Abstract: Methods, compositions and kits for detecting analytes of interest in a sample using electrogenerated chemiluminescence are provided. Compositions comprising at least one solid support that entraps or contains an electrogenerated chemiluminescent moiety also provided.

Abstract: A method for nucleic acid sequencing includes disposing template polynucleotide strands in defined spaces on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed according to a predetermined ordering; and determining, for each of the series of flows of nucleotide species, how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands, wherein the predetermined ordering (a) is not a series of consecutive repetitions of a 4-flow permutation of four different nucleotide species, (b) is not specifically tailored to a particular combination of a particular template polynucleotide strand to be sequenced and a particular sequencing primer to be used, and (c) comprises a phase-protecting flow ordering.

Abstract: The present invention provides a method for amplifying a pool of polynucleotide molecules in a sample, characterized by the steps of a) obtaining a sample or RNA and reverse transcription of entire RNA molecules thus creating full length cDNA or obtaining a sample of full length cDNA, b) tailing the 3? end of the transcribed cDNA with a polynucleotide tail after the 3? end, c) amplification of the cDNA using a pair of primers, wherein a first 3? primer is specific for the 5? end of the cDNA and a second 5? primer is specific for the a upstream portion of the polynucleotide tail and the next 1 to 10 nucleotides upstream of the 3?polynucleotide tail of the cDNA.

Abstract: Described herein are approaches for the detection, identification, and/or quantification of target nucleic acids, including, but not limited to partially, substantially randomly, degraded target nucleic acids, in a biological sample, such as a formalin-fixed, paraffin-embedded (FFPE) sample. These approaches provide a means of detecting, identifying, and/or quantifying target nucleic acid molecules, including DNA and RNA molecules, further including RNAs of different classes, from the same sample, and in the same reaction, by using “expander oligonucleotides,” as the term is defined herein, to convert fragments of target nucleic acids into discretely sized DNA fragments, each with a chosen length characteristic for the target nucleic acid from which it is derived.

Abstract: This invention provides for compositions for use in real time nucleic acid detection processes. Such real time nucleic acid detection processes are carried out with energy transfer elements attached to nucleic acid primers, nucleotides, nucleic acid probes or nucleic acid binding agents. Real time nucleic acid detection allows for the qualitative or quantitative detection or determination of single-stranded or double-stranded nucleic acids of interest in a sample. Other processes are provided by this invention including processes for removing a portion of a homopolymeric sequence, e.g., poly A sequence or tail, from an analyte or library of analytes. Compositions useful in carrying out such removal processes are also described and provided. Paneling and multiplex analyzes of more than one nucleic acid analyte using one sample are also provided.

Abstract: This invention provides for compositions for use in real time nucleic acid detection processes. Such real time nucleic acid detection processes are carried out with energy transfer elements attached to nucleic acid primers, nucleotides, nucleic acid probes or nucleic acid binding agents. Real time nucleic acid detection allows for the qualitative or quantitative detection or determination of single-stranded or double-stranded nucleic acids of interest in a sample. Other processes are provided by this invention including processes for removing a portion of a homopolymeric sequence, e.g., poly A sequence or tail, from an analyte or library of analytes. Compositions useful in carrying out such removal processes are also described and provided.

Abstract: Certain embodiments provide a method for capturing a genomic fragment. The method may comprise: obtaining a substrate comprising a first population of surface-bound oligonucleotides and a second population of surface-bound oligonucleotides; hybridizing a first member of the first population of surface-bound oligonucleotides to a selection oligonucleotide comprising a region that hybridizes with the first member and a region that contains a genomic sequence; extending the first member of the first population of surface-bound oligonucleotides to produce a support-bound selection primer that comprises a sequence that is complementary to the genomic sequence; hybridizing the support-bound selection primer to a nucleic acid fragment comprising the genomic sequence; extending the support-bound selection primer to produce an extension product that contains a sequence that flanks the genomic sequence, e.g., in a genome; and amplifying the extension product on the substrate.

Abstract: The invention relates generally to methods and apparatus for conducting analyzes, particularly microfluidic devices for the detection of target analytes.

Abstract: Methods are provided for nucleic acid analysis wherein a target nucleic acid that is at least partially double stranded is mixed with a dsDNA binding dye having a percent saturation of at least 50% to form a mixture. In one embodiment, the nucleic acid is amplified in the presence of the dsDNA binding dye, and in another embodiment a melting curve is generated for the target nucleic acid by measuring fluorescence from the dsDNA binding dye as the mixture is heated. Dyes for use in nucleic acid analysis and methods for making dyes are also provided.

