Abstract: Methods, kits and systems are disclosed for analyzing one or more molecules in a sample. Analyzing the one or more molecules may comprise quantitation of the one or more molecules. Individual molecules may quantitated by PCR, arrays, beads, emulsions, droplets, or sequencing. Quantitation of individual molecules may further comprise stochastic labeling of the one or more molecules with a plurality of oligonucleotide tags to produce one or more stochastically labeled molecules. The methods may further comprise amplifying, sequencing, detecting, and/or quantifying the stochastically labeled molecules. The molecules may be DNA, RNA and/or proteins.

Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.

Abstract: Methods are provided for monitoring a subject having a graft for an acute rejection (AR) response, e.g., to predict, to diagnose, and/or to characterize an AR response. In practicing the subject methods, the expression level of at least one gene in a sample from the subject, e.g., a blood or biopsy sample, is evaluated, e.g., at the nucleic acid and/or protein level, to monitor the subject. Also provided are compositions, systems, kits and computer program products that find use in practicing the subject methods.

Abstract: Processes for the serotype specific detection and identification of one or more Salmonella serotypes are provided. A family of specific primers and probes are provided that allow screening of biological or environmental samples for robust, rapid, and reproducible detection and identification of one or more Salmonella serotypes in the sample.

Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

Abstract: The present invention relates to an oligonucleotide having a novel structure and a method of synthesizing nucleic acid by using the same as a primer. This oligonucleotide is provided at the 5?-side of the primer with a nucleotide sequence substantially the same as a region synthesized with this primer as the origin of synthesis. The present invention realizes synthesis of nucleic acid based on an isothermal reaction with a simple constitution of reagents. Further, the present invention provides a method of synthesizing highly specific nucleic acid on the basis of this method of synthesizing nucleic acid.

Abstract: Provided herein are compositions and methods for determining the structure of individual targets using nucleic acid caliper by determining long-range distances within such targets.

Abstract: The present invention relates to a novel method for detection of target nucleic acid sequences on a solid phase using dual-labeled immobilized probes and its resistance to a 5? to 3? exonuclease activity of a DNA polymerase. Because the label is remained on the solid substrate by resistance to nucleases due to labeling of a base component the internal nucleotide, the present invention requires no consideration of a suitability of position of the label for remaining on the solid substrate. The present invention ensures to minimize background signal by positioning labels at a site on probes suitable to maximize quenching efficiency of the dual label system, since it permits to freely determine the position of the internal label on probes.

Abstract: The present invention relates to the detection of a target nucleic acid sequence by a PCE-SH (PTO Cleavage and Extension-Dependent Signaling Oligonucleotide Hybridization) assay. The present invention does not use probes to be hybridized with target nucleic acid sequences for providing target signals. Interestingly, the present invention uses probes (signaling oligonucleotides) to be hybridized with the extended strand formed in a target-dependent manner in which the extended strand is synthesized using the CTO artificially selected as templates.

Abstract: Methods for detecting endometrial diseases or an endometrium phase in a subject are described comprising measuring endometrial markers or polynucleotides encoding the markers in a sample from the subject. The invention also provides localization or imaging methods for endometrial diseases, and kits for carrying out the methods of the invention. The invention also contemplates therapeutic applications for endometrial diseases employing endometrial markers, polynucleotides encoding the markers, and/or binding agents for the markers.

Abstract: A method and assembly for electrochemically identifying target nucleotide sequences. The method includes supplying a biological sample that may contain a predetermined target nucleotide sequence; supplying activatable amplification materials comprising free nucleotides to form replicated target nucleotide sequences; supplying an oxido-reducible compound capable of being inserted during replication between the nucleotides forming the replicated target sequences; and activating the activatable amplification materials before applying an electric field to the sample in order to activate the oxido-reducible compound. The replicated target sequences cause inhibition of electrochemical activity of the inserted oxido-reducible compound, and the presence of the predetermined target nucleotide sequence is determined in instances where the electric current decreases.

