Abstract: The present invention is directed to methods, compositions and reaction mixtures for conducting COLD-PCR, by controlling and varying a preferential denaturation time.

Abstract: Improved methods and compositions are provided herein for primer extension target enrichment of target polynucleotides.

Abstract: A method for amplifying a CYP21A2 gene and/or a CYP21A2 gene chimera from a sample is provided. In some embodiments, the method may comprise amplifying a product from a sample comprising human genomic DNA by PCR using a forward primer that is complementary to a sequence that is duplicated in a bimodular human RCCX locus and a reverse primer that is complementary to a sequence that occurs only once in the bimodular human RCCX locus at a position that is downstream of the CYP21A2 gene. Methods for analyzing the amplification product are also provided.

Abstract: Provided are methods, kits, and systems useful in the performance of analysis and reporting of highly polymorphic loci, including, in particular, the performance of analysis and reporting of HLA typing. Combining one-step sequencing and sequence-specific oligonucleotide probe hybridization, the methods, kits, and systems offer improved efficiency of HLA typing while providing detailed sequencing information. In certain embodiments the methods and systems comprise one or more software applications to facilitate data acquisition, processing, and reporting.

Abstract: Ultra-sensitive assays for the detection of mutations, e.g., from blood-based sources of tumor genetic material (circulating tumor cells or plasma), or other settings in which limiting amounts of DNA, e.g., tumor DNA, is available. The assay is exemplified in the estrogen receptor, but is broadly customizable to target mutations in other genes.

Abstract: This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.

Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.

Abstract: Compositions, methods, kits, and uses are provided for detecting or quantifying an Human Parainfluenza virus 1 (HPIV-1), HPIV-2, HPIV-3, and/or HPIV-4 nucleic acid, e.g., using nucleic acid amplification and hybridization assays. In some embodiments, the compositions, methods, kits, and uses target the HN gene of HPIV-1, HPIV-2, and/or HPIV-3 and/or the NP gene of HPIV-4.

Abstract: In a method of nucleic acid extraction using a support, the present invention realizes collection of a nucleic acid from a liquid containing the nucleic acid at an extremely low concentration at which collection cannot be achieved with polyacrylamide. A method of extracting a nucleic acid, comprising allowing the nucleic acid to be adsorbed onto a support in the presence of a chaotropic salt and an alcohol in coexistence with an anionic polymer. A reagent for nucleic acid extraction, comprising an anionic polymer, a chaotropic salt, an alcohol and a support.

Abstract: The present invention relates to a highly automatable method for isolation and/or purification of nucleic acids from a biological sample, which is particularly suitable for nucleic acids-shorter than 250 bp and can be performed without a proteolytic pre-digestion step in an automated system, preferably a cartridge-based system. In a further aspect, the present invention also provides automated nucleic acid detection methods based on said isolation and/or purification method, as well as buffers and kits to be used in performing said methods.

Abstract: Disclosed is a method of quality control of nucleic acid amplification using quality control oligonucleotide. The method comprises a nucleic acid detection step and a determination step. The nucleic acid detection step comprises the steps of: preparing a nucleic acid sample containing a target nucleic acid and a quality control polynucleotide; preparing a compartment containing one molecule of the target nucleic acid and a compartment containing one molecule of the quality control polynucleotide; and carrying out nucleic acid amplification of the target nucleic acid and the quality control polynucleotide, in the compartments, and carrying out signal detection using a detection probe to detect a signal originated from the detection probe. In the determination step, it is determined as to whether or not the nucleic acid detection step is proper on the basis of the result obtained in the signal detection step.

Abstract: The present invention provides methods and systems for sequencing long nucleic acid fragments. In one aspect of the invention, methods, systems and reagent kits are provided for sequencing nucleic acid target sequences. Some embodiments of the methods, systems and reagent kits are particularly suitable for sequencing a large number of fragments, particularly long fragments.

Abstract: The present invention provides methods for rapidly identifying an RNA viral infection using an isothermal nucleic acid amplification reaction that can be carried out extracted RNA in the context of a crude biological sample.

