77 results about "Nucleic acid hybridisation" patented technology

The invention discloses a universal nucleic acid probe design method based on hybridization thermodynamics and kinetics, which comprises the following steps: 1) determining a target amplification region according to a fragment interval, generating a primer pair which meets the length requirement and covers a target fragment, calculating the Gibbs free energy change of nucleic acid hybridization by adopting an intelligent nucleic acid hybridization algorithm, and calculating the Gibbs free energy change of the target fragment according to the Gibbs free energy change; by combining chemical thermodynamics, kinetic parameters, sequence complementarity and enzymatic reaction characteristics, generating an optimal primer pair under a multi-dimensional constraint condition; and 2) on the basis of the generated optimal primer pair, generating a probe combination meeting a free energy difference threshold as a candidate pool, screening the probe combination with the highest objective function value from the candidate pool through an iterative process, and updating the candidate pool step by step until the primer pair and the probe combination with the highest objective function value are output. By introducing an intelligent algorithm and combining a thermodynamic model, a dynamic model and specificity evaluation, an optimal primer and probe combination is automatically generated, and the stability and reliability of design are ensured.

The present disclosure relates, in some aspects, to methods and compositions for analyzing a biological sample. In some aspects, the methods comprise use of a probe set comprising a first and second polynucleotide which hybridize to a target nucleic acid in the biological sample and form a circularized probe. In some aspects, the methods and compositions provided herein improve the detection of nucleic acids in a biological sample.

Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

In certain embodiments, the present invention provides a panel of probes associated with glioblastoma that hybridize to nucleic acid and kits that comprise a collection of panels of probes associated with glioblastoma. In certain embodiments, the present invention provides a method of detecting the presence of biomarkers associated with an increased risk of glioblastoma in a human subject. In certain embodiments, the present invention provides a method of treating a human subject for glioblastoma.

The present disclosure concerns phosphoramidite compounds useful for nucleic acid hybridization probes, the probes containing them, and related methods of use and preparation.

The present invention discloses variant polypeptides that support the adherent growth and long-term culture of hPSCs in vitro, as well as their design and applications. The present invention designs variants with VN polypeptides as the object to obtain the variant polypeptides, and the content of the variants is selected from any one of the following: (1) a polypeptide composed of an amino acid sequence obtained by deletion, substitution, insertion, and / or addition of one or more amino acids in the amino acid sequence of the VN polypeptide and having the function of supporting the growth of human pluripotent stem cells; (2) a polypeptide composed of an amino acid sequence having more than 70% amino acid homology with the amino acid sequence of the VN polypeptide and having the same function as the VN polypeptide; (3) a polypeptide encoded by a nucleic acid that hybridizes with the nucleic acid encoding the amino acid sequence of the VN polypeptide under stringent conditions and having the same function as the VN polypeptide. Based on the simple design, high synthesis efficiency, economic applicability, and excellent performance of the RGD-containing variant polypeptides, the present invention can ideally support the adherent growth and long-term amplification of hPSCs in vitro.

The present disclosure provides systems and methods for transposing a cargo nucleotide sequence into a target nucleic acid site in a target nucleic acid. These systems and methods may comprise a double-stranded nucleic acid comprising the cargo nucleotide sequence, wherein the cargo nucleotide sequence interacts with a transposase recognition complex, an effector complex comprising an effector and at least one engineered guide polynucleotide that hybridizes to the target nucleic acid, and the transposase recognition complex wherein the transposase recognition complex recruits the cargo nucleotide to the target nucleic acid site.

Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

Multivalent assemblies for target hybridization are described. The multivalent assemblies include oligonucleotide sets that hybridize to a target nucleic acid to permit capture of the target nucleic acid. In an embodiment, the multivalent assemblies are heteromultivalent such that the oligonucleotide sets include different oligonucleotides that bind to different regions of the target nucleic acid.

A method for extracting a target nucleic acid from a sample liquid includes providing a heating device having a heating element in contact with the sample liquid. The heating element is conjugated with at least one functional nucleic acid. The functional nucleic acid is adapted to hybridize to the target nucleic acid and bind the target nucleic acid to the heating element. Further, the method includes generating relative movement between the heating element and the sample liquid and extracting the target nucleic acid from the sample liquid by separating the heating element from the sample liquid.

