Munir

2017-05-01

Full Text Available Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs. Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131.

Field-based species identification in eukaryotes using real-time nanopore sequencing.

OpenAIRE

Papadopulos, Alexander; Devey, Dion; Helmstetter, Andrew; Parker, Joe

2017-01-01

Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, the generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potenti...

A novel SERRS sandwich-hybridization assay to detect specific DNA target.

Directory of Open Access Journals (Sweden)

Cécile Feuillie

Full Text Available In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR. In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.

Nanoporous thermosetting polymers.

Science.gov (United States)

Raman, Vijay I; Palmese, Giuseppe R

2005-02-15

Potential applications of nanoporous thermosetting polymers include polyelectrolytes in fuel cells, separation membranes, adsorption media, and sensors. Design of nanoporous polymers for such applications entails controlling permeability by tailoring pore size, structure, and interface chemistry. Nanoporous thermosetting polymers are often synthesized via free radical mechanisms using solvents that phase separate during polymerization. In this work, a novel technique for the synthesis of nanoporous thermosets is presented that is based on the reactive encapsulation of an inert solvent using step-growth cross-linking polymerization without micro/macroscopic phase separation. The criteria for selecting such a monomer-polymer-solvent system are discussed based on FTIR analysis, observed micro/macroscopic phase separation, and thermodynamics of swelling. Investigation of resulting network pore structures by scanning electron microscopy (SEM) and small-angle X-ray scattering following extraction and supercritical drying using carbon dioxide showed that nanoporous polymeric materials with pore sizes ranging from 1 to 50 nm can be synthesized by varying the solvent content. The differences in the porous morphology of these materials compared to more common free radically polymerized analogues that exhibit phase separation were evident from SEM imaging. Furthermore, it was demonstrated that the chemical activity of the nanoporous materials obtained by our method could be tailored by grafting appropriate functional groups at the pore interface.

Nanoporous hybrid electrolytes

KAUST Repository

Schaefer, Jennifer L.

2011-01-01

Oligomer-suspended SiO2-polyethylene glycol nanoparticles are studied as porous media electrolytes. At SiO2 volume fractions, , bracketing a critical value y ≈ 0.29, the suspensions jam and their mechanical modulus increase by more than seven orders. For >y, the mean pore diameter is close to the anion size, yet the ionic conductivity remains surprisingly high and can be understood, at all , using a simple effective medium model proposed by Maxwell. SiO 2-polyethylene glycol hybrid electrolytes are also reported to manifest attractive electrochemical stability windows (0.3-6.3 V) and to reach a steady-state interfacial impedance when in contact with metallic lithium. © 2010 The Royal Society of Chemistry.

Three-dimensional bicontinuous nanoporous Au/polyaniline hybrid films for high-performance electrochemical supercapacitors

Science.gov (United States)

Lang, Xingyou; Zhang, Ling; Fujita, Takeshi; Ding, Yi; Chen, Mingwei

2012-01-01

We report three-dimensional bicontinuous nanoporous Au/polyaniline (PANI) composite films made by one-step electrochemical polymerization of PANI shell onto dealloyed nanoporous gold (NPG) skeletons for the applications in electrochemical supercapacitors. The NPG/PANI based supercapacitors exhibit ultrahigh volumetric capacitance (∼1500 F cm-3) and energy density (∼0.078 Wh cm-3), which are seven and four orders of magnitude higher than these of electrolytic capacitors, with the same power density up to ∼190 W cm-3. The outstanding capacitive performances result from a novel nanoarchitecture in which pseudocapacitive PANI shells are incorporated into pore channels of highly conductive NPG, making them promising candidates as electrode materials in supercapacitor devices combing high-energy storage densities with high-power delivery.

Identification of DNA viruses by membrane filter hybridization.

OpenAIRE

Stålhandske, P; Pettersson, U

1982-01-01

The use of membrane filter hybridization for the identification of DNA viruses is described. We designed and used a procedure for identification of herpes simplex virus. This method can discriminate between herpes simplex virus types 1 and 2 in a simple way.

Sensitive detection of mercury and copper ions by fluorescent DNA/Ag nanoclusters in guanine-rich DNA hybridization.

Science.gov (United States)

Peng, Jun; Ling, Jian; Zhang, Xiu-Qing; Bai, Hui-Ping; Zheng, Liyan; Cao, Qiu-E; Ding, Zhong-Tao

2015-02-25

In this work, we designed a new fluorescent oligonucleotides-stabilized silver nanoclusters (DNA/AgNCs) probe for sensitive detection of mercury and copper ions. This probe contains two tailored DNA sequence. One is a signal probe contains a cytosine-rich sequence template for AgNCs synthesis and link sequence at both ends. The other is a guanine-rich sequence for signal enhancement and link sequence complementary to the link sequence of the signal probe. After hybridization, the fluorescence of hybridized double-strand DNA/AgNCs is 200-fold enhanced based on the fluorescence enhancement effect of DNA/AgNCs in proximity of guanine-rich DNA sequence. The double-strand DNA/AgNCs probe is brighter and stable than that of single-strand DNA/AgNCs, and more importantly, can be used as novel fluorescent probes for detecting mercury and copper ions. Mercury and copper ions in the range of 6.0-160.0 and 6-240 nM, can be linearly detected with the detection limits of 2.1 and 3.4 nM, respectively. Our results indicated that the analytical parameters of the method for mercury and copper ions detection are much better than which using a single-strand DNA/AgNCs. Copyright © 2014 Elsevier B.V. All rights reserved.

Hand-assisted hybrid laparoscopic-robotic total proctocolectomy with ileal pouch--anal anastomosis.

Science.gov (United States)

Morelli, Luca; Guadagni, Simone; Mariniello, Maria Donatella; Furbetta, Niccolò; Pisano, Roberta; D'Isidoro, Cristiano; Caprili, Giovanni; Marciano, Emanuele; Di Candio, Giulio; Boggi, Ugo; Mosca, Franco

2015-08-01

Few studies have reported minimally invasive total proctocolectomy with ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC) and familial adenomatous polyposis (FAP). We herein report a novel hand-assisted hybrid laparoscopic-robotic technique for patients with FAP and UC. Between February 2010 and March 2014, six patients underwent hand-assisted hybrid laparoscopic-robotic total proctocolectomy with IPAA. The abdominal colectomy was performed laparoscopically with hand assistance through a transverse suprapubic incision, also used to fashion the ileal pouch. The proctectomy was carried out with the da Vinci Surgical System. The IPAA was hand-sewn through a trans-anal approach. The procedure was complemented by a temporary diverting loop ileostomy. The mean hand-assisted laparoscopic surgery (HALS) time was 154.6 (±12.8) min whereas the mean robotic time was 93.6 (±8.1) min. In all cases, a nerve-sparing proctectomy was performed, and no conversion to traditional laparotomy was required. The mean postoperative hospital stay was 13.2 (±7.4) days. No anastomotic leakage was observed. To date, no autonomic neurological disorders have been observed with a mean of 5.8 (±1.3) bowel movements per day. The hand-assisted hybrid laparoscopic-robotic approach to total proctocolectomy with IPAA has not been previously described. Our report shows the feasibility of this hybrid approach, which surpasses most of the limitations of pure laparoscopic and robotic techniques. Further experience is necessary to refine the technique and fully assess its potential advantages.

Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors

Science.gov (United States)

Star, Alexander; Tu, Eugene; Niemann, Joseph; Gabriel, Jean-Christophe P.; Joiner, C. Steve; Valcke, Christian

2006-01-01

We report carbon nanotube network field-effect transistors (NTNFETs) that function as selective detectors of DNA immobilization and hybridization. NTNFETs with immobilized synthetic oligonucleotides have been shown to specifically recognize target DNA sequences, including H63D single-nucleotide polymorphism (SNP) discrimination in the HFE gene, responsible for hereditary hemochromatosis. The electronic responses of NTNFETs upon single-stranded DNA immobilization and subsequent DNA hybridization events were confirmed by using fluorescence-labeled oligonucleotides and then were further explored for label-free DNA detection at picomolar to micromolar concentrations. We have also observed a strong effect of DNA counterions on the electronic response, thus suggesting a charge-based mechanism of DNA detection using NTNFET devices. Implementation of label-free electronic detection assays using NTNFETs constitutes an important step toward low-cost, low-complexity, highly sensitive and accurate molecular diagnostics. hemochromatosis | SNP | biosensor

Instrumentation for low noise nanopore-based ionic current recording under laser illumination

Science.gov (United States)

Roelen, Zachary; Bustamante, José A.; Carlsen, Autumn; Baker-Murray, Aidan; Tabard-Cossa, Vincent

2018-01-01

We describe a nanopore-based optofluidic instrument capable of performing low-noise ionic current recordings of individual biomolecules under laser illumination. In such systems, simultaneous optical measurements generally introduce significant parasitic noise in the electrical signal, which can severely reduce the instrument sensitivity, critically hindering the monitoring of single-molecule events in the ionic current traces. Here, we present design rules and describe simple adjustments to the experimental setup to mitigate the different noise sources encountered when integrating optical components to an electrical nanopore system. In particular, we address the contributions to the electrical noise spectra from illuminating the nanopore during ionic current recording and mitigate those effects through control of the illumination source and the use of a PDMS layer on the SiNx membrane. We demonstrate the effectiveness of our noise minimization strategies by showing the detection of DNA translocation events during membrane illumination with a signal-to-noise ratio of ˜10 at 10 kHz bandwidth. The instrumental guidelines for noise minimization that we report are applicable to a wide range of nanopore-based optofluidic systems and offer the possibility of enhancing the quality of synchronous optical and electrical signals obtained during single-molecule nanopore-based analysis.

Alpha-Helical Fragaceatoxin C Nanopore Engineered for Double-Stranded and Single-Stranded Nucleic Acid Analysis

NARCIS (Netherlands)

Wloka, Carsten; Mutter, Natalie Lisa; Soskine, Misha; Maglia, Giovanni

2016-01-01

Nanopores are used in single-molecule DNA analysis and sequencing. Herein, we show that Fragaceatoxin C (FraC), an α-helical pore-forming toxin from an actinoporin protein family, can be reconstituted in sphingomyelin-free standard planar lipid bilayers. We engineered FraC for DNA analysis and show

Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool.

Science.gov (United States)

Hoenen, Thomas; Groseth, Allison; Rosenke, Kyle; Fischer, Robert J; Hoenen, Andreas; Judson, Seth D; Martellaro, Cynthia; Falzarano, Darryl; Marzi, Andrea; Squires, R Burke; Wollenberg, Kurt R; de Wit, Emmie; Prescott, Joseph; Safronetz, David; van Doremalen, Neeltje; Bushmaker, Trenton; Feldmann, Friederike; McNally, Kristin; Bolay, Fatorma K; Fields, Barry; Sealy, Tara; Rayfield, Mark; Nichol, Stuart T; Zoon, Kathryn C; Massaquoi, Moses; Munster, Vincent J; Feldmann, Heinz

2016-02-01

Rapid sequencing of RNA/DNA from pathogen samples obtained during disease outbreaks provides critical scientific and public health information. However, challenges exist for exporting samples to laboratories or establishing conventional sequencers in remote outbreak regions. We successfully used a novel, pocket-sized nanopore sequencer at a field diagnostic laboratory in Liberia during the current Ebola virus outbreak.

Thermodynamic framework to assess low abundance DNA mutation detection by hybridization

Science.gov (United States)

Willems, Hanny; Jacobs, An; Hadiwikarta, Wahyu Wijaya; Venken, Tom; Valkenborg, Dirk; Van Roy, Nadine; Vandesompele, Jo; Hooyberghs, Jef

2017-01-01

The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine. PMID:28542229

Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties

Energy Technology Data Exchange (ETDEWEB)

RamIrez, Patricio [Departament de Fisica Aplicada, Universitat Politecnica de Valencia, E-46022 Valencia (Spain); Apel, Pavel Yu [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie street 6, 141980 Dubna (Russian Federation); Cervera, Javier; Mafe, Salvador [Departament de Fisica de la Terra i Termodinamica, Universitat de Valencia, E-46100 Burjassot (Spain)], E-mail: patraho@fis.upv.es

2008-08-06

We present a complete theoretical study of the relationship between the structure (tip shape and dimensions) and function (selectivity and rectification) of asymmetric nanopores on the basis of previous experimental studies. The theoretical model uses a continuum approach based on the Nernst-Planck equations. According to our results, the nanopore transport properties, such as current-voltage (I-V) characteristics, conductance, rectification ratio, and selectivity, are dictated mainly by the shape of the pore tip (we have distinguished bullet-like, conical, trumpet-like, and hybrid shapes) and the concentration of pore surface charges. As a consequence, the nanopore performance in practical applications will depend not only on the base and tip openings but also on the pore shape. In particular, we show that the pore opening dimensions estimated from the pore conductance can be very different, depending on the pore shape assumed. The results obtained can also be of practical relevance for the design of nanopores, nanopipettes, and nanoelectrodes, where the electrical interactions between the charges attached to the nanostructure and the mobile charges confined in the reduced volume of the inside solution dictate the device performance in practical applications. Because single tracks are the elementary building blocks for nanoporous membranes, the understanding and control of their individual properties should also be crucial in protein separation, water desalination, and bio-molecule detection using arrays of identical nanopores.

Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties

International Nuclear Information System (INIS)

RamIrez, Patricio; Apel, Pavel Yu; Cervera, Javier; Mafe, Salvador

2008-01-01

We present a complete theoretical study of the relationship between the structure (tip shape and dimensions) and function (selectivity and rectification) of asymmetric nanopores on the basis of previous experimental studies. The theoretical model uses a continuum approach based on the Nernst-Planck equations. According to our results, the nanopore transport properties, such as current-voltage (I-V) characteristics, conductance, rectification ratio, and selectivity, are dictated mainly by the shape of the pore tip (we have distinguished bullet-like, conical, trumpet-like, and hybrid shapes) and the concentration of pore surface charges. As a consequence, the nanopore performance in practical applications will depend not only on the base and tip openings but also on the pore shape. In particular, we show that the pore opening dimensions estimated from the pore conductance can be very different, depending on the pore shape assumed. The results obtained can also be of practical relevance for the design of nanopores, nanopipettes, and nanoelectrodes, where the electrical interactions between the charges attached to the nanostructure and the mobile charges confined in the reduced volume of the inside solution dictate the device performance in practical applications. Because single tracks are the elementary building blocks for nanoporous membranes, the understanding and control of their individual properties should also be crucial in protein separation, water desalination, and bio-molecule detection using arrays of identical nanopores

Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties.

Science.gov (United States)

Ramírez, Patricio; Apel, Pavel Yu; Cervera, Javier; Mafé, Salvador

2008-08-06

We present a complete theoretical study of the relationship between the structure (tip shape and dimensions) and function (selectivity and rectification) of asymmetric nanopores on the basis of previous experimental studies. The theoretical model uses a continuum approach based on the Nernst-Planck equations. According to our results, the nanopore transport properties, such as current-voltage (I-V) characteristics, conductance, rectification ratio, and selectivity, are dictated mainly by the shape of the pore tip (we have distinguished bullet-like, conical, trumpet-like, and hybrid shapes) and the concentration of pore surface charges. As a consequence, the nanopore performance in practical applications will depend not only on the base and tip openings but also on the pore shape. In particular, we show that the pore opening dimensions estimated from the pore conductance can be very different, depending on the pore shape assumed. The results obtained can also be of practical relevance for the design of nanopores, nanopipettes, and nanoelectrodes, where the electrical interactions between the charges attached to the nanostructure and the mobile charges confined in the reduced volume of the inside solution dictate the device performance in practical applications. Because single tracks are the elementary building blocks for nanoporous membranes, the understanding and control of their individual properties should also be crucial in protein separation, water desalination, and bio-molecule detection using arrays of identical nanopores.

Femtomolar detection of single mismatches by discriminant analysis of DNA hybridization events using gold nanoparticles.

Science.gov (United States)

Ma, Xingyi; Sim, Sang Jun

2013-03-21

Even though DNA-based nanosensors have been demonstrated for quantitative detection of analytes and diseases, hybridization events have never been numerically investigated for further understanding of DNA mediated interactions. Here, we developed a nanoscale platform with well-designed capture and detection gold nanoprobes to precisely evaluate the hybridization events. The capture gold nanoprobes were mono-laid on glass and the detection probes were fabricated via a novel competitive conjugation method. The two kinds of probes combined in a suitable orientation following the hybridization with the target. We found that hybridization efficiency was markedly dependent on electrostatic interactions between DNA strands, which can be tailored by adjusting the salt concentration of the incubation solution. Due to the much lower stability of the double helix formed by mismatches, the hybridization efficiencies of single mismatched (MMT) and perfectly matched DNA (PMT) were different. Therefore, we obtained an optimized salt concentration that allowed for discrimination of MMT from PMT without stringent control of temperature or pH. The results indicated this to be an ultrasensitive and precise nanosensor for the diagnosis of genetic diseases.

Nuclear DNA content of the hybrid plant pathogen Phytophthora andina determined by flow cytometry.

Science.gov (United States)

Wang, Jianan; Presser, Jackson W; Goss, Erica M

2016-09-01

Phytophthora andina is a heterothallic plant pathogen of Andean solanaceous hosts and is an interspecific hybrid of P. infestans and an unknown Phytophthora species. The objective of this study was to estimate the nuclear DNA content of isolates in three clonal lineages of P. andina relative to P. infestans Twelve isolates of P. andina and six isolates of P. infestans were measured for nuclear DNA content by propidium iodide-stained flow cytometry. We found that the DNA content of P. andina was similar but slightly smaller, on average, than that of our sample of P. infestans isolates. This is consistent with P. andina being a homoploid hybrid rather than allopolyploid hybrid. Nuclear DNA content was more variable among a smaller sample of P. infestans isolates, including a putative triploid isolate from Mexico, but small differences in nuclear DNA content were also observed among P. andina isolates. Both species appear to be able to tolerate significant variation in genome size. © 2016 by The Mycological Society of America.

Fluorescent in situ hybridization of mitochondrial DNA and RNA

Czech Academy of Sciences Publication Activity Database

Alán, Lukáš; Zelenka, Jaroslav; Ježek, Jan; Dlasková, Andrea; Ježek, Petr

2010-01-01

Roč. 57, č. 4 (2010), s. 403-408 ISSN 0001-527X R&D Projects: GA ČR GAP302/10/0346; GA ČR GPP304/10/P204; GA AV ČR KJB500110902 Institutional research plan: CEZ:AV0Z50110509 Keywords : mitochondrial DNA and RNA * nucleoids of mitochondrial DNA * molecular beacon fluorescent hybridization probes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.234, year: 2010

Multilayer DNA Origami Packed on Hexagonal and Hybrid Lattices

DEFF Research Database (Denmark)

Ke, Yonggang; Voigt, Niels Vinther; Shih, William M.

2012-01-01

“Scaffolded DNA origami” has been proven to be a powerful and efficient approach to construct two-dimensional or three-dimensional objects with great complexity. Multilayer DNA origami has been demonstrated with helices packing along either honeycomb-lattice geometry or square-lattice geometry....... Here we report successful folding of multilayer DNA origami with helices arranged on a close-packed hexagonal lattice. This arrangement yields a higher density of helical packing and therefore higher resolution of spatial addressing than has been shown previously. We also demonstrate hybrid multilayer...... DNA origami with honeycomb-lattice, square-lattice, and hexagonal-lattice packing of helices all in one design. The availability of hexagonal close-packing of helices extends our ability to build complex structures using DNA nanotechnology....

Multilayer DNA origami packed on hexagonal and hybrid lattices.

Science.gov (United States)

Ke, Yonggang; Voigt, Niels V; Gothelf, Kurt V; Shih, William M

2012-01-25

"Scaffolded DNA origami" has been proven to be a powerful and efficient approach to construct two-dimensional or three-dimensional objects with great complexity. Multilayer DNA origami has been demonstrated with helices packing along either honeycomb-lattice geometry or square-lattice geometry. Here we report successful folding of multilayer DNA origami with helices arranged on a close-packed hexagonal lattice. This arrangement yields a higher density of helical packing and therefore higher resolution of spatial addressing than has been shown previously. We also demonstrate hybrid multilayer DNA origami with honeycomb-lattice, square-lattice, and hexagonal-lattice packing of helices all in one design. The availability of hexagonal close-packing of helices extends our ability to build complex structures using DNA nanotechnology. © 2011 American Chemical Society

Nanoporous gold synthesized by plasma-assisted inert gas condensation: room temperature sintering, nanoscale mechanical properties and stability against high energy electron irradiation

Science.gov (United States)

Weyrauch, S.; Wagner, C.; Suckfuell, C.; Lotnyk, A.; Knolle, W.; Gerlach, J. W.; Mayr, S. G.

2018-02-01

With a plasma assisted gas condensation system it is possible to achieve high-purity nanoporous Au (np-Au) structures with minimal contaminations and impurities. The structures consist of single Au-nanoparticles, which partially sintered together due to their high surface to volume ratio. Through electron microscopy investigations a porosity  >50% with ligament sizes between 20-30 nm was revealed. The elastic modulus of the np-Au was determined via peak force quantitative nanomechanical mapping and resulted in values of 7.5  ±  1.5 GPa. The presented structures partially sintered at room temperature, but proved to be stable to electron irradiation with energies of 7 MeV up to doses of 100 MGy. The electron irradiation stability opens the venue for electron assisted functionalization with biomolecules.

Nanoporous polymer electrolyte

Science.gov (United States)

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

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.

Non-Covalent Fluorescent Labeling of Hairpin DNA Probe Coupled with Hybridization Chain Reaction for Sensitive DNA Detection.

Science.gov (United States)

Song, Luna; Zhang, Yonghua; Li, Junling; Gao, Qiang; Qi, Honglan; Zhang, Chengxiao

2016-04-01

An enzyme-free signal amplification-based assay for DNA detection was developed using fluorescent hairpin DNA probes coupled with hybridization chain reaction (HCR). The hairpin DNAs were designed to contain abasic sites in the stem moiety. Non-covalent labeling of the hairpin DNAs was achieved when a fluorescent ligand was bound to the abasic sites through hydrogen bonding with the orphan cytosine present on the complementary strand, accompanied by quench of ligand fluorescence. As a result, the resultant probes, the complex formed between the hairpin DNA and ligand, showed almost no fluorescence. Upon hybridization with target DNA, the probe underwent a dehybridization of the stem moiety containing an abasic site. The release of ligand from the abasic site to the solution resulted in an effective fluorescent enhancement, which can be used as a signal. Compared with a sensing system without HCR, a 20-fold increase in the sensitivity was achieved using the sensing system with HCR. The fluorescent intensity of the sensing system increased with the increase in target DNA concentration from 0.5 nM to 100 nM. A single mismatched target ss-DNA could be effectively discriminated from complementary target DNA. Genotyping of a G/C single-nucleotide polymorphism of polymerase chain reaction (PCR) products was successfully demonstrated with the sensing system. Therefore, integrating HCR strategy with non-covalent labeling of fluorescent hairpin DNA probes provides a sensitive and cost-effective DNA assay. © The Author(s) 2016.

Sensitive electrochemical monitoring of nucleic acids coupling DNA nanostructures with hybridization chain reaction

International Nuclear Information System (INIS)

Zhuang, Junyang; Fu, Libing; Xu, Mingdi; Yang, Huanghao; Chen, Guonan; Tang, Dianping

2013-01-01

Graphical abstract: -- Highlights: •A new signal-on metallobioassay was developed for detection of nucleic acids. •Target-triggered long-range self-assembled DNA nanostructures are used for amplification of electronic signal. •Hybridization chain reaction is utilized for construction of long-range DNA nanostructures. -- Abstract: Methods based on metal nanotags have been developed for metallobioassay of nucleic acids, but most involve complicated labeling or stripping procedures and are unsuitable for routine use. Herein, we report the proof-of-concept of a novel and label-free metallobioassay for ultrasensitive electronic determination of human immunodeficiency virus (HIV)-related gene fragments at an ultralow concentration based on target-triggered long-range self-assembled DNA nanostructures and DNA-based hybridization chain reaction (HCR). The signal is amplified by silver nanotags on the DNA duplex. The assay mainly consists of capture probe, detection probe, and two different DNA hairpins. In the presence of target DNA, the capture probe immobilized on the sensor sandwiches target DNA with the 3′ end of detection probe. Another exposed part of detection probe at the 5′ end opens two alternating DNA hairpins in turn, and propagates a chain reaction of hybridization events to form a nicked double-helix. Finally, numerous silver nanotags are immobilized onto the long-range DNA nanostructures, each of which produces a strong electronic signal within the applied potentials. Under optimal conditions, the target-triggered long-range DNA nanostructures present good electrochemical behaviors for the detection of HIV DNA at a concentration as low as 0.5 fM. Importantly, the outstanding sensitivity can make this approach a promising scheme for development of next-generation DNA sensors without the need of enzyme labeling or fluorophore labeling

Programmable display of DNA-protein chimeras for controlling cell-hydrogel interactions via reversible intermolecular hybridization.

Science.gov (United States)

Zhang, Zhaoyang; Li, Shihui; Chen, Niancao; Yang, Cheng; Wang, Yong

2013-04-08

Extensive studies have been recently carried out to achieve dynamic control of cell-material interactions primarily through physicochemical stimulation. The purpose of this study was to apply reversible intermolecular hybridization to program cell-hydrogel interactions in physiological conditions based on DNA-antibody chimeras and complementary oligonucleotides. The results showed that DNA oligonucleotides could be captured to and released from the immobilizing DNA-functionalized hydrogels with high specificity via DNA hybridization. Accordingly, DNA-antibody chimeras were captured to the hydrogels, successfully inducing specific cell attachment. The cell attachment to the hydrogels reached the plateau at approximately half an hour after the functionalized hydrogels and the cells were incubated together. The attached cells were rapidly released from the bound hydrogels when triggering complementary oligonucleotides were introduced to the system. However, the capability of the triggering complementary oligonucleotides in releasing cells was affected by the length of intermolecular hybridization. The length needed to be at least more than 20 base pairs in the current experimental setting. Notably, because the procedure of intermolecular hybridization did not involve any harsh condition, the released cells maintained the same viability as that of the cultured cells. The functionalized hydrogels also exhibited the potential to catch and release cells repeatedly. Therefore, this study demonstrates that it is promising to regulate cell-material interactions dynamically through the DNA-programmed display of DNA-protein chimeras.

A Novel Method for Rapid Hybridization of DNA to a Solid Support

Science.gov (United States)

Pettersson, Erik; Ahmadian, Afshin; Ståhl, Patrik L.

2013-01-01

Here we present a novel approach entitled Magnetic Forced Hybridization (MFH) that provides the means for efficient and direct hybridization of target nucleic acids to complementary probes immobilized on a glass surface in less than 15 seconds at ambient temperature. In addition, detection is carried out instantly since the beads become visible on the surface. The concept of MFH was tested for quality control of array manufacturing, and was combined with a multiplex competitive hybridization (MUCH) approach for typing of Human Papilloma Virus (HPV). Magnetic Forced Hybridization of bead-DNA constructs to a surface achieves a significant reduction in diagnostic testing time. In addition, readout of results by visual inspection of the unassisted eye eliminates the need for additional expensive instrumentation. The method uses the same set of beads throughout the whole process of manipulating and washing DNA constructs prior to detection, as in the actual detection step itself. PMID:23950946

Facile fabrication of superhydrophobic hybrid nanotip and nanopore arrays as surface-enhanced Raman spectroscopy substrates

Science.gov (United States)

Li, Yuxin; Li, Juan; Wang, Tiankun; Zhang, Zhongyue; Bai, Yu; Hao, Changchun; Feng, Chenchen; Ma, Yingjun; Sun, Runguang

2018-06-01

We demonstrate the fabrication of superhydrophobic hybrid nanotip and nanopore arrays (NTNPAs) that can act as sensitive surface-enhanced Raman spectroscopy (SERS) substrates. The large-area substrates were fabricated by following a facile, low-cost process consisting of the one-step voltage-variation anodization of Al foil, followed by Ag nanoparticle deposition and fluorosilane (FS) modification. Uniformly distributed, large-area (5 × 5 cm2) NTNPAs can be obtained rapidly by anodizing Al foil for 1560 s followed by Ag deposition for 400 s, which showed good SERS reproducibility as using1 μM Rhodamine 6G (R6G) as analyte. SERS performances of superhydrophobic NTNPAs with different FS modification and Ag nanoparticle deposition orders were also studied. The nanosamples with FS modification followed by Ag nanoparticle deposition (FS-Ag) showed better SERS sensitivity than the nanosamples with Ag nanoparticle deposition followed by FS modification (Ag-FS). The detection limit of a directly dried R6G droplet can reach 10-8 M on the FS-Ag nanosamples. The results can help create practical high sensitive SERS substrates, which can be used in developing advanced bio- and chemical sensors.

