Showing papers on "Nucleic acid methods published in 2010"

Binary probes for nucleic acid analysis.

Abstract: Over the last four decades nucleic acid hybridization techniques have been widely used for the detection of specific nucleic acid sequences. In this approach a 15-nucleotide or longer DNA or RNA strand (the probe) forms complementary duplexes with the analyzed nucleic acid (analyte). Since the development of the first hybridization-based procedures by Hall and Spiegeleman1 and by Bolton and McCarty,2 oligoand polynucleotide probes have become routinely used as laboratory tools for nucleic acid analysis. The examples of such techniques include Southern3 and Northern4 blots, fluorescent in situ hybridization,5 and DNA microarrays.6 Furthermore, the introduction of real-time detection approaches, such as molecular beacon (MB) probes,7,8 has enabled fast assays, in which the fluorescence change is detected immediately after probe hybridization, thus avoiding the need to separate the probe-analyte hybrid from the excess of the unbound probe. However, low selectivity of the probe-analyte hybridization creates complications in the analysis of single-base differences between two polynucleotides. Indeed, a 15-nucleotide-long probe has a similar affinity to a fully complementary analyte and to an analyte containing a single noncomplementary base.9

Nucleic acid purification

Abstract: The inventive self-contained apparatus for isolating nucleic acid, cell lysates and cell suspensions from unprocessed samples apparatus, to be used with an instrument, comprises at least one input, and: (i) a macrofluidic component, comprising a chamber for receiving said unprocessed sample from a collection device and at least one filled liquid purification reagent storage reservoir; and (ii) a microfluidic component in communication with said macrofluidic component via at least one microfluidic element, said microfluidic component further comprising at least one nucleic acid purification matrix; and (iii) a drive mechanism on said instrument for driving said liquid purification reagent, through said microfluidic element and said nucleic acid purification matrix, wherein the only inputs to said apparatus are via said chamber and said drive mechanism.

Compositions for nucleic acid delivery

Abstract: A method for delivering a nucleic acid to a cell can include exposing sample cells to a composition which includes charged lipids.

Oligonucleotide end caps

Abstract: Modified nucleic acids are described herein, including pharmaceutical compositions comprising the modified nucleic acids, and methods of using the modified nucleic acids.

Lyophilization of nucleic acids in lactate-containing solutions

Abstract: The present invention is directed to the lyophilization of nucleic acids in a lactate-containing solution or formulation. The present invention is particularly suitable for enhancing and improving storage and shipping capabilities of nucleic acids for multiple purposes. The present invention is furthermore directed to methods of lyophilization suitable to prepare such inventive lyophilized nucleic acids, to the use of a lactate-containing solution or formulation for the preparation of such lyophilized nucleic acids or the use of a solution containing at least one nucleic acid (sequence) and (free) lactate for lyophilization of at least one nucleic acid (sequence), to the use of such lyophilized nucleic acids in the preparation of pharmaceutical compositions, to first and second medical indications using such lyophilized nucleic acids and to kits, particularly to kit of parts, comprising such lyophilized nucleic acids.

Method for sequencing a heteropolymeric target nucleic acid sequence

Abstract: The invention relates to a method for sequencing a heteropolymeric target nucleic acid sequence that involves stochastic sensing. The invention also relates to a method for improving a pore for sequencing a target nucleic acid sequence by modifying one or more sites in the pore.

Feasibility of methods based on nucleic acid amplification techniques to fulfil the requirements for microbiological analysis of water quality.

