30 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.

To provide compositions, methods and kits for detecting Treponema pallidum.SOLUTION: Presented are oligonucleotide hybridization probes, primer sets, methods, reaction mixtures, and kits for detecting nucleic acids of Treponema pallidum, the causative agent of syphilis. Disclosed assays are both highly sensitive and specific for detection of T. pallidum nucleic acids. Nucleic acid sequences of T. pallidum can be detected at a level of 100% positivity using test samples having only 30 copies / ml of a model in vitro transcript. The presence of potentially cross-reacting non-target microorganisms does not negatively impact assay results.SELECTED DRAWING: Figure 1A

The present invention provides a method that makes it possible to separate different workflow steps for barcoding of a target nucleic acid and thus provide optimal reaction conditions for each workflow step, especially a template conversion reaction. Furthermore, the method provides an opportunity to perform a reaction, such as a barcoding reaction, of two different nucleic acid molecules, such as RNA and genomic DNA molecules, from one cell in a single step. The method comprises the steps of: (a) providing a plurality of cells comprising a target RNA molecule and at least one solid support comprising a capture oligonucleotide and a barcode oligonucleotide for the target RNA molecule; (b) partitioning the plurality of cells and the solid support such that each cell is contained in a separate partition and each partition comprises a solid support; (c) lysing the cells, thereby obtaining a mixture of target RNA molecules and non-target RNA molecules; (d) hybridizing the target RNA molecule to a capture oligonucleotide of the target RNA molecule, thereby obtaining a target RNA molecule attached to the solid support; (e) disrupting the partitions and separating non-target RNA molecules from the target RNA molecules attached to the solid support; (f) generating a double stranded nucleic acid from the target RNA molecule by nucleic acid synthesis wherein the capture oligonucleotide is used as a primer and the target RNA molecule is used as a template; (g) attaching a barcoded oligonucleotide to the double stranded nucleic acid from the target RNA molecule, thereby producing a barcoded nucleic acid from the target RNA molecule; characterized in that, in step a), the plurality of cells additionally comprise a target genomic DNA molecule and the at least one solid support additionally comprises a capture oligonucleotide of the target genomic DNA molecule, and in that the target RNA and the capture oligonucleotide of the target genomic DNA molecule are different.

The improved nucleic acid capturing method comprises the following steps: hybridizing a random probe and an oligonucleotide chain fixed on a capturing chip through a splint oligonucleotide, reversely transcribing RNA (Ribonucleic Acid) in a sample captured by the random probe into cDNA (Complementary Deoxyribonucleic Acid), connecting the cDNA to the oligonucleotide chain, and carrying out reverse transcription and connection in the same reaction system. In the process, RNA is subjected to reverse transcription to form cDNA, and meanwhile, the cDNA is connected to an oligonucleotide chain fixed on a chip by virtue of fixed oligonucleotide sequences at two ends hybridized by splint. Through the method, the number of captured genes can be increased, the loss of cDNA (complementary deoxyribonucleic acid) is reduced, the original three steps are combined into one step, and the duration of the process can be further shortened.

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.

Disclosed herein include systems, methods, compositions, and kits for preventing antibody oligonucleotide extension. In some embodiments, blocking oligonucleotides are provided. In some embodiments, the blocking oligonucleotide comprises a binding region capable of hybridizing to the barcoded oligonucleotide to form a protected duplex. The blocking oligonucleotide may be a locked nucleic acid (LNA), a peptide nucleic acid (PNA), a DNA, an LNA / PNA chimera, an LNA / DNA chimera, or a PNA / DNA chimera. In some embodiments, the 3'terminal of the blocking oligonucleotide cannot be extended by a reverse transcriptase or polymerase, In some embodiments, the blocking oligonucleotide of the protected duplex cannot be removed by the strand displacement activity of the reverse transcriptase or polymerase.

Probe-based nucleic acid and protein analysis is provided herein, and in particular, systems and methods for processing biomolecules (e.g., nucleic acid molecules, proteins) from a sample are provided. A method for treating a biomolecule can include 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 derivative thereof. Such methods may include performing nucleic acid reactions, such as extension, denaturation, and amplification. Methods for processing a sample can include hybridizing a probe to (i) a target region of a nucleic acid molecule (e.g., an RNA molecule) and (ii) a reporter oligonucleotide of a characteristic binding group, and barcoding the molecule associated with the probe. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well.

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.

The present invention relates to antisense oligonucleotides that are capable of modulating expression of Tau in a target cell. The oligonucleotides hybridize to MAPT mRNA. The present invention further relates to conjugates of the oligonucleotide and pharmaceutical compositions and methods for treatment of Tauopathies, Alzheimzer's disease, fronto-temporal dementia (FTD), FTDP-17, progressive supranuclear palsy (PSP), chronic traumatic encephalopathy (CTE), corticobasal ganglionic degeneration (CBD), epilepsy, Dravet syndrome, depression, seizure disorders and movement disorders.