Tuneable graphene nanopores for single biomolecule detection.

Science.gov (United States)

Al-Dirini, Feras; Mohammed, Mahmood A; Hossain, Md Sharafat; Hossain, Faruque M; Nirmalathas, Ampalavanapillai; Skafidas, Efstratios

2016-05-21

Solid-state nanopores are promising candidates for next generation DNA and protein sequencing. However, once fabricated, such devices lack tuneability, which greatly restricts their biosensing capabilities. Here we propose a new class of solid-state graphene-based nanopore devices that exhibit a unique capability of self-tuneability, which is used to control their conductance, tuning it to levels comparable to the changes caused by the translocation of a single biomolecule, and hence, enabling high detection sensitivities. Our presented quantum simulation results suggest that the smallest amino acid, glycine, when present in water and in an aqueous saline solution can be detected with high sensitivity, up to a 90% change in conductance. Our results also suggest that passivating the device with nitrogen, making it an n-type device, greatly enhances its sensitivity, and makes it highly sensitive to not only the translocation of a single biomolecule, but more interestingly to intramolecular electrostatics within the biomolecule. Sensitive detection of the carboxyl group within the glycine molecule, which carries a charge equivalent to a single electron, is achieved with a conductance change that reaches as high as 99% when present in an aqueous saline solution. The presented findings suggest that tuneable graphene nanopores, with their capability of probing intramolecular electrostatics, could pave the way towards a new generation of single biomolecule detection devices.

Hybrid video-assisted and limited open (VALO) resection of superior sulcus tumors.

Science.gov (United States)

Nun, Alon Ben; Simansky, David; Rokah, Merav; Zeitlin, Nona; Avi, Roni Ben; Soudack, Michalle; Golan, Nir; Apel, Sarit; Bar, Jair; Yelin, Alon

2016-06-01

To compare the postoperative recovery of patients with superior sulcus tumors (Pancoast tumors) following conventional open surgery vs. a hybrid video-assisted and limited open approach (VALO). The subjects of this retrospective study were 20 patients we operated on to resect a Pancoast tumor. All patients received induction chemo-radiation followed by surgery, performed via either a conventional thoracotomy approach (n = 10) or the hybrid VALO approach (n = 10). In the hybrid VALO group, lobectomy and internal chest wall preparation were performed using a video technique, with rib resection and specimen removal through a limited incision. There was no mortality in either group. Two patients from the thoracotomy group required mechanical ventilation, but there was no major morbidity in the hybrid VALO group. The operative times were similar for the two procedures. The average length of hospital stay was shorter and the average pain scores were significantly lower in the hybrid VALO group. The incidence of chronic pain was 10 % in the hybrid VALO group vs. 50 % in the thoracotomy group. Hybrid VALO resection of Pancoast tumors is feasible and safe, resulting in faster patient recovery and a significantly lower incidence of severe chronic pain than open thoracotomy. We conclude that centers experienced with video-assisted lobectomy should consider hybrid VALO surgery as the procedure of choice for Pancoast tumors.

The chloroplast and mitochondrial DNA type are correlated with the nuclear composition of somatic hybrid calli of Solanum tuberosum and Nicotiana plumbaginifolia.

Science.gov (United States)

Wolters, A M; Koornneef, M; Gilissen, L J

1993-09-01

This paper describes the analysis of chloroplast (cp) DNA and mitochondrial (mt) DNA in 21 somatic hybrid calli of Solanum tuberosum and Nicotiana plumbaginifolia by means of Southern-blot hybridization. Each of these calli contained only one type of cpDNA; 14 had the N. plumbaginifolia (Np) type and seven the S. tuberosum (St) type. N. plumbaginifolia cpDNA was present in hybrids previously shown to contain predominantly N. plumbaginifolia chromosomes whereas hybrids in which S. tuberosum chromosomes predominated possessed cpDNA from potato. We have analyzed the mtDNA of these 21 somatic hybrid calli using four restriction enzyme/probe combinations. Most fusion products had only, or mostly, mtDNA fragments from the parent that predominated in the nucleus. The hybrids containing mtDNA fragments from only one parent (and new fragments) also possessed chloroplasts from the same species. The results suggest the existence of a strong nucleo-cytoplasmic incongruity which affects the genome composition of somatic hybrids between distantly related species.

An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays

Directory of Open Access Journals (Sweden)

Laurenzi Ian J

2009-12-01

Full Text Available Abstract Background Although oligonucleotide microarray technology is ubiquitous in genomic research, reproducibility and standardization of expression measurements still concern many researchers. Cross-hybridization between microarray probes and non-target ssDNA has been implicated as a primary factor in sensitivity and selectivity loss. Since hybridization is a chemical process, it may be modeled at a population-level using a combination of material balance equations and thermodynamics. However, the hybridization reaction network may be exceptionally large for commercial arrays, which often possess at least one reporter per transcript. Quantification of the kinetics and equilibrium of exceptionally large chemical systems of this type is numerically infeasible with customary approaches. Results In this paper, we present a robust and computationally efficient algorithm for the simulation of hybridization processes underlying microarray assays. Our method may be utilized to identify the extent to which nucleic acid targets (e.g. cDNA will cross-hybridize with probes, and by extension, characterize probe robustnessusing the information specified by MAGE-TAB. Using this algorithm, we characterize cross-hybridization in a modified commercial microarray assay. Conclusions By integrating stochastic simulation with thermodynamic prediction tools for DNA hybridization, one may robustly and rapidly characterize of the selectivity of a proposed microarray design at the probe and "system" levels. Our code is available at http://www.laurenzi.net.

Structured nanoporous surfaces from hybrid block copolymer micelle films with metal ions

International Nuclear Information System (INIS)

Kim, Minsoo P; Yi, Gi-Ra; Kim, Hyeong Jun; Kim, Bumjoon J

2015-01-01

We present a novel method for producing structured nanoporous thin films using block copolymer (BCP) micelles loaded with metallic ions. The BCP micellar thin films containing gold (Au) ions were prepared by spin-coating poly(styrene-block-4-vinylpyridine) (PS-b-P4VP) micelle solutions in which Au precursors (AuCl 4 − ) were selectively loaded onto the P4VP core. When the micellar films were exposed to cetyltrimethylammonium bromide (CTAB) solutions, the Au precursors were selectively extracted from the P4VP domains due to their strong electrostatic interaction with CTAB, leading to the formation of pores in the micelles. Consequently, regularly patterned nanoporous surfaces were formed. By controlling the molecular weight (M n ) of PS-b-P4VP and the amount of Au precursors (λ) that were loaded in the P4VP domains, the pore size and depth could be tuned precisely. In particular, when a sufficient amount of Au precursors was loaded (λ  ≥ 0.3), the porous surface nanostructure was well developed. In addition, the pore size and depth of the nanostructure increased as the λ value increased. For instance, when the λ value increased from 0.3 to 1.0, the pore size increased from 22.8 nm to 28.8 nm, and the pore depth increased from 2.1 nm to 3.2 nm. Interestingly, the transition from the nonporous structures to the porous structures in the micellar film could be reversibly controlled by adding and removing the Au precursors in the film. Moreover, our method for the preparation of nanoporous films can be extended to micellar film by incorporating other metal ions such as silver (Ag) and iron (Fe). (paper)

Multiway study of hybridization in nanoscale semiconductor labeled DNA based on fluorescence resonance energy transfer

DEFF Research Database (Denmark)

Gholami, Somayeh; Kompany Zare, Mohsen

2013-01-01

donor-QD acceptor) upon hybridization with a label free target was monitored by two-dimensional photoluminescence excitation spectroscopy (2D-PLE). Detection of a target oligonucleotide strand, using sandwiched nanoassembly in a separation-free format, was performed with the appearance of a new feature...... and model based analysis of 2D-PLE data was implemented by means of PAR-AFAC and hard trilinear decomposition (HTD), allowing to fit a proper model for FRET-based sandwich DNA hybridization systems. This study is the first successful application of a multiway chemometric technique to consider FRET based DNA...... hybridization in sandwiched nanoassemblies. A multi-equilibria model was properly fitted to the data and confirmed there is a competition between ternary and binary complex formation. Equilibrium constants of DNA hybridization in sandwiched nanoassemblies were estimated for the first time. Equilibrium constants...

Influence of DNA treatments on Southern blot hybridization analysis ...

African Journals Online (AJOL)

STORAGESEVER

2008-06-03

Jun 3, 2008 ... DNA samples obtained by a non-phenol/chloroform isolation method, from three races of Fusarium oxysporum f. sp. lycopersici ... Key words: Fusarium oxysporum, DIG-IGS Probe, Southern hybridization. INTRODUCTION .... Detection of Fusarium spp in plants with monoclonal antibody. Ann. Phytopathol.

Optical reflectance studies of highly specular anisotropic nanoporous (111) InP membrane

International Nuclear Information System (INIS)

Steele, J A; Lewis, R A; Sirbu, L; Enachi, M; Tiginyanu, I M; Skuratov, V A

2015-01-01

High-precision optical angular reflectance measurements are reported for a specular anisotropic nanoporous (111) InP membrane prepared by doping-assisted wet-electrochemical etching. The membrane surface morphology was investigated using scanning electron microscope imaging and revealed a quasi-uniform and self-organized nanoporous network consisting of semiconductor ‘islands’ in the sub-wavelength regime. The optical response of the nanoporous InP surface was studied at 405 nm (740 THz; UV), 633 nm (474 THz; VIS) and 1064 nm (282 THz; NIR), and exhibited a retention of basic macro-dielectric properties. Refractive index determinations demonstrate an optical anisotropy for the membrane which is strongly dependent on the wavelength of incident light, and exhibits an interesting inversion (positive anisotropy to negative) between 405 and 633 nm. The inversion of optical anisotropy is attributed to a strongly reduced ‘metallic’ behaviour in the membrane when subject to above-bandgap illumination. For the simplest case of sub-bandgap incident irradiation, the optical properties of the nanoporous InP sample are analysed in terms of an effective refractive index n eff and compared to effective media approximations. (invited article)

Hybrid-hybrid matrix structural refinement of a DNA three-way junction from 3D NOESY-NOESY

International Nuclear Information System (INIS)

Thiviyanathan, Varatharasa; Luxon, Bruce A.; Leontis, Neocles B.; Illangasekare, Nishantha; Donne, David G.; Gorenstein, David G.

1999-01-01

Homonuclear 3D NOESY-NOESY has shown great promise for the structural refinement of large biomolecules. A computationally efficient hybrid-hybrid relaxation matrix refinement methodology, using 3D NOESY-NOESY data, was used to refine the structure of a DNA three-way junction having two unpaired bases at the branch point of the junction. The NMR data and the relaxation matrix refinement confirm that the DNA three-way junction exists in a folded conformation with two of the helical stems stacked upon each other. The third unstacked stem extends away from the junction, forming an acute angle (∼60 deg.) with the stacked stems. The two unpaired bases are stacked upon each other and are exposed to the solvent. Helical parameters for the bases in all three strands show slight deviations from typical values expected for right-handed B-form DNA. Inter-nucleotide imino-imino NOEs between the bases at the branch point of the junction show that the junction region is well defined. The helical stems show mobility (± 20 deg.) indicating dynamic processes around the junction region. The unstacked helical stem adjacent to the unpaired bases shows greater mobility compared to the other two stems. The results from this study indicate that the 3D hybrid-hybrid matrix MORASS refinement methodology, by combining the spectral dispersion of 3D NOESY-NOESY and the computational efficiency of 2D refinement programs, provides an accurate and robust means for structure determination of large biomolecules. Our results also indicate that the 3D MORASS method gives higher quality structures compared to the 2D complete relaxation matrix refinement method

Development of Ionic Liquid Modified Disposable Graphite Electrodes for Label-Free Electrochemical Detection of DNA Hybridization Related to Microcystis spp.

Directory of Open Access Journals (Sweden)

Ceren Sengiz

2015-09-01

Full Text Available In this present study, ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate (IL modified pencil graphite electrode (IL-PGEs was developed for electrochemical monitoring of DNA hybridization related to Microcystis spp. (MYC. The characterization of IL-PGEs was performed using microscopic and electrochemical techniques. DNA hybridization related to MYC was then explored at the surface of IL-PGEs using differential pulse voltammetry (DPV technique. After the experimental parameters were optimized, the sequence-selective DNA hybridization related to MYC was performed in the case of hybridization between MYC probe and its complementary DNA target, noncomplementary (NC or mismatched DNA sequence (MM, or and in the presence of mixture of DNA target: NC (1:1 and DNA target: MM (1:1.

Hydrophilic nanoporous materials

DEFF Research Database (Denmark)

2010-01-01

The present application discloses a method for preparing and rendering hydrophilic a nanoporous material of a polymer matrix which has a porosity of 0.1-90 percent (v/v), such that the ratio between the final water absorption (percent (w/w)) and the porosity (percent (v/v)) is at least 0.05, the ......The present application discloses a method for preparing and rendering hydrophilic a nanoporous material of a polymer matrix which has a porosity of 0.1-90 percent (v/v), such that the ratio between the final water absorption (percent (w/w)) and the porosity (percent (v/v)) is at least 0.......05, the method comprising the steps of: (a) preparing a precursor material comprising at least one polymeric component and having a first phase and a second phase; (b) removal of at least a part of the first phase of the precursor material prepared in step (a) so as to leave behind a nanoporous material...... of the polymer matrix; (c) irradiating at least a part of said nanoporous material with light of a wave length of in the range of 250-400 nm (or 200-700 nm) in the presence of oxygen and/or ozone. Corresponding hydrophilic nanoporous materials are also disclosed. L...

Nanopore formation on Au coated pyramid under electron beam irradiations (plasmonic nanopore on pyramid

Directory of Open Access Journals (Sweden)

Seong Soo Choi

2016-03-01

Full Text Available There have been tremendous interests about the single molecule analysis using a sold-state nanopore. The solid-state nanopore can be fabricated either by drilling technique, or diffusion technique by using electron beam irradiations. The solid-state SiN nanopore device with electrical detection technique recently fabricated, however, the solid-state Au nanopore with optical detection technique can be better utilized as the next generation single molecule sensor. In this report, the nanometer size openings with its size less than 10 nm on the diffused membrane on the 200 nm Au pyramid were fabricated by using field emission scanning electron microscopy (FESEM electron beam irradiations, transmission electron microscopy (TEM, etc. After the sample was being kept under a room environment for several months, several Au (111 clusters with ~6 nm diameter formed via Ostwald ripening are observed using a high resolution TEM imaging. The nanopore with Au nanoclusters on the diffused membrane can be utilized as an optical nanopore device. Keywords: Electron beam irradiation, Surface diffusion, Carbon contamination, Au cluster, Ostwald ripening

rDNA genetic imbalance and nucleolar chromatin restructuring is induced by distant hybridization between Raphanus sativus and Brassica alboglabra.

Directory of Open Access Journals (Sweden)

Hong Long

Full Text Available The expression of rDNA in hybrids inherited from only one progenitor refers to nucleolar dominance. The molecular basis for choosing which genes to silence remains unclear. We report genetic imbalance induced by distant hybridization correlates with formation of rDNA genes (NORs in the hybrids between Raphanus sativus L. and Brassica alboglabra Bailey. Moreover, increased CCGG methylation of rDNA in F1 hybrids is concomitant with Raphanus-derived rDNA gene silencing and rDNA transcriptional inactivity revealed by nucleolar configuration restriction. Newly formed rDNA gene locus occurred through chromosomal in F1 hybrids via chromosomal imbalance. NORs are gained de novo, lost, and/or transposed in the new genome. Inhibition of methyltransferases leads to changes in nucleolar architecture, implicating a key role of methylation in control of nucleolar dominance and vital nucleolar configuration transition. Our findings suggest that gene imbalance and methylation-related chromatin restructuring is important for rDNA gene silencing that may be crucial for synthesis of specific proteins.

DNA assisted self-assembly of PAMAM dendrimers.

Science.gov (United States)

Mandal, Taraknath; Kumar, Mattaparthi Venkata Satish; Maiti, Prabal K

2014-10-09

We report DNA assisted self-assembly of polyamidoamine (PAMAM) dendrimers using all atom Molecular Dynamics (MD) simulations and present a molecular level picture of a DNA-linked PAMAM dendrimer nanocluster, which was first experimentally reported by Choi et al. (Nano Lett., 2004, 4, 391-397). We have used single stranded DNA (ssDNA) to direct the self-assembly process. To explore the effect of pH on this mechanism, we have used both the protonated (low pH) and nonprotonated (high pH) dendrimers. In all cases studied here, we observe that the DNA strand on one dendrimer unit drives self-assembly as it binds to the complementary DNA strand present on the other dendrimer unit, leading to the formation of a DNA-linked dendrimer dimeric complex. However, this binding process strongly depends on the charge of the dendrimer and length of the ssDNA. We observe that the complex with a nonprotonated dendrimer can maintain a DNA length dependent inter-dendrimer distance. In contrast, for complexes with a protonated dendrimer, the inter-dendrimer distance is independent of the DNA length. We attribute this observation to the electrostatic complexation of a negatively charged DNA strand with the positively charged protonated dendrimer.

Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases

International Nuclear Information System (INIS)

Ahmed, Towfiq; Haraldsen, Jason T; Balatsky, Alexander V; Rehr, John J; Di Ventra, Massimiliano; Schuller, Ivan

2014-01-01

Nanopore-based sequencing has demonstrated a significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multilayered graphene-based nanopore device architecture for the recognition of single biomolecules. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to-noise ratio and the accuracy, we implement a new ‘multi-point cross-correlation’ technique for identification of DNA bases or other molecules on the single molecular level. We demonstrate that the cross-correlations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multilayered graphene nanopore system to illustrate the advantages of the proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology. (paper)

Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases

Science.gov (United States)

Ahmed, Towfiq; Haraldsen, Jason T.; Rehr, John J.; Di Ventra, Massimiliano; Schuller, Ivan; Balatsky, Alexander V.

2014-03-01

Nanopore-based sequencing has demonstrated a significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multilayered graphene-based nanopore device architecture for the recognition of single biomolecules. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to-noise ratio and the accuracy, we implement a new ‘multi-point cross-correlation’ technique for identification of DNA bases or other molecules on the single molecular level. We demonstrate that the cross-correlations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multilayered graphene nanopore system to illustrate the advantages of the proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology.

Graphene Nanopres for DNA Fingerprinting

Science.gov (United States)

Ahmed, Towfiq; Balatsky, Alexander V.; Haraldsen, J. T.; Schuller, Ivan K.; di Ventra, M.; Wikfeldt, K. T.

2013-03-01

The recent progress in nanopore experiments with transverse current is important for the development of fast, accurate and cheap finger-printing techniques for single nucleotide. Despite its enormous potential for the next generation DNA sequencing technology, the presence of large noise in the temporal spectrum of transverse current remains a big challenge for getting highly accurate interpretation of data. In this paper we present our abinitio calculations, and propose graphene based device for DNA fingerprinting. We calculate transmission current through graphene for each DNA base (A,C,G,T). As shown in our work, a proper time-series analysis of a signal provides a higher quality information in identifying single bio-molecule is translocating through the nanopores. This work is supported by LANL, Nordita, US DOE, AFOSR, and NIH.

DNA Sequencing by Capillary Electrophoresis

Science.gov (United States)

Karger, Barry L.; Guttman, Andras

2009-01-01

Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

Tail-labelling of DNA probes using modified deoxynucleotide triphosphates and terminal deoxynucleotidyl tranferase. Application in electrochemical DNA hybridization and protein-DNA binding assays

Czech Academy of Sciences Publication Activity Database

Horáková Brázdilová, Petra; Macíčková-Cahová, Hana; Pivoňková, Hana; Špaček, Jan; Havran, Luděk; Hocek, Michal; Fojta, Miroslav

2011-01-01

Roč. 9, č. 5 (2011), s. 1366-1371 ISSN 1477-0520 R&D Projects: GA MŠk(CZ) LC06035; GA MŠk(CZ) LC512; GA AV ČR(CZ) IAA400040901 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : DNA tail- labelling * protein-DNA binding * DNA hybridization Subject RIV: BO - Biophysics Impact factor: 3.696, year: 2011

Non-uniform binding of single-stranded DNA binding proteins to hybrids of single-stranded DNA and single-walled carbon nanotubes observed by atomic force microscopy in air and in liquid

Energy Technology Data Exchange (ETDEWEB)

Umemura, Kazuo, E-mail: meicun2006@163.com; Ishizaka, Kei; Nii, Daisuke; Izumi, Katsuki

2016-12-01

Highlights: • Conjugates of protein, DNA, and SWNTs were observed by AFM in liquid. • Non-uniform binding of proteins was visualized in liquid. • Thickness of DNA molecules on SWNT surfaces was well characterized in liquid. - Abstract: Using atomic force spectroscopy (AFM), we observed hybrids of single-stranded DNA (ssDNA) and single-walled carbon nanotubes (SWNTs) with or without protein molecules in air and in an aqueous solution. This is the first report of ssDNA–SWNT hybrids with proteins in solution analyzed by AFM. In the absence of protein, the height of the ssDNA–SWNT hybrids was 1.1 ± 0.3 nm and 2.4 ± 0.6 nm in air and liquid, respectively, suggesting that the ssDNA molecules adopted a flexible structure on the SWNT surface. In the presence of single-stranded DNA binding (SSB) proteins, the heights of the hybrids in air and liquid increased to 6.4 ± 3.1 nm and 10.0 ± 4.5 nm, respectively. The AFM images clearly showed binding of the SSB proteins to the ssDNA–SWNT hybrids. The morphology of the SSB–ssDNA–SWNT hybrids was non-uniform, particularly in aqueous solution. The variance of hybrid height was quantitatively estimated by cross-section analysis along the long-axis of each hybrid. The SSB–ssDNA–SWNT hybrids showed much larger variance than the ssDNA–SWNT hybrids.

Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies

KAUST Repository

Lundberg, Erik P.

2011-09-27

We demonstrate the stepwise assembly of a fully addressable polycyclic DNA hexagon nanonetwork for the preparation of a four-ring system, one of the biggest networks yet constructed from tripodal building blocks. We find that the yield exhibits a distinct upper level <100%, a fundamental problem of thermodynamic DNA assembly that appears to have been overlooked in the DNA nanotechnology literature. A simplistic model based on a single step-yield parameter y can quantitatively describe the total yield of DNA assemblies in one-pot reactions as Y = yduplex n, with n the number of hybridization steps. Experimental errors introducing deviations from perfect stoichiometry and the thermodynamics of hybridization equilibria contribute to decreasing the value of yduplex (on average y = 0.96 for our 10 base pair hybridization). For the four-ring system (n = 31), the total yield is thus less than 30%, which is clearly unsatisfactory if bigger nanoconstructs of this class are to be designed. Therefore, we introduced site-specific click chemistry for making and purifying robust building blocks for future modular constructs of larger assemblies. Although the present yield of this robust module was only about 10%, it demonstrates a first step toward a general fabrication approach. Interestingly, we find that the click yields follow quantitatively a binomial distribution, the predictability of which indicates the usefulness of preparing pools of pure and robust building blocks in this way. The binomial behavior indicates that there is no interference between the six simultaneous click reactions but that step-yield limiting factors such as topological constraints and Cu(I) catalyst concentration are local and independent. © 2011 American Chemical Society.

Atomistic details of the molecular recognition of DNA-RNA hybrid ...

Indian Academy of Sciences (India)

conformations corresponding to typical A- and B-type nucleic acids and the .... protein chains and five base pairs in DNA-RNA hybrid ... employed to treat the long range electrostatic interac- .... The solvent accessible surface areas (SASA) of.

Organization and variation analysis of 5S rDNA in different ploidy-level hybrids of red crucian carp × topmouth culter.

Science.gov (United States)

He, Weiguo; Qin, Qinbo; Liu, Shaojun; Li, Tangluo; Wang, Jing; Xiao, Jun; Xie, Lihua; Zhang, Chun; Liu, Yun

2012-01-01

Through distant crossing, diploid, triploid and tetraploid hybrids of red crucian carp (Carassius auratus red var., RCC♀, Cyprininae, 2n = 100) × topmouth culter (Erythroculter ilishaeformis Bleeker, TC♂, Cultrinae, 2n = 48) were successfully produced. Diploid hybrids possessed 74 chromosomes with one set from RCC and one set from TC; triploid hybrids harbored 124 chromosomes with two sets from RCC and one set from TC; tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from TC. The 5S rDNA of the three different ploidy-level hybrids and their parents were sequenced and analyzed. There were three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) in RCC and two monomeric 5S rDNA classes (designated class IV: 188 bp, and class V: 286 bp) in TC. In the hybrid offspring, diploid hybrids inherited three 5S rDNA classes from their female parent (RCC) and only class IV from their male parent (TC). Triploid hybrids inherited class II and class III from their female parent (RCC) and class IV from their male parent (TC). Tetraploid hybrids gained class II and class III from their female parent (RCC), and generated a new 5S rDNA sequence (designated class I-N). The specific paternal 5S rDNA sequence of class V was not found in the hybrid offspring. Sequence analysis of 5S rDNA revealed the influence of hybridization and polyploidization on the organization and variation of 5S rDNA in fish. This is the first report on the coexistence in vertebrates of viable diploid, triploid and tetraploid hybrids produced by crossing parents with different chromosome numbers, and these new hybrids are novel specimens for studying the genomic variation in the first generation of interspecific hybrids, which has significance for evolution and fish genetics.

Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization in Populus species.

Science.gov (United States)

Prado, E A; Faivre-Rampant, P; Schneider, C; Darmency, M A

1996-10-01

Fluorescent in situ hybridization (FISH) was applied to related Populus species (2n = 19) in order to detect rDNA loci. An interspecific variability in the number of hybridization sites was revealed using as probe an homologous 25S clone from Populus deltoides. The application of image analysis methods to measure fluorescence intensity of the hybridization signals has enabled us to characterize major and minor loci in the 18S-5.8S-25S rDNA. We identified one pair of such rDNA clusters in Populus alba; two pairs, one major and one minor, in both Populus nigra and P. deltoides; and three pairs in Populus balsamifera, (two major and one minor) and Populus euroamericana (one major and two minor). FISH results are in agreement with those based on RFLP analysis. The pBG13 probe containing 5S sequence from flax detected two separate clusters corresponding to the two size classes of units that coexist within 5S rDNA of most Populus species. Key words : Populus spp., fluorescent in situ hybridization, FISH, rDNA variability, image analysis.

Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

DEFF Research Database (Denmark)

Kushon, S A; Jordan, J P; Seifert, J L

2001-01-01

The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA...... structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic...

