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At least 127 records · Page 7Linked to original sources
PubMed2006

Fast and sensitive DNA hybridization assays using microwave-accelerated metal-enhanced fluorescence.

A new, fast, and sensitive DNA hybridization assay platform based on microwave-accelerated metal-enhanced fluorescence (MAMEF) is presented. Thiolated oligonucleotide anchors were immobilized onto silver nanoparticles on a glass substrate. The hybridization of the complementary fluorescein-labeled DNA target with the surface-bound oligonucleotides was completed within 20 s upon heating with low-power microwaves. In addition, the signal is optically amplified, a consequence of close proximity of the fluorophore to the silvered substrate. In this proof-of-principle methodology, as low as 50 nM of a target DNA was detected, although we envisage far-lower detection limits. Control experiments, where the surface-bound oligonucleotide was omitted, were also performed to determine the extent of non-specific binding. In these studies a significantly reduced non-specific adsorption was found when using microwave heating near to silvered structures as compared to room temperature incubation. These findings suggest that MAMEF could be a most useful alternative to the DNA hybridization assays used today, especially with regard to substantially increasing both the assay rapidity and sensitivity.

Aminoacridines↗
PubMed2004

Secondary structure prediction of interacting RNA molecules.

Computational tools for prediction of the secondary structure of two or more interacting nucleic acid molecules are useful for understanding mechanisms for ribozyme function, determining the affinity of an oligonucleotide primer to its target, and designing good antisense oligonucleotides, novel ribozymes, DNA code words, or nanostructures. Here, we introduce new algorithms for prediction of the minimum free energy pseudoknot-free secondary structure of two or more nucleic acid molecules, and for prediction of alternative low-energy (sub-optimal) secondary structures for two nucleic acid molecules. We provide a comprehensive analysis of our predictions against secondary structures of interacting RNA molecules drawn from the literature. Analysis of our tools on 17 sequences of up to 200 nucleotides that do not form pseudoknots shows that they have 79% accuracy, on average, for the minimum free energy predictions. When the best of 100 sub-optimal foldings is taken, the average accuracy increases to 91%. The accuracy decreases as the sequences increase in length and as the number of pseudoknots and tertiary interactions increases. Our algorithms extend the free energy minimization algorithm of Zuker and Stiegler for secondary structure prediction, and the sub-optimal folding algorithm by Wuchty et al. Implementations of our algorithms are freely available in the package MultiRNAFold.

Algorithms↗
PubMed2005

Thermodynamics of DNA hybridization on gold nanoparticles.

Dynamic light scattering is used as a sensitive probe of hybridization on DNA-functionalized colloidal gold nanoparticles. When a target DNA strand possesses an 8 base "dangling end", duplex formation on the surface of the nanoparticles leads to an increase in hydrodynamic radius. Duplex melting is manifested in a drop in hydrodynamic radius with increasing temperature, and the concentration dependence of the melting temperature provides a measure of the thermodynamics of binding. The hybridization thermodynamics are found to be significantly lower at higher hybridization densities than those previously reported for initial hybridization events. The pronounced deviation from Langmuir adsorption behavior is greater for longer duplexes, and it is, therefore, consistent with electrostatic repulsion between densely packed oligonucleotides. The results have implications for sensing and DNA-directed nanoparticle assembly.

DNA↗
PubMed2006

Highly sensitive biomolecular fluorescence detection using nanoscale ZnO platforms.

Fluorescence detection is currently one of the most widely used methods in the areas of basic biological research, biotechnology, cellular imaging, medical testing, and drug discovery. Using model protein and nucleic acid systems, we demonstrate that engineered nanoscale zinc oxide structures can significantly enhance the detection capability of biomolecular fluorescence. Without any chemical or biological amplification processes, nanoscale zinc oxide platforms enabled increased fluorescence detection of these biomolecules when compared to other commonly used substrates such as glass, quartz, polymer, and silicon. The use of zinc oxide nanorods as fluorescence enhancing substrates in our biomolecular detection permitted sub-picomolar and attomolar detection sensitivity of proteins and DNA, respectively, when using a conventional fluorescence microscope. This ultrasensitive detection was due to the presence of ZnO nanomaterials which contributed greatly to the increased signal-to-noise ratio of biomolecular fluorescence. We also demonstrate the easy integration potential of zinc oxide nanorods into periodically patterned nanoplatforms which, in turn, will promote the assembly and fabrication of these materials into multiplexed, high-throughput, optical sensor arrays. These zinc oxide nanoplatforms will be extremely beneficial in accomplishing highly sensitive and specific detection of biological samples involving nucleic acids, proteins and cells, particularly under detection environments involving extremely small sample volumes of ultratrace-level concentrations.

