The subject invention pertains to composition and methods of using said composition as an in vitro biosensor of small molecules in biological and/or environmental samples using enzyme-assisted nucleic acid reactions. The methods and compositions can be used to sense and/or transduce the signal of a sensing event mediated by allosteric proteins, endonucleases and nucleic acid reactions. This invention allows the rapid development and setup of one-pot assays to provide results in minutes. The methods and compositions may be used to generate an electrochemical, fluorescent, colorimetric, and/or luminescent output and the methods can be performed in different modalities, including a solution-based or paper-based assay.

The subject invention pertains to composition and methods of using said composition as an in vitro biosensor of small molecules in biological and/or environmental samples using enzyme-assisted nucleic acid reactions. The methods and compositions can be used to sense and/or transduce the signal of a sensing event mediated by allosteric proteins, endonucleases and nucleic acid reactions. This invention allows the rapid development and setup of one-pot assays to provide results in minutes. The methods and compositions may be used to generate an electrochemical, fluorescent, colorimetric, and/or luminescent output and the methods can be performed in different modalities, including a solution-based or paper-based assay.

The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.

The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.

A method for synthesizing single-stranded DNA, specifically a process for producing single-stranded DNA without base mutations, is provided, by which single-stranded DNA is produced by uracil-specific excision reagent (USER)-mediated self-looping of double-stranded DNA combined with rolling circle replication.

A method for synthesizing single-stranded DNA, specifically a process for producing single-stranded DNA without base mutations, is provided, by which single-stranded DNA is produced by uracil-specific excision reagent (USER)-mediated self-looping of double-stranded DNA combined with rolling circle replication.

This disclosure relates to analyzing the end-to-end sequence and the relative distributions in heterogeneous mixtures of polynucleotides and methods and enabling reagents related thereto. In certain embodiments this method relates to the complete full length sequencing and quantitative profiling of mRNAs present in the transcriptomes of cells or tissues of, but not limited to, higher multicellular organisms that possess interrupted genes subject to complex post-transcriptional RNA processing

This disclosure relates to analyzing the end-to-end sequence and the relative distributions in heterogeneous mixtures of polynucleotides and methods and enabling reagents related thereto. In certain embodiments this method relates to the complete full length sequencing and quantitative profiling of mRNAs present in the transcriptomes of cells or tissues of, but not limited to, higher multicellular organisms that possess interrupted genes subject to complex post-transcriptional RNA processing

The present invention concerns a method of sequencing immobilized polynucleotides in which beads which are tethered to the solid support are used as labels to identify bases within the polynucleotides. The beads carry sets of probes or bases which can bind to the polynucleotide allowing identification of the target base(s). Identification of the base(s) is achieved through sequential application of different cleavage means specific to different probes/bases carried on the beads. Also provided is an apparatus for performing the method and a kit comprising the apparatus and other components necessary for performing the method.

The present invention concerns a method of sequencing immobilized polynucleotides in which beads which are tethered to the solid support are used as labels to identify bases within the polynucleotides. The beads carry sets of probes or bases which can bind to the polynucleotide allowing identification of the target base(s). Identification of the base(s) is achieved through sequential application of different cleavage means specific to different probes/bases carried on the beads. Also provided is an apparatus for performing the method and a kit comprising the apparatus and other components necessary for performing the method.