Abstract: Molecular methods based on nucleic acid recognition and amplification are valuable tools to complement and support water management decisions. At present, these decisions are mostly supported by the principle of end-point monitoring for indicators and a small number of selected measured by traditional methods. Nucleic acid methods show enormous potential for identifying isolates from conventional culture methods, providing data on cultivable and noncultivable micro-organisms, informing on the presence of pathogens in waters, determining the causes of waterborne outbreaks, and, in some cases, detecting emerging pathogens. However, some features of water microbiology affect the performance of nucleic acid-based molecular techniques and thus challenge their suitability for routine water quality control. These features include the variable composition of target water samples, the generally low numbers of target micro-organisms, the variable water quality required for different uses and the physiological status or condition of such micro-organisms. The standardization of these molecular techniques is also an important challenge for its routine use in terms of accuracy (trueness and precision) and robustness (reproducibility and reliability during normal usage). Most of national and international water regulations recommend the application of standard methods, and any new technique must be validated respect to established methods and procedures. Moreover, molecular methods show a high cost-effectiveness value that limits its practicability on some microbial water analyses. However, new molecular techniques could contribute with new information or at least to supplement the limitation of traditional culture-based methods. Undoubtedly, challenges for these nucleic acid-based methods need to be identified and solved to improve their feasibility for routine microbial water monitoring.

Fret-labeled compounds and uses therefor

Abstract: FRET-labeled compounds are provided for use in analytical reactions. In certain embodiments, FRET-labeled nucleotide analogs are used in place of naturally occurring nucleoside triphosphates or other analogs in analytical reactions comprising nucleic acids, for example, template-directed nucleic acid synthesis, DNA sequencing, RNA sequencing, single-base identification, hybridization, binding assays, and other analytical reactions.

Nucleic acid amplification and sequencing by synthesis with fluorogenic nucleotides

Abstract: In general, the invention features methods and systems for sequencing of nucleic acids based on the measurement of the incorporation of fluorogenic nucleotides in microreactors. The invention provides numerous advantages over previous systems such as unambiguous determination of sequence, fast cycle time, long read lengths, low overall cost of reagents, low instrument cost, and high throughput. The invention also features methods and kits for nucleic acid amplification. The amplification and sequencing aspects of the invention may or may not be employed in conjunction with one another. The invention also features fluorogenic nucleotides that may be used in the sequencing methods of the invention.

Advantages of peptide nucleic acids as diagnostic platforms for detection of nucleic acids in resource-limited settings

Abstract: Peptide nucleic acids are a class of nondegradable oligonucleotide mimics that can be used as probes for nucleic acid sequences and could convey the necessary stability to be a diagnostic tool for use in a resource-limited setting. In this review, there is a brief introduction to the field of peptide nucleic acids and their potential benefits as probes for DNA and RNA sequences, followed by highlights of ways by which peptide nucleic acids could benefit a number of established diagnostic tools for human immunodeficiency virus detection.

Nucleic acid analyzer

Abstract: A nucleic acid analyzer includes a nucleic acid purification kit yielding a nucleic acid solution by isolating and purifying nucleic acid from a specimen; a nucleic acid analysis chip having a rotation axis positioned at a center thereof, with reaction containers at an outer portion than the rotation axis, and feeding the acid to the containers through centrifugal force; a specimen-introducing part on which the kit is placed; an analysis chip holder at the specimen-introducing part and supporting the chip; a purification treatment unit injecting the nucleic acid solution containing the nucleic acid into the chip; a centrifugal liquid feed unit feeding the nucleic acid solution to the containers by rotating the chip about the rotation axis; an analysis unit analyzing reaction products in the containers; and a transport part transporting the specimen-introducing part to the purification treatment unit, the centrifugal liquid feed unit, and the analysis unit.

Detection of nucleic acids in crude matrices

Abstract: A method includes contacting a crude matrix with components of an isothermal nucleic acid amplification reaction for a target nucleic acid species, thereby providing a mixture; incubating the mixture under conditions sufficient for the isothermal nucleic acid amplification reaction to proceed, thereby providing a product; and determining whether an indicator of the target nucleic acid species is present in the product.

Methods, compositions, and kits for generating nucleic acid products substantially free of template nucleic acid

Abstract: Methods, kits, and compositions which enable the generation of double stranded DNA products from various substrates such as low abundance RNAs or whole transcriptosomes are provided. The double stranded DNA products are suitable for downstream applications involving microarray analysis or sequencing.