A method for analyzing planar sample is provided. In some cases the method comprises: (a) labelling the planar sample with a capture agent that is linked to a nucleic acid, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the nucleic acid, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

A CRISPR-Cas system and applications thereof are provided, also related to a Cas protein, a fusion protein and a guide polynucleotide. The Cas protein has at least 50% sequence identity compared to the sequence set forth in any one of SEQ ID NOs: 1-184, 426-428. The fusion protein comprises the Cas protein fused to a protein domain and / or a polypeptide tag. The guide polynucleotide comprises a direct repeat sequence having at least 70% sequence identity to any one of SEQ ID NOs: 185-199, 245-247, 287-303, 369 and 370-373, and a guide sequence engineered to hybridize to a target nucleic acid. The CRISPR-Cas system comprises a Cas protein having at least 90% sequence identity compared to the sequence set forth in any one of SEQ ID NOs: 1-184, 426-428, or a nucleic acid encoding thereof, and a guide polynucleotide or a nucleic acid encoding thereof.

The present invention relates to a method for preparing an in vitro evolution-basedhotspot-derived peptide-nucleic acid hybrid molecule. According to the method of the present invention, a hotspot-derived peptide-nucleic acid hybrid molecule that can bind with high affinity to viruses and effectively block the binding between the virus and the receptor can be rapidly prepared and screened in response to various virus mutations among numerous candidates. Therefore, it can be used very effectively for the development of therapeutics against various viral mutations.

The present disclosure relates in some aspects to methods and compositions for matrix-assisted spatial analysis, where a biological sample is embedded in a matrix (e.g., a hydrogel matrix) and a target nucleic acid from the biological sample is tethered to the matrix, followed by removing the biological sample (e.g., by clearing the sample) from the matrix while the target nucleic acid remains tethered to the matrix. After sample removal, one or more probes can be hybrized to the tethered target nucleic acid. The target nucleic acid, the one or more probes, a product of the target nucleic acid, and / or a product of the one or more probes can be released from the matrix for capturing on an array, spatial barcoding on the array, and subsequent sequence analysis of spatially barcoded molecules, for example, using a next-generation sequencing method.

To provide an inexpensive method of easy design and detection, and high-sensitivity mutation detection means capable of detecting even a difference of modification mode.SOLUTION: Provided is a nucleobase detection agent for detecting a predetermined base in a test nucleic acid that includes nucleic acid molecules including a base sequence region hybridizable with the test nucleic acid, wherein the base sequence region includes a detection domain consisting of one acting base, and one display base adjacent to the acting base. The nucleic acid molecule has a constitution in which, when hybridized with the test nucleic acid, the detection domain forms a right-wound double-stranded structure together with one shared base included in the test nucleic acid, and a different base pair is formed depending on whether or not the shared base is a predetermined base. Also provided is a detection method using the nucleobase detection agent.SELECTED DRAWING: None

Binding complexes including a detectable nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The binding complexes allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array-based applications.

Provided is a method for extracting a target nucleic acid (12) from a sample fluid (30). The method comprises providing a sample fluid (30) comprising the target nucleic acid (12) in a reaction container (22) and providing magnetic microparticles (10) in the sample fluid (30), each functionalized with at least one extraction nucleic acid (16), wherein the extraction nucleic acids (16) are at least partially complementary to the target nucleic acid (12). Further, the method comprises hybridizing at least a part of the target nucleic acid (12) with one of the extraction nucleic acids (16) and binding the target nucleic acid (12) via the extraction nucleic acid (16) to one of the magnetic microparticles (10). Furthermore, the method comprises providing a magnetic field in the reaction container (22) in such a manner that at least a part of the magnetic microparticles (10) associated with the target nucleic acid (12) sediments on a container wall (22a, 22b, 22c) of the reaction container (22). Further provided are devices and methods for amplifying a target nucleic acid (12), using magnetic microparticles (10) for extraction of a target nucleic acid (12), and a magnetic microparticle.

