Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “DNA Nanostructures”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8Linked to original sources
PubMedDate not supplied

Detection of point mutations in the HBV polymerase gene using a fluorescence intercalator in reverse micelles.

We report a novel and simple method for mutation detection in DNA oligonucleotides using a double-stranded DNA specific dye (SYBR Green I) in nanostructured molecular assemblies, called reverse micelles. The intercalation of SYBR Green I into the duplex DNA exhibits fluorescent emission in a CTAB/isooctane reverse micellar system as well as in an aqueous solution. We found marked differences in the fluorescence intensity between perfectly matched and mismatched 52-mer synthetic oligonucleotides, which were designed to contain the YMDD motif of the hepatitis B virus (HBV) polymerase gene, in a reverse micellar solution. Using this method, we successfully detected a mutation in PCR-amplified oligonucleotides of the HBV polymerase gene in sera of four patients with chronic hepatitis B. This detection method does not require DNA immobilization, chemical modification of DNA, or any special apparatus; it only needs a normal fluorescence spectrophotometer, an inexpensive dye, and just 10 pmol of sample DNA.

Base Pair Mismatch↗
PubMed2006

Molecular hurdles in polyfectin design and mechanistic background to polycation induced cytotoxicity.

Synthetic polymer based Polyfectins (cationic polymer-DNA complex) have received intensive scientific research as they can potentially circumvent problems associated with viral vectors for gene therapy. These cationic macromolecules can readily condense DNA or RNA into stable nanostructures for use in gene delivery. Recently two commonly used polycations, poly(ethylenimine) (PEI) and poly(L-lysine) have demonstrated their ability to induce apoptosis in a range of human cell lines. This may be the explanation for short-term gene transfection observed with polyfectins. It is the aim of this review to discuss these and other factors behind observed toxicities including the inherent polydisperse nature of polymeric macromolecules and their behaviour in vivo. Strategies for reduction of toxicity are included such as new polymeric synthetic technologies and vector pegylation. There is a clear and immediate need for understanding of the mechanisms which cause polyfectin toxicity which will ultimately facilitate improved vector design and safer gene delivery.

Animals↗
PubMed2004

Sparsely cross-linked "nanogel" matrixes as fluid, mechanically stabilized polymer networks for high-throughput microchannel DNA sequencing.

We have developed sparsely cross-linked "nanogels", subcolloidal polymer structures composed of covalently linked, linear polyacrylamide chains, as novel replaceable DNA sequencing matrixes for capillary and microchip electrophoresis. Nanogels were synthesized via inverse emulsion (water-in-oil) copolymerization of acrylamide and a low percentage (approximately 10(-4) mol %) of N,N-methylene bisacrylamide (Bis). Nanogels and nanogel networks were characterized by multiangle laser light scattering and rheometry, respectively, and tested for DNA sequencing in both capillaries and chips with four-color LIF detection. Typical nanogels have an average radius of approximately 230 nm, with approximately 75% of chains incorporating a Bis cross-linker. The properties and performance of nanogel matrixes are compared here to those of a linear polyacrylamide (LPA) network, matched for both polymer weight-average molar mass (M(w)) and the extent of interchain entanglements (c/c). At sequencing concentrations, the two matrixes have similar flow characteristics, important for capillary and microchip loading. However, because of the physical network stability provided by the internally cross-linked structure of the nanogels, substantially longer average read lengths are obtained under standard conditions with the nanogel matrix at a 98.5% accuracy of base-calling (for CE: 680 bases, an 18.7% improvement over LPA, with the best reads as long as 726 bases, compared to 568 bases for the LPA matrix). We further investigated the use of the nanogel matrixes in a high-throughput microfabricated DNA sequencing device consists of 96 separation channels densely fabricated on a 6-in. glass wafer. Again, preliminary DNA sequencing results show that the nanogel matrixes are capable of delivering significantly longer average read length, compared to an LPA matrix of comparable properties. Moreover, nanogel matrixes require 30% less polymer per unit volume than LPA. The addition of a small amount of low molar mass LPA or ultrahigh molar mass LPA to the optimized nanogel sequencing matrix further improves read length as well as the reproducibility of read length (RSD < 1.6%). This is the first report of a replaceable DNA sequencing matrix that provides better performance than LPA, in a side-by-side comparison of polymer matrixes appropriately matched for molar mass and the extent of interchain entanglements. These results could have significant implications for the improvement of microchip-based DNA sequencing technology.

