Abstract: A biochip used for quantitative analysis of a target DNA contained in a sample. The biochip includes a type I chamber that includes a primer designed to bind to the target DNA, an internal standard DNA of a first amount that has a sequence different from a sequence of the target DNA, and is amplifiable with the primer, and a fluorescent probe that is designed to bind to a part of a PCR product of the target DNA and to a part of a PCR product of the internal standard DNA. The fluorescent probe fluoresces differently for the PCR product of the target DNA and the PCR product of the internal standard DNA. The biochip also includes a type II chamber that includes the internal standard DNA of a second amount, the primer, and the fluorescent probe. The first and second amounts are different.

Abstract: A method of sequencing nucleic acids, which can include steps of (a) providing a substrate having a surface having a repeating pattern of features, wherein the features are spatially separated from each other on the surface of the substrate; (b) contacting the repeating pattern of features with a solution of different target nucleic acids to seed a subset of the features that contact the solution, wherein no more than the subset of the features that contact the solution is seeded with the target nucleic acids; (c) amplifying the target nucleic acids at the subset of features; (d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of different nucleic acid colonies; and (e) detecting sequencing reactions at the different nucleic acid colonies on the surface.

Abstract: A region of the Chlamydia trachomatis pmpA gene has been identified which is useful for performing amplification assays to determine specifically whether C. trachomatis is present in the sample being tested. Oligonucleotides useful for detecting this gene by performing the polymerase chain reaction (PCR) are disclosed. The disclosed oligonucleotides can be used in an assay which is specific for multiple strains or serovars of C. trachomatis, including the variant E serovar, and which does not show cross reactivity with the genomes of other microorganisms or with human DNA. In addition, the disclosed oligonucleotides can be used to in a multiplex system. This invention also contemplates a kit including oligonucleotides, and optionally other reagents, for the detection of C. trachomatis using PCR.

Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

Abstract: The invention is in the field of nucleic acid amplification, hi particular, methods are described which utilize stem primers that improve the rapid and specific amplification of a test sample.

Abstract: Methods for detecting Legionella (such as Legionella spp., Legionella pneumophila, Legionella pneumophila serogroup 1, Legionella bozemanii, Legionella dumoffii, Legionella feeleii, Legionella longbeachae, and/or Legionella micdadei) are disclosed. A sample suspected of containing one or more Legionella nucleic acids is screened for the presence or absence of that nucleic acid. Determining whether Legionella nucleic acid is present in the sample can be accomplished by contacting the sample with detectably labeled probes capable of hybridizing to a Legionella nucleic acid and detecting hybridization between the probes and nucleic acids in the sample. Detection of hybridization indicates that a Legionella nucleic acid is present in the sample. Also disclosed are probes and primers for the detection of Legionella, and kits that contain the disclosed probes and/or primers.

Abstract: A biochip used for quantitative analysis of a target DNA contained in a sample. The biochip includes a type I chamber that includes a primer designed to bind to the target DNA, an internal standard DNA of a first amount that has a sequence different from a sequence of the target DNA, and is amplifiable with the primer, and a fluorescent probe that is designed to bind to a part of a PCR product of the target DNA and to a part of a PCR product of the internal standard DNA. The fluorescent probe fluoresces differently for the PCR product of the target DNA and the PCR product of the internal standard DNA. The biochip also includes a type II chamber that includes the internal standard DNA of a second amount, the primer, and the fluorescent probe. The first and second amounts are different.

Abstract: A method for the amplification of nucleic acids, in which nanoparticles in a reaction volume transfer heat to their environment through excitation. The method comprises a step of providing nanoparticles with the nucleic acids in a reaction volume and one or more heating steps. In at least one of the heating steps, the heating is achieved at least partially through the excitation of the nanoparticles. The interval of the excitation is chosen to be shorter or equal to a critical excitation time.

Abstract: A longstanding challenge in forensics is resolving the genetic profile of a minor contributor in a mixed contributor sample. The instant disclosure provides for differentially labeling the products resulting from the amplification of a template from a major contributor relative to that of a minor contributor. Based on this differential labeling, the genetic profile of the minor contributor can be resolved from that of a major contributor.

Abstract: A method of sample analysis is provided. In certain embodiments, the method involves: a) amplifying a product from a sample that comprises both wild type copies of a genomic locus and mutant copies of the genomic locus that have a point mutation relative to said wild type copies of the genomic locus, to produce an amplified sample, where: i. the amplifying is done using a first primer and a second primer; and ii. the first primer comprises a 3? terminal nucleotide that base pairs with the point mutation and also comprises a nucleotide sequence that is fully complementary to a sequence in the locus with the exception of a single base mismatch within 6 bases of the 3? terminal nucleotide; and b) detecting the presence of said product in said amplified sample using a flap assay that employs an invasive oligonucleotide. A kit for performing the method is also provided.

