17 results about "Oligonucleotide hybridization" patented technology

Methods for determining a location of a feature on an array include: (a) providing a first array with a first plurality of features immobilized on a first substrate; (b) providing a second array with a second plurality of features immobilized on a second substrate; (c) aligning the first array with the second array; (d) hybridizing a first barcoded oligonucleotide of the first array to a second barcoded oligonucleotide of the second array, thereby producing a combined nucleic acid that includes first and second spatial barcodes; (e) determining all or a portion of the sequence of the combined nucleic acid; and (f) identifying the second barcoded oligonucleotide associated with the first barcoded oligonucleotide in the combined nucleic acid, and determining the location of a second feature in the second array.

The invention provides a method which allows the separation of different workflow steps for barcoding of target nucleic acids and therefore providing optimal reaction conditions for each workflow step, especially for template switching reactions. Moreover this method provides the opportunity to perform the reactions such as barcoding reactions of two different nucleic acid molecules from one cell such as RNA and genomic DNA molecules in a single step. The method comprises the steps: (a) Providing a plurality of cells comprising target RNA molecules and at least one solid support comprising capture oligonucleotides for said target RNA molecules and barcode oligonucleotides; (b) Partitioning said plurality of cells and said solid supports such that each cell is included into a separate partition and each partition comprises a solid support; (c) Lysing said cell, thereby obtaining a mixture of target and non, target RNA molecules; (d) Hybridizing said target RNA molecules to the capture oligonucleotides for said target RNA molecules, thereby obtaining target RNA molecules attached to said solid support (e) Disrupting the partitions and separating the non-target RNA molecules from the target RNA molecules attached to said solid support (f) Generating double stranded nucleic acids from the target RNA molecules by nucleic acid synthesis, wherein the capture oligonucleotides serve as primer and the target RNA molecules serve as templates (g) Attaching the barcode oligonucleotides to the double stranded nucleic acids from target RNA molecules, thereby generating barcoded nucleic acids from target RNA molecules; Characterized in that in step a) said plurality of cells additionally comprise target genomic DNA molecules and said at least one solid support additionally comprise capture oligonucleotides for target genomic DNA molecules and in that the capture oligonucleotides for target RNA and target genomic DNA molecules are different.

The present invention provides a single-stranded antisense oligonucleotide or pharmaceutically acceptable salt thereof for regulating the expression and / or function of the ATXN7 gene. In the single-stranded antisense oligonucleotide, each nucleotide is bonded by a phosphate group and / or modified phosphate group. The single-stranded antisense oligonucleotide includes a gap region, a 3' wing region bonded to the 3' terminal of the gap region, and a 5' wing region bonded to the 5' terminal of the gap region. The gap region is a deoxyribose-constituted nucleic acid in which a nucleic acid modified by a sugar moiety may be included. The 3' wing region and the 5' wing region are modified nucleic acids. The sugar modification constituting the single-stranded antisense oligonucleotide is a modified nucleic acid represented by formula (A1). The single-stranded antisense oligonucleotide has a base length of 12-30 mer. The base sequence of the antisense oligonucleotide is: a base sequence having a sequence identity of 90-100% with a base sequence that is complementary to at least one target region constituted at the same base length as the antisense oligonucleotide in the base sequence shown in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, or SEQ ID NO: 5; a base sequence that is complementary to the base sequence obtained by deleting, substituting, inserting, or adding one or more bases in the target region; or a base sequence that, under stringent conditions, hybridizes with an oligonucleotide having the target region.

1. The present invention relates to methods and kits for isolating a target nucleic acid by in-gel affinity electrophoresis. The method comprises the steps of: a. covalently immobilizing an anchor oligonucleotide during polyacrylamide polymerization in a polyacrylamide binding gel, wherein the anchor oligonucleotide comprises (a) a binding element that covalently binds to acrylamide of the polyacrylamide binding gel and (b) a first coupling nucleotide sequence that is complementary to a nucleotide sequence of a bridge oligonucleotide to hybridize the anchor oligonucleotide to the bridge oligonucleotide, wherein the bridge oligonucleotide comprises (a) a second coupling nucleotide sequence that is complementary to the first coupling sequence of the anchor oligonucleotide and (b) a landing site with at least one complementary target nucleotide sequence, b. hybridization of the anchor oligonucleotide to the bridge oligonucleotide, c. performing a polyacrylamide gel electrophoresis (PAGE) to enrich target nucleic acid by in-gel hybridization, d. depletion of undesired species by in-gel nucleic acid depletion, e. isolating the hybridized target nucleic acid from the binding gel.

