Abstract: A new fluorescence detection method called pyrophosphorolysis activated fluorescence was developed to measure PAP amplification of nucleic acid. A fluorophore-quencher dual-attached blocked primer was used for PAP which has a fluorophore attached to a nucleotide in the internal region or at the 5? end and a quencher attached to a blocked nucleotide at the 3? end. Multiple fluorophore-quencher dual-labeled blocked primers were also used for multiplex PAP, which are attached with different fluorophores to distinguish multiple templates in a reaction.

Abstract: Disclosed herein are primers and probes related to the detection of beta actin [Homo sapiens (human)] via nucleic acid amplification testing (NAAT), for example to amplify and determine the presence of ?-actin present in test samples. Specifically, the present disclosure describes primers and probes that bind to the beta actin gene for detection via loop mediated isothermal amplification (LAMP) and molecular beacon hybridization.

Abstract: Methods and compositions for nucleic acid amplification, detection, and genotyping techniques are disclosed. In one embodiment, a nucleic acid molecule having a target-specific primer sequence; an anti-tag sequence 5? of the target-specific primer sequence; a tag sequence 5? of the anti-tag sequence; and a blocker between the anti-tag sequence and the tag sequence is disclosed. Compositions containing such a nucleic acid molecule and methods of using such a nucleic acid molecule are also disclosed.

Abstract: The present invention provides an approach to increase the effective read length of commercially available sequencing platforms to several kilobases and be broadly applied to obtain long sequence reads from mixed template populations. A method for generating extended sequence reads of long DNA molecules in a sample, comprising the steps of: assigning a specific barcode sequence to each template DNA molecule in a sample to obtain barcode-tagged molecules; amplifying the barcode-tagged molecules to obtain barcode-containing fragments; juxtaposing the barcode-containing fragments to random short segments of the original DNA template molecule during the process of generating a sequencing library to obtain demultiplexed reads; and assembling the demultiplexed reads to obtain extended sequence reads for each DNA template molecule, is disclosed.

Abstract: Aspects of the technology disclosed herein relate to methods for preparing and analyzing nucleic acids. In some embodiments, methods for preparing nucleic acids for sequence analysis (e.g., using next-generation sequencing) are provided herein.

Abstract: A method for detecting Candida auris, including subjecting a nucleic acid sample obtained from a specimen to a nucleic acid amplification reaction by the LAMP method and detecting an amplification product, wherein, in the primer set to be used in the LAMP method, FIP is a polynucleotide including 5 to 20 nucleotides located on the 5?-terminal side and 5 to 20 nucleotides located on the 3?-terminal side in the nucleotide sequence represented by SEQ ID NO: 1, BIP is a polynucleotide including 5 to 20 nucleotides located on the 5?-terminal side and 5 to 20 nucleotides located on the 3?-terminal side in the nucleotide sequence represented by SEQ ID NO: 2, F3 is a polynucleotide including SEQ ID NO: 3, and B3 is a polynucleotide including SEQ ID NO: 4.

Abstract: The present invention provides a reagent and method for detecting a replication-competent lentivirus (RCL) by fluorescence quantitative real-time polymerase chain reaction (PCR). In particular, the present invention provides a primer and probe combination for detecting RCL, and a method for performing detection using said primer and probe; the present invention also provides a reagent kit comprising said primer and probe. The primer and probe combination of the present invention detects RCL with high amplification efficiency and good specificity, and can be used for RCL detection and RCL monitoring of clinical patient peripheral blood samples which may occur during a production process.

Abstract: The present disclosure provides a method of amplifying a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample comprising or suspected of comprising the target nucleic acid, (ii) multiple primer pairs, wherein at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid, and each primer pair has at least one blocking primer comprising a blocking group capable of blocking polymerase extension, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primers; and (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid and a kit used for the method. The present disclosure further provides a method of sequencing a target nucleic acid and a kit used for the method.

Abstract: Disclosed herein include systems, methods, compositions, and kits for labeling nucleic acid targets in a sample. In some embodiments, nucleic acid targets (e.g., mRNAs) are initially barcoded on the 3? end and are subsequently barcoded on the 5? end following a template switching reaction and intermolecular and/or intramolecular hybridization and extension. There are provided, in some embodiments, methods of 5?-based and 3?-based gene expression profiling. Immune repertoire profiling methods are also provided in some embodiments.

Abstract: Provided herein are methods, compositions, and kits for forming amplification products. In various embodiments provided herein, transposomes comprising transposases are used in forming tagged polynucleotides for downstream amplification and polynucleotide processing steps.

