MOLECULES COMPRISING BRANCHED LINKERS AND METHODS OF USE

    公开(公告)号:US20240175082A1

    公开(公告)日:2024-05-30

    申请号:US18488502

    申请日:2023-10-17

    Inventor: Justin COSTA

    CPC classification number: C12Q1/6841 C12Q1/682

    Abstract: The present disclosure in some aspects relates to methods and compositions for analyzing a biological sample comprising contacting the biological sample with a molecule comprising a branched linker. In some embodiments, the molecule is a detectable probe comprising branches each comprising one or more detectable labels and/or one or more sequences for hybridizing to a detectably labeled probe. In some embodiments, the molecule comprises an oligonucleotide linked to photoactivatable functional moieties via a branched linker.

    METHODS AND COMPOSITIONS FOR ROLLING CIRCLE AMPLIFICATION

    公开(公告)号:US20230242974A1

    公开(公告)日:2023-08-03

    申请号:US18088330

    申请日:2022-12-23

    CPC classification number: C12Q1/6841 C12Q1/6855

    Abstract: The present disclosure in some aspects relates to methods and compositions for detecting and quantifying multiple analytes present in a biological sample by rolling circle amplification (RCA). In some aspects, the methods and compositions provided herein address issues associated with control of signal spot size and intensity for RCA products (RCPs) in a sample. In some aspects, provided herein are methods and compositions (e.g., probes and/or reaction mixtures) for slowing down RCA and/or decreasing the size of RCA products. In some embodiments, nucleotides or nucleotide analogs having a hydrophobic group (e.g., a hydrophobic modification on the base) are included in nucleotides for RCA and incorporated into the RCP product, leading to reduction of RCP size without the need of crosslinking an incorporated hydrophobic nucleotide or nucleotide analog to the RCP itself or another molecule.

    CIRCULAR PROBES AND METHODS FOR SAMPLE ANALYSIS

    公开(公告)号:US20230159997A1

    公开(公告)日:2023-05-25

    申请号:US17993793

    申请日:2022-11-23

    CPC classification number: C12Q1/6841 C12Q1/682 C12Q1/6844

    Abstract: The present disclosure relates in some aspects to methods and compositions for analyzing a target nucleic acid, such as in situ detection of a region of interest in a polynucleotide in a cell or tissue sample. In some aspects, provided herein are circular probes (e.g., dumbbell probes) for analyzing a target nucleic acid, as well as methods comprising an enzymatic treatment to de-circularize unbound or non-specifically bound circular probes. Circular probes specifically bound to target nucleic acids remain intact during and after the enzymatic treatment and can be detected, e.g., via rolling circle amplification (RCA) of the circular probes and detection of the RCA products.

    NUCLEIC ACID CONCATEMERS AND METHODS FOR STABILIZING AND/OR COMPACTING THE SAME

    公开(公告)号:US20230057571A1

    公开(公告)日:2023-02-23

    申请号:US17816995

    申请日:2022-08-02

    Abstract: The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures, such as RCPs, in the biological sample without the use of exogenously added oligonucleotide compaction probes. In some embodiments, provided herein are methods involving the use of self-hybridizing hybridizing regions for compacting and/or stabilizing nucleic acid concatemers (e.g., RCPs). In some embodiments, dynamic inter-strand annealing between tandem units of an RCP is used for compaction and/or stabilization. In some embodiments, short palindromic regions in an RCP are used for compaction and/or stabilization.

    METHODS FOR PROCESSING RIBONUCLEIC ACIDS IN BIOLOGICAL SAMPLES

    公开(公告)号:US20250163502A1

    公开(公告)日:2025-05-22

    申请号:US18955449

    申请日:2024-11-21

    Abstract: The present disclosure relates in some aspects to methods and compositions for repairing and/or immobilizing ribonucleic acid analytes in biological samples, and more specifically fragmented ribonucleic acids. A workflow is provided for polishing and repairing fragmented ribonucleic acids in a biological sample, for improving nucleic acid quality for downstream applications, such as in situ, spatial array, or single-cell based analysis. Ribonucleic acid analytes may be tethered covalently or non-covalently to a matrix-forming agent, for example, matrix-forming agent that can form a three-dimensional polymerized matrix.

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