Hybridization change of DNA and nuclear RNA synthesized immediately after ionizing irradiation in spleen cells isolated from 615 mice

International Nuclear Information System (INIS)

Meng Ziqiang

1986-01-01

DNA hybridization with nuclear RNA(nRNA) synthesized immediately after 60 Co Gamma-irradiation in the spleen cells freshly isolated from inbred line 615 mice was investigated, using the technique of Gillespie and Spiegelman. In RNA/DNA hybridization percentage experiment, it was showed that the hybridization of normal DNA with labelled nRNA synthesized in irradiated cells reached the saturation point at a much faster rate than with labelled normal nRNA. The hybridization percentage of nRNA synthesized in irradiated cells was higher than that of normal nRNA during the different reaction time before the saturation point of DNA with nRNA synthesized in irradiated cells, but it was lower than that of normal nRNA after the zone of high repetitive DNA sequences was stimulated, however, the transcription of some base sequences in the zone of low repetitive DNA sequences was seriously inhibited. Measurements of the exhaustion rates of pulse-labelled nRNA were carried out as described by Greene and Flickinger Biochim. In these studies, pulse-labelled nRNA synthesized in unirradiated and irradiated cells were compared by exhausion with DNA at hybridization time of 4 or 24 hours, When the hybridization time was 4 hours, the nRNA synthesized in irradiated cells displayed a faster exhaustion rate than the control nRNA. But if the hybridization time was 24 hours, the exhaustion rate of nRNA synthesized in irradiated cells reduced. These results demostrated that Gamma-irradiation changed the proportion of transcription of some nRNA species and implayed that the sensitivities of the transcription activeties of the different repetitive DNA sequences to Gamma-irradiation were different, and so were the transcription activeties of the different base sequences in the same repetitive DNA sequences

Mixing of maize and wheat genomic DNA by somatic hybridization in regenerated sterile maize plants.

Science.gov (United States)

Szarka, B.; Göntér, I.; Molnár-Láng, M.; Mórocz, S.; Dudits, D.

2002-07-01

Intergeneric somatic hybridization was performed between albino maize ( Zea mays L.) protoplasts and mesophyll protoplasts of wheat ( Triticum aestivum L.) by polyethylene glycol (PEG) treatments. None of the parental protoplasts were able to produce green plants without fusion. The maize cells regenerated only rudimentary albino plantlets of limited viability, and the wheat mesophyll protoplasts were unable to divide. PEG-mediated fusion treatments resulted in hybrid cells with mixed cytoplasm. Six months after fusion green embryogenic calli were selected as putative hybrids. The first-regenerates were discovered as aborted embryos. Regeneration of intact, green, maize-like plants needed 6 months of further subcultures on hormone-free medium. These plants were sterile, although had both male and female flowers. The cytological analysis of cells from callus tissues and root tips revealed 56 chromosomes, but intact wheat chromosomes were not observed. Using total DNA from hybrid plants, three RAPD primer combinations produced bands resembling the wheat profile. Genomic in situ hybridization (GISH) using total wheat DNA as a probe revealed the presence of wheat DNA islands in the maize chromosomal background. The increased viability and the restored green color were the most-significant new traits as compared to the original maize parent. Other intermediate morphological traits of plants with hybrid origin were not found.

Branched-DNA signal amplification combined with paper chromatography hybridization assay and used in hepatitis B virus DNA detection

International Nuclear Information System (INIS)

Fu, F.Z.; Liu, L.X.; Wang, W.Q.; Sun, S. H.; Liu, L.B.

2002-01-01

Nucleic acids detection method is vital to the clinical pathogen diagnosis. The established method can be classified into target direct amplification and signal amplification format according to the target DNA or RNA being directly amplified or not. Those methods have advantages and disadvantages respectively in the clinical application. In the United States of American, branched-DNA as a strong signal amplifier is broadly used in the quantification of the nucleic acids. To gain satisfied sensitivity, some expensive label molecular and instruments should be adopted. Personnel should be special trained to perform. Hence, those can't be widely carried out in the Third World. To avoid those disadvantages, we used the branched-DNA amplifier in the paper chromatography hybridization assay. Methods: Branched DNA signal amplifier and series of probes complementary to the nucleic acid sequence of hepatitis B virus (HBV) have been synthesized. HBV-DNA or it's capture probe were immobilized on the high flow nitrocellulose strip. Having loaded at one end of the strip in turn, probes or HBV-DNA in the hybridization solution migrate to the opposite end of the strip by capillary forces and hybridizes to the immobilized DNA. The branched-DNA signal amplifier and probe labeled with biotin or 32P were then loaded. Through streptavidin-alkaline phosphatase (SA-AP) conjugate and NBT/BCIP ( the specific chromogenic substrate of AP) or autoradiography, the result can be visualized by color reaction or image production on the X-ray film. Results: The sensitivity of this HBV-DNA detection method used probe labeled with biotin and 32P are 1ng and 10pg. The method using the probe labeled with biotin is simple and rapid (2h) without depending on special instruments, it also avoids the pollution of EtBr which can lead to tumor. And the method using the probe labeled with 32P is simple and sensitive, with the exception of long time autoradiography and the inconvenient isotopic disposal

An impedimetric study of DNA hybridization on paper-supported inkjet-printed gold electrodes

International Nuclear Information System (INIS)

Ihalainen, Petri; Määttänen, Anni; Peltonen, Jouko; Pettersson, Fredrik; Pesonen, Markus; Österbacka, Ronald; Viitala, Tapani

2014-01-01

In this study, two different supramolecular recognition architectures for impedimetric detection of DNA hybridization have been formed on disposable paper-supported inkjet-printed gold electrodes. The gold electrodes were fabricated using a gold nanoparticle based ink. The first recognition architecture consists of subsequent layers of biotinylated self-assembly monolayer (SAM), streptavidin and biotinylated DNA probe. The other recognition architecture is constructed by immobilization of thiol-functionalized DNA probe (HS-DNA) and subsequent backfill with 11-mercapto-1-undecanol (MUOH) SAM. The binding capacity and selectivity of the recognition architectures were examined by surface plasmon resonance (SPR) measurements. SPR results showed that the HS-DNA/MUOH system had a higher binding capacity for the complementary DNA target. Electrochemical impedance spectroscopy (EIS) measurements showed that the hybridization can be detected with impedimetric spectroscopy in picomol range for both systems. EIS signal indicated a good selectivity for both recognition architectures, whereas SPR showed very high unspecific binding for the HS-DNA/MUOH system. The factors affecting the impedance signal were interpreted in terms of the complexity of the supramolecular architecture. The more complex architecture acts as a less ideal capacitive sensor and the impedance signal is dominated by the resistive elements. (paper)

Mediated Electron Transfer at Vertically Aligned Single-Walled Carbon Nanotube Electrodes During Detection of DNA Hybridization

Science.gov (United States)

Wallen, Rachel; Gokarn, Nirmal; Bercea, Priscila; Grzincic, Elissa; Bandyopadhyay, Krisanu

2015-06-01

Vertically aligned single-walled carbon nanotube (VASWCNT) assemblies are generated on cysteamine and 2-mercaptoethanol (2-ME)-functionalized gold surfaces through amide bond formation between carboxylic groups generated at the end of acid-shortened single-walled carbon nanotubes (SWCNTs) and amine groups present on the gold surfaces. Atomic force microscopy (AFM) imaging confirms the vertical alignment mode of SWCNT attachment through significant changes in surface roughness compared to bare gold surfaces and the lack of any horizontally aligned SWCNTs present. These SWCNT assemblies are further modified with an amine-terminated single-stranded probe-DNA. Subsequent hybridization of the surface-bound probe-DNA in the presence of complementary strands in solution is followed using impedance measurements in the presence of Fe(CN)6 3-/4- as the redox probe in solution, which show changes in the interfacial electrochemical properties, specifically the charge-transfer resistance, due to hybridization. In addition, hybridization of the probe-DNA is also compared when it is attached directly to the gold surfaces without any intermediary SWCNTs. Contrary to our expectations, impedance measurements show a decrease in charge-transfer resistance with time due to hybridization with 300 nM complementary DNA in solution with the probe-DNA attached to SWCNTs. In contrast, an increase in charge-transfer resistance is observed with time during hybridization when the probe-DNA is attached directly to the gold surfaces. The decrease in charge-transfer resistance during hybridization in the presence of VASWCNTs indicates an enhancement in the electron transfer process of the redox probe at the VASWCNT-modified electrode. The results suggest that VASWCNTs are acting as mediators of electron transfer, which facilitate the charge transfer of the redox probe at the electrode-solution interface.

Wettability transition induced transformation and entrapment of polymer nanostructures in cylindrical nanopores.

Science.gov (United States)

Feng, Xunda; Mei, Shilin; Jin, Zhaoxia

2011-12-06

We apply the concept of wettability transition to manipulate the morphology and entrapment of polymer nanostructures inside cylindrical nanopores of anodic aluminum oxide (AAO) membranes. When AAO/polystyrene (PS) hybrids, i.e., AAO/PS nanorods or AAO/PS nanotubes, are immersed into a polyethylene glycol (PEG) reservoir above the glass transition temperature of PS, a wettability transition from wetting to nonwetting of PS can be triggered due to the invasion of the more wettable PEG melt. The wettability transition enables us to develop a nondestructive method to entrap hemispherically capped nanorods inside nanopores. Moreover, we can obtain single nanorods with the desired aspect ratio by further dissolving the AAO template, in contrast to the drawbacks of nonuniformity or destructiveness from the conventional ultrasonication method. In the case of AAO/PS nanotubes, the wettability transition induced dewetting of PS nanotube walls results in the disconnection and entrapment of nonwetting PS domains (i.e., nanospheres, nanocapsules, or capped nanorods). Moreover, PEG is then washed to recover the pristine wettability of PS on the alumina surface; further annealing of the PS nanospheres inside AAO nanopores under vacuum can generate some unique nanostructures, particularly semicylindrical nanorods. © 2011 American Chemical Society

Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing.

Science.gov (United States)

Euskirchen, Philipp; Bielle, Franck; Labreche, Karim; Kloosterman, Wigard P; Rosenberg, Shai; Daniau, Mailys; Schmitt, Charlotte; Masliah-Planchon, Julien; Bourdeaut, Franck; Dehais, Caroline; Marie, Yannick; Delattre, Jean-Yves; Idbaih, Ahmed

2017-11-01

Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making. Here, we explored the potential of a pocket-size nanopore sequencing device for multimodal and rapid molecular diagnostics of cancer. Low-pass whole genome sequencing was used to simultaneously generate copy number (CN) and methylation profiles from native tumor DNA in the same sequencing run. Single nucleotide variants in IDH1, IDH2, TP53, H3F3A, and the TERT promoter region were identified using deep amplicon sequencing. Nanopore sequencing yielded ~0.1X genome coverage within 6 h and resulting CN and epigenetic profiles correlated well with matched microarray data. Diagnostically relevant alterations, such as 1p/19q codeletion, and focal amplifications could be recapitulated. Using ad hoc random forests, we could perform supervised pan-cancer classification to distinguish gliomas, medulloblastomas, and brain metastases of different primary sites. Single nucleotide variants in IDH1, IDH2, and H3F3A were identified using deep amplicon sequencing within minutes of sequencing. Detection of TP53 and TERT promoter mutations shows that sequencing of entire genes and GC-rich regions is feasible. Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost. It

A nanoporous gold membrane for sensing applications

Directory of Open Access Journals (Sweden)

Swe Zin Oo

2016-03-01

Full Text Available Design and fabrication of three-dimensionally structured, gold membranes containing hexagonally close-packed microcavities with nanopores in the base, are described. Our aim is to create a nanoporous structure with localized enhancement of the fluorescence or Raman scattering at, and in the nanopore when excited with light of approximately 600 nm, with a view to provide sensitive detection of biomolecules. A range of geometries of the nanopore integrated into hexagonally close-packed assemblies of gold micro-cavities was first evaluated theoretically. The optimal size and shape of the nanopore in a single microcavity were then considered to provide the highest localized plasmon enhancement (of fluorescence or Raman scattering at the very center of the nanopore for a bioanalyte traversing through. The optimized design was established to be a 1200 nm diameter cavity of 600 nm depth with a 50 nm square nanopore with rounded corners in the base. A gold 3D-structured membrane containing these sized microcavities with the integrated nanopore was successfully fabricated and ‘proof of concept’ Raman scattering experiments are described. Keywords: Nanopore, Polymer sphere, Gold membrane, Plasmons, Sensing, SERS

Using Protein Dimers to Maximize the Protein Hybridization Efficiency with Multisite DNA Origami Scaffolds

Science.gov (United States)

Verma, Vikash; Mallik, Leena; Hariadi, Rizal F.; Sivaramakrishnan, Sivaraj; Skiniotis, Georgios; Joglekar, Ajit P.

2015-01-01

DNA origami provides a versatile platform for conducting ‘architecture-function’ analysis to determine how the nanoscale organization of multiple copies of a protein component within a multi-protein machine affects its overall function. Such analysis requires that the copy number of protein molecules bound to the origami scaffold exactly matches the desired number, and that it is uniform over an entire scaffold population. This requirement is challenging to satisfy for origami scaffolds with many protein hybridization sites, because it requires the successful completion of multiple, independent hybridization reactions. Here, we show that a cleavable dimerization domain on the hybridizing protein can be used to multiplex hybridization reactions on an origami scaffold. This strategy yields nearly 100% hybridization efficiency on a 6-site scaffold even when using low protein concentration and short incubation time. It can also be developed further to enable reliable patterning of a large number of molecules on DNA origami for architecture-function analysis. PMID:26348722

Using Protein Dimers to Maximize the Protein Hybridization Efficiency with Multisite DNA Origami Scaffolds.

Directory of Open Access Journals (Sweden)

Vikash Verma

Full Text Available DNA origami provides a versatile platform for conducting 'architecture-function' analysis to determine how the nanoscale organization of multiple copies of a protein component within a multi-protein machine affects its overall function. Such analysis requires that the copy number of protein molecules bound to the origami scaffold exactly matches the desired number, and that it is uniform over an entire scaffold population. This requirement is challenging to satisfy for origami scaffolds with many protein hybridization sites, because it requires the successful completion of multiple, independent hybridization reactions. Here, we show that a cleavable dimerization domain on the hybridizing protein can be used to multiplex hybridization reactions on an origami scaffold. This strategy yields nearly 100% hybridization efficiency on a 6-site scaffold even when using low protein concentration and short incubation time. It can also be developed further to enable reliable patterning of a large number of molecules on DNA origami for architecture-function analysis.

Detection of DNA hybridization based on SnO2 nanomaterial enhanced fluorescence

International Nuclear Information System (INIS)

Gu Cuiping; Huang Jiarui; Ni Ning; Li Minqiang; Liu Jinhuai

2008-01-01

In this paper, enhanced fluorescence emissions were firstly investigated based on SnO 2 nanomaterial, and its application in the detection of DNA hybridization was also demonstrated. The microarray of SnO 2 nanomaterial was fabricated by the vapour phase transport method catalyzed by patterned Au nanoparticles on a silicon substrate. A probe DNA was immobilized on the substrate with patterned SnO 2 nanomaterial, respectively, by covalent and non-covalent linking schemes. When a fluorophore labelled target DNA was hybridized with a probe DNA on the substrate, fluorescence emissions were only observed on the surface of SnO 2 nanomaterial, which indicated the property of enhancing fluorescence signals from the SnO 2 nanomaterial. By comparing the different fluorescence images from covalent and non-covalent linking schemes, the covalent method was confirmed to be more effective for immobilizing a probe DNA. With the combined use of SnO 2 nanomaterial and the covalent linking scheme, the target DNA could be detected at a very low concentration of 10 fM. And the stability of SnO 2 nanomaterial under the experimental conditions was also compared with silicon nanowires. The findings strongly suggested that SnO 2 nanomaterial could be extensively applied in detections of biological samples with enhancing fluorescence property and high stability

Correlation between ultraviolet survival and DNA repair efficiency in mouse cell hybrids and their parent lines

International Nuclear Information System (INIS)

Limbosch, S.

1982-01-01

Three hybrid cell lines formed between mouse lymphoma (LS) and mouse fibroblasts (A9) have been tested for their capacity to perform unscheduled DNA synthesis; their recovery characteristics after uv irradiation have also been studied to determine if DNA repair is implicated in the high survival observed in one hybrid (clone 3). The results of these investigations indicate that hybrid clone 3 was distinguishable from the more uv sensitive parental and other hybrid cell lines by its higher uv-induced unscheduled DNA synthesis, its greater clonogenic survival in plateau phase, and its faster recovery when maintained in conditioned medium after irradiation. The simultaneous increase of these three properties in hybrid clone 3 suggest that, by three different approaches, we have evidenced the same molecular process, a process involved in the elimination of potentially lethal damage, most probably the excision repair pathway. This report also shows that the low efficiency in excision repair in the parent line A9 is probably not due to deletion but rather to repression of the relevant gene(s) and that somatic cell hybridization can result in a stimulation of a previously poorly expressed repair process

Tailoring uniform gold nanoparticle arrays and nanoporous films for next-generation optoelectronic devices

Science.gov (United States)

Farid, Sidra; Kuljic, Rade; Poduri, Shripriya; Dutta, Mitra; Darling, Seth B.

2018-06-01

High-density arrays of gold nanodots and nanoholes on indium tin oxide (ITO)-coated glass surfaces are fabricated using a nanoporous template fabricated by the self-assembly of diblock copolymers of poly (styrene-block-methyl methacrylate) (PS-b-PMMA) structures. By balancing the interfacial interactions between the polymer blocks and the substrate using random copolymer, cylindrical block copolymer microdomains oriented perpendicular to the plane of the substrate have been obtained. Nanoporous PS films are created by selectively etching PMMA cylinders, a straightforward route to form highly ordered nanoscale porous films. Deposition of gold on the template followed by lift off and sonication leaves a highly dense array of gold nanodots. These materials can serve as templates for the vapor-liquid-solid (VLS) growth of semiconductor nanorod arrays for next generation hybrid optoelectronic applications.

A versatile and highly sensitive homogeneous electrochemical strategy based on the split aptamer binding-induced DNA three-way junction and exonuclease III-assisted target recycling.

Science.gov (United States)

Hou, Ting; Li, Wei; Zhang, Lianfang; Li, Feng

2015-08-21

Herein, a highly sensitive and versatile homogeneous electrochemical biosensing strategy is proposed, based on the split aptamer-incorporated DNA three-way junction and the exonuclease (Exo) III-assisted target recycling. The aptamer of adenosine triphosphate (ATP, chosen as the model analyte) is split into two fragments and embedded in single-stranded DNA1 and DNA2, respectively. ATP specifically binds with the split aptamers, bringing DNA1 and DNA2 close to each other, thus inducing the DNA three-way junction formation through the partial hybridization among DNA1, DNA2 and the methylene blue-labelled MB-DNA. Subsequently, MB-DNA is specifically digested by Exo III, releasing a MB-labelled mononucleotide, as well as a DNA1-ATP-DNA2 complex, which acts as the recycled target and hybridizes with another intact MB-DNA to initiate the subsequent cycling cleavage process. As a result, large amounts of MB-labelled mononucleotides are released, generating a significantly amplified electrochemical signal toward the ATP assay. To the best of our knowledge, it is the first example to successfully incorporate split aptamers into DNA three-way junctions and to be adopted in a homogeneous electrochemical assay. In addition to high sensitivity, this strategy also exhibits the advantages of simplicity and convenience, because it is carried out in a homogeneous solution, and sophisticated electrode modification processes are avoided. By simply changing the sequences of the split aptamer fragments, this versatile strategy can be easily adopted to assay a large spectrum of targets. Due to its advantages of high sensitivity, excellent selectivity, versatility and simple operation, the as-proposed approach has great potential to be applied in biochemical research and clinical practices.

Preparation of fluorescent-dye-labeled cDNA from RNA for microarray hybridization.

Science.gov (United States)

Ares, Manuel

2014-01-01

This protocol describes how to prepare fluorescently labeled cDNA for hybridization to microarrays. It consists of two steps: first, a mixture of anchored oligo(dT) and random hexamers is used to prime amine-modified cDNA synthesis by reverse transcriptase using a modified deoxynucleotide with a reactive amine group (aminoallyl-dUTP) and an RNA sample as a template. Second, the cDNA is purified and exchanged into bicarbonate buffer so that the amine groups in the cDNA react with the dye N-hydroxysuccinimide (NHS) esters, covalently joining the dye to the cDNA. The dye-coupled cDNA is purified again, and the amount of dye incorporated per microgram of cDNA is determined.

Nanoporous Polymeric Grating-Based Biosensors

KAUST Repository

Gao, Tieyu; Hsiao, Vincent; Zheng, Yue Bing; Huang, Tony Jun

2012-01-01

We demonstrate the utilization of an interferometrically created nanoporous polymeric gratings as a platform for biosensing applications. Aminopropyltriethoxysilane (APTES)-functionalized nanoporous polymeric gratings was fabricated by combining holographic interference patterning and APTES-functionalization of pre-polymer syrup. The successful detection of multiple biomolecules indicates that the biofunctionalized nanoporous polymeric gratings can act as biosensing platforms which are label-free, inexpensive, and applicable as high-throughput assays. Copyright © 2010 by ASME.

Nanoporous Polymeric Grating-Based Biosensors

KAUST Repository

Gao, Tieyu

2012-05-02

We demonstrate the utilization of an interferometrically created nanoporous polymeric gratings as a platform for biosensing applications. Aminopropyltriethoxysilane (APTES)-functionalized nanoporous polymeric gratings was fabricated by combining holographic interference patterning and APTES-functionalization of pre-polymer syrup. The successful detection of multiple biomolecules indicates that the biofunctionalized nanoporous polymeric gratings can act as biosensing platforms which are label-free, inexpensive, and applicable as high-throughput assays. Copyright © 2010 by ASME.

The intrinsic role of nanoconfinement in chemical equilibrium: evidence from DNA hybridization.

Science.gov (United States)

Rubinovich, Leonid; Polak, Micha

2013-05-08

Recently we predicted that when a reaction involving a small number of molecules occurs in a nanometric-scale domain entirely segregated from the surrounding media, the nanoconfinement can shift the position of equilibrium toward products via reactant-product reduced mixing. In this Letter, we demonstrate how most-recently reported single-molecule fluorescence measurements of partial hybridization of ssDNA confined within nanofabricated chambers provide the first experimental confirmation of this entropic nanoconfinement effect. Thus, focusing separately on each occupancy-specific equilibrium constant, quantitatively reveals extra stabilization of the product upon decreasing the chamber occupancy or size. Namely, the DNA hybridization under nanoconfined conditions is significantly favored over the identical reaction occurring in bulk media with the same reactant concentrations. This effect, now directly verified for DNA, can be relevant to actual biological processes, as well as to diverse reactions occurring within molecular capsules, nanotubes, and other functional nanospaces.

Hybrid procedure for total laryngectomy with a flexible robot-assisted surgical system.

Science.gov (United States)

Schuler, Patrick J; Hoffmann, Thomas K; Veit, Johannes A; Rotter, Nicole; Friedrich, Daniel T; Greve, Jens; Scheithauer, Marc O

2017-06-01

Total laryngectomy is a standard procedure in head-and-neck surgery for the treatment of cancer patients. Recent clinical experiences have indicated a clinical benefit for patients undergoing transoral robot-assisted total laryngectomy (TORS-TL) with commercially available systems. Here, a new hybrid procedure for total laryngectomy is presented. TORS-TL was performed in human cadavers (n = 3) using a transoral-transcervical hybrid procedure. The transoral approach was performed with a robotic flexible robot-assisted surgical system (Flex®) and compatible flexible instruments. Transoral access and visualization of anatomical landmarks were studied in detail. Total laryngectomy is feasible with a combined transoral-transcervical approach using the flexible robot-assisted surgical system. Transoral visualization of all anatomical structures is sufficient. The flexible design of the robot is advantageous for transoral surgery of the laryngeal structures. Transoral robot assisted surgery has the potential to reduce morbidity, hospital time and fistula rates in a selected group of patients. Initial clinical studies and further development of supplemental tools are in progress. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Nanoporous metals for advanced energy technologies

CERN Document Server

Ding, Yi

2016-01-01

This book covers the state-of-the-art research in nanoporous metals for potential applications in advanced energy fields, including proton exchange membrane fuel cells, Li batteries (Li ion, Li-S, and Li-O2), and supercapacitors. The related structural design and performance of nanoporous metals as well as possible mechanisms and challenges are fully addressed. The formation mechanisms of nanoporous metals during dealloying, the microstructures of nanoporous metals and characterization methods, as well as miscrostructural regulation of nanoporous metals through alloy design of precursors and surface diffusion control are also covered in detail. This is an ideal book for researchers, engineers, graduate students, and government/industry officers who are in charge of R&D investments and strategy related to energy technologies.

PCR associated with hybridization with DNA radioactive probes for diagnosis of asymptomatic infection caused by Leishmania Chagasi

International Nuclear Information System (INIS)

Andrade, Antero Silva Ribeiro de; Moreno, Elizabeth Castro; Gomes, Rosangela Fatima; Melo, Maria Norma de; Carneiro, Mariangela; Fernandes, Octavio

2002-01-01

Detection systems for diagnosis of leishmaniasis based on PCR are very promising due to their sensitivity and specificity. Secondary detection by specific radioactive DNA probes, able to type the PCR amplified products, increase the specificity and raise about tem-fold the sensitivity of the assay. The aim of this work was evaluate PCR and hybridization as a tool to identify Leishmania (Leishmania) chagasi (the specie that cause the visceral leishmaniasis in Brazil) infection in asymptomatic persons living in a endemic area. Material and Methods: A group of 226 asymptomatic individuals, living in General Carneiro (MG), was selected. Blood samples were harvested and the DNA extracted from the mononucleate cells. PCR was performed using primers addressed to the kinetoplast DNA minicircles. This protocol gives a positive reaction for all Leishmania species. The amplified products were further hybridized with cloned L.chagasi minicircles labeled with 32 P. Results: were identified 111 samples PCR positive, 2 of them hybridization negative and 133 samples hybridization positive, 24 of them PCR negative. The occurrence of samples with hybridization positive and PCR negative was expected since hybridization, with DNA probes labeled with 32 P, increase the sensitivity of the assay. The samples that presented positive PCR and negative hybridization were probably due the presence of other Leishmania species, likely L. (V.) braziliensis (that produce tegumentary leishmaniasis in the region), since L. (L.) chagasi cloned minicircles were used as hybridization probe. We conclude that this procedure is a valuable tool to access subclinical L. (L.) chagasi infections in epidemiological studies. (author)

Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus).

Science.gov (United States)

Moody, Michael L; Rieseberg, Loren H

2012-07-01

The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.

Voltammetry of osmium-modified DNA at a mercury film electrode application in detecting DNA hybridization

Czech Academy of Sciences Publication Activity Database

Kostečka, Pavel; Havran, Luděk; Pivoňková, Hana; Fojta, Miroslav

2004-01-01

Roč. 63, 1-2 (2004), s. 245-248 ISSN 1567-5394 R&D Projects: GA AV ČR IAA4004108; GA AV ČR KJB4004302 Institutional research plan: CEZ:AV0Z5004920 Keywords : osmium * DNA hybridization * mercury film electrode Subject RIV: BO - Biophysics Impact factor: 2.261, year: 2004

Photoluminescence Enhancement of Poly(3-methylthiophene Nanowires upon Length Variable DNA Hybridization

Directory of Open Access Journals (Sweden)

Jingyuan Huang

2018-01-01

Full Text Available The use of low-dimensional inorganic or organic nanomaterials has advantages for DNA and protein recognition due to their sensitivity, accuracy, and physical size matching. In this research, poly(3-methylthiophene (P3MT nanowires (NWs are electrochemically prepared with dopant followed by functionalization with probe DNA (pDNA sequence through electrostatic interaction. Various lengths of pDNA sequences (10-, 20- and 30-mer are conjugated to the P3MT NWs respectively followed with hybridization with their complementary target DNA (tDNA sequences. The nanoscale photoluminescence (PL properties of the P3MT NWs are studied throughout the whole process at solid state. In addition, the correlation between the PL enhancement and the double helix DNA with various lengths is demonstrated.

