78 results about "DNA Modification" patented technology

The technology described herein relates to new CRISPR / Cas systems and components thereof, vectors, proteins, fusion proteins, ribonucleoprotein complexes and methods of using the new system and components. The new system can be used in CRISPRi applications and can be fused to any number of effector domain modalities, such as nucleases, base editors, prime editors and the like to perform various DNA modifications.

The technology described herein relates to novel CRISPR / Cas systems and components thereof, vectors, proteins, fusion proteins, ribonucleoprotein complexes and methods of using the novel systems and components. The new system can be used in CRIS PRi applications and can be fused with any number of effector domain patterns, such as nuclease, base editor, leader editor, and the like, to conduct a variety of DNA modifications.

The invention relates to the technical field of biology, in particular to an oligo A-tailed DNA-nanogold material with high modification density and a preparation method of the oligo A-tailed DNA-nanogold material. The oligo A-tag DNA-nanogold material is prepared from AuNPs (AuNPs), and / or AuNRs (AuNPs) and modified oligo A-tag DNA (Deoxyribose Nucleic Acid), wherein the AuNRs are AuNPs, AuNRs and the modified oligo A-tag DNA; and an oligo A-tag DNA (Deoxyribose Nucleic Acid) sequence is as shown in SEQ ID No 1. The preparation method is low in cost and easy to operate, high-density oligoA-tailed DNA modification on the surfaces of the nanogold with different morphologies can be achieved, and stability is high.

In one aspect, the disclosure relates to a gene modification tool that fuses a Cas protein with a polymerase. This DSB-independent approach utilizes a DNA-RNA chimeric prime-editor-like guide RNAs (chimeric pegRNAs or cpegRNAs) to enable programmable DNA sequence replacement or excision at endogenous human genomic sites. The Cas9 and RNA portion of cpegRNA helps with targeting a gene, while the DNA portion of cpegRNA is used as a template by the polymerase to repair. Furthermore, the disclosed method can be used to introduce large DNA modifications in the genome.

The present disclosure provides systems, compositions, and methods for nucleic acid modification. More particularly, the present disclosure provides systems comprising a TnpA protein, a TnpB protein, an IscB protein, or a combination thereof, and methods using thereof.

The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and / or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and / or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

Provided herein are compositions, methods, and systems for DNA modification. In particular, provided herein are compositions, and systems comprising TnpB-like nuclease-dead repressors (dTnpB / TldRs), dCas12f or dCas12f-like proteins, and / or a TnpB-transposase fusion proteins and methods using thereof.

The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and / or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and / or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

The invention discloses a preparation method and application of an i-motif-containing DNA surface modified carbon quantum dot, and the carbon dot is prepared by the following steps: synthesizing a carbon dot, and then carrying out DNA modification. The preparation method comprises the following steps: dissolving phenylenediamine in a polymer solution, uniformly mixing, transferring the solution into a polytetrafluoroethylene inner container, putting the inner container into a stainless steel high-pressure kettle, and heating and reacting in a muffle furnace. And after the reaction is finished, cooling a reaction system to room temperature, then polymerizing DNA containing i-motif as a cross-linking agent with CDs, after the polymerization reaction is finished, freeze-drying the solution, taking out the solution, putting the solution into a dialysis bag, and carrying out dialysis purification to obtain DNA-CDs after dialysis is finished. And then carrying out bionic treatment on the MV-DNA-CDs, so as to obtain the MV-DNA-CDs disclosed by the invention. The nano-carrier prepared by the invention is high in yield and good in stability, has responsiveness and targeting property, and can be used for precise treatment of tumors.

Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and / or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA / RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA / RNA modifications in parallel.

The present inventions generally relate to site-specific delivery of nucleic acid modifiers and includes novel DNA-binding proteins and effectors that can be rapidly programmed to make site-specific DNA modifications. The present inventions also provide a synthetic all-in-one genome editor (SAGE) systems comprising designer DNA sequence readers and a set of small molecules that induce double-strand breaks, enhance cellular permeability, inhibit NHEJ and activate HDR, as well as methods of using and delivering such systems.

Systems and methods for producing multiple unique edits in T1 seeds of a plant are provided. In one example, the method includes transforming at least one expression cassette into a plant cell or plant tissue. The at least one expression cassette may include a nucleic acid encoding a DNA modification enzyme; optionally, a nucleic acid encoding at least one guide RNA (gRNA); and a floral mosaic (FMOS) regulatory sequence, wherein the FMOS regulatory sequence (i) mediates the expression of the DNA modification enzyme in at least one of a flower primordium cell and a flower reproductive organ, and (ii) mediates multiple edits in at least one of the flower primordium and the flower reproductive organ. The method may also include regenerating the plant cell or plant tissue into a TO plant having multiple T1 seeds, wherein the T1 seeds contain multiple unique edits.