Abstract: The present invention relates to a method for determining a nucleotide sequence of a target nucleic acid. The method comprises: providing a pool of amplicons; sequencing each amplicon in the pool of amplicons to obtain sequence information of each amplicon; comparing a part of the sequence information of each amplicon with at least a part of the sequence of the target specific primer section, wherein the part of the sequence information of each amplicon is a sequence starting from position X+1; determining whether the part of the sequence information of each amplicon comprises at least the part of the sequence of the target specific primer section; and determining accurate sequence of the target region using sequence information which comprises at least the part of the sequence of the target-specific primer section.

Abstract: Disclosed is a method for determining a nucleotide sequence of a target nucleic acid. The method comprises: providing a pool of amplicons; sequencing each amplicon in the pool of amplicons to obtain sequence information of each amplicon; comparing a part of the sequence information of each amplicon with at least a part of the sequence of the target specific primer section, wherein the part of the sequence information of each amplicon is a sequence starting from position X-y and y is positive integer; determining whether the part of the sequence information of each amplicon comprises at least the part of the sequence of the target specific primer section; and determining accurate sequence of the target region using sequence information which comprises at least the part of the sequence of the target-specific primer section.

Abstract: The present disclosure provides methods, systems, and kits for processing nucleic acid molecules. A method may comprise providing a template nucleic acid fragment (e.g., within a cell, cell bead, or cell nucleus) within a partition (e.g., a droplet or well) and subjecting the template nucleic acid fragment to one or more processes including a barcoding process and a single primer extension or amplification process. The processed template nucleic acid fragment may then be recovered from the partition and subjected to further amplification to provide material for subsequent sequencing analysis. The methods provided herein may permit simultaneous processing and analysis of both DNA and RNA molecules originating from the same cell, cell bead, or cell nucleus.

Abstract: This disclosure provides for methods and reagents for rapid multiplex RPA reactions and improved methods for detection of multiplex RPA reaction products. In addition, the disclosure provides new methods for eliminating carryover contamination between RPA processes.

Abstract: The present invention provides a means for accurately discriminating whether an onion is an onion with no pungent taste and/or tear-inducing property. The present invention relates to a method of discriminating traits of an onion, comprising a first determination step of determining presence of the nucleotide sequence of SEQ ID NO:1 corresponding to alliinase gene 1 in a nucleic acid derived from the onion, and a second determination step of determining presence of the nucleotide sequence of SEQ ID NO:2 corresponding to alliinase gene 2, wherein the onion is discriminated to be an onion with no pungent taste and/or tear-inducing property if the presence of the nucleotide sequence of SEQ ID NO:1 is not determined in the first determination step and the presence of the nucleotide sequence of SEQ ID NO:2 is determined in the second determination step.

Abstract: The present invention has an object to provide a simpler and quicker method for diagnosing tinea, method for detecting a Trichophyton, or method for detecting the Trichophyton gene. Use of at least four kinds of specific primers each designed based on a DNA sequence of the Trichophyton gene makes it possible to simply and quickly detect the Trichophyton gene.

Abstract: In some embodiments, the present teachings provide compositions, systems, methods and kits for generating a population of nucleic acid fragments. In some embodiments, nucleic acids can be fragmented enzymatically. For example, methods for generating a population of nucleic acid fragments can include a nucleic acid nicking reaction. In one embodiment, the methods can include a nick translation reaction. A nicking reaction can introduce nicks at random positions on either strand of a double-stranded nucleic acid. A nick translation reaction can move the position of nicks to a new position so that the new positions of two of the nicks are aligned to create a double-stranded break. In some embodiments, methods for generating a population of nucleic acid fragments can include joining at least one end of a fragmented nucleic acid to one or more oligonucleotide adaptors.

Abstract: A method for enriching or amplifying a target nucleic acid including providing a system having a guide nucleic acid, and a Cas or Argonaute protein or a variant thereof. The guide nucleic acid contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid, and contacting the target nucleic acid with the system to form a complex.

Abstract: The present invention features compositions and methods for amplifying a target oligonucleotide in a sample, including detection of the target oligonucleotide in real time.

Abstract: Methods of producing an amplified double stranded deoxyribonucleic acid (dsDNA) from a nucleic acid sample are provided. Aspects of the methods include amplifying using a single product nucleic acid primer and a template switch oligonucleotide to produce an amplified dsDNA product. Compositions and kits for use in performing the methods are also provided.