Label-free DNA hybridization detection and single base-mismatch discrimination using CE-ICP-MS assay.

Science.gov (United States)

Li, Yan; Sun, Shao-kai; Yang, Jia-lin; Jiang, Yan

2011-12-07

Detecting a specific DNA sequence and discriminating single base-mismatch is critical to clinical diagnosis, paternity testing, forensic sciences, food and drug industry, pathology, genetics, environmental monitoring, and anti-bioterrorism. To this end, capillary electrophoresis (CE) coupled with the inductively coupled plasma mass spectrometry (ICP-MS) method is developed using the displacing interaction between the target ssDNA and the competitor Hg(2+) for the first time. The thymine-rich capture ssDNA 1 is interacted with the competitor Hg(2+), forming an assembled complex in a hairpin-structure between the thymine bases arrangement at both sides of the capture ssDNA 1. In the presence of a target ssDNA with stronger affinity than that of the competitor Hg(2+), the energetically favorable hybridization between capture ssDNA 1 and the target ssDNA destroys the hairpin-structure and releases the competitor as free Hg(2+), which was then read out and accurately quantified by CE-ICP-MS assay. Under the optimal CE separation conditions, free Hg(2+) ions and its capture ssDNA 1 adduct were baseline separated and detected on-line by ICP-MS; the increased peak intensity of free Hg(2+) against the concentration of perfectly complementary target ssDNA was linear over the concentration range of 30-600 nmol L(-1) with a limit of detection of 8 nmol L(-1) (3s, n = 11) in the pre-incubated mixture containing 1 μmol L(-1) Hg(2+) and 0.2 μmol L(-1) capture ssDNA 1. This new assay method is simple in design since any target ssDNA binding can in principle result in free Hg(2+) release by 6-fold Hg(2+) signal amplification, avoiding oligonucleotide labeling or assistance by excess signal transducer and signal reporter to read out the target. Due to element-specific detection of ICP-MS in our assay procedure, the interference from the autofluorescence of substrata was eliminated.

On the specific surface area of nanoporous materials

NARCIS (Netherlands)

Detsi, E.; De Jong, E.; Zinchenko, A.; Vukovic, Z.; Vukovic, I.; Punzhin, S.; Loos, K.; ten Brinke, G.; De Raedt, H. A.; Onck, P. R.; De Hosson, J. T. M.

2011-01-01

A proper quantification of the specific surface area of nanoporous materials is necessary for a better understanding of the properties that are affected by the high surface-area-to-volume ratio of nanoporous metals, nanoporous polymers and nanoporous ceramics. In this paper we derive an analytical

Detection of DNA fingerprints of cultivated rice by hybridization with a human minisatellite DNA probe

International Nuclear Information System (INIS)

Dallas, J.F.

1988-01-01

A human minisatellite DNA probe detects several restriction fragment length polymorphisms in cultivars of Asian and African rice. Certain fragments appear to be inherited in a Mendelian fashion and may represent unlinked loci. The hybridization patterns appear to be cultivar-specific and largely unchanged after the regeneration of plants from tissue culture. The results suggest that these regions of the rice genome may be used to generate cultivar-specific DNA fingerprints. The demonstration of similarity between a human minisatellite sequence and polymorphic regions in the rice genome suggests that such regions also occur in the genomes of many other plant species

CNTs grown on nanoporous carbon from zeolitic imidazolate frameworks for supercapacitors.

Science.gov (United States)

Kim, Jeonghun; Young, Christine; Lee, Jaewoo; Park, Min-Sik; Shahabuddin, Mohammed; Yamauchi, Yusuke; Kim, Jung Ho

2016-10-27

Carbon nanotubes (CNT) grown on nanoporous carbon (NPC), which yields coexisting amorphous and graphitic nanoarchitectures, have been prepared on a large scale from zeolitic imidazolate framework (ZIF) by introducing bimetallic ions (Co 2+ and Zn 2+ ). Interestingly, the hybrid Co/Zn-ZIF-derived NPC showed rich graphitic CNTs on the surface. This NPC was utilized for a coin-type supercapacitor cell with an aqueous electrolyte, which showed enhanced retention at high current density and good stability over 10 000 cycles.

Neighboring genes for DNA-binding proteins rescue male sterility in Drosophila hybrids.

Science.gov (United States)

Liénard, Marjorie A; Araripe, Luciana O; Hartl, Daniel L

2016-07-19

Crosses between closely related animal species often result in male hybrids that are sterile, and the molecular and functional basis of genetic factors for hybrid male sterility is of great interest. Here, we report a molecular and functional analysis of HMS1, a region of 9.2 kb in chromosome 3 of Drosophila mauritiana, which results in virtually complete hybrid male sterility when homozygous in the genetic background of sibling species Drosophila simulans. The HMS1 region contains two strong candidate genes for the genetic incompatibility, agt and Taf1 Both encode unrelated DNA-binding proteins, agt for an alkyl-cysteine-S-alkyltransferase and Taf1 for a subunit of transcription factor TFIID that serves as a multifunctional transcriptional regulator. The contribution of each gene to hybrid male sterility was assessed by means of germ-line transformation, with constructs containing complete agt and Taf1 genomic sequences as well as various chimeric constructs. Both agt and Taf1 contribute about equally to HMS1 hybrid male sterility. Transgenes containing either locus rescue sterility in about one-half of the males, and among fertile males the number of offspring is in the normal range. This finding suggests compensatory proliferation of the rescued, nondysfunctional germ cells. Results with chimeric transgenes imply that the hybrid incompatibilities result from interactions among nucleotide differences residing along both agt and Taf1 Our results challenge a number of preliminary generalizations about the molecular and functional basis of hybrid male sterility, and strongly reinforce the role of DNA-binding proteins as a class of genes contributing to the maintenance of postzygotic reproductive isolation.

Mixed DNA/Oligo(ethylene glycol) Functionalized Gold Surface Improve DNA Hybridization in Complex Media

International Nuclear Information System (INIS)

Lee, C.; Gamble, L.; Grainger, D.; Castner, D.

2006-01-01

Reliable, direct 'sample-to-answer' capture of nucleic acid targets from complex media would greatly improve existing capabilities of DNA microarrays and biosensors. This goal has proven elusive for many current nucleic acid detection technologies attempting to produce assay results directly from complex real-world samples, including food, tissue, and environmental materials. In this study, we have investigated mixed self-assembled thiolated single-strand DNA (ssDNA) monolayers containing a short thiolated oligo(ethylene glycol) (OEG) surface diluent on gold surfaces to improve the specific capture of DNA targets from complex media. Both surface composition and orientation of these mixed DNA monolayers were characterized with x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS). XPS results from sequentially adsorbed ssDNA/OEG monolayers on gold indicate that thiolated OEG diluent molecules first incorporate into the thiolated ssDNA monolayer and, upon longer OEG exposures, competitively displace adsorbed ssDNA molecules from the gold surface. NEXAFS polarization dependence results (followed by monitoring the N 1s→π* transition) indicate that adsorbed thiolated ssDNA nucleotide base-ring structures in the mixed ssDNA monolayers are oriented more parallel to the gold surface compared to DNA bases in pure ssDNA monolayers. This supports ssDNA oligomer reorientation towards a more upright position upon OEG mixed adlayer incorporation. DNA target hybridization on mixed ssDNA probe/OEG monolayers was monitored by surface plasmon resonance (SPR). Improvements in specific target capture for these ssDNA probe surfaces due to incorporation of the OEG diluent were demonstrated using two model biosensing assays, DNA target capture from complete bovine serum and from salmon genomic DNA mixtures. SPR results demonstrate that OEG incorporation into the ssDNA adlayer improves surface resistance to both nonspecific DNA and protein

DNA Immobilization and Hybridization Detection by the Intrinsic Molecular Charge Using Capacitive Field-Effect Sensors Modified with a Charged Weak Polyelectrolyte Layer.

Science.gov (United States)

Bronder, Thomas S; Poghossian, Arshak; Scheja, Sabrina; Wu, Chunsheng; Keusgen, Michael; Mewes, Dieter; Schöning, Michael J

2015-09-16

Miniaturized setup, compatibility with advanced micro- and nanotechnologies, and ability to detect biomolecules by their intrinsic molecular charge favor the semiconductor field-effect platform as one of the most attractive approaches for the development of label-free DNA chips. In this work, a capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensor covered with a layer-by-layer prepared, positively charged weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was used for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization. The negatively charged probe single-stranded DNA (ssDNA) molecules were electrostatically adsorbed onto the positively charged PAH layer, resulting in a preferentially flat orientation of the ssDNA molecules within the Debye length, thus yielding a reduced charge-screening effect and a higher sensor signal. Each sensor-surface modification step (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), reducing an unspecific adsorption by a blocking agent, incubation with noncomplementary DNA (ncDNA) solution) was monitored by means of capacitance-voltage and constant-capacitance measurements. In addition, the surface morphology of the PAH layer was studied by atomic force microscopy and contact-angle measurements. High hybridization signals of 34 and 43 mV were recorded in low-ionic strength solutions of 10 and 1 mM, respectively. In contrast, a small signal of 4 mV was recorded in the case of unspecific adsorption of fully mismatched ncDNA. The density of probe ssDNA and dsDNA molecules as well as the hybridization efficiency was estimated using the experimentally measured DNA immobilization and hybridization signals and a simplified double-layer capacitor model. The results of field-effect experiments were supported by fluorescence measurements, verifying the DNA-immobilization and hybridization event.

Double positive effect of adding hexaethyelene glycol when optimizing the hybridization efficiency of a microring DNA detection assay

Energy Technology Data Exchange (ETDEWEB)

Van Eeghem, Anabelle, E-mail: anabelle.vaneeghem@gmail.com [Polymer Chemistry and Biomaterials Research Group, Department of Organic and Macromolecular Chemistry, Ghent University (Belgium); Center for Nano- and Biophotonics, Ghent University (Belgium); Werquin, Sam [Center for Nano- and Biophotonics, Ghent University (Belgium); Photonics Research Group, Department of Information Technology, Ghent University – IMEC (Belgium); Hoste, Jan-Willem, E-mail: janwillem.hoste@ugent.be [Center for Nano- and Biophotonics, Ghent University (Belgium); Photonics Research Group, Department of Information Technology, Ghent University – IMEC (Belgium); Goes, Arne [Polymer Chemistry and Biomaterials Research Group, Department of Organic and Macromolecular Chemistry, Ghent University (Belgium); Agrosavfe NV, Technologiepark 4 (Bio-incubator), Zwijnaarde (Belgium); Vanderleyden, Els [Polymer Chemistry and Biomaterials Research Group, Department of Organic and Macromolecular Chemistry, Ghent University (Belgium); Center for Nano- and Biophotonics, Ghent University (Belgium); Bienstman, Peter [Center for Nano- and Biophotonics, Ghent University (Belgium); Photonics Research Group, Department of Information Technology, Ghent University – IMEC (Belgium); Dubruel, Peter [Polymer Chemistry and Biomaterials Research Group, Department of Organic and Macromolecular Chemistry, Ghent University (Belgium); Center for Nano- and Biophotonics, Ghent University (Belgium)

2017-05-31

Highlights: • The hybridization efficiency of a DNA assay was investigated based on SOI microring resonators. • A 4-fold increase in efficiency was obtained by using HEG as backfilling agent, as well as improving robustness. • The dual polarization microring technique shows that HEG reorients the DNA in an upright position. • Hybridizing at 35 °C and with a buffer containing 50 v/v% of formamide greatly improves the robustness. - Abstract: In this paper, a method for detection of DNA molecules using silicon-on-insulator (SOI) microring resonators is described. The influence of temperature and the use of formamide on the hybridization efficiency were studied. It was shown that 50 v/v% of formamide in the hybridization buffer can ensure hybridization when working close to physiological temperature. Furthermore, the use of hexaethylene glycol (HEG) as backfilling agent was studied in order to resolve issues of non-specific adsorption to the surface. The results indicated that not only non-specific binding was reduced significantly but also that HEG improves the orientation of the DNA probes on the surface. This led to a 4-fold increase in hybridization efficiency and thus in an equal decrease in the detection limit, compared to hybridization without the use of HEG. An improvement in robustness of the assay was also observed. This DNA reorientation hypothesis was confirmed by studying the thickness and density of the layers by using dual polarization microring sensing. Finally, the different steps in the sensing experiment were characterized in more detail by static contact angle (SCA) and X-ray photoelectron spectroscopy (XPS) analysis. The results showed quantitatively that the surface modifications were successful.

Parental DNA methylation states are associated with heterosis in epigenetic hybrids

NARCIS (Netherlands)

Lauss, Kathrin; Wardenaar, René; Oka, Rurika; van Hulten, Marieke H A; Guryev, Victor; Keurentjes, Joost J B; Stam, Maike; Johannes, Frank

Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood. Recent studies have implicated changes in DNA methylation and small RNAs in hybrid performance, however, it remains unclear whether

Parental DNA methylation states are associated with heterosis in epigenetic hybrids

NARCIS (Netherlands)

Lauss, K.; Wardenaar, R.; Oka, R.; van Hulten, M.H.A.; Guryev, V.; Keurentjes, J.J.B.; Stam, M.; Johannes, F.

Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood. Recent studies have implicated changes in DNA methylation and small RNAs in hybrid performance; however, it remains unclear whether

Parental DNA methylation states are associated with heterosis in epigenetic hybrids

NARCIS (Netherlands)

Lauss, Kathrin; Wardenaar, R.; Oka, Rurika; Hulten, M.H.A.; Guryev, Victor; Keurentjes, J.J.B.; Stam, Maike; Johannes, Frank

2018-01-01

Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood. Recent studies have implicated changes in DNA methylation and small RNAs in hybrid performance, however, it remains unclear whether

"Multicolor" electrochemical labeling of DNA hybridization probes with osmium tetroxide complexes

Czech Academy of Sciences Publication Activity Database

Fojta, Miroslav; Kostečka, Pavel; Trefulka, Mojmír; Havran, Luděk; Paleček, Emil

2007-01-01

Roč. 79, č. 3 (2007), s. 1022-1029 ISSN 0003-2700 R&D Projects: GA AV ČR(CZ) IAA4004402; GA ČR(CZ) GA203/05/0043; GA ČR(CZ) GA203/04/1325; GA MPO(CZ) 1H-PK/42; GA MŠk(CZ) LC06035 Institutional research plan: CEZ:AV0Z50040507 Keywords : DNA labeling * osmium tetroxide complexes * DNA hybridization Subject RIV: BO - Biophysics Impact factor: 5.287, year: 2007

Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA

Directory of Open Access Journals (Sweden)

Weixin Qian

2014-08-01

Full Text Available The electrokinetic transport dynamics of deoxyribonucleic acid (DNA molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the translocation mechanism of a DNA-like polymer chain in a nanofluidic channel was investigated using Langevin dynamics simulations. A coarse-grained bead-spring model was developed to simulate the dynamics of a long polymer chain passing through a rectangular cross-section nanopore embedded in a nanochannel, under the influence of a nonuniform electric field. Varying the cross-sectional area of the nanopore was found to allow optimization of the translocation process through modification of the electric field in the flow channel, since a drastic drop in the electric potential at the nanopore was induced by changing the cross-section. Furthermore, the configuration of the polymer chain in the nanopore was observed to determine its translocation velocity. The competition between the strength of the electric field and confinement in the small pore produces various transport mechanisms and the results of this study thus represent a means of optimizing the design of nanofluidic devices for single molecule detection.

A hybrid swarm population of Pinus densiflora x P. sylvestris hybrids inferred from sequence analysis of chloroplast DNA and morphological characters

Science.gov (United States)

To confirm a hybrid swarm population of Pinus densiflora × P. sylvestris in Jilin, China and to study whether shoot apex morphology of 4-year old seedlings can be correlated with the sequence of a chloroplast DNA simple sequence repeat marker (cpDNA SSR), needles and seeds from P. densiflora, P. syl...

Label-free detection of DNA hybridization and single point mutations in a nano-gap biosensor

International Nuclear Information System (INIS)

Zaffino, R L; Mir, M; Samitier, J

2014-01-01

We describe a conductance-based biosensor that exploits DNA-mediated long-range electron transport for the label-free and direct electrical detection of DNA hybridization. This biosensor platform comprises an array of vertical nano-gap biosensors made of gold and fabricated through standard photolithography combined with focused ion beam lithography. The nano-gap walls are covalently modified with short, anti-symmetric thiolated DNA probes, which are terminated by 19 bases complementary to both the ends of a target DNA strand. The nano-gaps are separated by a distance of 50nm, which was adjusted to fit the length of the DNA target plus the DNA probes. The hybridization of the target DNA closes the gap circuit in a switch on/off fashion, in such a way that it is readily detected by an increase in the current after nano-gap closure. The nano-biosensor shows high specificity in the discrimination of base-pair mismatching and does not require signal indicators or enhancing molecules. The design of the biosensor platform is applicable for multiplexed detection in a straightforward manner. The platform is well-suited to mass production, point-of-care diagnostics, and wide-scale DNA analysis applications. (paper)

Ultra-Thin Solid-State Nanopores: Fabrication and Applications

Science.gov (United States)

Kuan, Aaron Tzeyang

Solid-state nanopores are a nanofluidic platform with unique advantages for single-molecule analysis and filtration applications. However, significant improvements in device performance and scalable fabrication methods are needed to make nanopore devices competitive with existing technologies. This dissertation investigates the potential advantages of ultra-thin nanopores in which the thickness of the membrane is significantly smaller than the nanopore diameter. Novel, scalable fabrication methods were first developed and then utilized to examine device performance for water filtration and single molecule sensing applications. Fabrication of nanometer-thin pores in silicon nitride membranes was achieved using a feedback-controlled ion beam method in which ion sputtering is arrested upon detection of the first few ions that drill through the membrane. Performing fabrication at liquid nitrogen temperatures prevents surface atom rearrangements that have previously complicated similar processes. A novel cross-sectional imaging method was also developed to allow careful examination of the full nanopore geometry. Atomically-thin graphene nanopores were fabricated via an electrical pulse method in which sub-microsecond electrical pulses applied across a graphene membrane in electrolyte solution are used to create a defect in the membrane and controllably enlarge it into a nanopore. This method dramatically increases the accuracy and reliability of graphene nanopore production, allowing consistent production of single nanopores down to subnanometer sizes. In filtration applications in which nanopores are used to selectively restrict the passage of dissolved contaminants, ultra-thin nanopores minimize the flow resistance, increasing throughput and energy-efficiency. The ability of graphene nanopores to separate different ions was characterized via ionic conductance and reversal potential measurements. Graphene nanopores were observed to conduct cations preferentially over

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

KAUST Repository

Teng, Haotian; Cao, Minh Duc; Hall, Michael B; Duarte, Tania; Wang, Sheng; Coin, Lachlan J M

2018-01-01

Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

KAUST Repository

Teng, Haotian

2018-04-10

Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.

Recent Advances in Nanoporous Membranes for Water Purification

Directory of Open Access Journals (Sweden)

Zhuqing Wang

2018-01-01

Full Text Available Nanoporous materials exhibit wide applications in the fields of electrocatalysis, nanodevice fabrication, energy, and environmental science, as well as analytical science. In this review, we present a summary of recent studies on nanoporous membranes for water purification application. The types and fabrication strategies of various nanoporous membranes are first introduced, and then the fabricated nanoporous membranes for removing various water pollutants, such as salt, metallic ions, anions, nanoparticles, organic chemicals, and biological substrates, are demonstrated and discussed. This work will be valuable for readers to understand the design and fabrication of various nanoporous membranes, and their potential purification mechanisms towards different water pollutants. In addition, it will be helpful for developing new nanoporous materials for quick, economic, and high-performance water purification.

Water-assisted growth of graphene-carbon nanotube hybrids in plasma

Science.gov (United States)

Tewari, Aarti; Ghosh, Santanu; Srivastava, Pankaj

2018-04-01

The enhanced growth of graphene-carbon nanotube (CNT) hybrids in a hydrocarbon and hydrogen plasma assisted by water is numerically formulated. The catalyst activity and agglomeration of catalyst particles are the rate determining factors in the growth of hybrids and their constituents, i.e., the CNT and graphene. The water vapor concentration is varied to investigate its effect on the growth process. The enhanced catalyst activity on account of oxidation by hydroxyl ions of water to impede the agglomeration of catalyst particles and the removal of amorphous carbon through etching by hydrogen ions of water are seen to be the main driving forces behind the many fold increase in the dimensions of constituent nanostructures and the hybrids with water vapor concentration. Importantly, beyond a certain specific water vapor concentration, the growth rates dropped due to active oxidation of the catalyst particle.

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

Science.gov (United States)

Kitajima, Akira; Nonaka, Keisuke; Yoshioka, Terutaka; Ohta, Satoshi; Goto, Shingo; Toyoda, Atsushi; Fujiyama, Asao; Mochizuki, Takako; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2016-01-01

Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies. PMID:27902727

Proximity hybridization-regulated catalytic DNA hairpin assembly for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles

International Nuclear Information System (INIS)

Zhou, Fuyi; Yao, Yao; Luo, Jianjun; Zhang, Xing; Zhang, Yu; Yin, Dengyang; Gao, Fenglei; Wang, Po

2017-01-01

Novel hybridization proximity-regulated catalytic DNA hairpin assembly strategy has been proposed for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles as signal label. The DNA template-synthesized Pd nanoparticles were characterized with atomic force microscopic and X-ray photoelectron spectroscopy. The highly efficient electrocatalysis by DNA template synthesized Pd nanoparticles for NaBH 4 oxidation produced an intense detection signal. The label-free electrochemical method achieved the detection of carcinoembryonic antigen (CEA) with a linear range from 10 −15 to 10 −11  g mL −1 and a detection limit of 0.43 × 10 −15  g mL −1 . Through introducing a supersandwich reaction to increase the DNA length, the electrochemical signal was further amplified, leading to a detection limit of 0.52 × 10 −16  g mL −1 . And it rendered satisfactory analytical performance for the determination of CEA in serum samples. Furthermore, it exhibited good reproducibility and stability; meanwhile, it also showed excellent specificity due to the specific recognition of antigen by antibody. Therefore, the DNA template synthesized Pd nanoparticles based signal amplification approach has great potential in clinical applications and is also suitable for quantification of biomarkers at ultralow level. - Graphical abstract: A novel label-free and enzyme-free electrochemical immunoassay based on proximity hybridization-regulated catalytic DNA hairpin assemblies for recycling of the CEA. - Highlights: • A novel enzyme-free electrochemical immunosensor was developed for detection of CEA. • The signal amplification was based on catalytic DNA hairpin assembly and DNA-template-synthesized Pd nanoparticles. • The biosensor could detect CEA down to 0.52 × 10 −16  g mL −1 level with a dynamic range spanning 5 orders of magnitude.

Applying Mesoporous Silica SBA-15 in Electrochemical Detection of DNA Hybridization

Czech Academy of Sciences Publication Activity Database

Josypčuk, Oksana; Fojta, Miroslav; Daňhel, Aleš; Josypčuk, Bohdan

2016-01-01

Roč. 28, č. 8 (2016), s. 1860-1864 ISSN 1040-0397 R&D Projects: GA ČR GAP206/11/1638 Institutional support: RVO:68081707 ; RVO:61388955 Keywords : voltammetry * sensor DNA hybridization * mesoporous silica Subject RIV: CG - Electrochemistry Impact factor: 2.851, year: 2016

Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

Science.gov (United States)

Roever, Stefan

2012-01-01

A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

Electrochemically fabricated polyaniline nanowire-modified electrode for voltammetric detection of DNA hybridization

International Nuclear Information System (INIS)

Zhu Ningning; Chang Zhu; He Pingang; Fang Yuzhi

2006-01-01

A novel and sensitive electrochemical DNA biosensor based on electrochemically fabricated polyaniline nanowire and methylene blue for DNA hybridization detection is presented. Nanowires of conducting polymers were directly synthesized through a three-step electrochemical deposition procedure in an aniline-containing electrolyte solution, by using the glassy carbon electrode (GCE) as the working electrode. The morphology of the polyaniline films was examined using a field emission scanning electron microscope (SEM). The diameters of the nanowires range from 80 to 100 nm. The polyaniline nanowires-coated electrode exhibited very good electrochemical conductivity. Oligonucleotides with phosphate groups at the 5' end were covalently linked onto the amino groups of polyaniline nanowires on the electrode. The hybridization events were monitored with differential pulse voltammetry (DPV) measurement using methylene blue (MB) as an indicator. The approach described here can effectively discriminate complementary from non-complementary DNA sequence, with a detection limit of 1.0 x 10 -12 mol l -1 of complementary target, suggesting that the polyaniline nanowires hold great promises for sensitive electrochemical biosensor applications

Development of a PCR/LDR/flow-through hybridization assay using a capillary tube, probe DNA-immobilized magnetic beads and chemiluminescence detection.

Science.gov (United States)

Hommatsu, Manami; Okahashi, Hisamitsu; Ohta, Keisuke; Tamai, Yusuke; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

2013-01-01

A polymerase chain reaction (PCR)/ligase detection reaction (LDR)/flow-through hybridization assay using chemiluminescence (CL) detection was developed for analyzing point mutations in gene fragments with high diagnostic value for colorectal cancers. A flow-through hybridization format using a capillary tube, in which probe DNA-immobilized magnetic beads were packed, provided accelerated hybridization kinetics of target DNA (i.e. LDR product) to the probe DNA. Simple fluid manipulations enabled both allele-specific hybridization and the removal of non-specifically bound DNA in the wash step. Furthermore, the use of CL detection greatly simplified the detection scheme, since CL does not require a light source for excitation of the fluorescent dye tags on the LDR products. Preliminary results demonstrated that this analytical system could detect both homozygous and heterozygous mutations, without the expensive instrumentation and cumbersome procedures required by conventional DNA microarray-based methods.

Removal of thorium (IV) ions from aqueous solution by a novel nanoporous ZnO: Isotherms, kinetic and thermodynamic studies.

Science.gov (United States)

Kaynar, Ümit H; Ayvacıklı, Mehmet; Hiçsönmez, Ümran; Kaynar, Sermin Çam

2015-12-01

The adsorption of thorium (IV) from aqueous solutions onto a novel nanoporous ZnO particles prepared by microwave assisted combustion was studied using batch methods under different experimental conditions. The effect of contact time, solution pH, initial concentration and temperature on adsorption process was studied. The ability of this material to remove Th (IV) from aqueous solution was characterises by Langmuir, Freunlinch and Temkin adsorption isotherms. The adsorption percent and distribution coefficient for nanoporous ZnO powders in optimum conditions were 97% ± 1.02; 8080 L kg(-1)for Th (IV), respectively. Based on the Langmuir model, the maximum adsorption capacity of nanoporous ZnO for Th (IV) was found to be 1500 g kg(-1). Thermodynamic parameters were determined and discussed. The results indicated that nanoporous ZnO was suitable as sorbent material for recovery and adsorption of Th (IV) ions from aqueous solutions. The radioactive Th (VI) in surface water, sea water and waste waters from technologies producing nuclear fuels, mining (uranium and thorium) and laboratories working with radioactive materials (uranium and thorium) can be removed with this nanoporous ZnO. Copyright © 2015 Elsevier Ltd. All rights reserved.

DNA hybridization evidence for the Australasian affinity of the American marsupial Dromiciops australis.

OpenAIRE

Kirsch, J A; Dickerman, A W; Reig, O A; Springer, M S

1991-01-01

DNA hybridization was used to compare representatives of the major groups of marsupials and a eutherian outgroup. Because of the large genetic distances separating marsupial families, trees were calculated from normalized percentages of hybridization; thermal-melting statistics, however, gave identical topologies for the well-supported clades. The most notable results were the association of the only extant microbiotheriid, Dromiciops australis, an American marsupial, with the Australasian Di...