DNA↗
PubMed2005

Periodic DNA nanotemplates synthesized by rolling circle amplification.

Rolling circle amplification (RCA) is an elegant biochemical method by which long single-stranded DNA molecules with a repeating sequence motif can be readily synthesized. In RCA, small circular single-stranded oligonucleotides serve as templates for the polymerization of the complementary strand. A DNA polymerase with an efficient strand displacement activity can copy the circular template without stopping. This results in a long DNA strand with periodic sequence. We here demonstrate that this method, using DNA recognition and biotin-streptavidin binding, provides a simple procedure for DNA-directed nanoscale organization of matter. As an example, a 74 nucleotide (nt) long circular DNA molecule is amplified into a sequence-periodic single strand with a length up to several micrometers. Hybridization of this long periodic DNA template to the biotinylated complement of the sequence motif results in a long DNA duplex with a periodic arrangement of biotin binding sites. On this duplex, streptavidin-coated particles can be organized into one-dimensional arrays. The resulting DNA constructs are characterized by gel electrophoresis and atomic force microscopy.

Biotin↗
PubMed2005

Slowing DNA translocation in a solid-state nanopore.

Reducing a DNA molecule's translocation speed in a solid-state nanopore is a key step toward rapid single molecule identification. Here we demonstrate that DNA translocation speeds can be reduced by an order of magnitude over previous results. By controlling the electrolyte temperature, salt concentration, viscosity, and the electrical bias voltage across the nanopore, we obtain a 3 base/micros translocation speed for 3 kbp double-stranded DNA in a 4-8 nm diameter silicon nitride pore. Our results also indicate that the ionic conductivity inside such a nanopore is smaller than it is in bulk.

DNA↗
PubMed2005

In vitro non-viral gene delivery with nanofibrous scaffolds.

Extracellular and intracellular barriers typically prevent non-viral gene vectors from having an effective transfection efficiency. Formulation of a gene delivery vehicle that can overcome the barriers is a key step for successful tissue regeneration. We have developed a novel core-shelled DNA nanoparticle by invoking solvent-induced condensation of plasmid DNA (beta-galactosidase or GFP) in a solvent mixture [94% N,N-dimethylformamide (DMF) + 6% 1x TE buffer] and subsequent encapsulation of the condensed DNA globule in a triblock copolymer, polylactide-poly(ethylene glycol)-polylactide (L8E78L8), in the same solvent environment. The polylactide shell protects the encapsulated DNA from degradation during electrospinning of a mixture of encapsulated DNA nanoparticles and biodegradable PLGA (a random copolymer of lactide and glycolide) to form a nanofibrous non-woven scaffold using the same solution mixture. The bioactive plasmid DNA can then be released in an intact form from the scaffold with a controlled release rate and transfect cells in vitro.

Animals↗
PubMed2005

Magnetic force probe for nanoscale biomolecules.

We present a new technique to measure the mechanical properties of small biomolecules. This technique uses long range repulsive colloidal forces together with magnetic attraction as a force probing tool. The biomolecules are grafted between superparamagnetic particles, which are regularly spaced within long chains maintained by an external magnetic field. Varying the magnetic field results in compression or extension of the molecules between the particles. In order to demonstrate this technique we use, as a size controlled model molecule, a short double stranded DNA (151 base pairs) for which the force-extension law is determined and found in agreement with existing predictions.

Biopolymers↗
PubMedDate not supplied

[Functionalized nanocomposite coating of a glass surface for oligonucleotide immobilization].

A new type of coating for manufacturing DNA chips was constructed of the basis of an organic-inorganic nanocomposite based on the polyvinylbutyral-tetraethoxysilane copolymer. The organosilicon composite was functionalized by introduction of ethanolamine vinyl ether copolymers, which contain amino groups and anchor vinyloxide units capable of reacting with silanol groups of the nanocomposite. The resulting coatings form a film on glass slides with a high surface density of amino groups (up to 700 groups/nm2) suitable for three-dimensional immobilization of oligonucleotides. The use of bifunctional reagents (e.g., phenylene diisothiocyanate) for the attachment of oligonucleotides bearing amino linkers to the amino-containing surface provides an immobilization density of 0.5-1.6 pmol/mm2. Immobilization with a higher density (10-12 pmol/mm2) was achieved for attachment to amino-containing glass slides upon the use of oligonucleotides containing selectively activated terminal phosphate groups. The activation of oligonucleotides was carried out with the triphenylphosphine-dithiodipyridine pair in the presence of dimethylaminopyridine N-oxide. The resulting DNA chips were shown to be useful in principle for DNA detection.

