Showing papers on "Nucleic acid methods published in 2011"

Methods for sequencing individual nucleic acids under tension

Abstract: The invention provides apparatuses and methods of use thereof for sequencing nucleic acids subjected to a force, and thus considered under tension. The methods may employ but are not dependent upon incorporation of extrinsically detectably labeled nucleotides.

Method and Apparatus for Rapid Nucleic Acid Sequencing

Abstract: Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Integrated Glass Microdevice for Nucleic Acid Purification, Loop-Mediated Isothermal Amplification, and Online Detection

Abstract: A microdevice made of glass for genetic analysis has been fabricated, for the first time, for integration of extraction of nucleic acids and loop-mediated isothermal amplification (LAMP), followed by online fluorescence detection of amplification products on a single chip. The nucleic acid (NA) extraction region consists of a microfabricated serpentine channel in which micropillars were etched to increase the channel surface area and the capture efficiency of NAs. Nucleic acid molecules were bound to these pillars and channel surface in the presence of the chaotropic salt guanidine hydrochloride and eluted into a downstream amplification chamber with low ionic strength buffer where loop-mediated isothermal amplification was efficiently performed. Amplification can be detected online by the increase of fluorescence intensity at 540 nm when a low concentration of SYBR Green I, a fluorescent dsDNA intercalating dye, is employed. Flow control was accomplished by using laminar flow and differential channel flo...

Methods of generating nucleic acid fragments

Abstract: Provided herein are methods of using a Cas1 polypeptide to generate nucleic fragments from a DNA substrate. These methods may be performed in vitro or in vivo. Also provided are methods of screening for modulators of Cas1.

Metal-containing peptide nucleic acid conjugates.

Abstract: Peptide Nucleic Acids (PNAs) are non-natural DNA/RNA analogues with favourable physico-chemical properties and promising applications. Discovered nearly 20 years ago, PNAs have recently re-gained quite a lot of attention. In this Perspective article, we discuss the latest advances on the preparation and utilisation of PNA monomers and oligomers containing metal complexes. These metal- conjugates have found applications in various research fields such as in the sequence-specific detection of nucleic acids, in the hydrolysis of nucleic acids and peptides, as radioactive probes or as modulators of PNA˙DNA hybrid stability, and last but not least as probes for molecular and cell biology.

Nucleic acid isolation methods

Abstract: The present invention provides methods for selectively enriching a biological sample for short nucleic acids, such as fetal DNA in a maternal sample or apoptic DNA in a biological sample from a cancer patient and for subsequently analyzing the short nucleic acids for genotype, mutation, and/or aneuploidy.

B7-H1 antibodies and method of use

Abstract: The invention provides novel polypeptides useful for co-stimulating T cells, isolated nucleic acid molecules encoding them, vectors containing the nucleic acid molecules, and cells containing the vectors. Also included are methods of making and using these co-stimulatory polypeptides.

Nucleic acid compounds with conformationally restricted monomers and uses thereof

Abstract: This disclosure provides single-stranded and multi-stranded nucleic acid compounds having one or more double-stranded regions that regulate the function or expression of nucleic acid molecules expressed in a cell or a cell regulatory system dependent upon a nucleic acid. The disclosure provides a range of nucleic acid compounds having one or more conformationally restricted nucleomonomers (CRN). Certain nucleic acid compounds may have one or more conformationally restricted nucleomonomers and one or more hydroxymethyl substituted nucleomonomers (UNA). The nucleic acid compounds are useful in various therapeutic modalities.

Modified proteins and methods of making and using same

Abstract: Methods, compositions, systems, apparatuses and kits comprising modified proteins, particularly modified nucleic acid-binding proteins with altered buffering properties are provided. For example, in some embodiments, methods of forming modified proteins including one or more amino acid modifications to achieve desired pKa values are described. Furthermore, the invention provides methods for using such modified proteins in ion-producing reactions, such as ion-based nucleic acid sequencing reactions.

Methods and Kits for Nucleic Acid Amplification

Abstract: Compositions and methods are provided for amplifying nucleic acid molecules. The nucleic acid molecules can be used in various research and diagnostic applications, such as gene expression studies involving nucleic acid microarrays.

Methods of in situ detection of nucleic acids

Abstract: Methods of detecting the presence or absence of a class of nucleic acid targets in single cells through direct or indirect capture of labels to the nucleic acids are provided, where such labels to the class of nucleic acid targets are indistinguishable from each other. Also described are methods of detecting individual cells, particularly a cell of a specific type from large heterogeneous cell populations, through detection of one or more of nucleic acid targets, where the labels to the one or more of nucleic acid targets are indistinguishable from each other. Related kits are also described.