Thermal conductivity model for nanoporous thin films

Science.gov (United States)

Huang, Congliang; Zhao, Xinpeng; Regner, Keith; Yang, Ronggui

2018-03-01

Nanoporous thin films have attracted great interest because of their extremely low thermal conductivity and potential applications in thin thermal insulators and thermoelectrics. Although there are some numerical and experimental studies about the thermal conductivity of nanoporous thin films, a simplified model is still needed to provide a straightforward prediction. In this paper, by including the phonon scattering lifetimes due to film thickness boundary scattering, nanopore scattering and the frequency-dependent intrinsic phonon-phonon scattering, a fitting-parameter-free model based on the kinetic theory of phonon transport is developed to predict both the in-plane and the cross-plane thermal conductivities of nanoporous thin films. With input parameters such as the lattice constants, thermal conductivity, and the group velocity of acoustic phonons of bulk silicon, our model shows a good agreement with available experimental and numerical results of nanoporous silicon thin films. It illustrates that the size effect of film thickness boundary scattering not only depends on the film thickness but also on the size of nanopores, and a larger nanopore leads to a stronger size effect of the film thickness. Our model also reveals that there are different optimal structures for getting the lowest in-plane and cross-plane thermal conductivities.

Thermal stability of DNA quadruplex-duplex hybrids.

Science.gov (United States)

Lim, Kah Wai; Khong, Zi Jian; Phan, Anh Tuân

2014-01-14

DNA has the capacity to adopt several distinct structural forms, such as duplex and quadruplex helices, which have been implicated in cellular processes and shown to exhibit important functional properties. Quadruplex-duplex hybrids, generated from the juxtaposition of these two structural elements, could find applications in therapeutics and nanotechnology. Here we used NMR and CD spectroscopy to investigate the thermal stability of two classes of quadruplex-duplex hybrids comprising fundamentally distinct modes of duplex and quadruplex connectivity: Construct I involves the coaxial orientation of the duplex and quadruplex helices with continual base stacking across the two components; Construct II involves the orthogonal orientation of the duplex and quadruplex helices with no base stacking between the two components. We have found that for both constructs, the stability of the quadruplex generally increases with the length of the stem-loop incorporated, with respect to quadruplexes comprising nonstructured loops of the same length, which showed a continuous drop in stability with increasing loop length. The stability of these complexes, particularly Construct I, can be substantially influenced by the base-pair steps proximal to the quadruplex-duplex junction. Bulges at the junction are largely detrimental to the adoption of the desired G-quadruplex topology for Construct I but not for Construct II. These findings should facilitate future design and prediction of quadruplex-duplex hybrids.

Sequencing of megabase plus DNA by hybridization: Method development ENT. Final technical progress report

Energy Technology Data Exchange (ETDEWEB)

Crkvenjakov, R.; Drmanac, R.

1991-01-31

Sequencing by hybridization (SBH) is the only sequencing method based on the experimental determination of the content of oligonucleotide sequences. The data acquisition relies on the natural process of base pairing. It is possible to determine the content of complementary oligosequences in the target DNA by the process of hybridization with oligonucleotide probes of known sequences.

DNA origami/gold nanorod hybrid nanostructures for the circumvention of drug resistance.

Science.gov (United States)

Song, Linlin; Jiang, Qiao; Liu, Jianbing; Li, Na; Liu, Qing; Dai, Luru; Gao, Yuan; Liu, Weili; Liu, Dongsheng; Ding, Baoquan

2017-06-14

We herein demonstrate that DNA origami can work as a multifunctional platform integrating a chemotherapeutic drug (doxorubicin), gold nanorods and a tumour-specific aptamer MUC-1, to realize the effective circumvention of drug resistance. Doxorubicin (DOX) was loaded efficiently onto DNA origami through base pair intercalation and surface-modified gold nanorods (AuNRs) were assembled onto the DNA origami through DNA hybridization. Due to the active targeting effect of the assembled aptamers, the multifunctional nanostructures achieved increased cellular internalization of DOX and AuNRs. Upon near-infrared (NIR) laser irradiation, the P-glycoprotein (multidrug resistance pump) expression of multidrug resistant MCF-7 (MCF-7/ADR) cells was down-regulated, achieving the synergistically chemotherapeutic (DOX) and photothermal (AuNRs) effects.

Highly active thermally stable nanoporous gold catalyst

Energy Technology Data Exchange (ETDEWEB)

Biener, Juergen; Wittstock, Arne; Biener, Monika M.; Bagge-Hansen, Michael; Baeumer, Marcus; Wichmann, Andre; Neuman, Bjoern

2016-12-20

In one embodiment, a system includes a nanoporous gold structure and a plurality of oxide particles deposited on the nanoporous gold structure; the oxide particles are characterized by a crystalline phase. In another embodiment, a method includes depositing oxide nanoparticles on a nanoporous gold support to form an active structure and functionalizing the deposited oxide nanoparticles.

Adiabatic burst evaporation from bicontinuous nanoporous membranes

Science.gov (United States)

Ichilmann, Sachar; Rücker, Kerstin; Haase, Markus; Enke, Dirk

2015-01-01

Evaporation of volatile liquids from nanoporous media with bicontinuous morphology and pore diameters of a few 10 nm is an ubiquitous process. For example, such drying processes occur during syntheses of nanoporous materials by sol–gel chemistry or by spinodal decomposition in the presence of solvents as well as during solution impregnation of nanoporous hosts with functional guests. It is commonly assumed that drying is endothermic and driven by non-equilibrium partial pressures of the evaporating species in the gas phase. We show that nearly half of the liquid evaporates in an adiabatic mode involving burst-like liquid-to-gas conversions. During single adiabatic burst evaporation events liquid volumes of up to 107 μm3 are converted to gas. The adiabatic liquid-to-gas conversions occur if air invasion fronts get unstable because of the built-up of high capillary pressures. Adiabatic evaporation bursts propagate avalanche-like through the nanopore systems until the air invasion fronts have reached new stable configurations. Adiabatic cavitation bursts thus compete with Haines jumps involving air invasion front relaxation by local liquid flow without enhanced mass transport out of the nanoporous medium and prevail if the mean pore diameter is in the range of a few 10 nm. The results reported here may help optimize membrane preparation via solvent-based approaches, solution-loading of nanopore systems with guest materials as well as routine use of nanoporous membranes with bicontinuous morphology and may contribute to better understanding of adsorption/desorption processes in nanoporous media. PMID:25926406

Blue shift of CdSe/ZnS nanocrystal-labels upon DNA-hybridization

Directory of Open Access Journals (Sweden)

Palme Klaus

2008-05-01

Full Text Available Abstract Luminescence color multiplexing is one of the most intriguing benefits, which might occur by using semiconductor Quantum Dots (QDs as labels for biomolecules. It was found, that the luminescence of QDs can be quenched, and replaced by a luminescence peak at approximately 460 nm on hybridization with certain regions of Arabidopsis thaliana tissue. This effect is site selective, and it is unclear whether it occurs due to an energy transfer process, or due to quenching and scattering of the excitation light. The article describes methods for phase-transfer of differently coloured, hydrophobically ligated QDs, coupling of DNA strands to the QD's surface, and hybridization of the labelled DNA to different cell types of Arabidopsis thaliana. The reason for the luminescence blue-shift was studied systematically, and narrowed down to the above mentioned causes.

Mapping Base Modifications in DNA by Transverse-Current Sequencing

Science.gov (United States)

Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

2018-02-01

Sequencing DNA modifications and lesions, such as methylation of cytosine and oxidation of guanine, is even more important and challenging than sequencing the genome itself. The traditional methods for detecting DNA modifications are either insensitive to these modifications or require additional processing steps to identify a particular type of modification. Transverse-current sequencing in nanopores can potentially identify the canonical bases and base modifications in the same run. In this work, we demonstrate that the most common DNA epigenetic modifications and lesions can be detected with any predefined accuracy based on their tunneling current signature. Our results are based on simulations of the nanopore tunneling current through DNA molecules, calculated using nonequilibrium electron-transport methodology within an effective multiorbital model derived from first-principles calculations, followed by a base-calling algorithm accounting for neighbor current-current correlations. This methodology can be integrated with existing experimental techniques to improve base-calling fidelity.

Patterns of DNA methylation in development, division of labor and hybridization in an ant with genetic caste determination.

Directory of Open Access Journals (Sweden)

Chris R Smith

Full Text Available BACKGROUND: DNA methylation is a common regulator of gene expression, including acting as a regulator of developmental events and behavioral changes in adults. Using the unique system of genetic caste determination in Pogonomyrmex barbatus, we were able to document changes in DNA methylation during development, and also across both ancient and contemporary hybridization events. METHODOLOGY/PRINCIPAL FINDINGS: Sodium bisulfite sequencing demonstrated in vivo methylation of symmetric CG dinucleotides in P. barbatus. We also found methylation of non-CpG sequences. This validated two bioinformatics methods for predicting gene methylation, the bias in observed to expected ratio of CpG dinucleotides and the density of CpG/TpG single nucleotide polymorphisms (SNP. Frequencies of genomic DNA methylation were determined for different developmental stages and castes using ms-AFLP assays. The genetic caste determination system (GCD is probably the product of an ancestral hybridization event between P. barbatus and P. rugosus. Two lineages obligately co-occur within a GCD population, and queens are derived from intra-lineage matings whereas workers are produced from inter-lineage matings. Relative DNA methylation levels of queens and workers from GCD lineages (contemporary hybrids were not significantly different until adulthood. Virgin queens had significantly higher relative levels of DNA methylation compared to workers. Worker DNA methylation did not vary among developmental stages within each lineage, but was significantly different between the currently hybridizing lineages. Finally, workers of the two genetic caste determination lineages had half as many methylated cytosines as workers from the putative parental species, which have environmental caste determination. CONCLUSIONS/SIGNIFICANCE: These results suggest that DNA methylation may be a conserved regulatory mechanism moderating division of labor in both bees and ants. Current and historic

Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing.

Science.gov (United States)

Liu, Chang; Xiao, Fangzhou; Hoisington-Lopez, Jessica; Lang, Kathrin; Quenzel, Philipp; Duffy, Brian; Mitra, Robi David

2018-04-03

Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunologic compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. We developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) identifies candidate alleles with the highest read coverage at different resolution levels that are represented as branching nodes and leaves of a tree structure, iii) generates consensus sequences by remapping the reads to the candidate alleles, and iv) calls the final diploid genotype by blasting consensus sequences against the reference database. Using two independent data sets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the two-field resolution. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Controlling the role of nanopore morphology in capillary condensation.

Science.gov (United States)

Casanova, Fèlix; Chiang, Casey E; Ruminski, Anne M; Sailor, Michael J; Schuller, Ivan K

2012-05-01

The effect of pore morphology on capillary condensation and evaporation in nanoporous silicon is studied experimentally. A variety of cooperative and local effects are observed in tailored nanopores with well-defined regions by directly probing gas adsorption in each region using optical interferometry. All observations are ascribed to the ability of the nanopore region to access the gas reservoir directly and the nucleation of liquid bridges at local heterogeneities within the nanopore region. These assumptions, consistent with recent simulations, can be extended to any real nanoporous system.

In-situ electrochemical doping of nanoporous anodic aluminum oxide with indigo carmine organic dye

International Nuclear Information System (INIS)

Stępniowski, Wojciech J.; Norek, Małgorzata; Budner, Bogusław; Michalska-Domańska, Marta; Nowak-Stępniowska, Agata; Bombalska, Aneta; Kaliszewski, Miron; Mostek, Anna; Thorat, Sanjay; Salerno, Marco; Giersig, Michael; Bojar, Zbigniew

2016-01-01

Nanoporous anodic aluminum oxide was formed in sulfuric acid with addition of indigo carmine. During anodizing, the organic dye was incorporated into the porous oxide walls. X-ray photoelectron spectroscopy revealed the presence of nitrogen and sulfur in the anodic aluminum oxide. Two types of incorporated sulfur were found: belonging to the sulfate anions SO_4"2"− of the electrolyte and belonging to the C-SO_3"− side groups of the indigo carmine. Raman spectroscopy confirmed the incorporation and showed that the inorganic–organic hybrid material inherited optical properties from the indigo carmine. Typical modes from pyrrolidone rings, unique for indigo carmine in the investigated system (650 and 1585 cm"−"1), were found to be the strongest for the greatest anodizing voltages used. Despite the indigo carmine incorporation, the morphology of the oxide is still nanoporous and its geometry is still tuned by the voltage applied during aluminum anodization. This work presents an inexpensive and facile approach to doping an inorganic oxide material with organic compounds. - Highlights: • Nanoporous anodic alumina was formed in electrolyte with indigo carmine. • XPS confirmed the presence of N and S in anodic alumina. • Raman spectroscopy revealed indigo carmine bands in anodic alumina. • The higher the voltage, the more indigo carmine was incorporated.

Proximity hybridization-regulated catalytic DNA hairpin assembly for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Zhou, Fuyi [School of Chemistry and Chemical Engineering, Jiangsu Normal University, Xuzhou 221116 (China); Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical College, 221004, Xuzhou (China); Yao, Yao; Luo, Jianjun; Zhang, Xing; Zhang, Yu; Yin, Dengyang [Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical College, 221004, Xuzhou (China); Gao, Fenglei, E-mail: jsxzgfl@sina.com [Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical College, 221004, Xuzhou (China); Wang, Po, E-mail: wangpo@jsnu.edu.cn [School of Chemistry and Chemical Engineering, Jiangsu Normal University, Xuzhou 221116 (China)

2017-05-29

Novel hybridization proximity-regulated catalytic DNA hairpin assembly strategy has been proposed for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles as signal label. The DNA template-synthesized Pd nanoparticles were characterized with atomic force microscopic and X-ray photoelectron spectroscopy. The highly efficient electrocatalysis by DNA template synthesized Pd nanoparticles for NaBH{sub 4} oxidation produced an intense detection signal. The label-free electrochemical method achieved the detection of carcinoembryonic antigen (CEA) with a linear range from 10{sup −15} to 10{sup −11} g mL{sup −1} and a detection limit of 0.43 × 10{sup −15} g mL{sup −1}. Through introducing a supersandwich reaction to increase the DNA length, the electrochemical signal was further amplified, leading to a detection limit of 0.52 × 10{sup −16} g mL{sup −1}. And it rendered satisfactory analytical performance for the determination of CEA in serum samples. Furthermore, it exhibited good reproducibility and stability; meanwhile, it also showed excellent specificity due to the specific recognition of antigen by antibody. Therefore, the DNA template synthesized Pd nanoparticles based signal amplification approach has great potential in clinical applications and is also suitable for quantification of biomarkers at ultralow level. - Graphical abstract: A novel label-free and enzyme-free electrochemical immunoassay based on proximity hybridization-regulated catalytic DNA hairpin assemblies for recycling of the CEA. - Highlights: • A novel enzyme-free electrochemical immunosensor was developed for detection of CEA. • The signal amplification was based on catalytic DNA hairpin assembly and DNA-template-synthesized Pd nanoparticles. • The biosensor could detect CEA down to 0.52 × 10{sup −16} g mL{sup −1} level with a dynamic range spanning 5 orders of magnitude.

Exciton-controlled fluorescence: application to hybridization-sensitive fluorescent DNA probe.

Science.gov (United States)

Okamoto, Akimitsu; Ikeda, Shuji; Kubota, Takeshi; Yuki, Mizue; Yanagisawa, Hiroyuki

2009-01-01

A hybridization-sensitive fluorescent probe has been designed for nucleic acid detection, using the concept of fluorescence quenching caused by the intramolecular excitonic interaction of fluorescence dyes. We synthesized a doubly thiazole orange-labeled nucleotide showing high fluorescence intensity for a hybrid with the target nucleic acid and effective quenching for the single-stranded state. This exciton-controlled fluorescent probe was applied to living HeLa cells using microinjection to visualize intracellular mRNA localization. Immediately after injection of the probe into the cell, fluorescence was observed from the probe hybridizing with the target RNA. This fluorescence rapidly decreased upon addition of a competitor DNA. Multicoloring of this probe resulted in the simple simultaneous detection of plural target nucleic acid sequences. This probe realized a large, rapid, reversible change in fluorescence intensity in sensitive response to the amount of target nucleic acid, and facilitated spatiotemporal monitoring of the behavior of intracellular RNA.

Detection of TTV-DNA in PBMC using digoxigenin labelled probe by in situ hybridization

International Nuclear Information System (INIS)

Liu Yang; Qi Qige

2002-01-01

To determine TTV-DNA in PBMC in patients with viral hepatitis, a study of in situ hybridization using digoxigenin labelled probe by PCR method to the TTV ORF1 region was performed on PBMC. Results showed that the detection rate of TTV-DNA using double-stranded probe in TTV-DNA positive group in sera was 58.06 (18/31), and the detection rate of TTV-DNA using double-stranded probe in TTV-DNA negative group in sera was 27.59 (8/29). For TTV-DNA positive group detected by double- stranded probe, then we use negative- stranded probe to detect their replication. The detection rate was 22.2%(4/18). Conclusions: TTV can infect PBMC and replicate in PBMC

Gold nano particle decorated graphene core first generation PAMAM dendrimer for label free electrochemical DNA hybridization sensing.

Science.gov (United States)

Jayakumar, K; Rajesh, R; Dharuman, V; Venkatasan, R; Hahn, J H; Pandian, S Karutha

2012-01-15

A novel first generation (G1) poly(amidoamine) dendrimer (PAMAM) with graphene core (GG1PAMAM) was synthesized for the first time. Single layer of GG1PAMAM was immobilized covalently on mercaptopropionic acid (MPA) monolayer on Au transducer. This allows cost effective and easy deposition of single layer graphene on the Au transducer surface than the advanced vacuum techniques used in the literature. Au nano particles (17.5 nm) then decorated the GG1PAMAM and used for electrochemical DNA hybridization sensing. The sensor discriminates selectively and sensitively the complementary double stranded DNA (dsDNA, hybridized), non-complementary DNA (ssDNA, un-hybridized) and single nucleotide polymorphism (SNP) surfaces. Interactions of the MPA, GG1PAMAM and the Au nano particles were characterized by Ultra Violet (UV), Fourier Transform Infrared (FTIR), Raman spectroscopy (RS), Thermo gravimetric analysis (TGA), Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Cyclic Voltmetric (CV), Impedance spectroscopy (IS) and Differntial Pulse Voltammetry (DPV) techniques. The sensor showed linear range 1×10(-6) to 1×10(-12) M with lowest detection limit 1 pM which is 1000 times lower than G1PAMAM without graphene core. Copyright © 2011 Elsevier B.V. All rights reserved.

Gyroid nanoporous scaffold for conductive polymers

DEFF Research Database (Denmark)

Guo, Fengxiao; Schulte, Lars; Zhang, Weimin

2011-01-01

Conductive nanoporous polymers with interconnected large surface area have been prepared by depositing polypyrrole onto nanocavity walls of nanoporous 1,2-polybutadiene films with gyroid morphology. Vapor phase polymerization of pyrrole was used to generate ultrathin films and prevent pore blocking...

Nanoporous titanium niobium oxide and titanium tantalum oxide compositions and their use in anodes of lithium ion batteries

Science.gov (United States)

Dai, Sheng; Guo, Bingkun; Sun, Xiao-Guang; Qiao, Zhenan

2017-10-31

Nanoporous metal oxide framework compositions useful as anodic materials in a lithium ion battery, the composition comprising metal oxide nanocrystals interconnected in a nanoporous framework and having interconnected channels, wherein the metal in said metal oxide comprises titanium and at least one metal selected from niobium and tantalum, e.g., TiNb.sub.2-x Ta.sub.xO.sub.y (wherein x is a value from 0 to 2, and y is a value from 7 to 10) and Ti.sub.2Nb.sub.10-vTa.sub.vO.sub.w (wherein v is a value from 0 to 2, and w is a value from 27 to 29). A novel sol gel method is also described in which sol gel reactive precursors are combined with a templating agent under sol gel reaction conditions to produce a hybrid precursor, and the precursor calcined to form the anodic composition. The invention is also directed to lithium ion batteries in which the nanoporous framework material is incorporated in an anode of the battery.

Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study.

Science.gov (United States)

Suresh, Gorle; Priyakumar, U Deva

2015-09-01

Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2'-position attribute special properties to nucleic acids when compared to other modifications. 2'-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2'-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2'-O-methyl modified counterparts to investigate the effect of 2'-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes. Copyright © 2015 Elsevier Inc. All rights reserved.

Magnetoresistive sensors for measurements of DNA hybridization kinetics - effect of TINA modifications

DEFF Research Database (Denmark)

Rizzi, Giovanni; Dufva, Martin; Hansen, Mikkel Fougt

2017-01-01

We present the use of magnetoresistive sensors integrated in a microfluidic system for real-time studies of the hybridization kinetics of DNA labeled with magnetic nanoparticles to an array of surface-tethered probes. The nanoparticles were magnetized by the magnetic field from the sensor current....... A local negative reference ensured that only the specific binding signal was measured. Analysis of the real-time hybridization using a two-compartment model yielded both the association and dissociation constants kon, and koff. The effect of probe modifications with ortho-Twisted Intercalating Nucleic...

The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation

International Nuclear Information System (INIS)

Chen, Chung H.

2004-01-01

The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation

Direct deposition of inorganic–organic hybrid semiconductors and their template-assisted microstructures

International Nuclear Information System (INIS)

Dwivedi, V.K.; Baumberg, J.J.; Prakash, G. Vijaya

2013-01-01

A straight-forward method is developed to deposit a new class of self-organized inorganic–organic (IO) hybrid, (C 12 H 25 NH 3 ) 2 PbI 4 . These IO hybrid structures are stacked-up as natural multiple quantum well structures and exhibit strong room-temperature exciton emission and other multifunctional features. Here it is successfully demonstrated that these materials can be directly carved into 2D photonic structures from the inexpensive template-assisted electrochemical deposition followed by solution processing. The applicability of this method for many such varieties of IO-hybrids is also explored. By appropriately controlling the deposition conditions and the self-assembly templates, target structures are developed for new-generation low-cost photonic devices. -- Highlights: ► New fabrication methodology for self-organized inorganic–organic hybrids. ► Strongly confined exciton emission and photoconductive properties. ► Simple bottom-up fabrication for device applications.

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. II. Isothermal signal amplification in process of DNA analysis by minisequencing].

Science.gov (United States)

Dmitrienko, E V; Khomiakova, E A; Pyshnaia; Bragin, A G; Vedernikov, V E; Pyshnyĭ, D V

2010-01-01

The isothermal amplification of reporter signal via limited probe extension (minisequencing) upon hybridization of nucleic acids has been studied. The intensity of reporter signal has been shown to increase due to enzymatic labeling of multiple probes upon consecutive hybridization with one DNA template both in homophase and heterophase assays using various kinds of detection signal: radioisotope label, fluorescent label, and enzyme-linked assay. The kinetic scheme of the process has been proposed and kinetic parameters for each step have been determined. The signal intensity has been shown to correlate with physicochemical characteristics of both complexes: probe/DNA and product/DNA. The maximum intensity has been observed at minimal difference between the thermodynamic stability of these complexes, provided the reaction temperature has been adjusted near their melting temperature values; rising or lowering the reaction temperature reduces the amount of reporting product. The signal intensity has been shown to decrease significantly upon hybridization with the DNA template containing single-nucleotide mismatches. Limited probe extension assay is useful not only for detection of DNA template but also for its quantitative characterization.

5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH

Directory of Open Access Journals (Sweden)

Jaime Gosálvez

2013-02-01

Full Text Available We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH. A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL, 10 with high-grade SIL (HG-SIL, and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1.

5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH).

Science.gov (United States)

Cortés-Gutiérrez, Elva I; Ortíz-Hernández, Brenda L; Dávila-Rodríguez, Martha I; Cerda-Flores, Ricardo M; Fernández, José Luis; López-Fernández, Carmen; Gosálvez, Jaime

2013-02-19

We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH). A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL), 10 with high-grade SIL (HG-SIL), and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1.

An easy two-step microwave assisted synthesis of SnO2/CNT hybrids

CSIR Research Space (South Africa)

Motshekga, SC

2011-11-01

Full Text Available Tin oxide (SnO2) - decorated carbon nanotube (CNT) heterostructures were synthesized by microwave assisted wet impregnation method. CNTs of three different aspect ratios were compared. The hybrid samples were characterized by powder X...

Antibacterial activity of zinc oxide-coated nanoporous alumina

Energy Technology Data Exchange (ETDEWEB)

Skoog, S.A. [Joint Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Box 7115, Raleigh, NC 27695-7115 (United States); Bayati, M.R. [Department of Materials Science and Engineering, North Carolina State University, Box 7907, Raleigh, NC 27695-7907 (United States); Petrochenko, P.E. [Joint Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Box 7115, Raleigh, NC 27695-7115 (United States); Division of Biology, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD 20993 (United States); Stafslien, S.; Daniels, J.; Cilz, N. [Center for Nanoscale Science and Engineering, North Dakota State University, 1805 Research Park Drive, Fargo, ND 58102 (United States); Comstock, D.J.; Elam, J.W. [Energy Systems Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Narayan, R.J., E-mail: roger_narayan@msn.com [Joint Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Box 7115, Raleigh, NC 27695-7115 (United States); Department of Materials Science and Engineering, North Carolina State University, Box 7907, Raleigh, NC 27695-7907 (United States)

2012-07-25

Highlights: Black-Right-Pointing-Pointer Atomic layer deposition was used to deposit ZnO on nanoporous alumina membranes. Black-Right-Pointing-Pointer Scanning electron microscopy showed continuous coatings of zinc oxide nanocrystals. Black-Right-Pointing-Pointer Activity against B. subtilis, E. coli, S. aureus, and S. epidermidis was shown. - Abstract: Nanoporous alumina membranes, also known as anodized aluminum oxide membranes, are being investigated for use in treatment of burn injuries and other skin wounds. In this study, atomic layer deposition was used for coating the surfaces of nanoporous alumina membranes with zinc oxide. Agar diffusion assays were used to show activity of zinc oxide-coated nanoporous alumina membranes against several bacteria found on the skin surface, including Bacillus subtilis, Escherichia coli, Staphylococcus aureus, and Staphylococcus epidermidis. On the other hand, zinc oxide-coated nanoporous alumina membranes did not show activity against Pseudomonas aeruginosa, Enterococcus faecalis, and Candida albicans. These results suggest that zinc oxide-coated nanoporous alumina membranes have activity against some Gram-positive and Gram-negative bacteria that are associated with skin colonization and skin infection.

A microfabricated hybrid device for DNA sequencing.

Science.gov (United States)

Liu, Shaorong

2003-11-01

We have created a hybrid device of a microfabricated round-channel twin-T injector incorporated with a separation capillary in order to extend the straight separation distance for high speed and long readlength DNA sequencing. Semicircular grooves on glass wafers are obtained using a photomask with a narrow line-width and a standard isotropic photolithographic etching process. Round channels are made when two etched wafers are face-to-face aligned and bonded. A two-mask fabrication process has been developed to make channels of two different diameters. The twin-T injector is formed by the smaller channels whose diameter matches the bore of the separation capillary, and the "usual" separation channel, now called the connection channel, is formed by the larger ones whose diameter matches the outer diameter of the separation capillary. The separation capillary is inserted through the connection channel all the way to the twin-T injector to allow the capillary bore flush with the twin-T injector channels. The total dead-volume of the connection is estimated to be approximately 5 pL. To demonstrate the efficiency of this hybrid device, we have performed four-color DNA sequencing on it. Using a 200 microm twin-T injector coupled with a separation capillary of 20 cm effective separation distance, we have obtained readlengths of 800 plus bases at an accuracy of 98.5% in 56 min, compared to about 650 bases in 100 min on a conventional 40 cm long capillary sequencing machine under similar conditions. At an increased separation field strength and using a diluted sieving matrix, the separation time has been reduced to 20 min with a readlength of 700 bases at 98.5% base-calling accuracy.