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.

In accordance with an aspect of the present disclosure, there is provided a method of reducing linker-dimers in a sequencing library, comprising: hybridizing an excess of 3 '-linkers to blocker oligonucleotides to form a hybrid complex such that the excess of 3'-linkers cannot form linker-dimers, the hybrid complex comprising: a first blocker oligonucleotide 3 '-terminal, a second blocker oligonucleotide 3'-terminal, a third blocker oligonucleotide 3 '-terminal, and a fourth blocker oligonucleotide 3'-terminal; the first blocker oligonucleotide 3'end is adjacent to the adenylated nucleotide at the 5'end of the first unlinked 3 'linker, and the second blocker oligonucleotide 3' end is adjacent to the adenylated nucleotide at the 5 'end of the second unlinked 3' linker, where the first blocker oligonucleotide has a 5 'moiety complementary and hybridized to the first unlinked 3' linker, and the second blocker oligonucleotide 3 'end is adjacent to the adenylated nucleotide at the 5' end of the second unlinked 3 'linker. The second blocker oligonucleotide has a 5'portion complementary and hybridized to the second unlinked 3 'linker, and the first blocker oligonucleotide has a 3' portion complementary and hybridized to the 3 'portion of the second blocker oligonucleotide. The first and second blocker oligonucleotides may be the same oligonucleotide comprising a palindromic sequence that allows self-hybridization.

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.

Pore-forming peptides or proteins modified by DNA nanotechnology can determine and control the size of the pores, increase stability after insertion into the lipid membrane, and have membrane affinity. Compounds can be easily chemically modified by hybridization with oligonucleotides connected to peptides or proteins. The compound can be hybridized with a DNA template to determine the number of monomers assembled into the pore, thereby determining the size of the pore formed. The range of DNA templates can be a unique single strand composed of multiple hybridization sites separated by a flexible connector, or a complex rigid DNA nanoconstruct, such as a ring based on DNA origami, as a scaffold for pore formation. Hydrophilic modifications at the transmembrane segment or end of the peptide provide long-lived pores and keep the compound in a transmembrane conformation. The compound can be combined with various groups and hydrophilic modifications on the transmembrane end (inserted into the lipid membrane during pore formation), and there are many possible connection positions.

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.

Lipid bilayer particles, such as extracellular vesicles (EVs), are labeled with lipid-tagged single-stranded DNA (ssDNA), which is amplified by polymerase chain reaction (PCR) to quantify particles captured via surface marker interactions or complementary oligonucleotide hybridization.

A method for generating probes on a carrier, and a method for detecting target substance in a sample includes the following steps: hybridizing a probe template with oligonucleotides immobilized on a carrier, extending the oligonucleotides to obtain probes having different spatial barcode segments; performing first amplification to the probes to form probe clusters; sequencing the spatial barcode segments of the probes; performing re-amplification to the probe clusters; and forming capture segments for capturing the target substance on the probes. In this application, after sequencing to determine the spatial barcodes, re-amplification of the probe clusters is performed. The re-amplification by using the excess oligonucleotides on the carrier increases the number of the probes, such that the target substance in the sample can more readily “contact” the probes without relying on long-distance diffusion, which effectively addresses the problem of spatially uneven capture of target substance and enhances capture efficiency.

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.

The present report relates to hybridizing single-stranded (ss-) oligonucleotides which entirely consist of locked nucleic acid (LNA) monomers. The present document shows hybridization experiments with pairs of entirely complementary ss-oligonucleotides which fail to form a duplex within a given time interval. The present report provides methods to identify such incompatible oligonucleotide pairs. In another aspect, the present report provides pairs of complementary ss-oligonucleotides which are capable of rapid duplex formation. The present report also provides methods to identify and select compatible oligonucleotide pairs. In yet another aspect the present report provides use of compatible oligonucleotide pairs as binding partners in binding assays, e.g. receptor-based assays.

Provided herein are systems and methods for processing biomolecules (e.g., nucleic acid molecules, proteins) from a sample. A method for treating a biomolecule can include 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 derivative thereof. Such methods may include performing nucleic acid reactions, such as extension, denaturation, and amplification. Methods for processing a sample can include hybridizing a probe to (i) a target region of a nucleic acid molecule (e.g., an RNA molecule) and (ii) a reporter oligonucleotide of a characteristic binding group, and barcoding the molecule associated with the probe. One or more processes of the methods described herein may be performed within a partition, such as within a droplet or a well.

To provide methods and compositions for analyzing nucleic acid.SOLUTION: In some aspects, the technology relates to methods and compositions for preparing a nucleic acid library from single-stranded nucleic acid fragments. In some aspects, provided are compositions comprising: a nucleic acid composition comprising single-stranded nucleic acid (ssNA); a first oligonucleotide; and a plurality of first scaffold polynucleotide species each comprising an ssNA hybridization region and a first oligonucleotide hybridization region.SELECTED DRAWING: None

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.