Selective enrichment of nucleic acids

Abstract: Methods for the selective enrichment of nucleic acids are described including obtaining a population of nucleic acids, comprising a target; contacting the population of nucleic acids with a nickase to produce a population of nicked nucleic acids; contacting the population of nicked nucleic acids with an exonuclease to generate a nucleic acid having a single-stranded portion, comprising at least a portion of said target; contacting a capture probe to the portion of the target to hybridize to said target; and separating a nucleic acid hybridized to said capture probe from a nucleic acid not bound to said capture probe.

Nucleic acid detection and quantification by post-hybridization labeling and universal encoding

Abstract: The present invention provides, among other things, methods and compositions for encoding a substrate for detecting and quantifying target nucleic acids.

A method for isolation of nucleic acids and a kit thereof

Abstract: The present disclosure provides a method to isolate natural & artificial nucleic acids like deoxyribonucleic acid (DNA), ribonucleic acid (RNA) and peptide nucleic acid (PNA) from a solid or liquid sample using cotton. The cotton packed is such that, a solution containing nucleic acids passes through it and the nucleic acids in solution are bound to the cotton in a medium optimal for binding. The nucleic acids are bound to cotton in such a way that, the bound nucleic acids can withstand multiple washes with liquid comprising water and gets eluted in an aqueous buffer, with which eluted nucleic acids can be directly used for amplification using PCR or for any other biochemical or molecular biology needs.

Compounds and methods for modulating interaction between proteins and target nucleic acids

Abstract: Provided herein are antisense compounds and methods for recruiting one or more non-cleaving protein to a target nucleic acid in a cell. In certain instances such recruitment of a non-cleaving protein alters the function or activity of the target nucleic acid. In certain such instances, the target nucleic acid a pre-mRNA and the recruitment of the non-cleaving protein results in a change in splicing of the pre-mRNA.

Methods and devices for in situ nucleic acid synthesis

Abstract: Disclosed are compositions, methods and devices for the in situ synthesis of nucleic acids. In an exemplary embodiment, a support-bound oligonucleotide is elongated by addition of one or more nucleotides by hybridization of a partially double-stranded oligonucleotide, ligation and removal of unwanted nucleotides.

Compositions and methods for detecting, identifying and quantitating mycobacterial-specific nucleic acids

Abstract: Disclosed are compositions and methods for isolating, detecting, amplifying, and quantitating Mycobacterium-specific nucleic acids in a sample. Also disclosed are compositions and diagnostic kits comprising Mycobacterium IS6110-specific oligonucleotide amplification primers and labeled oligonucleotide detection probes that specifically bind to the amplification products obtained therefrom. Also disclosed are compositions and methods for the isolation and characterization of nucleic acids that are specific to one or more tubercular pathogens, including Mycobacterium tuberculosis, in particular, from a wide variety of samples including those of biological, environmental, clinical and/or veterinary origin.

Self-assembled polynucleotide structure

Abstract: The present application provides polynucleotide structures such as nucleic acid ribbons and nucleic acid tubes, methods for making the polynucleotide structures, and methods for making two-dimensional or three-dimensional objects comprising the nucleic acid ribbons and nucleic acid tubes.

Orthogonal amplification and assembly of nucleic acid sequences

Abstract: Methods and compositions for synthesizing nucleic acid sequences of interest from heterogeneous mixtures of oligonucleotide sequences are provided.

Facile synthesis of peptide nucleic acids and peptide nucleic acid‐peptide conjugates on an automated peptide synthesizer

Abstract: Peptide nucleic acids (PNAs) are DNA mimics with a neutral peptide backbone instead of the negatively charged sugar phosphates. PNAs exhibit several attractive features such as high chemical and thermal stability, resistance to enzymatic degradation, and stable binding to their RNA or DNA targets in a sequence-specific manner. Therefore, they are widely used in molecular diagnosis of antisense-targetedtherapeutic drugsor probes and in pharmaceuticalapplications. However, themain hindrance to the effective use of PNAs is their poor uptake by cells as well as the difficult and laborious chemical synthesis. In order to achieve an efficient delivery of PNAs into cells, there are already many published reports of peptides being used for transport across the cell membrane. In this protocol, we describe the automated as well as cost-effective semi-automated synthesisofPNAsandPNA-peptideconstructsonanautomatedpeptidesynthesizer.ThefacilesynthesisofPNAswillbehelpful in generatingPNA librariesusable, e.g. for high-throughputscreening in biomolecular studies. Efficient syntheticschemes,the automated procedure, the reduced consumption of costly reagents, and the high purity of the products are attractive features of the reported procedure. Copyright c � 2010 European Peptide Society and John Wiley & Sons, Ltd.