Abstract: The reaction-medicated amplification methods and applications include a new type of ligase. The general amplification and detection of the downstream with the ligase reaction includes 3 linking probes. It achieves the effect of eliminating nonspecific signal interference by respectively filling the detection tag sequence, upstream primer tag sequence, and downstream primer combination tag sequence into 3 different linking probes. Wherein the linking probe containing detection tag sequence forms a cystic structure and the specific hybridization sequences on both sides of the cystic structure form a “hybridization community” when being hybrid to the target sequences. Being hybrid closely at the adjacent positions to the target sequences, 3 linking probes finally form a complete probe chain containing 3 “tag” sequences with the effect of ligase. This technique achieves the goals of reducing reaction background, enhancing signal-noise-ration and avoiding false positive.

Abstract: Provided herein is technology relating to isolating nucleic acids. In particular, the technology relates to methods and kits for extracting nucleic acids from problematic samples such as stool.

Abstract: [Problem] To provide a method for detecting a nucleic acid (such as DNA and RNA) under isothermal conditions, in particular a method by which a short-chain nucleic acid can be directly detected. [Solution] A method for detecting a target nucleic acid in a sample of the present invention comprises: (a) a step of preparing a first oligonucleotide which comprises, in the direction from 5? to 3?, a first arbitrary sequence, an endonuclease recognition site that is used in a nicking reaction, and a sequence complementary to the target nucleic acid; (b) a step of carrying out a nucleic acid amplification reaction using the target nucleic acid contained in the sample as a primer in the presence of an endonuclease which recognizes the endonuclease recognition site that is used in a nicking reaction; and (c) a step of detecting an oligonucleotide which is obtained by the nucleic acid amplification reaction and comprises a sequence complementary to the first arbitrary sequence.

Abstract: Provided are unimolecular oligonucleotide probes for detecting a target in a sample. The probes use target binding-induced structural changes to detect the presence of the target in the sample. Also provided are methods of using the probes to detect a target in a sample.

Abstract: A method for determining whether a lysate contains sufficient biological sample material for a nucleic acid amplification reaction that includes preparing the lysate in the presence of at least one compound that inhibits the amplification reaction if insufficient biological sample material was present during preparation of the lysate, but does not inhibit the amplification reaction if sufficient biological sample material was present during preparation of the lysate, subjecting the lysate to the amplification reaction, and analyzing a result of the amplification reaction. Due to the presence of the compound in the amplification reaction, no amplification signal is obtained if insufficient biological sample material was present during preparation of the lysate but an amplification signal is obtained if sufficient biological sample material was present during preparation of the lysate.

Abstract: The present invention provides highly sensitive methods used for diagnosing and monitoring various diseases and disorders by detecting and analyzing “ultra short” (20-50 base pair) nucleic acids obtained from bodily fluids.

Abstract: An embodiment of a device for automatically executing a process of generating an emulsion containing nucleic acids, amplifying the nucleic acids in the emulsion, breaking the emulsion, and separating and purifying said amplified nucleic acids, is described that comprises an emulsion generation unit for sealing beads to which nucleic acids are bound in a water-in-oil type emulsion; a nucleic acid amplification unit provided with a reaction vessel for amplifying said nucleic acids and a heating and cooling part for heating and cooling the reaction vessel; an emulsion breaking unit for breaking the emulsion after nucleic acid amplification; and a nucleic acid purification unit for recovering said amplified nucleic acids from said emulsion breaking unit.

Abstract: Disclosed herein are compositions and methods for the processing, amplification and detection of polynucleotides using target-specific oligonucleotides (TSOs). Hybridization of TSOs to target polynucleotides guides target processing into and purification of small target fragments that then can be amplified and detected with high sensitivity and reproducibility. The method is specifically beneficial for highly degraded polynucleotides found in biological samples.

Abstract: The present invention relates to primers, probes, primer sets, primer and probe sets, methods and kits for detecting human papillomaviruses, human beta globin sequences and human papillomaviruses and human beta globin sequences in a test sample.