Abstract: The subject invention pertains to the rapid amplification and real-time monitoring of nucleic acid sequences at a constant temperature. Specifically, fluorescent or electroactive-labeled loop probes and primers are designed to be specific to identified regions of a target nucleic acid sequences and subsequently amplify and permit the identification of the presence of the target sequence. In this method, a DNA polymerase with no 5? to 3? exonuclease activity is added to extend the primers and probes, while a nicking endonuclease is added to specifically identify the amplified nucleic acid product and cleave the label from the loop probe-extended DNA duplex.

Abstract: The invention provides methods of digital amplification using primers of limited nucleotide composition. Limited nucleotide composition means that the primers are underrepresented in at least one nucleotide type. Such primers have much reduced capacity to prime from each other or to extend initiated by mispriming from other than at their intended primer binding sites in a target nucleic acid.

Abstract: The technology relates in part to methods and compositions for detecting one or more pathogens in plants. In some aspects, the technology relates to methods and compositions for detecting hops latent viroid in plants. In some aspects, the technology relates to methods and compositions for detecting hops latent viroid in cannabis plants. In some aspects, the technology relates to methods and compositions for classifying a hops latent viroid genotype. In certain aspects, the technology relates to methods and compositions for determining the presence, absence and/or amount of one or more pathogens in plants, either independently or simultaneously. In aspects, the pathogen is a virus. In some aspects, the virus is selected from among one or more of hops latent viroid, beet curly top virus and alfalfa mosaic virus.

Abstract: The present disclosure relates to a PCR detection kit for rapidly identifying Salmonella of specific serotypes. The kit includes primers for detecting tcpS gene, the primers for detecting the tcpS gene including a forward primer having a nucleotide sequence as set forth in SEQ ID NO. 1 and a reverse primer having a nucleotide sequence as set forth in SEQ ID NO. 2. The kit can identify Salmonella of enteritidis, pullorum/gallinarum, and dublin serotypes rapidly and in a high throughput, which can be used as an auxiliary method for the conventional serotyping of Salmonella.

Abstract: Molecules may be analyzed (e.g., sequencing of nucleic acid molecules) by tunneling recognition at a tunneling junction. Embodiments of the present invention may allow detecting individual nucleotides and the sequencing of a nucleic acid molecule using a tunneling junction. By labeling a specific nucleotide with a moiety, tunneling junctions may generate a signal with a suitable signal-to-noise ratio. The tunneling recognition uses a tunneling current that is mostly through the moiety rather than mostly through the nucleotide or a portion of the molecule of interest. Because a single nucleotide can be detected with a signal with a suitable signal-to-noise ratio resulting from the tunneling current passing through the moiety, embodiments of the present invention may allow for fast detection of nucleotides using a tunneling current.

Abstract: Provided are a composition for a polymerase reaction, containing a nucleic acid polymerase and a 2-methacryloyloxyethyl phosphorylcholine (MPC)-containing zwitterionic copolymer detergent, a tube for a polymerase reaction, and a kit for a polymerase reaction. The stability of the composition for a polymerase reaction can be improved and the reliability of the results of polymerase reaction such as nucleic acid polymerization or amplification can be improved.

Abstract: Methods for enhancing specificity of an analyte binding moiety or probe oligonucleotide to an analyte are provided herein. For example, methods provided herein include blocking a capture binding domain, thereby preventing hybridization to the capture domain of the capture probe affixed to a substrate. Further methods include releasing the block from the capture binding domain, thereby allowing the capture binding domain to specifically bind to the capture domain of the capture probe on the substrate.

Abstract: Disclosed are methods of identifying a methicillin-resistant Staphylococcus aureus (MRSA) in a sample wherein the methods involve detecting a S. aureus-specific nucleic acid sequence, mecA and mecC, in the sample. Kits for determining the presence of MRSA in a sample are also provided.

Abstract: Disclosed are methods and systems for detecting RNA and sequencing RNA in a wide range of samples such as samples with low concentrations of nucleic acid, samples with degraded nucleic acid, samples that would not otherwise be amenable to conventional sequencing or RNA detection methods, poor quality samples, high quality samples in which rare mutations are sought, formalin-fixed paraffin-embedded samples, blood samples, etc. The methods of the present invention may use paired, large panels of primers to amplify many short fragments that overlap between but not within each panel. Each panel's amplicon set may fill the gaps between those of the opposing panel, thereby providing complete gene or genomic coverage. A preliminary, multiplex amplification step amplifies target nucleic acid for all downstream reactions such as Sanger sequencing, cloning, and Next Generation Sequencing (NGS).