Aptamer detection techniques with chemistry attachment with proximity hybridization and extension are described in an aptamer-based assay. In an embodiment, capture oligonucleotides can be used such that the capture oligonucleotides attach to spatially-fixed analytes in a fixed tissue sample. Aptamers that hybridize to the capture oligonucleotides are tagged with an extension sequence that can then be used for subsequent capture and spatial tagging steps.

Provided are methods of producing a nucleic acid complex. In certain aspects, the methods include combining a sample including ribosomal RNA (rRNA) and a probe complement oligonucleotide with an oligonucleotide probe. The oligonucleotide probe includes a 3′ region complementary to a 3′ region of a rRNA, and a 5′ region complementary to the probe complement oligonucleotide. The combining is under conditions in which the 3′ region of the oligonucleotide probe hybridizes to the 3′ region of the rRNA and the 5′ region of the oligonucleotide probe hybridizes to the probe complement oligonucleotide, thereby producing a nucleic acid complex. In certain aspects, the methods find use in producing rRNA libraries that find use, e.g., in rRNA sequencing applications. Oligonucleotide probes, libraries thereof, compositions, and kits that find use, e.g., in practicing the methods of the present disclosure, are also provided.

An improved nucleic acid capture method, comprising the following steps: by means of a splint oligonucleotide hybridization random probe and an oligonucleotide strand fixed on a capture chip, an RNA in a sample captured by the random probe undergoing reverse transcription into a cDNA, and linking the cDNA to the oligonucleotide strand, the reverse transcription and the linking being carried out in the same reaction system. During the process, while the RNA undergoes the reverse transcription into the cDNA, the cDNA is linked, by means of splint hybridization of fixed oligonucleotide sequences at two ends, to the oligonucleotide strand fixed on the chip. The method can increase the number of captured genes, and reduce the loss of cDNA; in addition, the method combines what was originally three steps into one step, thus further shortening the duration of the process.

The present invention relates to the detection of a target nucleic acid sequence by a PTOCE (PTO Cleavage and Extension) assay. The present invention detects a target nucleic acid sequence in which the PTO (Probing and Tagging Oligonucleotide) hybridized with the target nucleic acid sequence is cleaved to release a fragment and the fragment is hybridized with the CTO (Capturing and Templating Oligonucleotide) to form an extended duplex, followed by detecting the presence of the extended duplex. The extended duplex provides signals (generation, increase, extinguishment or decrease of signals) from labels indicating the presence of the extended duplex and has adjustable Tm value, which are well adoptable for detection of the presence of the target nucleic acid sequence.

A method includes inserting a fluid including a sample into a cartridge, lysing the sample in an extraction chamber to release nucleic acids of interest from the sample, collecting a first set of hybridized magnetic particles hybridized to a first type of nucleic acids of interest by: hybridizing the first type of nucleic acids of interest with an oligonucleotide attached to magnetic particles, holding the first set of hybridized magnetic particles on a side of the extraction chamber, suspending the first set of hybridized magnetic particles with a wash buffer, transporting the first set of hybridized magnetic particles to a detection chamber, collecting a second set of hybridized magnetic particles hybridized to a second type of nucleic acids of interest, amplifying the sets of hybridized magnetic particles, and detecting a plurality of amplification products indicative of the presence, absence, or amount of the types of nucleic acids of interest.

Provided is a method for multiplexed fluorescence microscopy comprising contacting a fixed sample with a set of binding agent-T-oligonucleotide conjugates to allow the binding agents to bind to any binding partners present in the sample, wherein the set comprises a plurality of binding agents having different specificities and the sequence of the T-oligonucleotide is unique to the binding agent to which it is conjugated, contacting the sample and any bound binding agents resulting from step a with a FRET-oligonucleotide, illuminating the sample with a wavelength to cause excitation of the FRET-oligonucleotide's emitter molecule, and observing the fluorescent kinetic profile of the sample at the FRET-oligonucleotide emitter molecule's emission wavelength at one or more pixels over time, wherein the FRET-oligonucleotide can hybridise to multiple T-oligonucleotides in the set, to form multiple pairs, and wherein the dissociation and reassociation between each different pair generates a fluorescent kinetic profile that is unique within that set to that pair. Also provided are associated kits, sets of binding agent T-oligonucleotide conjugates and corresponding FRET-oligonucleotides, and methods of designing such sets.

Provided herein are systems and methods for processing biomolecules (e.g., nucleic acid molecules, proteins) from a sample. A method for processing biomolecules may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule) and barcoding the probe-nucleic acid molecule complex or derivatives thereof. Such a method can comprise performing a nucleic acid reaction, e.g., extension, denaturation, and amplification. A method for processing a sample may comprise hybridizing probes to (i) target regions of a nucleic acid molecule (e.g., RNA molecule) and (ii) a reporter oligonucleotide of a feature binding group, and barcoding the probe-associated molecules. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well.