Acrylic Resins↗
PubMed2003

Surface-enhanced Raman scattering substrate based on a self-assembled monolayer for use in gene diagnostics.

The development of surface-enhanced Raman scattering (SERS)-active substrates for cancer gene detection is described. The detection method uses Raman active dye-labeled DNA gene probes, self-assembled monolayers, and nanostructured metallic substrates as SERS-active platforms. The mercaptohexane-labeled single-stranded DNA (SH-(CH(2))(6)-ssDNA)/6-mercapto-1-hexanol system formed on a silver surface is characterized by atomic force microscopy. The surface-enhanced Raman gene (SERGen) probes developed in this study can be used to detect DNA targets via hybridization to complementary DNA probes. The probes do not require the use of radioactive labels and have a great potential to provide both sensitivity and selectivity. The effectiveness of this approach and its application in cancer gene diagnostics (BRCA1 breast cancer gene) are investigated.

BRCA1 Protein↗
PubMed2005

Strategies for DNA vaccine delivery.

Strategies for gene delivery comprise a diverse range of live and synthetic approaches; DNA delivery for the purposes of immunisation in turn comprises a large part of this research. This review mainly discusses synthetic systems for application in the delivery of plasmid DNA vaccines, outlining polylactide-co-glycolide, liposome, chitosan and complex combination delivery systems. Areas of promise for DNA vaccine candidates include immune modulation of allergic responses and veterinarian application. The potential for realistic consideration of DNA vaccines as an alternative to existing approaches is dependent on the development of efficient DNA vaccine vectors and improved systems for DNA vaccine delivery. DNA vaccine technology may yet prove to be an important asset in an environment where there is a critical need for therapeutic and prophylactic strategies to combat a wide range of disease states.

Animals↗
PubMed2006

Wide-field optical imaging of surface nanostructures.

We present a new technique that increases the sensitivity of incoherent light optical microscopy to a point where it becomes possible to directly visualize ultrathin films (approximately nanometers) and isolated nano-objects. The technique is based on the use of nonreflecting substrate surfaces for cross-polarized reflected light microscopy. These surfaces generate a contrast enhancement of about 2 orders of magnitude, extending the application field of wide-field optical microscopy toward the nanoworld. The efficiency of the method is proven experimentally on well-characterized samples. Wide-field imaging of a nonlabeled lambda-DNA molecule is also presented.

DNA↗
PubMed2006

Fabrication of biological nanostructures by scanning near-field photolithography of chloromethylphenylsiloxane monolayers.

We demonstrate the fabrication of sub-100-nm DNA surface patterns by scanning near-field optical lithography using a near-field scanning optical microscope coupled to a UV laser and a chloromethylphenylsiloxane (CMPS) self-assembled monolayer (SAM). The process involves 244-nm exposure of the CMPS SAM to create nanoscale patterns of surface carboxylic acid functional groups, followed by their conversion to the N-hydroxysuccinimidyl ester and reaction of the active ester with DNA to spatially control DNA grafting with high selectivity.

Animals↗
PubMed2005

Plasmonics-based nanostructures for surface-enhanced Raman scattering bioanalysis.

Surface-enhanced Raman scattering (SERS) spectroscopy is a plasmonics-based spectroscopic technique that combines modern laser spectroscopy with unique optical properties of metallic nanostructures, resulting in strongly increased Raman signals when molecules are adsorbed on or near nanometer-size structures of special metals such as gold, silver, and transition metals. This chapter provides a synopsis of the development and application of SERS-active metallic nanostructures, especially for the analysis of biologically relevant compounds. Some highlights of this chapter include reports of SERS as an immunoassay readout method, SERS gene nanoprobes, near-field scanning optical microscopy SERS probes, SERS as a tool for single-molecule detection, and SERS nanoprobes for cellular studies.