Abstract: A method of performing a non-isothermal nucleic acid amplification reaction, the method comprising the steps of: (a) mixing a target sequence with one or more complementary single stranded primers in conditions which permit a hybridization event in which the primers hybridize to the target, which hybridization event, directly or indirectly, leads to the formation of a duplex structure comprising two nicking sites disposed at or near opposite ends of the duplex; and performing an amplification process by; (b) using a nicking enzyme to cause a nick at each of said nicking sites in the strands of the duplex; (c) using a polymerase to extend the nicked strands so as to form newly synthesized nucleic acid, which extension with the polymerase recreates nicking sites; (d) repeating steps (b) and (c) as desired so as to cause the production of multiple copies of the newly synthesized nucleic acid.

Abstract: Nucleic acid probes for detection of a target nucleic acid molecule by an RCA reaction in the presence of the target nucleic acid molecule, comprise a first circular template strand which is capable of acting as a template for RCA, and is protected from RCA in the absence of the target nucleic acid molecule by at least a second protector strand which comprises a region of complementarity to the first template strand and is hybridised thereto to form a double-stranded circular structure containing the first template strand inside the protector strand(s). At least one of the second and/or any further protector strands comprises a target binding site, such that upon binding of the probe to the target nucleic acid molecule the probe is able to undergo a strand displacement reaction which allows RCA of the first template strand. Methods of detecting target analytes use such probes.

Abstract: Provided herein are compositions, methods and uses that relate to an easy, accurate and reliable dual or duplex assay that determines both protein and nucleic acid amounts in a viral preparation in a single container and further determines full versus empty virion content.

Abstract: The present invention relates to a method for detecting a target nucleic acid, which induces any surrogate target to be amplified in the presence of the target nucleic acid and is useful for molecular diagnosis, prenatal diagnosis, early diagnosis, cancer diagnosis, genetic related diagnosis, genetic trait diagnosis, diagnosis of infectious bacteria, identification of drug-resistant bacteria, forensic medicine, species identification of organisms, and the like.

Abstract: This invention relates to methods and compositions for detecting the presence or absence of a Respiratory Syncytial Virus target nucleic acid in a biological sample using isothermal nucleic acid amplification.

Abstract: Disclosed are methods for detecting spatial proximity relationships between nucleic acid sequences in a cell. The methods include: providing a sample of one or more cells comprising nucleic acids; fragmenting the nucleic acids present in the cells, wherein the fragmented nucleic acids have ends capable of joining to other fragmented nucleic acids; joining ends of fragmented nucleic acids to other ends fragmented nucleic acid to create at least one nucleic acid concatemer having at least one junction between the joined fragmented nucleic acids, and wherein the at least one nucleic acid concatemer encodes the information about the proximity of the DNA sequences in the cell; and determining the sequence at least one junction of the at least one nucleic acid concatemer, thereby detecting spatial proximity relationships between nucleic acid sequences in a cell.

Abstract: Provided herein are systems and methods for high-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing.

Abstract: The present invention may provide a small RNA detection sensor comprising: at one end thereof, a first sensing region comprising nucleotides having a sequence complementary to target small RNA; and a PCR-capable region that is coupled to the first sensing region, the small RNA detection sensor to synthesize a replication region complementary to the PCR-capable region by a DNA polymerase by using the target small RNA as a primer, and amplify the PCR-capable region and the replication region.

Abstract: Disclosed is a method of performing a non-isothermal nucleic acid amplification reaction, wherein the temperature at which the method is performed is non-isothermal and subject to a reduction of at least 2° C. during amplification process steps. The present invention provides an improved nucleic acid amplification technique having one or more advantages over existing techniques including, for example, decreased reaction time, increased yield, and decreased non-specific amplification products.

Abstract: Integrated devices that include a sample preparation component integrated with a detection component are disclosed. The sample preparation component may be a digital microfluidics module or a surface acoustic wave module which modules are used for combing a sample droplet with a reagent droplet and for performing additional sample preparation step leading to a droplet that contains beads/particles/labels that indicate presence or absence of an analyte of interest in the sample. The beads/particles/labels may be detected by moving the droplet to the detection component of the device, which detection component includes an array of wells. The detection modules disclosed here can be used for detecting analytes of interest which analytes may have been enriched by amplification, isolation, or other techniques.

Abstract: The invention relates to reagents and methods for improving the efficiency of multiplex nucleic acid amplification, in particular where overlapping amplicons are to be generated. The invention also relates to reagents and methods for improving the efficiency of multistep nucleic acid amplification, in particular the performance of two separate amplification reactions designed to occur in sequence in the same reaction mixture or vessel. The invention further relates to reagents and methods for improving multistep nucleic acid amplification reactions by controlling the output of the first amplification reaction. In particular, primers are provided that minimise the formation of aberrant amplification products. Such primers are particularly useful where first and second amplification reactions take place in a single reaction mixture or vessel.