Stabilization of Pt nanoparticles by single stranded DNA and the binary assembly of Au and Pt nanoparticles without hybridization

International Nuclear Information System (INIS)

Yang, J.; Lee, Jim Yang; Too, Heng-Phon; Chow, Gan-Moog; Gan, Leong M.

2006-01-01

The non-specific interaction between single stranded DNA (ssDNA) and 12 nm Pt nanoparticles is investigated in this work. The data show a strong and non-specific interaction between the two which can be exploited for the stabilization of Pt nanoparticles in aqueous solutions. Based on the experimental findings, a non-hybridization based protocol to assemble 17 nm Au and Pt nanoparticles (12 nm cubic and 3.6 nm spherical) by single-stranded DNA was developed. Transmission electron microscopy (TEM) and UV-visible spectroscopy confirmed that Au and Pt nanoparticles could be assembled by the non-specific interaction in an orderly manner. The experimental results also caution against the potential pitfalls in using DNA melting point analysis to infer metal nanoparticle assembly by DNA hybridization

Synthesis of ordered large-scale ZnO nanopore arrays

International Nuclear Information System (INIS)

Ding, G.Q.; Shen, W.Z.; Zheng, M.J.; Fan, D.H.

2006-01-01

An effective approach is demonstrated for growing ordered large-scale ZnO nanopore arrays through radio-frequency magnetron sputtering deposition on porous alumina membranes (PAMs). The realization of highly ordered hexagonal ZnO nanopore arrays benefits from the unique properties of ZnO (hexagonal structure, polar surfaces, and preferable growth directions) and PAMs (controllable hexagonal nanopores and localized negative charges). Further evidence has been shown through the effects of nanorod size and thermal treatment of PAMs on the yielded morphology of ZnO nanopore arrays. This approach opens the possibility of creating regular semiconducting nanopore arrays for the application of filters, sensors, and templates

Polyelectrolyte layer-by-layer deposition in cylindrical nanopores.

Science.gov (United States)

Lazzara, Thomas D; Lau, K H Aaron; Abou-Kandil, Ahmed I; Caminade, Anne-Marie; Majoral, Jean-Pierre; Knoll, Wolfgang

2010-07-27

Layer-by-layer (LbL) deposition of polyelectrolytes within nanopores in terms of the pore size and the ionic strength was experimentally studied. Anodic aluminum oxide (AAO) membranes, which have aligned, cylindrical, nonintersecting pores, were used as a model nanoporous system. Furthermore, the AAO membranes were also employed as planar optical waveguides to enable in situ monitoring of the LbL process within the nanopores by optical waveguide spectroscopy (OWS). Structurally well-defined N,N-disubstituted hydrazine phosphorus-containing dendrimers of the fourth generation, with peripherally charged groups and diameters of approximately 7 nm, were used as the model polyelectrolytes. The pore diameter of the AAO was varied between 30-116 nm and the ionic strength was varied over 3 orders of magnitude. The dependence of the deposited layer thickness on ionic strength within the nanopores is found to be significantly stronger than LbL deposition on a planar surface. Furthermore, deposition within the nanopores can become inhibited even if the pore diameter is much larger than the diameter of the G4-polyelectrolyte, or if the screening length is insignificant relative to the dendrimer diameter at high ionic strengths. Our results will aid in the template preparation of polyelectrolyte multilayer nanotubes, and our experimental approach may be useful for investigating theories regarding the partitioning of nano-objects within nanopores where electrostatic interactions are dominant. Furthermore, we show that the enhanced ionic strength dependence of polyelectrolyte transport within the nanopores can be used to selectively deposit a LbL multilayer atop a nanoporous substrate.

Mapping DNA methylation by transverse current sequencing: Reduction of noise from neighboring nucleotides

Science.gov (United States)

Alvarez, Jose; Massey, Steven; Kalitsov, Alan; Velev, Julian

Nanopore sequencing via transverse current has emerged as a competitive candidate for mapping DNA methylation without needed bisulfite-treatment, fluorescent tag, or PCR amplification. By eliminating the error producing amplification step, long read lengths become feasible, which greatly simplifies the assembly process and reduces the time and the cost inherent in current technologies. However, due to the large error rates of nanopore sequencing, single base resolution has not been reached. A very important source of noise is the intrinsic structural noise in the electric signature of the nucleotide arising from the influence of neighboring nucleotides. In this work we perform calculations of the tunneling current through DNA molecules in nanopores using the non-equilibrium electron transport method within an effective multi-orbital tight-binding model derived from first-principles calculations. We develop a base-calling algorithm accounting for the correlations of the current through neighboring bases, which in principle can reduce the error rate below any desired precision. Using this method we show that we can clearly distinguish DNA methylation and other base modifications based on the reading of the tunneling current.

DNA Methylation Alterations at 5'-CCGG Sites in the Interspecific and Intraspecific Hybridizations Derived from Brassica rapa and B. napus.

Directory of Open Access Journals (Sweden)

Wanshan Xiong

Full Text Available DNA methylation is an important regulatory mechanism for gene expression that involved in the biological processes of development and differentiation in plants. To investigate the association of DNA methylation with heterosis in Brassica, a set of intraspecific hybrids in Brassica rapa and B. napus and interspecific hybrids between B. rapa and B. napus, together with parental lines, were used to monitor alterations in cytosine methylation at 5'-CCGG sites in seedlings and buds by methylation-sensitive amplification polymorphism analysis. The methylation status of approximately a quarter of the methylation sites changed between seedlings and buds. These alterations were related closely to the genomic structure and heterozygous status among accessions. The methylation status in the majority of DNA methylation sites detected in hybrids was the same as that in at least one of the parental lines in both seedlings and buds. However, the association between patterns of cytosine methylation and heterosis varied among different traits and between tissues in hybrids of Brassica, although a few methylation loci were associated with heterosis. Our data suggest that changes in DNA methylation at 5'-CCGG sites are not associated simply with heterosis in the interspecific and intraspecific hybridizations derived from B. rapa and B. napus.

Designing robust alumina nanowires-on-nanopores structures: superhydrophobic surfaces with slippery or sticky water adhesion.

Science.gov (United States)

Peng, Shan; Tian, Dong; Miao, Xinrui; Yang, Xiaojun; Deng, Wenli

2013-11-01

Hierarchical alumina surfaces with different morphologies were fabricated by a simple one-step anodization method. These alumina films were fabricated by a new raw material: silica gel plate (aluminum foil with a low purity of 97.17%). The modulation of anodizing time enabled the formation of nanowires-on-nanopores hybrid nanostructures having controllable nanowires topographies through a self-assembly process. The resultant structures were demonstrated to be able to achieve superhydrophobicity without any hydrophobic coating layer. More interestingly, it is found that the as-prepared superhydrophobic alumina surfaces exhibited high contrast water adhesion. Hierarchical alumina film with nanowire bunches-on-nanopores (WBOP) morphology presents extremely slippery property which can obtain a sliding angle (SA) as low as 1°, nanowire pyramids-on-nanopores (WPOP) structure shows strongly sticky water adhesion with the adhesive ability to support 15 μL inverted water droplet at most. The obtained superhydrophobic alumina surfaces show remarkable mechanical durability even treated by crimping or pressing without impact on the water-repellent performance. Moreover, the created surfaces also show excellent resistivity to ice water, boiling water, high temperature, organic solvent and oil contamination, which could expand their usefulness and efficacy in harsh conditions. Copyright © 2013 Elsevier Inc. All rights reserved.

Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus revealed by analyses of multiple mitochondrial and nuclear DNA loci

Directory of Open Access Journals (Sweden)

Wu Shi-Fang

2011-07-01

Full Text Available Abstract Background Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. Results Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. Conclusion This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.

UV Defined Nanoporous Liquid Core Waveguides

DEFF Research Database (Denmark)

Christiansen, Mads Brøkner; Gopalakrishnan, Nimi; Ndoni, Sokol

2011-01-01

Nanoporous liquid core waveguides, where both core and cladding are made from the same material, are presented. The nanoporous polymer used is intrinsically hydrophobic, but selective UV exposure enables it to infiltrate with an aqueous solution, thus raising the refractive index from 1.26 to 1...

Nanoparticle mechanics: deformation detection via nanopore resistive pulse sensing

Science.gov (United States)

Darvish, Armin; Goyal, Gaurav; Aneja, Rachna; Sundaram, Ramalingam V. K.; Lee, Kidan; Ahn, Chi Won; Kim, Ki-Bum; Vlahovska, Petia M.; Kim, Min Jun

2016-07-01

Solid-state nanopores have been widely used in the past for single-particle analysis of nanoparticles, liposomes, exosomes and viruses. The shape of soft particles, particularly liposomes with a bilayer membrane, can greatly differ inside the nanopore compared to bulk solution as the electric field inside the nanopores can cause liposome electrodeformation. Such deformations can compromise size measurement and characterization of particles, but are often neglected in nanopore resistive pulse sensing. In this paper, we investigated the deformation of various liposomes inside nanopores. We observed a significant difference in resistive pulse characteristics between soft liposomes and rigid polystyrene nanoparticles especially at higher applied voltages. We used theoretical simulations to demonstrate that the difference can be explained by shape deformation of liposomes as they translocate through the nanopores. Comparing our results with the findings from electrodeformation experiments, we demonstrated that the rigidity of liposomes can be qualitatively compared using resistive pulse characteristics. This application of nanopores can provide new opportunities to study the mechanics at the nanoscale, to investigate properties of great value in fundamental biophysics and cellular mechanobiology, such as virus deformability and fusogenicity, and in applied sciences for designing novel drug/gene delivery systems.Solid-state nanopores have been widely used in the past for single-particle analysis of nanoparticles, liposomes, exosomes and viruses. The shape of soft particles, particularly liposomes with a bilayer membrane, can greatly differ inside the nanopore compared to bulk solution as the electric field inside the nanopores can cause liposome electrodeformation. Such deformations can compromise size measurement and characterization of particles, but are often neglected in nanopore resistive pulse sensing. In this paper, we investigated the deformation of various

Controlling Ionic Transport for Device Design in Synthetic Nanopores

Science.gov (United States)

Kalman, Eric Boyd

Polymer nanopores present a number of behaviors not seen in microscale systems, such as ion current rectification, ionic selectivity, size exclusion and potential dependent ion concentrations in and near the pore. The existence of these effects stems from the small size of nanopores with respect to the characteristic length scales of surface interactions at the interface between the nanopore surface and the solution within it. The large surface-to-volume ratio due to the nanoscale geometry of a nanopore, as well as similarity in scale between geometry and interaction demands the solution interact with the nanopore walls. As surfaces in solution almost always carry residual charge, these surface forces are primarily the electrostatic interactions between the charge groups on the pore surface and the ions in solution. These interactions may be used by the experimentalist to control ionic transport through synthetic nanopores, and use them as a template for the construction of devices. In this research, we present our work on creating a number of ionic analogs to seminal electronic devices, specifically diodes, and transistors, by controlling ionic transport through the electrostatic interactions between a single synthetic nanopore and ions. Control is achieved by "doping" the effective charge carrier concentration in specific regions of the nanopore through manipulation of the pore's surface charge. This manipulation occurs through two mechanisms: chemical modification of the surface charge and electrostatic manipulation of the local internal nanopore potential using a gate electrode. Additionally, the innate selectivity of the charged nanopores walls allows for the separation of charges in solution. This well-known effect, which spawns measureable quantities, the streaming potential and current, has been used to create nanoscale water desalination membranes. We attempt to create a device using membranes with large nanopore densities for the desalination of water

Ab initio Calculations of Electronic Fingerprints of DNA bases on Graphene

Science.gov (United States)

Ahmed, Towfiq; Rehr, John J.; Kilina, Svetlana; Das, Tanmoy; Haraldsen, Jason T.; Balatsky, Alexander V.

2012-02-01

We have carried out first principles DFT calculations of the electronic local density of states (LDOS) of DNA nucleotide bases (A,C,G,T) adsorbed on graphene using LDA with ultra-soft pseudo-potentials. We have also calculated the longitudinal transmission currents T(E) through graphene nano-pores as an individual DNA base passes through it, using a non-equilibrium Green's function (NEGF) formalism. We observe several dominant base-dependent features in the LDOS and T(E) in an energy range within a few eV of the Fermi level. These features can serve as electronic fingerprints for the identification of individual bases from dI/dV measurements in scanning tunneling spectroscopy (STS) and nano-pore experiments. Thus these electronic signatures can provide an alternative approach to DNA sequencing.

AFM Imaging of Hybridization Chain Reaction-Mediated Signal Transmission Between two DNA Origami Structures

DEFF Research Database (Denmark)

Helmig, Sarah Wendelbo; Gothelf, Kurt Vesterager

2017-01-01

transfer between two connected DNA nanostructures, using the hybridization chain reaction (HCR). Two sets of metastable DNA hairpins - of which one is immobilized in specific points along tracks on DNA origami structures - are polymerized to form a continuous DNA duplex, which is visible using atomic force...... microscopy (AFM). Upon addition of a designed initiator, the initiation signal is efficiently transferred >200 nm from a specific location on one origami structure to an end point on another origami structure. The system shows no significant loss of signal when crossing from one nanostructure to another...

A polypeptide-DNA hybrid with selective linking capability applied to single molecule nano-mechanical measurements using optical tweezers.

Directory of Open Access Journals (Sweden)

Fatemeh Moayed

Full Text Available Many applications in biosensing, biomaterial engineering and single molecule biophysics require multiple non-covalent linkages between DNA, protein molecules, and surfaces that are specific yet strong. Here, we present a novel method to join proteins and dsDNA molecule at their ends, in an efficient, rapid and specific manner, based on the recently developed linkage between the protein StrepTactin (STN and the peptide StrepTag II (ST. We introduce a two-step approach, in which we first construct a hybrid between DNA and a tandem of two STs peptides (tST. In a second step, this hybrid is linked to polystyrene bead surfaces and Maltose Binding Protein (MBP using STN. Furthermore, we show the STN-tST linkage is more stable against forces applied by optical tweezers than the commonly used biotin-Streptavidin (STV linkage. It can be used in conjunction with Neutravidin (NTV-biotin linkages to form DNA tethers that can sustain applied forces above 65 pN for tens of minutes in a quarter of the cases. The method is general and can be applied to construct other surface-DNA and protein-DNA hybrids. The reversibility, high mechanical stability and specificity provided by this linking procedure make it highly suitable for single molecule mechanical studies, as well as biosensing and lab on chip applications.

Nanoporous hard data: optical encoding of information within nanoporous anodic alumina photonic crystals.

Science.gov (United States)

Santos, Abel; Law, Cheryl Suwen; Pereira, Taj; Losic, Dusan

2016-04-21

Herein, we present a method for storing binary data within the spectral signature of nanoporous anodic alumina photonic crystals. A rationally designed multi-sinusoidal anodisation approach makes it possible to engineer the photonic stop band of nanoporous anodic alumina with precision. As a result, the transmission spectrum of these photonic nanostructures can be engineered to feature well-resolved and selectively positioned characteristic peaks across the UV-visible spectrum. Using this property, we implement an 8-bit binary code and assess the versatility and capability of this system by a series of experiments aiming to encode different information within the nanoporous anodic alumina photonic crystals. The obtained results reveal that the proposed nanosized platform is robust, chemically stable, versatile and has a set of unique properties for data storage, opening new opportunities for developing advanced nanophotonic tools for a wide range of applications, including sensing, photonic tagging, self-reporting drug releasing systems and secure encoding of information.

Impact of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization method.

Science.gov (United States)

do Nascimento, Cássio; dos Santos, Janine Navarro; Pedrazzi, Vinícius; Pita, Murillo Sucena; Monesi, Nadia; Ribeiro, Ricardo Faria; de Albuquerque, Rubens Ferreira

2014-01-01

Molecular diagnosis methods have been largely used in epidemiological or clinical studies to detect and quantify microbial species that may colonize the oral cavity in healthy or disease. The preservation of genetic material from samples remains the major challenge to ensure the feasibility of these methodologies. Long-term storage may compromise the final result. The aim of this study was to evaluate the effect of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization. Saliva and supragingival biofilm were taken from 10 healthy subjects, aliquoted (n=364) and processed according to proposed protocols: immediate processing and processed after 2 or 4 weeks, and 6 or 12 months of storage at 4°C, -20°C and -80°C. Either total or individual microbial counts were recorded in lower values for samples processed after 12 months of storage, irrespective of temperatures tested. Samples stored up to 6 months at cold temperatures showed similar counts to those immediately processed. The microbial incidence was also significantly reduced in samples stored during 12 months in all temperatures. Temperature and time of oral samples storage have relevant impact in the detection and quantification of bacterial and fungal species by Checkerboard DNA-DNA hybridization method. Samples should be processed immediately after collection or up to 6 months if conserved at cold temperatures to avoid false-negative results. Copyright © 2013 Elsevier Ltd. All rights reserved.

Detection of genetic changes in Barrett's adenocarcinoma and Barrett's esophagus by DNA in situ hybridization and immunohistochemistry

NARCIS (Netherlands)

Krishnadath, K. K.; Tilanus, H. W.; Alers, J. C.; Mulder, A. H.; van Dekken, H.

1994-01-01

We have investigated the occurrence of chromosomal DNA and cell cycle-related protein changes in Barrett's epithelium and adenocarcinoma. The presence of numerical chromosomal aberrations was studied by applying nonisotopic in situ hybridization (ISH) with (peri-)centromeric DNA probes, specific for

Membrane-Assisted Growth of DNA Origami Nanostructure Arrays

Science.gov (United States)

2015-01-01

Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors—a three-layered rectangular block and a Y-shaped DNA structure—to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes. PMID:25734977

Membrane-assisted growth of DNA origami nanostructure arrays.

Science.gov (United States)

Kocabey, Samet; Kempter, Susanne; List, Jonathan; Xing, Yongzheng; Bae, Wooli; Schiffels, Daniel; Shih, William M; Simmel, Friedrich C; Liedl, Tim

2015-01-01

Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors--a three-layered rectangular block and a Y-shaped DNA structure--to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes.

Meso-/Nanoporous Semiconducting Metal Oxides for Gas Sensor Applications

Directory of Open Access Journals (Sweden)

Nguyen Duc Hoa

2015-01-01

Full Text Available Development and/or design of new materials and/or structures for effective gas sensor applications with fast response and high sensitivity, selectivity, and stability are very important issues in the gas sensor technology. This critical review introduces our recent progress in the development of meso-/nanoporous semiconducting metal oxides and their applications to gas sensors. First, the basic concepts of resistive gas sensors and the recent synthesis of meso-/nanoporous metal oxides for gas sensor applications are introduced. The advantages of meso-/nanoporous metal oxides are also presented, taking into account the crystallinity and ordered/disordered porous structures. Second, the synthesis methods of meso-/nanoporous metal oxides including the soft-template, hard-template, and temple-free methods are introduced, in which the advantages and disadvantages of each synthetic method are figured out. Third, the applications of meso-/nanoporous metal oxides as gas sensors are presented. The gas nanosensors are designed based on meso-/nanoporous metal oxides for effective detection of toxic gases. The sensitivity, selectivity, and stability of the meso-/nanoporous gas nanosensors are also discussed. Finally, some conclusions and an outlook are presented.

Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice

International Nuclear Information System (INIS)

Bhanjadeo, Madhabi M.; Nayak, Ashok K.; Subudhi, Umakanta

2017-01-01

DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices. - Highlights: • Al foil surface-assisted self-assembly of monomeric structures into larger branched DNA lattice. • FESEM study confirms the uniform distribution of two-dimensional bDNA lattice structures across the surface of Al foil. • Enzyme-free and economic strategy to prepare higher order structures from simpler DNA nanostructures have been confirmed by recovery assay. • Use of well proven sequences for the preparation of pure Y-shaped monomeric DNA nanostructure with high yield.

Individual capacity for DNA repair and maintenance of genomic integrity: a fertile ground for studies in the field of assisted reproduction

Directory of Open Access Journals (Sweden)

Radoslava Vazharova

2016-05-01

Full Text Available Many factors may affect the chances for successful pregnancy, especially at a later age. Fertility evaluations including genetic analysis are recommended to couples that have not achieved pregnancy within 6–12 months of unprotected intercourse. This review discusses some of the common polymorphisms in genes coding for proteins functioning in DNA damage identification and repair and maintenance of genomic integrity that may affect the chances of success in natural conception as well as in assisted reproduction (AR. Common polymorphisms in genes coding for proteins functioning in DNA damage identification and repair and maintenance of genomic integrity may affect the chances of success in assisted reproduction as well as in natural conception. The effects of carriership of different alleles of key genes of DNA repair may have differential effects in men and women and at different ages, suggesting complex interactions with the mechanisms controlling cell and tissue aging and programmed cell death. Future studies in the field are needed in order to elucidate the genotype–phenotype relationships and to translate the knowledge about individual repair capacity and maintenance of genomic integrity to potential clinical applications. Abbreviations: aCGH: microarray-based comparative genomic hybridization; AR: assisted reproduction; ATM: ataxia-telangiectasia mutated; ATP: adenosine triphosphate; BER: base excision repair; BFE: basic fertility evaluation; DMSO: dimethyl sulfoxide; FSH: follicle-stimulating hormone; GNRHR: gonadotropin-releasing hormone receptor; HMG: high-mobility group; ICSI: intracytoplasmic sperm injection; IUI: intrauterine insemination; IVF: in vitro fertilization; LH: luteinizing hormone; LIF: leukaemia inhibitory factor; MTR: methionine synthase; MTRR: methionine synthase reductase; NGS: next-generation sequencing; NER: nucleotide excision repair; NHEJ: non-homologous end joining; PAH: polycyclic aromatic hydrocarbons; PCOS

In-situ electrochemical doping of nanoporous anodic aluminum oxide with indigo carmine organic dye

Energy Technology Data Exchange (ETDEWEB)

Stępniowski, Wojciech J., E-mail: wojciech.stepniowski@wat.edu.pl [Department of Advanced Materials and Technology, Faculty of Advanced Technology and Chemistry, Military University of Technology, 2 Kaliskiego Str., 00-908 Warszawa (Poland); Norek, Małgorzata [Department of Advanced Materials and Technology, Faculty of Advanced Technology and Chemistry, Military University of Technology, 2 Kaliskiego Str., 00-908 Warszawa (Poland); Budner, Bogusław [Institute of Optoelectronics, Military University of Technology, 2 Kaliskiego Str., 00-908 Warszawa (Poland); Michalska-Domańska, Marta [Department of Advanced Materials and Technology, Faculty of Advanced Technology and Chemistry, Military University of Technology, 2 Kaliskiego Str., 00-908 Warszawa (Poland); Institute of Optoelectronics, Military University of Technology, 2 Kaliskiego Str., 00-908 Warszawa (Poland); Nowak-Stępniowska, Agata; Bombalska, Aneta; Kaliszewski, Miron [Institute of Optoelectronics, Military University of Technology, 2 Kaliskiego Str., 00-908 Warszawa (Poland); Mostek, Anna [Department of Advanced Materials and Technology, Faculty of Advanced Technology and Chemistry, Military University of Technology, 2 Kaliskiego Str., 00-908 Warszawa (Poland); Thorat, Sanjay; Salerno, Marco [Department of Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genova I-16163 (Italy); Giersig, Michael [Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin (Germany); Bojar, Zbigniew [Department of Advanced Materials and Technology, Faculty of Advanced Technology and Chemistry, Military University of Technology, 2 Kaliskiego Str., 00-908 Warszawa (Poland)

2016-01-01

Nanoporous anodic aluminum oxide was formed in sulfuric acid with addition of indigo carmine. During anodizing, the organic dye was incorporated into the porous oxide walls. X-ray photoelectron spectroscopy revealed the presence of nitrogen and sulfur in the anodic aluminum oxide. Two types of incorporated sulfur were found: belonging to the sulfate anions SO{sub 4}{sup 2−} of the electrolyte and belonging to the C-SO{sub 3}{sup −} side groups of the indigo carmine. Raman spectroscopy confirmed the incorporation and showed that the inorganic–organic hybrid material inherited optical properties from the indigo carmine. Typical modes from pyrrolidone rings, unique for indigo carmine in the investigated system (650 and 1585 cm{sup −1}), were found to be the strongest for the greatest anodizing voltages used. Despite the indigo carmine incorporation, the morphology of the oxide is still nanoporous and its geometry is still tuned by the voltage applied during aluminum anodization. This work presents an inexpensive and facile approach to doping an inorganic oxide material with organic compounds. - Highlights: • Nanoporous anodic alumina was formed in electrolyte with indigo carmine. • XPS confirmed the presence of N and S in anodic alumina. • Raman spectroscopy revealed indigo carmine bands in anodic alumina. • The higher the voltage, the more indigo carmine was incorporated.

Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

Science.gov (United States)

Tsukanov, A. A.; Psakhie, S. G.

2017-12-01

The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks

KAUST Repository

Mahfouz, Magdy M.

2011-01-24

Site-specific and rare cutting nucleases are valuable tools for genome engineering. The generation of double-strand DNA breaks (DSBs) promotes homologous recombination in eukaryotes and can facilitate gene targeting, additions, deletions, and inactivation. Zinc finger nucleases have been used to generate DSBs and subsequently, for genome editing but with low efficiency and reproducibility. The transcription activator-like family of type III effectors (TALEs) contains a central domain of tandem repeats that could be engineered to bind specific DNA targets. Here, we report the generation of a Hax3-based hybrid TALE nuclease with a user-selected DNA binding specificity. We show that the engineered TALE nuclease can bind to its target sequence in vitro and that the homodimeric TALE nuclease can cleave double-stranded DNA in vitro if the DNA binding sites have the proper spacing and orientation. Transient expression assays in tobacco leaves suggest that the hybrid nuclease creates DSB in its target sequence, which is subsequently repaired by nonhomologous end-joining repair. Taken together, our data show the feasibility of engineering TALE-based hybrid nucleases capable of generating site-specific DSBs and the great potential for site-specific genome modification in plants and eukaryotes in general.

Cleavable DNA-protein hybrid molecular beacon: A novel efficient signal translator for sensitive fluorescence anisotropy bioassay.

Science.gov (United States)

Hu, Pan; Yang, Bin

2016-01-15

Due to its unique features such as high sensitivity, homogeneous format, and independence on fluorescent intensity, fluorescence anisotropy (FA) assay has become a hotspot of study in oligonucleotide-based bioassays. However, until now most FA probes require carefully customized structure designs, and thus are neither generalizable for different sensing systems nor effective to obtain sufficient signal response. To address this issue, a cleavable DNA-protein hybrid molecular beacon was successfully engineered for signal amplified FA bioassay, via combining the unique stable structure of molecular beacon and the large molecular mass of streptavidin. Compared with single DNA strand probe or conventional molecular beacon, the DNA-protein hybrid molecular beacon exhibited a much higher FA value, which was potential to obtain high signal-background ratio in sensing process. As proof-of-principle, this novel DNA-protein hybrid molecular beacon was further applied for FA bioassay using DNAzyme-Pb(2+) as a model sensing system. This FA assay approach could selectively detect as low as 0.5nM Pb(2+) in buffer solution, and also be successful for real samples analysis with good recovery values. Compatible with most of oligonucleotide probes' designs and enzyme-based signal amplification strategies, the molecular beacon can serve as a novel signal translator to expand the application prospect of FA technology in various bioassays. Copyright © 2015 Elsevier B.V. All rights reserved.