Abstract: A method of amplifying a nucleic acid of interest comprises (i) treating a biological sample chemically or enzymatically to permit conversion of one type of nucleic acid base to another type of base, (ii) purifying the treated biological sample before adding amplification primers and amplification reagents to the biological sample, (iii) adding the amplification primers and amplification reagents to the biological sample, each primer being constituted of three different types of bases and being specific to a converted nucleic acid of interest or to a nucleic acid that is complementary to the converted nucleic acid of interest, and (iv) amplifying the converted nucleic acid of interest provided that the nucleic acid of interest was present in the biological sample. In the method, amplification of contaminating nucleic acids is avoided by converting the one type of nucleic acid base to another type of base prior to adding the amplification reagents to the biological sample.

Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

Abstract: Disclosed are compositions and methods for making differentiable amplicon species at unequal ratios using a single amplification system in a single vessel. The number of differentiable amplicons and their ratios to one another are chosen to span the required linear dynamic range for the amplification reaction and to accommodate limitations of the measuring system used to determine the amount of amplicon generated. Unequal amounts of distinguishable amplicon species are generated by providing unequal amounts of one or more amplification reaction components (e.g., distinguishable amplification oligomers, natural and unnatural NTP in an NTP mix, or the like). The amount of target nucleic acid present in a test sample is determined using the linear detection range generated from detection of one or more amplicon species having an amount within the dynamic range of detection.

Abstract: The presently disclosed subject matter relates to modified Kunkel mutagenesis methods that use a thermostable DNA polymerase and a thermostable DNA ligase.

Abstract: A nucleic acid extraction device includes a tube that is internally provided with, in the following order, a first plug composed of a first oil, a second plug composed of a first washing liquid, which is phase-separated from an oil and is used for washing a nucleic acid-binding solid-phase carrier having nucleic acids bound thereto, a third plug composed of a second oil, a fourth plug composed of a reverse transcription reaction solution, which is phase-separated from an oil and is used for performing a reverse transcription reaction, a fifth plug composed of a third oil, a sixth plug composed of an eluent, which is phase-separated from an oil and is used for eluting the nucleic acids from the nucleic acid-binding solid-phase carrier having nucleic acids bound thereto, and a seventh plug composed of a fourth oil.

Abstract: A system and method for processing and detecting nucleic acids from a set of biological samples, comprising: a capture plate and a capture plate module configured to facilitate binding of nucleic acids within the set of biological samples to magnetic beads; a molecular diagnostic module configured to receive nucleic acids bound to magnetic beads, isolate nucleic acids, and analyze nucleic acids, comprising a cartridge receiving module, a heating/cooling subsystem and a magnet configured to facilitate isolation of nucleic acids, a valve actuation subsystem configured to control fluid flow through a microfluidic cartridge for processing nucleic acids, and an optical subsystem for analysis of nucleic acids; a fluid handling system configured to deliver samples and reagents to components of the system to facilitate molecular diagnostic protocols; and an assay strip configured to combine nucleic acid samples with molecular diagnostic reagents for analysis of nucleic acids.

Abstract: The invention includes methods and apparatus for separating heteroduplexed nucleic acids from homoduplexed nucleic acids having similar sequences and being at a much higher concentration. The heteroduplexed nucleic acids may be separated through the application of a time varying driving field and a time-varying mobility field to a sample of heteroduplexed and homoduplexed nucleic acids in a separation medium. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.

Abstract: This disclosure describe three related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of the bacterial RecA and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods has the advantage of not requiring thermocycling or thermophilic enzymes. Further, the improved processivity of the disclosed methods allow amplification of DNA up to hundreds of megabases in length.

Abstract: The object of the present invention is to provide a novel method that addresses the problem of differentiating large sets of genomic sequences. The invention relates to a method for genotyping N loci present in a sample in a target nucleic acid molecule, wherein each locus is located in a genotype marker region of the nucleic acid molecule, and corresponds to two or more genotypes. Furthermore the invention relates to a kit for performing said method for genotyping. Also the invention relates to a method for designing and producing selection primers, as well as a method for producing detection primers, all of said primers to be used in the method for genotyping or in the kit for performing the genotyping method. The invention further relates to selection primers adapted for genotyping of loci in a target nucleic acid molecule and a computer program product for designing selection primers.

Abstract: The present invention relates to the detection of a target nucleic acid sequence using a target hybridization and detection primer (THD primer). The present invention allows for both a target amplification and a signal amplification by introducing a label into a primer used in PCR reactions, ensuring a real-time target detection by PCR reaction by no use of complicated oligonucleotides. The present invention could completely be free from the troublesome matters and shortcomings associated with conventional real-time PCR methods. The present invention allows for successful real-time target detection by using only a labeled primer. This feature makes it possible that the present invention exhibits excellent real-time target detection in multiplex manner.