Aspects of the present disclosure are directed to methods, compositions, and kits for detection and analysis of DNA and RNA cytosine methylation and / or RNA pseudouridylation. Certain aspects include methods, compositions and kits useful in bisulfite sequencing of methylated and / or pseudouridinylated nucleic acids, including methylated and / or pseudouridinylated nucleic acids from low-input samples such as cell-free DNA (cfDNA) and cell-free RNA, long fragment polynucleotides, and / or cfDNA and DNA from formalin-fixed paraffin-embedded (FFPE) samples. Also disclosed herein are methods, compositions and kits useful in bisulfite sequencing of methylated and / or pseudouridinylated nucleic acids with low nucleic acid damage, higher true positive results, and / or lower false negative results.

This invention relates to the field of biotechnology, and more particularly to a high-density oligoA-tailed DNA-gold nanomaterial and its preparation method. The oligoA-tailed DNA-gold nanomaterial comprises AuNPs, and / or AuNRs, and modified oligoA-tailed DNA; the oligoA-tailed DNA sequence is shown in SEQ ID No. 1. This preparation method is low-cost, easy to operate, and can achieve high-density oligoA-tailed DNA modification on the surface of gold nanoparticles with different morphologies, while exhibiting high stability.

Aspects of the present disclosure are directed to methods, compositions, and kits for detection and analysis of DNA and RNA cytosine methylation and / or RNA pseudouridylation. Certain aspects include methods, compositions and kits useful in bisulfite sequencing of methylated and / or pseudouridinylated nucleic acids, including methylated and / or pseudouridinylated nucleic acids from low-input samples such as cell-free DNA (cfDNA) and cell-free RNA, long fragment polynucleotides, and / or cfDNA and DNA from formalin-fixed paraffin-embedded (FFPE) samples. Also disclosed herein are methods, compositions and kits useful in bisulfite sequencing of methylated and / or pseudouridinylated nucleic acids with low nucleic acid damage, higher true positive results, and / or lower false negative results.

Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and / or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA / RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for identification and / or localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA / RNA modifications in parallel.

This invention relates to a method for preparing a functional DNA gel and its applications. Addressing the problems of existing methods for immobilizing functional nucleic acids requiring DNA modification, which increases immobilization costs, and the reduction of functionality due to chemical fixation, this invention mixes functional circular DNA with a gel monomer solution, and adds an initiator and a coagulant to initiate a cross-linking polymerization reaction. During the reaction, the gel monomers pass through the functional circular DNA, polymerizing into long chains and then cross-linking into a network structure. This allows the functional circular DNA to be enriched on the network structure in a suspended, fixed form, resulting in a functional DNA gel. The functional circular DNA is circular DNA containing functional nucleic acid sequences. This invention immobilizes functional circular DNA on the gel network structure without chemical modification, and the preparation method is simple. It can be used for the efficient and specific removal of pollutants such as heavy metal ions, toxins, veterinary drugs, and pesticides from solutions, as well as the enrichment of small molecule nucleic acids in solutions.

The present invention is directed to composition comprising modified DNA identifier sequences (MoDIS) comprising (i) a validation code nucleotide sequence (VC), (ii) a randomized index code nucleotide sequence (RIC) and (iii) an annealing site nucleotide sequence (AS) for specifically binding a primer for PCR amplification, wherein (a) AS is attached to an affinity tag or marker and / or affinity tag compound for the identification, enrichment and / or purification of MoDIS-bound nucleotide sequences; and (b) the nucleotide at the 5'-end of the MoDIS comprises a 5'- azido-modified moiety or a 5'-alkynyl-modified moiety.

The invention belongs to the technical field of DNA coding molecules, and provides a synthesis method of an on-DNA carbonyl compound, which comprises: providing an on-DNA amino compound and an on-DNA hydroxyl compound, the on-DNA amino compound comprising a DNA fragment and an amino group coupled to the DNA fragment, and the on-DNA hydroxyl compound comprising a DNA fragment and a hydroxyl group coupled to the DNA fragment; and reacting the on-DNA amino compound and / or the on-DNA hydroxyl compound with laccase and an auxiliary catalyst to obtain the on-DNA carbonyl compound, namely the on-DNA carbonyl compound containing a DNA fragment and carbonyl coupled with the DNA fragment. The synthesis method has the advantages of mild conditions, environmental friendliness and small damage to DNA, and is suitable for construction of a DNA coding molecular library, fluorescence labeled molecule coupling performed by using an on-DNA carbonyl reaction handle, DNA modification coupling and functional modification in targeted drug delivery.

The present invention relates to methods and compositions for modifying target sites in the genome of a cell. Fusion proteins are provided, which include one or more DNA binding domains and one or more heterologous domains, such as DNA modification domains, connected by improved linker sequences. Codon-optimized polynucleotides are provided, which encode fusion proteins including one or more DNA binding domains and one or more heterologous domains connected by improved linker sequences.