Abstract: Provided herein are mutant endonuclease V enzymes that are capable of nicking an inosine-containing DNA sequence. Nucleic acid assays and agents that employ such mutant endonuclease V enzymes to introduce a nick into a target DNA including one or more inosine, and uses a DNA polymerase to generate amplicons of a target DNA are also described.

Abstract: This application provides photoinduced electron transfer (PET) nucleic acid molecules that can be used detect and amplify nucleic acid molecules, such as target nucleic acid molecules. These PET tags can be attached to the 5?-end of a target sequence-specific primer, thereby generating a PET primer. In particular examples, a PET tag includes a 5?-labeled nucleotide that can be quenched by at least two consecutive Gs within the tag sequence, and is unquenched when the PET tag hybridizes with its complementary nucleic acid molecule. Also disclosed are methods of using PET primers in nucleic acid amplification, such as real-time PCR.

Abstract: Disclosed are nucleic acid-based sensors for measuring the pH of a sample, including cells, regions thereof, and whole organisms. The sensor includes an I-switch that is triggered by protons, and which functions as a FRET-based pH sensor inside living cells and organisms. Also disclosed are compositions and methods for measuring the pH of a specific region of a cell, such as vesicles, the nucleus, mitochondrial matrix, or the Golgi lumen.

Abstract: The present invention provides methods and compositions for performing illuminated reactions, particularly sequencing reactions, while mitigating and/or preventing photodamage to reactants that can result from prolonged illumination. In particular, the invention provides methods and compositions for incorporating photoprotective agents into conjugates comprising reporter molecules and nucleoside polyphosphates.

Abstract: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof.

Abstract: A new method of RNA-PAP was developed that can directly amplify RNA template without additional treatment. RNA-PAP brings in a new mechanism for amplification of RNA template in which RNA-dependent DNA pyrophosphorolysis and RNA-dependent DNA polymerization are serially coupled using 3? blocked primers. Due to this serial coupling, RNA-PAP has high selectivity against mismatches on the RNA template, providing highly specific amplification of RNA template. In addition, mutant polymerases were genetically engineered for higher efficiency of RNA-dependent DNA pyrophosphorolysis and RNA-dependent DNA polymerization.

Abstract: Assays and methods including mobile tagged single stranded nucleic acid reagents pre-loaded on an analysis device, which are preferably tagged, but not labeled and are complementary to a strand (preferably the anti-sense strand in double stranded DNA targets) of the target nucleic acid. The assay also includes a running buffer that includes a dye or other detectable label that nonspecifically binds only to double stranded nucleic acids. In addition, the analysis device includes a detection zone including one or more test zones that have an immobilized tag that binds to the tag on the mobile nucleic acid reagent.

Abstract: Target-specific hybrid capture (TSHC) provides a nucleic acid detection method that is not only rapid and sensitive, but is also highly specific and capable of discriminating highly homologous nucleic acid target sequences. The method produces DNA:RNA hybrids which can be detected by a variety of methods.

Abstract: A modified or isolated composition comprising a gel. The gel includes a plurality of first polymers, each of said first polymers having first functional groups comprising a first nucleic acid sequence attached as side-chains thereto. The gel includes a plurality of second polymers, each of said second polymers having second functional groups comprising a second nucleic acid sequence attached as side-chains thereto, said first and said second functional groups forming a reversible cross-link between said first and said second polymers, wherein said cross-link comprises a plurality of hydrogen bonds between complementary base portions of said first and said second nucleic acid sequences.

Abstract: Devices, containers, and methods are provided for performing biological analysis in a closed environment. Illustrative biological analyses include high density nucleic acid amplification and detection and immuno-PCR.

Abstract: The application relates generally to methods useful for the selective amplification of one or more target nucleic acid or fragments thereof, as well as compositions and kits comprising said amplification reaction mixtures. More specifically, the application relates to a composite primer that comprises a 5? promoter portion and a 3? target-recognition portion which is complementary to the 3? end portion of a target polynucleotide sequence; and optionally, a means for identifying the 5? end portion of the target polynucleotide sequence. The amplification reaction mixture comprises at least one handle-stem-loop structure which comprises a 5? single-stranded handle comprising the promoter portion and a double-stranded stem comprising at least one pair of self-folding segments hybridized to each other, and optionally, a single-stranded loop comprising the sequence between the pair of self-folding segments.