Single molecule spectroscopy for analysis of cell-free nucleic acid biomarkers

Abstract: The present invention relates, e.g., to a method for detecting a nucleic acid molecule of interest in a sample comprising cell-free nucleic acids, comprising fluorescently labeling the nucleic acid molecule of interest, by specifically binding a fluorescently labeled nanosensor or probe to the nucleic acid of interest, or by enzymatically incorporating a fluorescent probe or dye into the nucleic acid of interest, illuminating the fluorescently labeled nucleic acid molecule, causing it to emit fluorescent light, and measuring the level of fluorescence by single molecule spectroscopy, wherein the detection of a fluorescent signal is indicative of the presence of the nucleic acid of interest in the sample.

Nucleic acid preparation compositions and methods

Abstract: Provided herein are methods and compositions to extract and enrich by, physical separation or amplification, relatively short nucleic acids from a nucleic acid composition containing a high background of longer nucleic acids (e.g., host or maternal nucleic acids; genomic nucleic acid and the like).

Methods of detecting nucleic acid sequences with high specificity

Abstract: The invention relates to methods of detecting nucleic acids, including methods of detecting one or more target nucleic acid sequences in multiplex branched-chain DNA assays, are provided Nucleic acids captured on a solid support or suspending cells are detected, for example, through cooperative hybridization events that result in specific association of a label with the nucleic acids The invention further relates to methods to improve probe hybridization specificity and their application in genotyping The invention also relates to in situ detection of mis-joined nucleic acid sequences The invention relates to reducing false positive signals and improve signal-to-background ratio in hybridization-based nucleic acid detection assay The invention further relates to method to improve specificity in hybridization based nucleic acid using co-location probes Compositions, tissue slides, sample of suspended cells, kits, and systems related to the methods are also described

Targeted gene repair facilitated by peptide nucleic acids (PNA).

Abstract: Sequence specific gene targeting at the DNA level has been an important challenge for chemical biology for more than two decades. It has resulted in the development of several technologies, including triplex forming oligonucleotides (TFOs), minor groove binding hairpin polyamides, triplex forming and duplex invading peptide nucleic acids, and on the more molecular biology level, designed zinc-finger protein domains. In terms of biological and medicinal approaches, gene targeting has predominantly been aimed at inhibition and blockage of gene expression at the transcriptional level. However, more recently the prospect of inducing site specific gene repair in somatic cells and eventually in tissues in animals and humans are slowly emerging as reachable goals that could result in new modalities for treatment of genetic diseases. The principle is based on the observation that introduction into the cell of a short (twenty to a few thousand bases) single or double stranded DNA (dsDNA) molecule (a repair domain) that is homologous to but genetically different from part of the genome in the cell, can result—although at very low frequency, usually subpercent—in the exchange of genetic information, by which the base sequence from the repair domain is transferred to the genome. The cellular molecular mechanism(s) that are responsible for these events are not fully understood, but it is believed that homologous recombination is involved if not required in many cases. This contention is supported by recent developments demonstrating that the frequency (efficiency) of targeted repair is very significantly increased if a dsDNA break is introduced in the target gene in the cell, for example, by transfection with a genetically engineered, sequence specific zinc-finger nuclease. 10] Indeed in such systems chromosomal repair efficiencies reaching 20 % of the cells have been achieved. Although this method works well in cell culture especially if repaired cells can be selected for, and is being successfully exploited in plant biotechnology, prospects for in vivo animal and eventually human medical exploitation is less obvious. First of all, the zinc-finger nuclease must be introduced by gene delivery (transformation), and secondly, various genome changes other than the desired repair (side effects) are discovered at high frequency. Therefore, alternative ways of target-specific activation (recruitment) of homologous recombination could prove better suited in a drug discovery context. Indeed it has recently been found that oligonucleotide triplexes as well as various peptide nucleic acid (PNA) invasion complexes may enhance targeted gene repair events. The present review will focus on recent developments in targeting duplex DNA by PNA and the implications for further developments in targeted gene repair.