Provided are synthetic strands for nucleic acid sequencing. In some embodiments, the strands include a plurality of rotatable molecular disks. The plurality of rotatable molecular disks comprises molecular disks each comprising a first moiety that binds to adenine (A), a second moiety that binds to cytosine (C), a third moiety that binds to guanine (G), and a fourth moiety that binds to thymine (T), uracil (U), or both (T / U). The first, second, third, and fourth moieties are spaced about the perimeter of the molecular disk. The molecular disks enable hybridization of the synthetic strand to a nucleic acid, where the rotational positions of the molecular disks indicate the sequence of the nucleic acid. Also provided are methods of using the synthetic strands, as well as related compositions, kits, and nucleic acid sequencing systems. Stem-loop structure-based sequencing methods and related compositions, kits, and nucleic acid sequencing systems are also provided.

The invention provides a method for detecting escherichia coli O157 based on a CRISPR (clustered regularly interspaced short palindromic repeats) technology. The method comprises the following steps: S1, amplifying a sample to be detected to obtain an amplification product; amplification of the to-be-detected sample is to amplify the to-be-detected sample by using the RPA amplification primer group; s2, contacting the amplification product with Cas protein, sgRNA and a single-stranded nucleic acid detector, and detecting a detectable signal generated by cutting the single-stranded nucleic acid detector by the Cas protein, so as to detect the escherichia coli O157, the sequences of the RPA amplification primer group are as shown in SEQ ID No.2 and SEQ ID No.7, and the sequence of a target region hybridized with target nucleic acid in the sgRNA is as shown in SEQ ID No.9. The method disclosed by the invention has the advantages of good inclusiveness, strong specificity, high sensitivity and the like, and has a wide application prospect.

Provided are synthetic strands for nucleic acid sequencing. In some embodiments, the strands include a plurality of rotatable molecular disks. The plurality of rotatable molecular disks comprises molecular disks each comprising a first moiety that binds to adenine (A), a second moiety that binds to cytosine (C), a third moiety that binds to guanine (G), and a fourth moiety that binds to thymine (T), uracil (U), or both (T / U). The first, second, third, and fourth moieties are spaced about the perimeter of the molecular disk. The molecular disks enable hybridization of the synthetic strand to a nucleic acid, where the rotational positions of the molecular disks indicate the sequence of the nucleic acid. Also provided are methods of using the synthetic strands, as well as related compositions, kits, and nucleic acid sequencing systems. Stem-loop structure-based sequencing methods and related compositions, kits, and nucleic acid sequencing systems are also provided.

The present invention provides oligomeric compounds. Certain such oligomeric compounds are useful for hybridizing to a complementary nucleic acid, including but not limited, to nucleic acids in a cell. In certain embodiments, hybridization results in modulation of the amount activity or expression of the target nucleic acid in a cell.

The present application relates to spatially differentiated, multiplexed nucleic acid analysis of a biological sample, including a method of spatially tagging nucleic acids of a biological sample comprising the steps of: (a) providing a solid support comprising different nucleic acid probes randomly positioned on the solid support, wherein the different nucleic acid probes each comprise a barcode sequence that is different from the barcode sequences of the other randomly positioned probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequence on the solid support; (c) contacting a biological sample with the solid support having the randomly positioned probe; (d) hybridizing the randomly positioned probe to a target nucleic acid from a portion of the biological sample; and (e) modifying the randomly located probe hybridized to the target nucleic acid, thereby producing a modified probe comprising the barcode sequence and a target-specific modification, thereby spatially tagging the nucleic acid of the biological sample.

The application provides a method for detecting Staphylococcus aureus based on CRISPR technology, and the method comprises the following steps: S1, amplifying a to-be-detected sample to obtain an amplification product; the to-be-detected sample is amplified by using an RPA amplification primer group; S2, contacting the amplification product with Cas protein, sgRNA and single-stranded nucleic acid detector, detecting a detectable signal generated by the Cas protein cutting the single-stranded nucleic acid detector, and thus detecting Staphylococcus aureus; the sequence of the RPA amplification primer group is shown as SEQ ID No. 3 and SEQ ID No. 7, and the sequence of the target region in the sgRNA for hybridizing with the target nucleic acid is shown as SEQ ID No. 9. The method has the advantages of good inclusivity, strong specificity, high sensitivity and the like, and has a wide application prospect.