Method of making nucleic acid libraries

Abstract: A method of preparing a nucleic acid library in droplets in contact with oil, including: (a) blunt-ending nucleic acid fragments in a droplet in the oil to yield blunt-ended nucleic acid fragments; (b) phosphorylating the blunt-ended nucleic acid fragments in a droplet in the oil to yield phosphorylated nucleic acid fragments; coupling A-tails to the phosphorylated nucleic acid fragments in a droplet in the oil to yield A-tailed nucleic acid fragments; and (d) coupling nucleic acid adapters to the A-tailed nucleic acid fragments in a droplet in the oil to yield the nucleic acid library comprising adapter-ligated nucleic acid fragments.

Compositions and methods for sequencing nucleic acids

Abstract: The present invention provides a method for sequencing nucleic acids, comprising the use of nucleotide analogs and a nucleic acid polymerase enzyme or enzyme complex with proofreading activity. The nucleotide analogs may be incorporated into a replicating strand and induce the proofreading activity of the polymerase enzyme, thereby prolonging the duration of a signal associated with nucleotide incorporation.

Optimized Dyes for Protein and Nucleic Acid Detection

Abstract: Fluorescent homogeneous detection is widely used in modern biomedical techniques for analysis and quantification of nucleic acids and proteins. This method is based on the ability of low-fluorescent dye to bind noncovalently with target biomolecule with significant increase of dye’s emission intensity. A wide range of probes for homogeneous detection developed during last decades are reviewed here. Series of cyanine dyes were developed for using in visualization of nucleic acids in living cells and detection of amplification products in real-time PCR. Besides, the cyanines, and triphenylmethane dyes that are able to detect certain nucleic acid structures (double stranded, triplex, and quadruplex DNA) and styrylcyanine dyes for two-photon excited fluorescent detection and imaging of DNA are described. Dyes applied for nonspecific proteins detection belong to different classes, among them are complexes of Ru2+, merocyanines, and trimethine cyanines. Moreover, cyanine dyes sensitive to amyloid β-pleated protein formations and albumin-specific squaraine dyes are discussed here.

Compositions, Methods and Kits for Nucleic Acid Synthesis and Amplification

Abstract: The present invention is directed to compositions, methods and kits useful for the synthesis of nucleic acid molecules. More specifically, compositions, methods and kits are provided for the amplification of nucleic acid molecules in a one-step RT-PCR procedure comprising one or more agents used to increase tolerance to PCR inhibitors.

Methods and compositions for sequence-specific purification and multiplex analysis of nucleic acids

Abstract: Methods and materials for determining the presence of at least one nucleic acid in a sample are provided, said methods comprising (1) a purification step using sequence specific hybrid capture; (2) an amplification step; and (3) a detection step comprising contacting the target nucleic acid with a plurality of detectably labeled nucleic acid detection probes, wherein each (a) bears a different detectable label from the other detection probes, and/or (b) has a different melting temperature from probes bearing the same detectable label. Also disclosed are compositions and kits for use in such a method.

Detection of nucleic acids and proteins

Abstract: The invention generally relates to methods for detecting a target nucleic acid and a target protein in a single assay.

Multiplexed identification of nucleic acid sequences

Abstract: A method for the rapid identification of a target nucleic acid sequence is provided, as well as corresponding devices, products and kits. Such methods are useful for the rapid detection, identification and/or quantification of target nucleic acid sequences associated with, for example, a pathogen.

Methods and Compositions for Sequencing Nucleic Acids Using Charge

Abstract: The invention provides methods and compositions, and systems for determining the identity of nucleic acids in nucleotide sequences, including sequences with one or more homopolymer regions. The methods of the invention include improvements so as to accurately identify sequences, including the difficult homopolymer sequences that are encountered during nucleotide sequencing, such as pyrosequencing.

Method of dna sequencing by hybridisation

Abstract: The present invention relates to a method for the determination of a nucleic acid sequence by physical manipulation. In particular, the said method comprises the steps of denaturing a double-stranded nucleic acid molecule corresponding to the said nucleic acid sequence by applying a physical force to the said molecule; and detecting a blockage of the renaturation of the double-stranded nucleic acid molecule. More specifically, the method comprises the steps of denaturing a double-stranded nucleic acid molecule corresponding to the said nucleic acid sequence by applying a physical force to the said molecule; providing a single- stranded nucleic acid molecule;renaturing the said double stranded nucleic acid molecule in the presence of the said single-stranded nucleic acid molecule; and detecting a blockage of the renaturation of the double-stranded nucleic acid.