Abstract: Genomic DNA contains embedded ribonucleotides (rNMPs) that are incorporated during DNA replication and repair, or formed during DNA damage. The modifications have been linked to genome instability and disease, but no method currently exists to profile their locations genome-wide. rNMP incorporation has been extensively studied in recent years; however, locating sites of rNMP incorporation in genomic DNA has not yet been possible. Disclosed herein is a unique method for mapping rNMPs in genomic DNA that exploits the unique ligation mechanism of Arabidopsis thaliana tRNA ligase (AtRNL), normally involved in tRNA maturation. As disclosed herein AtRNL captures 2?,3?-cyclic phosphate or 2?-phosphate termini of DNA derived from alkaline cleavage of a DNA oligonucleotide (oligo) at an embedded rNMP, ligating the 2?-phosphate end to the 5?-phosphate terminus of the same DNA molecule and producing a ssDNA circle containing an embedded rNMP.

Abstract: A composition for use in amplifying cDNA synthesized by a reverse transcription reaction and detecting RNA that serves as a template of the reverse transcription reaction, the composition containing a thermostable DNA polymerase, a thermostable ribonuclease H, and an intercalating dye. Since the composition of the present invention can suppress the influences to the nucleic acid amplification reaction by RNA that serves as a template for cDNA synthesis, the composition is useful in the detection of RNA, and more useful in quantification of RNA having a desired sequence by real-time RT-PCR.

Abstract: A self-metering reaction device has a sample reservoir, configured to accept a varying amount of fluid; a metering reservoir, configured to be a subportion of the sample reservoir and to hold a reaction amount of the fluid; a reaction chamber fluidly connected to the metering reservoir; and a plunger comprising a tip configured to make a seal with the metering reservoir so that the reaction amount of the fluid is sealed within the metering reservoir when the plunger is in contact with the metering reservoir. The plunger can be configured to plunge the sealed reaction amount of the fluid from the metering reservoir into the reaction chamber.

Abstract: Compositions and methods related to transgenic high oleic acid/ALS inhibitor-tolerant soybean plants are provided. Specifically, the present invention provides soybean plants having a DP-305423-1 event which imparts a high oleic acid phenotype and tolerance to at least one ALS-inhibiting herbicide. The soybean plant harboring the DP-305423-1 event comprises genomic/transgene junctions having at least the polynucleotide sequence of SEQ ID NO:8, 9, 14, 15, 20, 21, 83 or 84. The characterization of the genomic insertion site of the DP-305423-1 event provides for an enhanced breeding efficiency and enables the use of molecular markers to track the transgene insert in the breeding populations and progeny thereof. Various methods and compositions for the identification, detection, and use of the soybean DP-305423-1 events are provided.

Abstract: Provided herein include compositions comprising a primer having the nucleic acid sequence of ACeIN-F3_c, a primer having the nucleic acid sequence of ACeIN-B3_a, a primer having the nucleic acid sequence of ACeIN-B3_b, a primer having the nucleic acid sequence of ACeIN-FIP_e, a primer having the nucleic acid sequence of ACeIN-FIP_f, a primer having the nucleic acid sequence of ACeIN-BIP (or ACeIN-BIP-song), a primer having the nucleic acid sequence of ACeIN-LF; and a primer having the nucleic acid sequence of ACeIN-LB. Also provided are methods of detecting human immunodeficiency virus (HIV) nucleic acids in a sample comprising performing reverse transcription-based loop mediated isothermal amplification (RT-LAMP) on a sample using the previously disclosed compositions.

Abstract: The purpose of the present invention is to provide a method and kit for highly precise DNA typing, in which ambiguity derived from phase ambiguity is eliminated. The present invention provides a method for the DNA typing of HLA, which is characterized by comprising: (1) a step of preparing a set of primers which can respectively anneal specifically to an upstream region and a downstream region of each of HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQB1, HLA-DPA1 and HLA-DPB1 gene in the nucleotide sequence for the human genome, and a set of primers which can respectively anneal specifically to exon-2 and a 3?-side non-translated region in HLA-DRB1; (2) a step of carrying out the PCR amplification of a sample to be tested (DNA) using the sets of primers; (3) a step of determining the nucleotide sequence for a PCR-amplified product; and (4) an optional step of carrying out the homology search in a data base.

Abstract: Compositions, reaction mixtures, kits and methods used in amplifying and detecting nucleic acids from various species of the class Mollicutes. Particular regions of the 23S rRNA or its gene have been identified as preferred targets for nucleic acid amplification reactions of a sample suspected containing at least one species of Mollicutes. Some oligomers comprise tag regions, target closing regions, promoter sequences, and/or binding moieties. Samples can be from any source suspected of containing a species of the class Mollicutes. Preferred sample sources include bioreactors, cell lines, cell culture wares and pharmaceutical manufacturing wares.