Provided herein are methods, compositions, and kits for the spatial analysis of target nucleic acids in biological samples by their 5′ end. An exemplary method includes: contacting a biological sample with a primer that hybridizes the target nucleic acid; hybridizing the primer to the target nucleic acid and extending using the target nucleic acid as a template to generate an extension product; incorporating a non-templated polynucleotide sequence including at least three nucleotides to the 3′ end of the extension product; hybridizing the polynucleotide sequence of the extension product to a capture domain on an array including a plurality of capture probes that include a spatial barcode and the capture domain; and determining the spatial barcode sequence, or complement thereof, and all or a portion of the extension product, or complement thereof, and using the determined sequences to determine the location of the target nucleic acid in the biological sample. The non-templated polynucleotide sequence may be C-C-C or C-G-C introduced by terminal transferase or may be introduced by SMART technology using reverse transcriptase.

The invention provides a method for detecting staphylococcus aureus based on a CRISPR (clustered regularly interspaced short palindromic repeats) technology. The method comprises the following steps: S1, amplifying a sample to be detected to obtain an amplification product; amplification of the to-be-detected sample is to amplify the to-be-detected sample by using the RPA amplification primer group; s2, enabling the amplification product to be in contact with Cas protein, sgRNA and a single-stranded nucleic acid detector, and detecting a detectable signal generated by cutting the single-stranded nucleic acid detector by the Cas protein, so as to detect the staphylococcus aureus, the sequences of the RPA amplification primer group are as shown in SEQ ID No.3 and SEQ ID No.7, and the sequence of a target region hybridized with target nucleic acid in the sgRNA is as shown in SEQ ID No.9. The method disclosed by the invention has the advantages of good inclusiveness, strong specificity, high sensitivity and the like, and has a wide application prospect.

This invention relates to the field of biosensors and microfluidics, and particularly to a method for treating interfering DNA based on an ultrasonic-driven device. The method includes an ultrasonic-driven device comprising a piezoelectric substrate, Rayleigh wave drive, microfluidic reaction, and drive control module. First, a nucleic acid hybridization system is constructed to achieve initial binding and recognition of interfering DNA. Then, Rayleigh waves are excited to generate physical shearing force. Based on the difference in binding force between the interfering DNA and the target DNA and probe, precise mechanical feature recognition is achieved. By adjusting the radio frequency signal parameters to make the shearing force between the two types of binding forces, the interfering DNA is dissociated and expelled, completing the selective removal process.

The invention discloses a fluorescent microsphere coding method for regulating and controlling FRET efficiency based on nucleic acid and application, and belongs to the technical field of DNA detection. The method comprises the following steps: combining DNA (deoxyribonucleic acid) coding probes with different lengths and two fluorescent probes marked with different fluorescent groups to the surfaces of magnetic beads through nucleic acid hybridization; the FRET efficiency of the two fluorophores is changed, so that the fluorescence intensity change on the carboxyl magnetic beads is realized; the method comprises the following steps: S1, combining a coupling probe with a microsphere: coupling a first coupling probe to the surface of a carboxylated magnetic bead through a carboxyl-amino covalent reaction; s2, hybridization reaction: taking magnetic beads obtained by coupling, adding a DNA coding probe, a first fluorescent probe and a second fluorescent probe, reacting for a period of time in a dark place, and washing to obtain coding microspheres; and S3, decoding: detecting the fluorescence intensity of FAM and Cy3 through a flow cytometry, and decoding according to the position difference of the microspheres in the two-dimensional scatter diagram. According to the invention, coding in two dimensions of wavelength and intensity can be realized.

The present disclosure provides systems and methods for transposing a cargo nucleotide sequence into a target nucleic acid site in a target nucleic acid. These systems and methods can include: a double-stranded nucleic acid comprising the cargo nucleotide sequence, where the cargo nucleotide sequence interacts with a recombinase complex; an effector complex, the effector complex comprising an effector and at least one engineered guide polynucleotide, the at least one engineered guide polynucleotide hybridizing to the target nucleic acid; and the recombinase recognition complex, wherein the recombinase recognition complex recruits the cargo nucleotide to the target nucleic acid site.