DNA↗
PubMed2005

Enhanced immunogenicity of microencapsulated multiepitope DNA vaccine encoding T and B cell epitopes of foot-and-mouth disease virus in mice.

The role of poly(D,L-lactic-co-glycolic acid, PLGA) microparticles on enhancing immune responses of multiepitope DNA vaccines was investigated in vitro and in vivo. pcDNA-SG encoding T and B cell epitopes of foot-and-mouth disease virus (FMDV) was encapsulated into PLGA microparticles. PLGA microparticles could protect themselves from nuclease degradation in vitro. PLGA-pcDNA-SG microparticles could be uptaken by cells and expressed His-tagged SG immunogen in vitro and in vivo. A prolonged expression and presentation of SG immunogen were observed by confocal laser scanning microscopy in the lymphocytes from the mice incubated with PLGA-pcDNA-SG microparticles, compared with the mice immunized with naked pcDNA-SG. PLGA-pcDNA-SG microparticles displayed a significant stronger immunogenicity than naked DNA vaccines with a higher titer of virus-specific antibody, elevated IFN-gamma production and enhanced lymphocyte proliferation. PLGA-DNA microparticle could elicit augmented humoral and cellular responses with reduced amounts and times of immunization.

Animals↗
PubMed2005

Nanoparticle-DNA conjugates bearing a specific number of short DNA strands by enzymatic manipulation of nanoparticle-bound DNA.

Self-assembling of metallic nanoparticles to form well-defined nanostructured structures is a field that has been receiving considerable research interest in recent years. In this field, DNA is a commonly used linker molecule to direct the assembly of the nanoscale building blocks because of its unique recognition capabilities, mechanical rigidity, and physicochemical stability. This study reported our novel approach to generate gold nanoparticle-DNA conjugates bearing specially designed DNA linker molecules that can be used as building blocks to construct nanoassemblies with precisely controlled structure or as nanoprobes for quantitative DNA sequence detection analysis. In our approach, gold nanoparticle-DNA conjugates bearing a specific number of long double-stranded DNA strands were prepared by gel electrophoresis. A restriction endonuclease enzyme was then used to manipulate the length of the nanoparticle-bound DNA. This enzymatic cleavage was confirmed by gel electrophoresis, and digestion efficiency of 90% or more was achieved. With this approach, nanoparticle conjugates bearing a specific number of strands of short DNA with less than 20-base can be achieved.

Cross-Linking Reagents↗
PubMed2004

Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes.

Nucleic acid diagnostics is dominated by fluorescence-based assays that use complex and expensive enzyme-based target or signal-amplification procedures. Many clinical diagnostic applications will require simpler, inexpensive assays that can be done in a screening mode. We have developed a 'spot-and-read' colorimetric detection method for identifying nucleic acid sequences based on the distance-dependent optical properties of gold nanoparticles. In this assay, nucleic acid targets are recognized by DNA-modified gold probes, which undergo a color change that is visually detectable when the solutions are spotted onto an illuminated glass waveguide. This scatter-based method enables detection of zeptomole quantities of nucleic acid targets without target or signal amplification when coupled to an improved hybridization method that facilitates probe-target binding in a homogeneous format. In comparison to a previously reported absorbance-based method, this method increases detection sensitivity by over four orders of magnitude. We have applied this method to the rapid detection of mecA in methicillin-resistant Staphylococcus aureus genomic DNA samples.

Bacterial Proteins↗
PubMed2004

Reversibly switchable DNA nanocompartment on surfaces.

Biological macromolecules have been used to fabricate many nanostructures, biodevices and biomimetics because of their physical and chemical properties. But dynamic nanostructure and biomachinery that depend on collective behavior of biomolecules have not been demonstrated. Here, we report the design of DNA nanocompartments on surfaces that exhibit reversible changes in molecular mechanical properties. Such molecular nanocompartments are used to encage molecules, switched by the collective effect of Watson-Crick base-pairing interactions. This effect is used to perform molecular recognition. Furthermore, we found that 'fuel' strands with single-base variation cannot afford an efficient closing of nanocompartments, which allows highly sensitive label-free DNA array detection. Our results suggest that DNA nanocompartments can be used as building blocks for complex biomaterials because its core functions are independent of substrates and mediators.