DNA↗
PubMed2004

Self-organized, highly luminescent CdSe nanorod-DNA complexes.

DNA molecules are useful building blocks and nanotemplates for controllable fabrication of various bioinorganic nanostructures due to their unique physical-chemical properties and recognition capabilities and the synthetic availability of desired nucleotide sequences and length. We have synthesized novel DNA complexes with positively charged, highly luminescent CdSe nanorods that can be self-organized into filamentary, netlike, or spheroidal nanostructures. DNA-CdSe-nanorod filaments possess strongly linearly polarized photoluminescence due to the unidirectional orientation of nanorods along the filaments.

Cadmium Compounds↗
PubMed2003

Surface-enhanced Raman scattering for cancer diagnostics: detection of the BCL2 gene.

A method of detection for cancer genes, such as B-cell lymphoma 2 gene, has been developed using surface-enhanced Raman scattering-active substrates. This method uses Raman active dye-labeled DNA gene probes and metallic nanostructures as surface-enhanced Raman scattering-active platforms. A self-assembled monolayer system composed of mercapto hexane-labeled, single-strand DNA (SH-(CH2)6-ssDNA/ 6-mercapto-1-hexanol) is formed on a silver surface. The Raman-active dye-labeled gene is hybridized with its complementary probe, which is immobilized on the silver surface. The surface-enhanced Raman gene probes in this study can be used to detect DNA targets via hybridization to complementary DNA probes. The probes do not involve the use of radioactive labels and have great potential to provide both sensitivity and selectivity. The utility of this approach is investigated.

DNA Probes↗
PubMed2004

Roles of anionic and cationic template components in biomineralization of CdS nanorods using self-assembled DNA-membrane complexes.

Complexes of anionic DNA and cationic liposomes self-assemble into a multilamellar structure where two-dimensional lipid sheets confine a periodic one-dimensional lattice of parallel DNA chains, between which Cd(2+) ions can condense, and be subsequently reacted with H(2)S to form CdS nanorods. In this work, we identify the synergistic roles of the anionic and cationic components within the DNA-membrane template; DNA is highly anionic and condenses the Cd(2+) ions, while the cationic membrane modulates the concentration of condensed Cd(2+) ions to control the final CdS nanorod dimensions. Due to the strong electrostatic interactions between the DNA sugar-phosphate backbone and the Cd(2+) ions, crystallographic control of CdS nanostructures is possible using these simple DNA-membrane templates, which we demonstrate using nanobeam electron diffraction experiments on individual templated CdS nanorods.

Animals↗
PubMed2006

Dendritic-like streptavidin/alkaline phosphatase nanoarchitectures for amplified electrochemical sensing of DNA sequences.

This study describes the development and characterization of a novel dendritic-like signal amplification pathway. Such an analytical strategy relies on the use of streptavidin and biotinylated alkaline phosphatase, which can be simply and conveniently self-assembled to build nanoarchitectures rich in enzyme labels. The performance of this enzyme-based amplification route was demonstrated in connection with the electrochemical sensing of DNA sequences. Compared to the commercially available streptavidin-conjugated alkaline phosphatase labels, a single generation of the streptavidin/biotinylated alkaline phosphatase assembly allowed a 15-20-fold enhancement of the electroanalytical signals. The higher sensitivity allowed by the dendritic-like route was attributed to the lower steric hindrance of the proteins employed for this amplification path. As low as 50 pmol/L of a 388-bp-long amplicon identifying Salmonella spp. was easily detected. The experimental results additionally demonstrated that the sensitivity of the method could be further increased in a linear fashion with the number of protein-enzyme generations.

Alkaline Phosphatase↗
PubMed2006

Coadsorption of guanine and cytosine on graphite: ordered structure based on GC pairing.

Nanostructures formed by coadsorption of the complementary DNA bases guanine (G) and cytosine (C) at a graphite surface in 1-octanol solvent were investigated by in situ scanning tunneling microscopy. The high-resolution observations showed for the first time a well-ordered coadsorption structure, attributed to rows formed from Watson-Crick G-C pairs, which was distinctly different from the structures observed for the individual G/C components. The observed coadsorption structure has been modeled by self-consistent charge density-functional-based tight-binding (SCC-DFTB) calculations, providing information on the intermolecular interactions underlying its formation.

Adsorption↗