Products for detecting a plurality of protein analytes comprise a plurality of proximity probe pairs comprising first and second proximity probes having an antibody or antibody fragment specific for the same protein analyte and a nucleic acid domain, which probes can simultaneously bind to the analyte. Each pair is specific for a different analyte. Each nucleic acid domain comprises an ID sequence and at least a first hybridisation sequence. In each probe pair, ID sequences correspond to a particular analyte, and the probes comprise paired hybridisation sequences. For each probe pair, a splint oligonucleotide comprises hybridisation sequences complementary to each of the paired hybridisation sequences. When probes bind to their protein analyte, the respective paired hybridisation sequences can hybridise to the splint oligonucleotide. At least one pair of hybridisation sequences is shared by at least two pairs of proximity probes. A plurality of sample index oligonucleotides is also included.

The present disclosure provides methods and compositions, e.g., kits, for isolating eukaryotic nucleic acid from a stool sample. In one embodiment, the method provided herein involves incubating the stool sample with a chaotropic salt, heating the stool sample, and using a substrate coupled to a locked nucleic acid (LNA) oligonucleotide to isolate the nucleic acids hybridized to the LNA oligonucleotide.

Methods, kits, and systems for analyzing a sample comprising extracellular vesicles. In various examples, a method comprises use of a fluidic device for the retention and discrete presentation of single extracellular vesicles for imaging-based analyses. In various examples, a method comprises use of a plurality of capture agents that are each linked to a different oligonucleotide and a corresponding plurality of labeled nucleic acid probes, where each of the labeled nucleic acid probes specifically hybridizes with one or more or each of the oligonucleotides of the capture agents, and sub-sets of the capture agents are detected by imaging-based means using iterative cycles using corresponding sub-sets of the labeled nucleic acid probes. In various examples, kits and systems are provided for carrying out a method of the disclosure.

Described herein are multiplexable aptamer-based systems and methods for detecting target ligands in a fluid sample. More specifically, described herein are ligand-sensing complexes comprising a ligand-binding oligonucleotide (LBO) hybridized to a corresponding short-release oligonucleotide (SRO) such that binding of a target ligand to the LBO drives a conformational change triggering release of a barcoded SRO or LBO. The released barcode, which comprises a sequence that is informative with respect to the target ligand bound, may then be captured, amplified and / or sequenced as a readout for the presence / concentration of the target ligand in the fluid sample. Also described herein is a method for preparing ligand-sensing complexes with error-free LBO / SRO pairing, as well as a method for improving the sensitivity and / or dynamic range of aptamer-based detection systems.

A single-stranded antisense oligonucleotide or a pharmaceutically acceptable salt thereof, which modulates the expression and / or function of the RPS25 gene, and which is characterized in that each nucleoside of the single-stranded antisense oligonucleotide is bonded via a phosphate group and / or a modified phosphate group, the single-stranded antisense oligonucleotide contains a gap region, a 3 '-wing region bonded to the 3'-terminal of the gap region, and a 5 '-wing region bonded to the 5'-terminal of the gap region, the gap region being a nucleic acid comprising deoxyribose optionally containing a nucleic acid in which a sugar part is modified, and the gap region containing at least one 5 '-CP nucleic acid; the 3 '-wing region and the 5'-wing region are modified nucleic acids having a substituent at the 2 '-position, and the base length of the single-stranded antisense oligonucleotide is 12-30 mer. The base sequence of the single-stranded antisense oligonucleotide is a base sequence having 90%-100% sequence identity with respect to a base sequence complementary to at least one target region comprising the same base length as the single-stranded antisense oligonucleotide in the base sequence depicted in SEQ ID NO: 1. A nucleotide sequence complementary to a nucleotide sequence in which one or more nucleotides have been deleted, substituted, inserted or added in the target region; or a base sequence capable of hybridizing with the oligonucleotide having the target region under strict conditions.

The present disclosure describes a system and methods for the generation of DNA strands and querying a DNA database rapidly and accurately. The method disclosed includes the generating at least one database single stranded DNA (ssDNA) strand, includes a plurality of functional oligonucleotides separated by introns. On one end of each intron there is a donor fluorophore and on the other end is an acceptor fluorophore. A query ssDNA strand is also generated that includes a series of complimentary oligonucleotides, which can hybridize with the functional oligonucleotides of the database ssDNA strand. Hybridization causes the intron regions of the database ssDNA strand to fold resulting in the donor fluorophore and acceptor fluorophore being placed in close proximity to one another. The close proximity enables Förster Resonance Energy Transfer (FRET) phenomena to occur, which is detected using a photodetector.