Base Pair Mismatch↗
PubMed2005

Single-molecule studies on DNA and RNA.

DNA and RNA are the most individual molecules known. Therefore, single-molecule experiments with these nucleic acids are particularly useful. This review reports on recent experiments with single DNA and RNA molecules. First, techniques for their preparation and handling are summarised including the use of AFM nanotips and optical or magnetic tweezers. As important detection techniques, conventional and near-field microscopy as well as fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) are touched on briefly. The use of single-molecule techniques currently includes force measurements in stretched nucleic acids and in their complexes with binding partners, particularly proteins, and the analysis of DNA by restriction mapping, fragment sizing and single-molecule hybridisation. Also, the reactions of RNA polymerases and enzymes involved in DNA replication and repair are dealt with in some detail, followed by a discussion of the transport of individual nucleic acid molecules during the readout and use of genetic information and during the infection of cells by viruses. The final sections show how the enormous addressability in nucleic acid molecules can be exploited to construct a single-molecule field-effect transistor and a walking single-molecule robot, and how individual DNA molecules can be used to assemble a single-molecule DNA computer.

Chromatin↗
PubMed2004

Silica-nanoparticle-based interface for the enhanced immobilization and sequence-specific detection of DNA.

A biocompatible and uniform interface based on silica nanoparticles derivatized with amino groups has been constructed for the effective immobilization and sensitive sequence-specific detection of calf thymus DNA. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) results showed that a monolayer of silica nanoparticles can be formed on a gold electrode under our experimental conditions using cysteine self-assembly monolayer as binder medium. Electrochemical impedance spectroscopy and X-ray photoelectron spectroscopy (XPS) verified the successful immobilization of DNA on silica-nanoparticle-modified gold electrodes. Quantitative results demonstrated that enhanced immobilization of single-strand DNA (ss-DNA) up to 1.6 x 10(-8) mol cm(-2) could be achieved owing to the larger surface area and the special properties of silica nanoparticles. In addition, hybridization experiments demonstrated that the immobilized ss-DNA on silica nanoparticles could specifically interact with complementary DNA in solutions.

Animals↗
PubMed2004

Oligonucleotide-displaced organic monolayer-protected silver nanoparticles and enhanced luminescence of their salted aggregates.

N-(2-mercaptopropionyl)glycine (tiopronin) monolayer-protected silver particles were partially displaced by single-stranded oligonucleotides through ligand exchanges. The oligonucleotide-displaced particles could be hybridized with complementary fluorophore-labeled oligonucleotides. Both the oligonucleotide-displaced and hybridized particles could be aggregated by electrostatic interactions with salt in buffer solution, and the aggregates displayed enhanced luminescence from fluorophores. This result suggests the possible application of surface-enhanced fluorescence from metallic nanoparticle aggregation for DNA detection.

DNA↗
PubMed2006

Label-free detection of biomolecules on microarrays using surface-colloid interaction.

Binding of charged nanoparticles to nonmodified DNA and RNA target molecules on microarrays allows detection of these nucleic acids by locating bound nanoparticles on microarray surface. Two computational models have been developed to study the ionic interaction of colloidal particles and biopolymer molecules on a microarray surface. One model represents a basic approach based on mass action law for simulation charge effects versus the chemical composition of the interacting array surface and nanoparticle. The second model is implementation of the advanced Gouy-Chapman-Stern-Graham model for describing effects on liquid-solid interface. We found that both models predict selective binding of colloidal particles to large target molecules on the surface with no binding to smaller capture molecules. This binding regime is considered to be very beneficial for application of charged nanoparticles for detection of nonmodified DNA and RNA target molecules on microarrays. The theoretical considerations are in qualitative agreement with the experimental results for detecting large target DNA and a 50-base long synthetic oligonucleotide on the amino-modified microarray substrate. The experimental and theoretical results of this study allow further development of the label-free microarray technology demonstrated previously for gene expression analysis that is free of reverse transcription and dye labeling.

Colloids↗