The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and / or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and / or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and / or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and / or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

This disclosure to the methods for nucleic acid modification, gene targeting, and gene tagging comprising an engineered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated transposon (CAST) system with a donor DNA comprising at least one engineered transposon end sequence and / or at least one integration co-factor protein. More particularly, the present disclosure provides systems comprising: an engineered CAST system or one or more nucleic acids encoding the engineered CAST system, wherein the CAST system comprises at least one or all of: i) at least one Cas protein, ii) one or more transposon-associated proteins, iii) at least one guide RNA (gRNA) complementary to at least a portion of a target nucleic acid sequence; and a donor nucleic acid comprising a cargo nucleic acid sequence flanked by at least one engineered transposon end sequence and / or at least one integration co-factor protein, or a nucleic acid encoding thereof.

Provided is a simple and efficient method of plant genome editing that does not involve the incorporation of a gene cassette for the expression system of a site-specific DNA modification protein. The method of the present invention comprises: (i) a step for mixing plant cells or a tissue containing plant cells together with a site-specific DNA modification protein and a needle-shaped inorganic compound in a liquid medium and making a disturbance to perforate the cells with the needle-shaped inorganic compound, thereby introducing the site-specific DNA modification protein into the cells; and (ii) a step for culturing the plant cells or the tissue containing the plant cells, into which the site-specific DNA modification protein has been introduced in step (i), thereby causing a DNA mutation specific to a target site in the genome of the plant cells.

The invention relates to a method for detecting DNA modification, in particular to a construction method of a DNA library with modified nucleotide, a detection method, a kit set and application. According to the scheme provided by the invention, the necessity of designing degenerate primers is avoided, the design difficulty of multiple primers is greatly reduced, the specificity of multiple PCR amplification is improved, and the formation of primer dimers is reduced.

To provide methods of profiling gene and protein expression of a plurality of nuclei from a single cell type.SOLUTION: Provided is a method of profiling nuclear epigenetic expression and / or nuclear structure, the method comprising: (a) processing a tissue sample containing a plurality of cell types to expose nuclei, the tissue sample comprising brain tissue, brain stem tissue, and / or spinal cord tissue; (b) contacting the nuclei with two or more affinity labels that bind to different nucleic acid transcripts or proteins that are specific to the nuclei of a cell type in the tissue sample to label the nuclei, the nucleic acid transcripts or proteins being encoded by genes selected from a specific group; (c) purifying the nuclei labeled with two or more affinity labels; and (d) (i) collecting information regarding histone modifications, binding of transcription factors, and DNA modifications for the labeled nuclei to profile the epigenetic expression of the nuclei, and / or (ii) collecting information on the chromosomal structure of the labeled nuclei to profile the nuclear structure.SELECTED DRAWING: Figure 1

The invention discloses a DNA modification and positioning method based on quantum dots, and relates to the technical field of DNA sequencing, and the method comprises the following steps: S1, combining CdSe quantum dots at the tail end of DNA to form a DNA and quantum dot compound; s2, enabling the DNA and quantum dot compound to pass through a nanopore of a nanopore detection system under the driving of an electric field, and collecting a tunneling current signal in real time by utilizing a current amplifier of the nanopore detection system; s3, performing filtering and noise reduction processing on the acquired tunneling current signal to obtain a processed current signal; s4, the processed current signals are subjected to feature recognition, the current base type and a recognition result are obtained, and the recognition result is recognition accuracy or recognition inaccuracy. According to the invention, the signal-to-noise ratio of single-base identification is improved, and the accuracy and stability of base identification are improved.

The present invention relates to a method of profiling covalent DNA modification(s) at a cellular or nuclei level comprising the steps of: providing a sample solution, comprising cell(s) comprising a nucleus comprising genomic DNA; adding a buffer comprising a nucleosome depletion agent to expose the genomic DNA; adding a fusion protein comprising a DNA modification binding domain and a nuclease part; incubating the fusion protein together with the exposed genomic DNA under conditions allowing the fusion protein to bind to the genomic DNA; washing the solution of step (d) with buffer to remove any excess fusion protein; incubating the solution of step (e) under conditions allowing the fusion protein to cut the genomic DNA in proximity of the DNA modification(s); and determining the sequence of the fusion protein incubated DNA of step (e) by high-throughput sequencing, thereby identifying the position(s) of the DNA modification(s) of the genomic DNA that have been sequenced. In other aspects, the invention also relates to a kit for use in performing the method.

Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and / or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA / RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for identification and / or localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA / RNA modifications in parallel.

Provided herein are methods and compositions for use in detecting on-target and / or off-target cleavage of genomic DNA in a cell by a nuclease. The on-target and off-target cleavage is detected by using oligonucleotides that bind to the single-stranded 3′-overhang created at the cleavage site. The nuclease may be an engineered nuclease comprising a nucleic acid binding domain that binds to a target nucleic acid of interest.