Multiply osmium-labeled reporter probes for electrochemical DNA hybridization assays: detection of trinucleotide repeats

Czech Academy of Sciences Publication Activity Database

Fojta, Miroslav; Havran, Luděk; Kizek, René; Paleček, Emil

2004-01-01

Roč. 20, č. 5 (2004), s. 985-994 ISSN 0956-5663 R&D Projects: GA MPO 1H-PK/42; GA AV ČR IAA4004108; GA AV ČR IBS5004355; GA AV ČR KJB4004302; GA AV ČR KSK4055109 Institutional research plan: CEZ:AV0Z5004920 Keywords : electrochemical sensors * DNA hybridization * DNA labeling Subject RIV: BO - Biophysics Impact factor: 3.251, year: 2004

Synthesis of DNA block copolymers with extended nucleic acid segments by enzymatic ligation : cut and paste large hybrid architectures

NARCIS (Netherlands)

Ayaz, Meryem S.; Kwak, Minseok; Alemdaroglu, Fikri E.; Wang, Jie; Berger, Ruediger; Herrmann, Andreas; Berger, Rüdiger

2011-01-01

Ultra-high molecular weight DNA/polymer hybrid materials were prepared employing molecular biology techniques. Nucleic acid restriction and ligation enzymes were used to generate linear DNA di- and triblock copolymers that contain up to thousands of base pairs in the DNA segments.

Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA.

Science.gov (United States)

Zhang, Jia-yu; Zheng, Ke-wei; Xiao, Shan; Hao, Yu-hua; Tan, Zheng

2014-01-29

We recently reported that a DNA:RNA hybrid G-quadruplex (HQ) forms during transcription of DNA that bears two or more tandem guanine tracts (G-tract) on the nontemplate strand. Putative HQ-forming sequences are enriched in the nearby 1000 nt region right downstream of transcription start sites in the nontemplate strand of warm-blooded animals, and HQ regulates transcription under both in vitro and in vivo conditions. Therefore, knowledge of the mechanism of HQ formation is important for understanding the biological function of HQ as well as for manipulating gene expression by targeting HQ. In this work, we studied the mechanism of HQ formation using an in vitro T7 transcription model. We show that RNA synthesis initially produces an R-loop, a DNA:RNA heteroduplex formed by a nascent RNA transcript and the template DNA strand. In the following round of transcription, the RNA in the R-loop is displaced, releasing the RNA in single-stranded form (ssRNA). Then the G-tracts in the RNA can jointly form HQ with those in the nontemplate DNA strand. We demonstrate that the structural cascade R-loop → ssRNA → HQ offers opportunities to intercept HQ formation, which may provide a potential method to manipulate gene expression.

Surface effects on the mechanical properties of nanoporous materials

International Nuclear Information System (INIS)

Xia Re; Li Xide; Feng Xiqiao; Qin Qinghua; Liu Jianlin

2011-01-01

Using the theory of surface elasticity, we investigate the mechanical properties of nanoporous materials. The classical theory of porous materials is modified to account for surface effects, which become increasingly important as the characteristic sizes of microstructures shrink to nanometers. First, a refined Timoshenko beam model is presented to predict the effective elastic modulus of nanoporous materials. Then the surface effects on the elastic microstructural buckling behavior of nanoporous materials are examined. In particular, nanoporous gold is taken as an example to illustrate the application of the proposed model. The results reveal that both the elastic modulus and the critical buckling behavior of nanoporous materials exhibit a distinct dependence on the characteristic sizes of microstructures, e.g. the average ligament width.

Surface effects on the mechanical properties of nanoporous materials

Energy Technology Data Exchange (ETDEWEB)

Xia Re [School of Power and Mechanical Engineering, Wuhan University, Wuhan 430072 (China); Li Xide; Feng Xiqiao [AML, Department of Engineering Mechanics, Tsinghua University, Beijing 100084 (China); Qin Qinghua [School of Engineering, Australian National University, Canberra, ACT 0200 (Australia); Liu Jianlin, E-mail: fengxq@tsinghua.edu.cn [Department of Engineering Mechanics, China University of Petroleum, Qingdao 266555 (China)

2011-07-01

Using the theory of surface elasticity, we investigate the mechanical properties of nanoporous materials. The classical theory of porous materials is modified to account for surface effects, which become increasingly important as the characteristic sizes of microstructures shrink to nanometers. First, a refined Timoshenko beam model is presented to predict the effective elastic modulus of nanoporous materials. Then the surface effects on the elastic microstructural buckling behavior of nanoporous materials are examined. In particular, nanoporous gold is taken as an example to illustrate the application of the proposed model. The results reveal that both the elastic modulus and the critical buckling behavior of nanoporous materials exhibit a distinct dependence on the characteristic sizes of microstructures, e.g. the average ligament width.

Chromosome specific DNA hybridization in suspension for flow cytometric detection of chimerism in bone marrow transplantation and leukemia

NARCIS (Netherlands)

G.J.A. Arkesteijn (Ger); C.A.J. Erpelinck (Claudia); A.C.M. Martens (Anton); A. Hagenbeek (Anton)

1995-01-01

textabstractFlow cytometry was used to measure the fluorescence intensity of nuclei that were subjected to fluorescent in situ hybridization in suspension with chromosome specific DNA probes. Paraformaldehyde-fixed nuclei were protein digested with trypsin and hybridized simultaneously with a

Sensitive optical bio-sensing of p-type WSe2 hybridized with fluorescent dye attached DNA by doping and de-doping effects

Science.gov (United States)

Han, Kyu Hyun; Kim, Jun Young; Jo, Seong Gi; Seo, Changwon; Kim, Jeongyong; Joo, Jinsoo

2017-10-01

Layered transition metal dichalcogenides, such as MoS2, WSe2 and WS2, are exciting two-dimensional (2D) materials because they possess tunable optical and electrical properties that depend on the number of layers. In this study, the nanoscale photoluminescence (PL) characteristics of the p-type WSe2 monolayer, and WSe2 layers hybridized with the fluorescent dye Cy3 attached to probe-DNA (Cy3/p-DNA), have been investigated as a function of the concentration of Cy3/DNA by using high-resolution laser confocal microscopy. With increasing concentration of Cy3/p-DNA, the measured PL intensity decreases and its peak is red-shifted, suggesting that the WSe2 layer has been p-type doped with Cy3/p-DNA. Then, the PL intensity of the WSe2/Cy3/p-DNA hybrid system increases and the peak is blue-shifted through hybridization with relatively small amounts of target-DNA (t-DNA) (50-100 nM). This effect originates from charge and energy transfer from the Cy3/DNA to the WSe2. For t-DNA detection, our systems using p-type WSe2 have the merit in terms of the increase of PL intensity. The p-type WSe2 monolayers can be a promising nanoscale 2D material for sensitive optical bio-sensing based on the doping and de-doping responses to biomaterials.

Hydrophilic nanoporous polystyrenes and 1,2-polybutadienes

DEFF Research Database (Denmark)

Guo, Fengxiao; Jankova Atanasova, Katja; Vigild, Martin Etchells

2008-01-01

Nanoporous polymers from ordered block copolymers having hydrophilic cavity surfaces were successfully prepared by two methodologies: ' 1. Nanoporous polystyrenes fromPtBA-b-PS diblock or PDMS-b-PtBA-b-PS triblock copolymer precursors by atom transfer radical polymerization (ATRP), or combination...... of living anionic polymerization~ and ATRP r~spectively. The one, PtBA block, can be modified to the hydrophilic PAA, where the dther, polydimethysiloxane (PDMS) block, can be fully degraded. Deprotection of the tert-butyl groups in PtBA and the selective etching of PDMS· chains were accomplished...... by applying HF or TFA in one step. Thus both the di- and triblock copolymers after such a treatment resulted. in nanoporous polystyrenes with hexagonal cavities of different nanosizes (6-11 nm, Figure 1). 2. Nanoporous I,2-polybutadienes (I,2-PB) by grafting various acrylic monomers onto the pore. surfaces...

Genetic relatedness of artichoke (Cynara scolymus L.) hybrids using random amplified polymorphic DNA (RAPD) fingerprinting.

Science.gov (United States)

Sharaf-Eldin, M A; Al-Tamimi, A; Alam, P; Elkholy, S F; Jordan, J R

2015-12-28

The artichoke (Cynara scolymus L.) is an important food and medicinal crop that is cultivated in Mediterranean countries. Morphological characteristics, such as head shape and diameter, leaf shape, and bract shape, are mainly affected by environmental conditions. A molecular marker approach was used to analyze the degree of polymorphism between artichoke hybrid lines. The degree of genetic difference among three artichoke hybrids was evaluated using random amplified polymorphic DNA-PCR (RAPD-PCR). In this study, the DNA fingerprints of three artichoke lines (A13-010, A11-018, and A12-179) were generated, and a total of 10 decamer primers were applied for RAPD-PCR analyses. Polymorphism  (16.66 to 62.50%) was identified using eight arbitrary decamers and total genomic DNA extracted from the hybrids. Of the 59 loci detected, there were 25 polymorphic and 34 monomorphic loci. Jaccard's similarity index (JSI) ranged between 1.0 and 0.84. Based on the unweighted pair group method with arithmetic mean (UPGMA) similarity matrix and dendrogram, the results indicated that two hybrids (A13-010 and A11-018) were closely related to each other, and the A12-179 line showed more divergence. When identifying correct accessions, consideration of the genetic variation and genetic relationships among the genotypes are required. The RAPD-PCR fingerprinting of artichoke lines clearly showed that it is possible to analyze the RAPD patterns for correlation between genetic means and differences or resemblance between close accessions (A13-010 and A11- 018) at the genomic level.

Nanopore Electrochemistry: A Nexus for Molecular Control of Electron Transfer Reactions

Science.gov (United States)

2018-01-01

Pore-based structures occur widely in living organisms. Ion channels embedded in cell membranes, for example, provide pathways, where electron and proton transfer are coupled to the exchange of vital molecules. Learning from mother nature, a recent surge in activity has focused on artificial nanopore architectures to effect electrochemical transformations not accessible in larger structures. Here, we highlight these exciting advances. Starting with a brief overview of nanopore electrodes, including the early history and development of nanopore sensing based on nanopore-confined electrochemistry, we address the core concepts and special characteristics of nanopores in electron transfer. We describe nanopore-based electrochemical sensing and processing, discuss performance limits and challenges, and conclude with an outlook for next-generation nanopore electrode sensing platforms and the opportunities they present. PMID:29392173

Nanopore Electrochemistry: A Nexus for Molecular Control of Electron Transfer Reactions

Directory of Open Access Journals (Sweden)

Kaiyu Fu

2018-01-01

Full Text Available Pore-based structures occur widely in living organisms. Ion channels embedded in cell membranes, for example, provide pathways, where electron and proton transfer are coupled to the exchange of vital molecules. Learning from mother nature, a recent surge in activity has focused on artificial nanopore architectures to effect electrochemical transformations not accessible in larger structures. Here, we highlight these exciting advances. Starting with a brief overview of nanopore electrodes, including the early history and development of nanopore sensing based on nanopore-confined electrochemistry, we address the core concepts and special characteristics of nanopores in electron transfer. We describe nanopore-based electrochemical sensing and processing, discuss performance limits and challenges, and conclude with an outlook for next-generation nanopore electrode sensing platforms and the opportunities they present.

Nanoporous polymer liquid core waveguides

DEFF Research Database (Denmark)

Gopalakrishnan, Nimi; Christiansen, Mads Brøkner; Ndoni, Sokol

2010-01-01

We demonstrate liquid core waveguides defined by UV to enable selective water infiltration in nanoporous polymers, creating an effective refractive index shift Δn=0.13. The mode confinement and propagation loss in these waveguides are presented.......We demonstrate liquid core waveguides defined by UV to enable selective water infiltration in nanoporous polymers, creating an effective refractive index shift Δn=0.13. The mode confinement and propagation loss in these waveguides are presented....

An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences.

Science.gov (United States)

Pollier, Jacob; González-Guzmán, Miguel; Ardiles-Diaz, Wilson; Geelen, Danny; Goossens, Alain

2011-01-01

cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis. A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts. The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.

Mechanisms of material removal and mass transport in focused ion beam nanopore formation

Energy Technology Data Exchange (ETDEWEB)

Das, Kallol, E-mail: das7@illinois.edu; Johnson, Harley T., E-mail: htj@illinois.edu [Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, 1206 West Green Street, MC-244, Urbana, Illinois 61801 (United States); Freund, Jonathan B., E-mail: jbfreund@illinois.edu [Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, 1206 West Green Street, MC-244, Urbana, Illinois 61801 (United States); Department of Aerospace Engineering, University of Illinois at Urbana-Champaign, 306 Talbot Laboratory, MC-236, 104 South Wright Street Urbana, Illinois 61801 (United States)

2015-02-28

Despite the widespread use of focused ion beam (FIB) processing as a material removal method for applications ranging from electron microscope sample preparation to nanopore processing for DNA sequencing, the basic material removal mechanisms of FIB processing are not well understood. We present the first complete atomistic simulation of high-flux FIB using large-scale parallel molecular dynamics (MD) simulations of nanopore fabrication in freestanding thin films. We focus on the root mechanisms of material removal and rearrangement and describe the role of explosive boiling in forming nanopores. FIB nanopore fabrication is typically understood to occur via sputter erosion. This can be shown to be the case in low flux systems, where individual ion impacts are sufficiently separated in time that they may be considered as independent events. But our detailed MD simulations show that in high flux FIB processing, above a threshold level at which thermal effects become significant, the primary mechanism of material removal changes to a significantly accelerated, thermally dominated process. Under these conditions, the target is heated by the ion beam faster than heat is conducted away by the material, leading quickly to melting, and then continued heating to nearly the material critical temperature. This leads to explosive boiling of the target material with spontaneous bubble formation and coalescence. Mass is rapidly rearranged at the atomistic scale, and material removal occurs orders of magnitude faster than would occur by simple sputtering. While the phenomenology is demonstrated computationally in silicon, it can be expected to occur at lower beam fluxes in other cases where thermal conduction is suppressed due to material properties, geometry, or ambient thermal conditions.

Resolution-improved in situ DNA hybridization detection based on microwave photonic interrogation.

Science.gov (United States)

Cao, Yuan; Guo, Tuan; Wang, Xudong; Sun, Dandan; Ran, Yang; Feng, Xinhuan; Guan, Bai-ou

2015-10-19

In situ bio-sensing system based on microwave photonics filter (MPF) interrogation method with improved resolution is proposed and experimentally demonstrated. A microfiber Bragg grating (mFBG) is used as sensing probe for DNA hybridization detection. Different from the traditional wavelength monitoring technique, we use the frequency interrogation scheme for resolution-improved bio-sensing detection. Experimental results show that the frequency shift of MPF notch presents a linear response to the surrounding refractive index (SRI) change over the range of 1.33 to 1.38, with a SRI resolution up to 2.6 × 10(-5) RIU, which has been increased for almost two orders of magnitude compared with the traditional fundamental mode monitoring technique (~3.6 × 10(-3) RIU). Due to the high Q value (about 27), the whole process of DNA hybridization can be in situ monitored. The proposed MPF-based bio-sensing system provides a new interrogation method over the frequency domain with improved sensing resolution and rapid interrogation rate for biochemical and environmental measurement.

Universal quantum gates for photon-atom hybrid systems assisted by bad cavities

Science.gov (United States)

Wang, Guan-Yu; Liu, Qian; Wei, Hai-Rui; Li, Tao; Ai, Qing; Deng, Fu-Guo

2016-01-01

We present two deterministic schemes for constructing a CNOT gate and a Toffoli gate on photon-atom and photon-atom-atom hybrid quantum systems assisted by bad cavities, respectively. They are achieved by cavity-assisted photon scattering and work in the intermediate coupling region with bad cavities, which relaxes the difficulty of their implementation in experiment. Also, bad cavities are feasible for fast quantum operations and reading out information. Compared with previous works, our schemes do not need any auxiliary qubits and measurements. Moreover, the schematic setups for these gates are simple, especially that for our Toffoli gate as only a quarter wave packet is used to interact the photon with each of the atoms every time. These atom-cavity systems can be used as the quantum nodes in long-distance quantum communication as their relatively long coherence time is suitable for multi-time operations between the photon and the system. Our calculations show that the average fidelities and efficiencies of our two universal hybrid quantum gates are high with current experimental technology. PMID:27067992

The formation of diploid and triploid hybrids of female grass carp × male blunt snout bream and their 5S rDNA analysis.

Science.gov (United States)

He, Weiguo; Xie, Lihua; Li, Tangluo; Liu, Shaojun; Xiao, Jun; Hu, Jie; Wang, Jing; Qin, Qinbo; Liu, Yun

2013-11-23

Hybridization is a useful strategy to alter the genotypes and phenotypes of the offspring. It could transfer the genome of one species to another through combing the different genome of parents in the hybrid offspring. And the offspring may exhibit advantages in growth rate, disease resistance, survival rate and appearance, which resulting from the combination of the beneficial traits from both parents. Diploid and triploid hybrids of female grass carp (Ctenopharyngodon idellus, GC, Cyprininae, 2n = 48) × male blunt snout bream (Megalobrama amblycephala, BSB, Cultrinae, 2n = 48) were successfully obtained by distant hybridization. Diploid hybrids had 48 chromosomes, with one set from GC and one set from BSB. Triploid hybrids possessed 72 chromosomes, with two sets from GC and one set from BSB.The morphological traits, growth rates, and feeding ecology of the parents and hybrid offspring were compared and analyzed. The two kinds of hybrid offspring exhibited significantly phenotypic divergence from GC and BSB. 2nGB hybrids showed similar growth rate compared to that of GC, and 3nGB hybrids significantly higher results. Furthermore, the feeding ecology of hybrid progeny was omnivorous.The 5S rDNA of GC, BSB and their hybrid offspring were also cloned and sequenced. There was only one type of 5S rDNA (designated type I: 180 bp) in GC and one type of 5S rDNA (designated type II: 188 bp) in BSB. However, in the hybrid progeny, diploid and triploid hybrids both inherited type I and type II from their parents, respectively. In addition, a chimera of type I and type II was observed in the genome of diploid and triploid hybrids, excepting a 10 bp of polyA insertion in type II sequence of the chimera of the diploid hybrids. This is the first report of diploid and triploid hybrids being produced by crossing GC and BSB, which have the same chromosome number. The obtainment of two new hybrid offspring has significance in fish genetic breeding. The results illustrate the effect

Enzymatic Amplification of DNA/RNA Hybrid Molecular Beacon Signaling in Nucleic Acid Detection

OpenAIRE

Jacroux, Thomas; Rieck, Daniel C.; Cui, Rong; Ouyang, Yexin; Dong, Wen-Ji

2012-01-01

A rapid assay operable under isothermal or non-isothermal conditions is described wherein the sensitivity of a typical molecular beacon (MB) system is improved by utilizing thermostable RNase H to enzymatically cleave an MB comprised of a DNA stem and RNA loop (R/D-MB). Upon hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7x above background) due to an opening of the probe and concomitant reduction in the Förster resonance energy transfer e...

Voltammetric behavior of osmium-labeled DNA at mercury meniscus-modified solid amalgam electrodes. Detecting DNA hybridization

Czech Academy of Sciences Publication Activity Database

Josypčuk, Bohdan; Fojta, Miroslav; Havran, Luděk; Heyrovský, Michael; Paleček, Emil

2006-01-01

Roč. 18, č. 2 (2006), s. 186-194 ISSN 1040-0397 R&D Projects: GA MPO 1H-PK/42; GA AV ČR IAA4004402; GA AV ČR KJB4004302; GA AV ČR IBS5004355 Institutional research plan: CEZ:AV0Z40400503; CEZ:AV0Z50040507 Keywords : voltammetry * solid amalgam electrodes * DNA-osmium complex * hybridization * catalytic hydrogen evolution Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.444, year: 2006

Single-step direct fabrication of pillar-on-pore hybrid nanostructures in anodizing aluminum for superior superhydrophobic efficiency.

Science.gov (United States)

Jeong, Chanyoung; Choi, Chang-Hwan

2012-02-01

Conventional electrochemical anodizing processes of metals such as aluminum typically produce planar and homogeneous nanopore structures. If hydrophobically treated, such 2D planar and interconnected pore structures typically result in lower contact angle and larger contact angle hysteresis than 3D disconnected pillar structures and, hence, exhibit inferior superhydrophobic efficiency. In this study, we demonstrate for the first time that the anodizing parameters can be engineered to design novel pillar-on-pore (POP) hybrid nanostructures directly in a simple one-step fabrication process so that superior surface superhydrophobicity can also be realized effectively from the electrochemical anodization process. On the basis of the characteristic of forming a self-ordered porous morphology in a hexagonal array, the modulation of anodizing voltage and duration enabled the formulation of the hybrid-type nanostructures having controlled pillar morphology on top of a porous layer in both mild and hard anodization modes. The hybrid nanostructures of the anodized metal oxide layer initially enhanced the surface hydrophilicity significantly (i.e., superhydrophilic). However, after a hydrophobic monolayer coating, such hybrid nanostructures then showed superior superhydrophobic nonwetting properties not attainable by the plain nanoporous surfaces produced by conventional anodization conditions. The well-regulated anodization process suggests that electrochemical anodizing can expand its usefulness and efficacy to render various metallic substrates with great superhydrophilicity or -hydrophobicity by directly realizing pillar-like structures on top of a self-ordered nanoporous array through a simple one-step fabrication procedure.

Sugar-influenced water diffusion, interaction, and retention in clay interlayer nanopores probed by theoretical simulations and experimental spectroscopies

Science.gov (United States)

Aristilde, Ludmilla; Galdi, Stephen M.; Kelch, Sabrina E.; Aoki, Thalia G.

2017-08-01

Understanding the hydrodynamics in clay nanopores is important for gaining insights into the trapping of water, nutrients, and contaminants in natural and engineered soils. Previous investigations have focused on the interlayer organization and molecular diffusion coefficients (D) of cations and water molecules in cation-saturated interlayer nanopores of smectite clays. Little is known, however, about how these interlayer dynamic properties are influenced by the ubiquitous presence of small organic compounds such as sugars in the soil environment. Here we probed the effects of glucose molecules on montmorillonite interlayer properties. Molecular dynamics simulations revealed re-structuring of the interlayer organization of the adsorptive species. Water-water interactions were disrupted by glucose-water H-bonding interactions. ;Dehydration; of the glucose-populated nanopore led to depletion in the Na solvation shell, which resulted in the accumulation of both Na ions (as inner-sphere complexes) and remaining hydrated water molecules at the mineral surface. This accumulation led to a decrease in both DNa and Dwater. In addition, the reduction in Dglucose as a function of increasing glucose content can be explained by the aggregation of glucose molecules into organic clusters H-bonded to the mineral surface on both walls of the nanopore. Experimental nuclear magnetic resonance and X-ray diffraction data were consistent with the theoretical predictions. Compared to clay interlayers devoid of glucose, increased intensities and new peaks in the 23Na nuclear magnetic resonance spectra confirmed increasing immobilization of Na as a function of increasing glucose content. And, the X-ray diffraction data indicated a reduced collapse of glucose-populated interlayers exposed to decreasing moisture conditions, which led to the maintenance of hydrated clay nanopores. The coupling of theoretical and experimental findings sheds light on the molecular to nanoscale mechanisms that

UV patterned nanoporous solid-liquid core waveguides

DEFF Research Database (Denmark)

Gopalakrishnan, Nimi; Sagar, Kaushal Shashikant; Christiansen, Mads Brøkner

2010-01-01

Nanoporous Solid-Liquid core waveguides were prepared by UV induced surface modification of hydrophobic nanoporous polymers. With this method, the index contrast (delta n = 0.20) is a result of selective water infiltration. The waveguide core is defined by UV light, rendering the exposed part...

Influence of nanopore surface charge and magnesium ion on polyadenosine translocation

International Nuclear Information System (INIS)

Lepoitevin, Mathilde; Bechelany, Mikhael; Janot, Jean-Marc; Balme, Sebastien; Coulon, Pierre Eugène; Cambedouzou, Julien

2015-01-01

We investigate the influence of a nanopore surface state and the addition of Mg 2+ on poly-adenosine translocation. To do so, two kinds of nanopores with a low aspect ratio (diameter ∼3–5 nm, length 30 nm) were tailored: the first one with a negative charge surface and the second one uncharged. It was shown that the velocity and the energy barrier strongly depend on the nanopore surface. Typically if the nanopore and polyA exhibit a similar charge, the macromolecule velocity increases and its global energy barrier of entrance in the nanopore decreases, as opposed to the non-charged nanopore. Moreover, the addition of a divalent chelating cation induces an increase of energy barrier of entrance, as expected. However, for a negative nanopore, this effect is counterbalanced by the inversion of the surface charge induced by the adsorption of divalent cations. (paper)

HyDEn: A Hybrid Steganocryptographic Approach for Data Encryption Using Randomized Error-Correcting DNA Codes

Directory of Open Access Journals (Sweden)

Dan Tulpan

2013-01-01

Full Text Available This paper presents a novel hybrid DNA encryption (HyDEn approach that uses randomized assignments of unique error-correcting DNA Hamming code words for single characters in the extended ASCII set. HyDEn relies on custom-built quaternary codes and a private key used in the randomized assignment of code words and the cyclic permutations applied on the encoded message. Along with its ability to detect and correct errors, HyDEn equals or outperforms existing cryptographic methods and represents a promising in silico DNA steganographic approach.

Gassmann Theory Applies to Nanoporous Media

Science.gov (United States)

Gor, Gennady Y.; Gurevich, Boris

2018-01-01

Recent progress in extraction of unconventional hydrocarbon resources has ignited the interest in the studies of nanoporous media. Since many thermodynamic and mechanical properties of nanoscale solids and fluids differ from the analogous bulk materials, it is not obvious whether wave propagation in nanoporous media can be described using the same framework as in macroporous media. Here we test the validity of Gassmann equation using two published sets of ultrasonic measurements for a model nanoporous medium, Vycor glass, saturated with two different fluids, argon, and n-hexane. Predictions of the Gassmann theory depend on the bulk and shear moduli of the dry samples, which are known from ultrasonic measurements and the bulk moduli of the solid and fluid constituents. The solid bulk modulus can be estimated from adsorption-induced deformation or from elastic effective medium theory. The fluid modulus can be calculated according to the Tait-Murnaghan equation at the solvation pressure in the pore. Substitution of these parameters into the Gassmann equation provides predictions consistent with measured data. Our findings set up a theoretical framework for investigation of fluid-saturated nanoporous media using ultrasonic elastic wave propagation.

Nanopore fabricated in pyramidal HfO2 film by dielectric breakdown method

Science.gov (United States)

Wang, Yifan; Chen, Qi; Deng, Tao; Liu, Zewen

2017-10-01

The dielectric breakdown method provides an innovative solution to fabricate solid-state nanopores on insulating films. A nanopore generation event via this method is considered to be caused by random charged traps (i.e., structural defects) and high electric fields in the membrane. Thus, the position and number of nanopores on planar films prepared by the dielectric breakdown method is hard to control. In this paper, we propose to fabricate nanopores on pyramidal HfO2 films (10-nm and 15-nm-thick) to improve the ability to control the location and number during the fabrication process. Since the electric field intensity gets enhanced at the corners of the pyramid-shaped film, the probability of nanopore occurrence at vertex and edge areas increases. This priority of appearance provides us chance to control the location and number of nanopores by monitoring a sudden irreversible discrete increase in current. The experimental results showed that the probability of nanopore occurrence decreases in an order from the vertex area, the edge area to the side face area. The sizes of nanopores ranging from 30 nm to 10 nm were obtained. Nanopores fabricated on the pyramid-shaped HfO2 film also showed an obvious ion current rectification characteristic, which might improve the nanopore performance as a biomolecule sequencing platform.

High quality self-separated GaN crystal grown on a novel nanoporous template by HVPE.