Novel nucleic acid prodrugs and methods use thereof

Abstract: Described herein are nucleic acid prodrugs and nucleic acid prodrugs comprising chiral phosphorous moieties. Also described herein are methods of making and using nucleic acid prodrugs and nucleic acid prodrugs comprising chiral phosphorous moieties.

Multiplex nucleic acid detection methods and systems

Abstract: The present invention relates to methods and systems for single molecule based clonal amplification and subsequent detection of nucleic acid molecules, and particularly to the determination of SNPs, mutations, and to the diagnosis of diseases associated with the changes of these nucleic acid molecules.

Regulatory nucleic acid molecules for enhancing seed-specific gene expression in plants promoting enhanced polyunsaturated fatty acid synthesis

Abstract: The invention in principle pertains to the field of recombinant manufacture of fatty acids. It provides novel nucleic acid molecules comprising nucleic acid sequences encoding fatty acid desaturases, elongases, acyltransferases, terminator sequences and high expressing seed-specific promoters operatively linked to the said nucleic acid sequences wherein nucleic acid expression enhancing nucleic acids (NEENAs) are functionally linked to said promoters.

Nucleic acid analysis

Abstract: A method for extracting high quality nucleic acids from a biological sample are disclosed The extractions obtained by the methods described herein are characterized by high yield and high integrity, making the extracted nucleic acids useful for various applications in which high quality nucleic acid extractions are preferred, e g, a diagnosis, prognosis or therapy evaluation for a medical condition

Polyunsaturated fatty acid synthase nucleic acid molecules and polypeptides, compositions, and methods of making and uses thereof

Abstract: The present invention is directed to isolated nucleic acid molecules and polypeptides of thraustochytrid polyunsaturated fatty acid (PUFA) synthases involved in the production of PUFAs, including PUFAs enriched in docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), or a combination thereof. The present invention is directed to vectors and host cells comprising the nucleic acid molecules, polypeptides encoded by the nucleic acid molecules, compositions comprising the nucleic acid molecules or polypeptides, and methods of making and uses thereof.

High throughput nucleic acid sequencing by expansion and related methods

Abstract: Nucleic acid sequencing methods and related products and methods for detection and presentation of the same are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid.

Method for selectively enriching and isolating microbial and optionally additional viral nucleic acids

Abstract: The present invention relates to a method for selectively enriching and/or isolating microbial and optionally additionally viral nucleic acids from samples that contain a mixture of microbial cells, freely circulating nucleic acids and higher eukaryotic cells, and optionally additionally viruses, in a liquid, and to a kit for selectively enriching and/or isolating intracellular and extracellular microbial nucleic acids, and optionally additionally viral nucleic acids, from samples that contain a mixture of microbial and higher eukaryotic cells, freely circulating nucleic acids, in particular extracellular microbial nucleic acids, and optionally additionally viruses in a liquid.

Efficient genomic DNA extraction from low target concentration bacterial cultures using SCODA DNA extraction technology.

Abstract: Methods for the extraction of nucleic acids are straightforward in instances where there is ample nucleic acid mass in the sample and contamination is minimal. However, applications in areas such as metagenomics, life science research, clinical research, and forensics, that are limited by smaller amounts of starting materials or more dilute samples, require sample preparation methods that are more efficient at extracting nucleic acids. Synchronous coefficient of drag alteration (SCODA) is a novel electrophoretic nucleic acid purification technology that has been tested successfully with both highly contaminated and dilute samples and is a promising candidate for new sample preparation challenges. In this article, as an example of SCODA's performance with limited sample material, we outline a genomic DNA (gDNA) extraction protocol from low abundance cultures of Escherichia coli DH10B. This method is equally well suited to high biomass samples.