Science.gov (United States)

Huo, Qin; Shao, Yongliang; Wu, Yongzhong; Zhang, Baoguo; Hu, Haixiao; Hao, Xiaopeng

2018-02-16

In this study, a novel nanoporous template was obtained by a two-step etching process from MOCVD-GaN/Al 2 O 3 (MGA) with electrochemical etching sequentially followed by chemical wet etching. The twice-etched MOCVD-GaN/Al 2 O 3 (TEMGA) templates were utilized to grow GaN crystals by hydride vapor phase epitaxy (HVPE) method. The GaN crystals were separated spontaneously from the TEMGA template with the assistance of voids formed by the etched nanopores. Several techniques were utilized to characterize the quality of the free-standing GaN crystals obtained from the TEMGA template. Results showed that the quality of the as-obtained GaN crystals was improved obviously compared with those grown on the MGA. This convenient technique can be applied to grow high-quality free-standing GaN crystals.

Impedance nanopore biosensor: influence of pore dimensions on biosensing performance.

Science.gov (United States)

Kant, Krishna; Yu, Jingxian; Priest, Craig; Shapter, Joe G; Losic, Dusan

2014-03-07

Knowledge about electrochemical and electrical properties of nanopore structures and the influence of pore dimensions on these properties is important for the development of nanopore biosensing devices. The aim of this study was to explore the influence of nanopore dimensions (diameter and length) on biosensing performance using non-faradic electrochemical impedance spectroscopy (EIS). Nanoporous alumina membranes (NPAMs) prepared by self-ordered electrochemical anodization of aluminium were used as model nanopore sensing platforms. NPAMs with different pore diameters (25-65 nm) and lengths (4-18 μm) were prepared and the internal pore surface chemistry was modified by covalently attaching streptavidin and biotin. The performance of this antibody nanopore biosensing platform was evaluated using various concentrations of biotin as a model analyte. EIS measurements of pore resistivity and conductivity were carried out for pores with different diameters and lengths. The results showed that smaller pore dimensions of 25 nm and pore lengths up to 10 μm provide better biosensing performance.

Alien DNA introgression and wheat DNA rearrangements in a stable wheat line derived from the early generation of distant hybridization.

Science.gov (United States)

Zhang, Lianquan; Liu, Dengcai; Yan, Zehong; Zheng, Youliang

2005-10-01

Polyploidy has been found to be common in plants. Bread or common wheat (Triticum aestivum L., 2n=42) is a good example of allopolyploid made up of three diploid genomes A, B and D. In recent years, by the study of mimicking the origination of common wheat, it was found that changes of DNA sequence and gene expression occurred at the early stages of artificial allohexaploid between tetraploid wheat and Aegilops tauschii, which was probably favorable to genetic diploidization of new synthetic hexaploid wheat. Common wheat 99L2 is a new line stable in genetic, which was derived from the early self-pollinated generation of wide hybrids between common wheat and rye. In this study, it was found that at least two rye DNA segments had been introgressed into 99L2. This result suggested that a mechanism of alien DNA introgression may exist, which was different from the traditional mechanism of chromosome pairing and DNA recombination between wheat and alien species. Meanwhile, during the introgression process of alien rye DNA segments, the changes in DNA sequences of wheat itself occurred.

Thermodynamics for the Formation of Double-Stranded DNA-Single-Walled Carbon Nanotube Hybrids.

Science.gov (United States)

Shiraki, Tomohiro; Tsuzuki, Akiko; Toshimitsu, Fumiyuki; Nakashima, Naotoshi

2016-03-24

For the first time, the thermodynamics are described for the formation of double-stranded DNA (ds-DNA)-single-walled carbon nanotube (SWNT) hybrids. This treatment is applied to the exchange reaction of sodium cholate (SC) molecules on SWNTs and the ds-DNAs d(A)20 -d(T)20 and nuclear factor (NF)-κB decoy. UV/Vis/near-IR spectroscopy with temperature variations was used for analyzing the exchange reaction on the SWNTs with four different chiralities: (n,m)=(8,3), (6,5), (7,5), and (8,6). Single-stranded DNAs (ss-DNAs), including d(A)20 and d(T)20, are also used for comparison. The d(A)20-d(T)20 shows a drastic change in its thermodynamic parameters around the melting temperature (Tm ) of the DNA oligomer. No such Tm dependency was measured, owing to high Tm in the NF-κB decoy DNA and no Tm in the ss-DNA. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study of polymer molecules and conformations with a nanopore

Science.gov (United States)

Golovchenko, Jene A.; Li, Jiali; Stein, Derek; Gershow, Marc H.

2010-12-07

The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

Potential Evaluation of Solar Heat Assisted Desiccant Hybrid Air Conditioning System

Science.gov (United States)

Tran, Thien Nha; Hamamoto, Yoshinori; Akisawa, Atsushi; Kashiwagi, Takao

The solar thermal driven desiccant dehumidification-absorption cooling hybrid system has superior advantage in hot-humid climate regions. The reasonable air processing of desiccant hybrid air conditioning system and the utility of clean and free energy make the system environment friendly and energy efficient. The study investigates the performance of the desiccant dehumidification air conditioning systems with solar thermal assistant. The investigation is performed for three cases which are combinations of solar thermal and absorption cooling systems with different heat supply temperature levels. Two solar thermal systems are used in the study: the flat plate collector (FPC) and the vacuum tube with compound parabolic concentrator (CPC). The single-effect and high energy efficient double-, triple-effect LiBr-water absorption cooling cycles are considered for cooling systems. COP of desiccant hybrid air conditioning systems are determined. The evaluation of these systems is subsequently performed. The single effect absorption cooling cycle combined with the flat plate collector solar system is found to be the most energy efficient air conditioning system.

DNA Origami: Folded DNA-Nanodevices That Can Direct and Interpret Cell Behavior

Science.gov (United States)

Kearney, Cathal J.; Lucas, Christopher R.; O'Brien, Fergal J.; Castro, Carlos E.

2016-01-01

DNA origami is a DNA-based nanotechnology that utilizes programmed combinations of short complementary oligonucleotides to fold a large single strand of DNA into precise 2-D and 3-D shapes. The exquisite nanoscale shape control of this inherently biocompatible material is combined with the potential to spatially address the origami structures with diverse cargos including drugs, antibodies, nucleic acid sequences, small molecules and inorganic particles. This programmable flexibility enables the fabrication of precise nanoscale devices that have already shown great potential for biomedical applications such as: drug delivery, biosensing and synthetic nanopore formation. In this Progress Report, we will review the advances in the DNA origami field since its inception several years ago and then focus on how these DNA-nanodevices can be designed to interact with cells to direct or probe their behavior. PMID:26840503

Integration of Multiplexed Microfluidic Electrokinetic Concentrators with a Morpholino Microarray via Reversible Surface Bonding for Enhanced DNA Hybridization.

Science.gov (United States)

Martins, Diogo; Wei, Xi; Levicky, Rastislav; Song, Yong-Ak

2016-04-05

We describe a microfluidic concentration device to accelerate the surface hybridization reaction between DNA and morpholinos (MOs) for enhanced detection. The microfluidic concentrator comprises a single polydimethylsiloxane (PDMS) microchannel onto which an ion-selective layer of conductive polymer poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) ( PSS) was directly printed and then reversibly surface bonded onto a morpholino microarray for hybridization. Using this electrokinetic trapping concentrator, we could achieve a maximum concentration factor of ∼800 for DNA and a limit of detection of 10 nM within 15 min. In terms of the detection speed, it enabled faster hybridization by around 10-fold when compared to conventional diffusion-based hybridization. A significant advantage of our approach is that the fabrication of the microfluidic concentrator is completely decoupled from the microarray; by eliminating the need to deposit an ion-selective layer on the microarray surface prior to device integration, interfacing between both modules, the PDMS chip for electrokinetic concentration and the substrate for DNA sensing are easier and applicable to any microarray platform. Furthermore, this fabrication strategy facilitates a multiplexing of concentrators. We have demonstrated the proof-of-concept for multiplexing by building a device with 5 parallel concentrators connected to a single inlet/outlet and applying it to parallel concentration and hybridization. Such device yielded similar concentration and hybridization efficiency compared to that of a single-channel device without adding any complexity to the fabrication and setup. These results demonstrate that our concentrator concept can be applied to the development of a highly multiplexed concentrator-enhanced microarray detection system for either genetic analysis or other diagnostic assays.

Modulation of Molecular Flux Using a Graphene Nanopore Capacitor.

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Shankla, Manish; Aksimentiev, Aleksei

2017-04-20

Modulation of ionic current flowing through nanoscale pores is one of the fundamental biological processes. Inspired by nature, nanopores in synthetic solid-state membranes are being developed to enable rapid analysis of biological macromolecules and to serve as elements of nanofludic circuits. Here, we theoretically investigate ion and water transport through a graphene-insulator-graphene membrane containing a single, electrolyte-filled nanopore. By means of all-atom molecular dynamics simulations, we show that the charge state of such a graphene nanopore capacitor can regulate both the selectivity and the magnitude of the nanopore ionic current. At a fixed transmembrane bias, the ionic current can be switched from being carried by an equal mixture of cations and anions to being carried almost exclusively by either cationic or anionic species, depending on the sign of the charge assigned to both plates of the capacitor. Assigning the plates of the capacitor opposite sign charges can either increase the nanopore current or reduce it substantially, depending on the polarity of the bias driving the transmembrane current. Facilitated by the changes of the nanopore surface charge, such ionic current modulations are found to occur despite the physical dimensions of the nanopore being an order of magnitude larger than the screening length of the electrolyte. The ionic current rectification is accompanied by a pronounced electro-osmotic effect that can transport neutral molecules such as proteins and drugs across the solid-state membrane and thereby serve as an interface between electronic and chemical signals.

DNA-based construction at the nanoscale: emerging trends and applications

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Lourdu Xavier, P.; Chandrasekaran, Arun Richard

2018-02-01

The field of structural DNA nanotechnology has evolved remarkably—from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes—in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

Simulation of a model nanopore sensor: Ion competition underlies device behavior

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Mádai, Eszter; Valiskó, Mónika; Dallos, András; Boda, Dezső

2017-12-01

We study a model nanopore sensor with which a very low concentration of analyte molecules can be detected on the basis of the selective binding of the analyte molecules to the binding sites on the pore wall. The bound analyte ions partially replace the current-carrier cations in a thermodynamic competition. This competition depends both on the properties of the nanopore and the concentrations of the competing ions (through their chemical potentials). The output signal given by the device is the current reduction caused by the presence of the analyte ions. The concentration of the analyte ions can be determined through calibration curves. We model the binding site with the square-well potential and the electrolyte as charged hard spheres in an implicit background solvent. We study the system with a hybrid method in which we compute the ion flux with the Nernst-Planck (NP) equation coupled with the Local Equilibrium Monte Carlo (LEMC) simulation technique. The resulting NP+LEMC method is able to handle both strong ionic correlations inside the pore (including finite size of ions) and bulk concentrations as low as micromolar. We analyze the effect of bulk ion concentrations, pore parameters, binding site parameters, electrolyte properties, and voltage on the behavior of the device.

Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.

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Steger, Doris; Berry, David; Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander

2011-01-01

The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.

Oligonucleotide PIK3CA/Chromosome 3 Dual in Situ Hybridization Automated Assay with Improved Signals, One-Hour Hybridization, and No Use of Blocking DNA.

Science.gov (United States)

Zhang, Wenjun; Hubbard, Antony; Baca-Parkinson, Leslie; Stanislaw, Stacey; Vladich, Frank; Robida, Mark D; Grille, James G; Maxwell, Daniel; Tsao, Tsu-Shuen; Carroll, William; Gardner, Tracie; Clements, June; Singh, Shalini; Tang, Lei

2015-09-01

The PIK3CA gene at chromosome 3q26.32 was found to be amplified in up to 45% of patients with squamous cell carcinoma of the lung. The strong correlation between PIK3CA amplification and increased phosphatidylinositol 3-kinase (PI3K) pathway activities suggested that PIK3CA gene copy number is a potential predictive biomarker for PI3K inhibitors. Currently, all microscopic assessments of PIK3CA and chromosome 3 (CHR3) copy numbers use fluorescence in situ hybridization. PIK3CA probes are derived from bacterial artificial chromosomes whereas CHR3 probes are derived mainly from the plasmid pHS05. These manual fluorescence in situ hybridization assays mandate 12- to 18-hour hybridization and use of blocking DNA from human sources. Moreover, fluorescence in situ hybridization studies provide limited morphologic assessment and suffer from signal decay. We developed an oligonucleotide-based bright-field in situ hybridization assay that overcomes these shortcomings. This assay requires only a 1-hour hybridization with no need for blocking DNA followed by indirect chromogenic detection. Oligonucleotide probes produced discrete and uniform CHR3 stains superior to those from the pHS05 plasmid. This assay achieved successful staining in 100% of the 195 lung squamous cell carcinoma resections and in 94% of the 33 fine-needle aspirates. This robust automated bright-field dual in situ hybridization assay for the simultaneous detection of PIK3CA and CHR3 centromere provides a potential clinical diagnostic method to assess PIK3CA gene abnormality in lung tumors. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Nanoporous Pirani sensor based on anodic aluminum oxide

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Jeon, Gwang-Jae; Kim, Woo Young; Shim, Hyun Bin; Lee, Hee Chul

2016-09-01

A nanoporous Pirani sensor based on anodic aluminum oxide (AAO) is proposed, and the quantitative relationship between the performance of the sensor and the porosity of the AAO membrane is characterized with a theoretical model. The proposed Pirani sensor is composed of a metallic resistor on a suspended nanoporous membrane, which simultaneously serves as the sensing area and the supporting structure. The AAO membrane has numerous vertically-tufted nanopores, resulting in a lower measurable pressure limit due to both the increased effective sensing area and the decreased effective thermal loss through the supporting structure. Additionally, the suspended AAO membrane structure, with its outer periphery anchored to the substrate, known as a closed-type design, is demonstrated using nanopores of AAO as an etch hole without a bulk micromachining process used on the substrate. In a CMOS-compatible process, a 200 μm × 200 μm nanoporous Pirani sensor with porosity of 25% was capable of measuring the pressure from 0.1 mTorr to 760 Torr. With adjustment of the porosity of the AAO, the measurable range could be extended toward lower pressures of more than one decade compared to a non-porous membrane with an identical footprint.

Resolved single-molecule detection of individual species within a mixture of anti-biotin antibodies using an engineered monomeric nanopore.

Science.gov (United States)

Fahie, Monifa; Chisholm, Christina; Chen, Min

2015-02-24

Oligomeric protein nanopores with rigid structures have been engineered for the purpose of sensing a wide range of analytes including small molecules and biological species such as proteins and DNA. We chose a monomeric β-barrel porin, OmpG, as the platform from which to derive the nanopore sensor. OmpG is decorated with seven flexible loops that move dynamically to create a distinct gating pattern when ionic current passes through the pore. Biotin was chemically tethered to the most flexible one of these loops. The gating characteristic of the loop's movement in and out of the porin was substantially altered by analyte protein binding. The gating characteristics of the pore with bound targets were remarkably sensitive to molecular identity, even providing the ability to distinguish between homologues within an antibody mixture. A total of five gating parameters were analyzed for each analyte to create a unique fingerprint for each biotin-binding protein. Our exploitation of gating noise as a molecular identifier may allow more sophisticated sensor design, while OmpG's monomeric structure greatly simplifies nanopore production.

Disposable urea biosensor based on nanoporous ZnO film fabricated from omissible polymeric substrate

International Nuclear Information System (INIS)

Rahmanian, Reza; Mozaffari, Sayed Ahmad; Abedi, Mohammad

2015-01-01

In the present study, a facile and simple fabrication method of a semiconductor based urea biosensor was reported via three steps: (i) producing a ZnO–PVA composite film by means of a polymer assisted electrodeposition of zinc oxide (ZnO) on the F-doped SnO 2 conducting glass (FTO) using water soluble polyvinyl alcohol (PVA), (ii) obtaining a nanoporous ZnO film by PVA omission via a subsequent post-treatment by annealing of the ZnO–PVA film, and (iii) preparation of a FTO/ZnO/Urs biosensor by exploiting a nanoporous ZnO film as an efficient and excellent platform area for electrostatic immobilization of urease enzyme (Urs) which was forced by the difference in their isoelectric point (IEP). The characterization techniques focused on the analysis of the ZnO–PVA film surfaces before and after annealing, which had a prominent effect on the porosity of the prepared ZnO film. The surface characterization of the nanostructured ZnO film by a field emission-scanning electron microscopy (FE–SEM), exhibited a film surface area as an effective bio-sensing matrix for enzyme immobilization. The structural characterization and monitoring of the biosensor fabrication was performed using UV–Vis, Fourier Transform Infrared (FT-IR), Raman Spectroscopy, Thermogravimetric Analysis (TGA), Cyclic Voltammetry (CV), and Electrochemical Impedance Spectroscopy (EIS) techniques. The impedimetric results of the FTO/ZnO/Urs biosensor showed a high sensitivity for urea detection within 8.0–110.0 mg dL −1 with the limit of detection as 5.0 mg dL −1 . - Highlights: • Novel disposable impedimetric urea biosensor fabrication based on ZnO–nanoporous transducer • Exploiting omissible PVA polymer as a simple strategy for ZnO–nanoporous film preparation • ZnO–nanoporous film as a good pore framework with large surface area/volume for enzyme immobilization • Application of impedimetric measurement for urea monitoring due to its rapidity, sensitivity, and repeatability

Disposable urea biosensor based on nanoporous ZnO film fabricated from omissible polymeric substrate

Energy Technology Data Exchange (ETDEWEB)

Rahmanian, Reza; Mozaffari, Sayed Ahmad, E-mail: mozaffari@irost.ir; Abedi, Mohammad

2015-12-01

In the present study, a facile and simple fabrication method of a semiconductor based urea biosensor was reported via three steps: (i) producing a ZnO–PVA composite film by means of a polymer assisted electrodeposition of zinc oxide (ZnO) on the F-doped SnO{sub 2} conducting glass (FTO) using water soluble polyvinyl alcohol (PVA), (ii) obtaining a nanoporous ZnO film by PVA omission via a subsequent post-treatment by annealing of the ZnO–PVA film, and (iii) preparation of a FTO/ZnO/Urs biosensor by exploiting a nanoporous ZnO film as an efficient and excellent platform area for electrostatic immobilization of urease enzyme (Urs) which was forced by the difference in their isoelectric point (IEP). The characterization techniques focused on the analysis of the ZnO–PVA film surfaces before and after annealing, which had a prominent effect on the porosity of the prepared ZnO film. The surface characterization of the nanostructured ZnO film by a field emission-scanning electron microscopy (FE–SEM), exhibited a film surface area as an effective bio-sensing matrix for enzyme immobilization. The structural characterization and monitoring of the biosensor fabrication was performed using UV–Vis, Fourier Transform Infrared (FT-IR), Raman Spectroscopy, Thermogravimetric Analysis (TGA), Cyclic Voltammetry (CV), and Electrochemical Impedance Spectroscopy (EIS) techniques. The impedimetric results of the FTO/ZnO/Urs biosensor showed a high sensitivity for urea detection within 8.0–110.0 mg dL{sup −1} with the limit of detection as 5.0 mg dL{sup −1}. - Highlights: • Novel disposable impedimetric urea biosensor fabrication based on ZnO–nanoporous transducer • Exploiting omissible PVA polymer as a simple strategy for ZnO–nanoporous film preparation • ZnO–nanoporous film as a good pore framework with large surface area/volume for enzyme immobilization • Application of impedimetric measurement for urea monitoring due to its rapidity, sensitivity, and

Instability of chromosome number and DNA methylation variation induced by hybridization and amphidiploid formation between Raphanus sativus L. and Brassica alboglabra Bailey

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Wang Yanjie

2010-09-01

Full Text Available Abstract Background Distant hybridization can result genome duplication and allopolyploid formation which may play a significant role in the origin and evolution of many plant species. It is unclear how the two or more divergent genomes coordinate in one nucleus with a single parental cytoplasm within allopolyploids. We used cytological and molecular methods to investigate the genetic and epigenetic instabilities associated with the process of distant hybridization and allopolyploid formation, measuring changes in chromosome number and DNA methylation across multiple generations. Results F1 plants from intergeneric hybridization between Raphanus sativus L. (2n = 18, RR and Brassica alboglabra Bailey (2n = 18, CC were obtained by hand crosses and subsequent embryo rescue. Random amplification of polymorphic DNA (RAPD markers were used to identify the F1 hybrid plants. The RAPD data indicated that the hybrids produced specific bands similar to those of parents and new bands that were not present in either parent. Chromosome number variation of somatic cells from allotetraploids in the F4 to F10 generations showed that intensive genetic changes occurred in the early generations of distant hybridization, leading to the formation of mixopolyploids with different chromosome numbers. DNA methylation variation was revealed using MSAP (methylation-sensitive amplification polymorphism, which showed that cytosine methylation patterns changed markedly in the process of hybridization and amphidiploid formation. Differences in cytosine methylation levels demonstrated an epigenetic instability of the allopolyploid of Raphanobrassica between the genetically stable and unstable generations. Conclusions Our results showed that chromosome instability occurred in the early generations of allopolyploidy and then the plants were reverted to largely euploidy in later generations. During this process, DNA methylation changed markedly. These results suggest that

A rapid and efficient branched DNA hybridization assay to titer lentiviral vectors.

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Nair, Ayyappan; Xie, Jinger; Joshi, Sarasijam; Harden, Paul; Davies, Joan; Hermiston, Terry

2008-11-01

A robust assay to titer lentiviral vectors is imperative to qualifying their use in drug discovery, target validation and clinical applications. In this study, a novel branched DNA based hybridization assay was developed to titer lentiviral vectors by quantifying viral RNA genome copy numbers from viral lysates without having to purify viral RNA, and this approach was compared with other non-functional (p24 protein ELISA and viral RT-qPCR) and a functional method (reporter gene expression) used commonly. The RT-qPCR method requires purification of viral RNA and the accuracy of titration therefore depends on the efficiency of purification; this requirement is ameliorated in the hybridization assay as RNA is measured directly in viral lysates. The present study indicates that the hybridization based titration assay performed on viral lysates was more accurate and has additional advantages of being rapid, robust and not dependent on transduction efficiency in different cell types.

Identification of Biomolecular Building Blocks by Recognition Tunneling: Stride towards Nanopore Sequencing of Biomolecules

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Sen, Suman

DNA, RNA and Protein are three pivotal biomolecules in human and other organisms, playing decisive roles in functionality, appearance, diseases development and other physiological phenomena. Hence, sequencing of these biomolecules acquires the prime interest in the scientific community. Single molecular identification of their building blocks can be done by a technique called Recognition Tunneling (RT) based on Scanning Tunneling Microscope (STM). A single layer of specially designed recognition molecule is attached to the STM electrodes, which trap the targeted molecules (DNA nucleoside monophosphates, RNA nucleoside monophosphates or amino acids) inside the STM nanogap. Depending on their different binding interactions with the recognition molecules, the analyte molecules generate stochastic signal trains accommodating their "electronic fingerprints". Signal features are used to detect the molecules using a machine learning algorithm and different molecules can be identified with significantly high accuracy. This, in turn, paves the way for rapid, economical nanopore sequencing platform, overcoming the drawbacks of Next Generation Sequencing (NGS) techniques. To read DNA nucleotides with high accuracy in an STM tunnel junction a series of nitrogen-based heterocycles were designed and examined to check their capabilities to interact with naturally occurring DNA nucleotides by hydrogen bonding in the tunnel junction. These recognition molecules are Benzimidazole, Imidazole, Triazole and Pyrrole. Benzimidazole proved to be best among them showing DNA nucleotide classification accuracy close to 99%. Also, Imidazole reader can read an abasic monophosphate (AP), a product from depurination or depyrimidination that occurs 10,000 times per human cell per day. In another study, I have investigated a new universal reader, 1-(2-mercaptoethyl)pyrene (Pyrene reader) based on stacking interactions, which should be more specific to the canonical DNA nucleosides. In addition

Guanine is indispensable for immunoglobulin switch region RNA-DNA hybrid formation

International Nuclear Information System (INIS)

Mizuta, Ryushin; Mizuta, Midori; Kitamura, Daisuke

2005-01-01

It is suggested that the formation of the switch (S) region RNA-DNA hybrid and the subsequent generation of higher-order chromatin structures including R-loop initiate a class switch recombination of the immunoglobulin gene. The primary factor of this recombination is the S-region derived noncoding RNA. However, the biochemical character of this guanine-rich (G-rich) transcript is poorly understood. The present study was performed to analyze the structure of this G-rich RNA using atomic force microscope (AFM). The in vitro transcribed S-region RNA was spread on a mica plate, air-dried and observed by non-contact mode AFM in air. The G-rich transcripts tend to aggregate on the template DNA and to generate a higher-order RNA-DNA complex. However, the transcripts that incorporated guanine analogues as substitutes for guanine neither aggregated nor generated higher-order structures. Incorporation of guanine analogues in transcribes RNA partially disrupts hydrogen bonds related to guanine, such as Watson-Crick GC-base pair and Hoogsteen bond GG-base pair. Thus, aggregation of S-region RNA and generation of the higher-order RNA-DNA complex are attributed to hydrogen bonds of guanine. (author)

An Engineered Kinetic Amplification Mechanism for Single Nucleotide Variant Discrimination by DNA Hybridization Probes.

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Chen, Sherry Xi; Seelig, Georg

2016-04-20

Even a single-nucleotide difference between the sequences of two otherwise identical biological nucleic acids can have dramatic functional consequences. Here, we use model-guided reaction pathway engineering to quantitatively improve the performance of selective hybridization probes in recognizing single nucleotide variants (SNVs). Specifically, we build a detection system that combines discrimination by competition with DNA strand displacement-based catalytic amplification. We show, both mathematically and experimentally, that the single nucleotide selectivity of such a system in binding to single-stranded DNA and RNA is quadratically better than discrimination due to competitive hybridization alone. As an additional benefit the integrated circuit inherits the property of amplification and provides at least 10-fold better sensitivity than standard hybridization probes. Moreover, we demonstrate how the detection mechanism can be tuned such that the detection reaction is agnostic to the position of the SNV within the target sequence. in contrast, prior strand displacement-based probes designed for kinetic discrimination are highly sensitive to position effects. We apply our system to reliably discriminate between different members of the let-7 microRNA family that differ in only a single base position. Our results demonstrate the power of systematic reaction network design to quantitatively improve biotechnology.

Energy absorption behaviors of nanoporous materials functionalized (NMF) liquids

OpenAIRE

Kim, Tae Wan

2011-01-01

For many decades, people have been actively investigating high-performance energy absorption materials, so as to develop lightweight and small-sized protective and damping devices, such as blast mitigation helmets, vehicle armors, etc. Recently, the high energy absorption efficiency of nanoporous materials functionalized (NMF) liquids has drawn considerable attention. A NMF liquid is usually a liquid suspension of nanoporous particles with large nanopore surface areas (100 - 2,000 m²/g). The ...

Identification of Lactobacillus UFV H2b20 (probiotic strain using DNA-DNA hybridization Identificação de Lactobacillus UFV H2b20 (linhagem probiótica através de hibridização DNA-DNA

Directory of Open Access Journals (Sweden)

J.T. de Magalhães

2008-09-01

Full Text Available Sequence analyses of the 16S rDNA gene and DNA-DNA hybridization tests were performed for identification of the species of the probiotic Lactobacillus UFV H2b20 strain. Using these two tests, we concluded that this strain, originally considered Lact. acidophilus, should be classified as Lact. delbrueckii.Análise da seqüência do gene 16S rDNA e ensaios de hibridização DNA_DNA foram empregados para identificar a espécie da cepa probiótica Lactobacillus UFV H2b20. Empregando-se estes dois testes, concluímos que esta cepa, originalmente considerada Lact. acidophilus, deve ser classificada como Lact. delbrueckii.