17 results about "Dna interaction" patented technology

The invention discloses a method and a device suitable for CUAMP. The invention discloses a method for extracting liriodendron tulipifera cell nucleuses by a Tag technology and application of the liriodendron tulipifera cell nucleuses. Hybridized liriodendron tulipifera calluses are used as materials, and protoplasts are released through enzymolysis solution vacuumizing and mild enzymolysis for 1.5 h; the method comprises the following steps: sequentially purifying by using a W5 solution and mannitol, detecting the activity by FDA, cracking by using an NE buffer solution, and washing by using a Wash buffer solution in two steps, thereby obtaining 2 * 10 < 6 >-3 * 10 < 6 > high-purity and high-integrity cell nucleuses. The obtained core is clean in background and complete in membrane structure, and can be directly used for CUTamp; tag is used for building a library, so that the magnetic bead capturing efficiency is improved by 46%, and protein-DNA interaction high-throughput sequencing under the condition of low sample size is realized. The method disclosed by the invention is simple and convenient to operate and good in repeatability, and provides key technical support for epigenetic research of rare tree species such as liriodendron tulipifera.

The embodiment of the present application provides a computer prediction method and system for protein-DNA-RNA triplets and their functions, which belongs to the field of biotechnology. The solution obtains target cells from a target cell line; obtains DNA-RNA interaction data of the target cells; obtains protein-DNA interaction data of the target cells; obtains protein-RNA interaction data of the target cells; processes the DNA-RNA interaction data of the target cells to obtain the DNA-RNA interaction score, protein-DNA-RNA interaction score, and protein-DNA-RNA triplet prediction results of the target cells; and obtains functional information of downstream target genes that regulate the interaction of protein-DNA-RNA triplet based on the prediction results. The present invention can explore the functions and effects of DNA, RNA and protein interactions in cells, and provide a new type of interactome data.

This invention relates to RPA compounds or pharmaceutically acceptable salts thereof, and for the use of the compounds to treat cancer.

The present invention discloses a method for capturing chromatin and / or chromosome conformation and reagents used therein, and belongs to the field of three-dimensional genomics. The method comprises: subjecting target cells to in vitro cross-linking, lysis, enzymatic digestion with blunt-end restriction endonucleases to add A bases at the ends, and connecting adjacent DNA ends with BP Linker; after labeling the target protein with a specific antibody, using Tn5 fusion protein to target and enrich DNA interactions mediated by the target protein, using biotin labeling to enrich the target fragments of "DNA-tag-DNA" to obtain adjacent ligated DNA fragments, sequencing and analyzing the adjacent ligated DNA fragments, and determining the adjacent ligated DNA bound to the target protein. Compared with traditional methods, the present invention has the advantages of using conventional experimental equipment and a small number of cells, high efficiency, short cycle, low data signal-to-noise ratio, and low cost.

Nucleic acid molecule libraries comprising 5' and 3' primer recognition sites and a plurality of molecules comprising a target sequence molecule and a plurality of variant sequence molecules are provided. Kits comprising the nucleic acid molecule libraries are also provided as are methods of determining protein association with a nucleotide sequence and identifying an inhibitor of protein-DNA interaction.

The invention provides a tumor-driven IncRNA screening method based on interaction and co-expression characteristics of a three-dimensional genome. The method comprises the following steps: acquiring tumor information containing tumor TAD, expression quantity data, tumor-driven PCG and lncRNA gene information; calculating CDT and RNA-DNA interaction characteristics and co-expression characteristics according to the tumor information; according to the CDT and RNA-DNA interaction characteristics and the co-expression characteristics, identifying the tumor driving lncRNA, and according to the co-expression characteristics, classifying the tumor driving lncRNA; and the tumor driving lncRNA comprises a cancer promoting lncRNA, a cancer inhibiting lncRNA and a dual-effect lncRNA. According to the method, three-dimensional genome interaction and co-expression characteristics are utilized to realize tumor lncRNA recognition directly influencing tumor driven PCG expression, and the recognition efficiency, accuracy and precision are improved.

Bead constructs of sizes in the nanometer to micrometer range with a primary functionalization of a lipid membrane with embedded anchor peptides are provided. The anchor peptides may be adapted for a secondary functionalization of active molecules that are bound to the anchor peptides by transpeptidation or similar process. The functionalized bead platform can be adaptable and used in many different applications including biochemical and cellular assays, molecular diagnostics such as protein-protein interactions, protein-DNA interactions, DNA detection, separations, purifications, imaging, and microfluidics.

A method for sequencing DNA wherein a sample comprising isolated cell nuclei is contacted with an antibody that forms a covalent conjugate with a first DNA adapter, and wherein the formed antibody-DNA conjugate can bind a protein of interest and ligate to an end of a dephosphorylated DNA fragment, and wherein the sample is then contacted with a second DNA adapter that coheres to the first DNA adapter of the antibody-DNA conjugate to obtain a second DNA adapter-first DNA adapter—DNA fragment product that allows for sequencing of an amplified product.

The present invention encompasses an in vitro method for evaluating the ability of a compound to disrupt or stabilize the interaction between one or more baits and one or more candidate preys in eukaryotic cells. In addition, the present invention encompasses compounds for use as medicaments identified by an in vitro method according to any of the preceding claims.

The invention discloses a protein-DNA interaction detection method aiming at whole genome open chromatin and independent of an antibody. The method comprises the steps of cell nucleus preparation, transposase reaction, ampDAP library construction, protein incubation and DNA library construction. The cell nucleus preparation comprises cell activity detection and cell nucleus extraction; the transposase reaction comprises transposon and DNA (Deoxyribose Nucleic Acid) recovery; the construction of the ampDAP library comprises the steps of PCR amplification and product purification; the protein incubation comprises protein in-vitro expression and protein-library incubation; dNA library building comprises PCR (polymerase chain reaction) amplification and product purification. According to the present invention, the protein-DNA interaction detection is achieved, the experiment target can be achieved by only requiring the in-vitro expression of the interested protein during the process, and the one library can simultaneously meet the detection of a plurality of proteins, such that the new idea and the new method are provided for the protein-DNA interaction detection.

A method for sequencing DNA wherein a sample comprising isolated cell nuclei is contacted with an antibody that forms a covalent conjugate with a first DNA adapter, and wherein the formed antibody-DNA conjugate can bind a protein of interest and ligate to an end of a dephosphorylated DNA fragment, and wherein the sample is then contacted with a second DNA adapter that coheres to the first DNA adapter of the antibody-DNA conjugate to obtain a second DNA adapter—first DNA adapter—DNA fragment product that allows for sequencing of an amplified product.

The present invention provides a method for enhancing chromatin interaction information based on RNA-DNA and DNA-DNA interaction information, and relates to the technical field of bioinformatics. The method comprises: collecting iMARGI data of RNA-DNA interaction and original Hi-C data of DNA-DNA interaction; performing feature extraction on the iMARGI data and calculating the Pearson correlation coefficient to obtain a DNA-DNA feature correlation coefficient matrix fused with RNA information; performing FAN completion processing on the original Hi-C data after downsampling to obtain a complete Hi-C matrix; constructing a CNN network model, using the above two parts as input, training the model, and outputting the enhanced Hi-C matrix; for the trained model, inputting data of different RNA types, and predicting the corresponding Hi-C matrix for downstream analysis. The present invention can integrate RNA interaction data and Hi-C data, realize multimodal data integration and analysis, and promote the further development of research on RNA and chromatin interactions.

The invention discloses a visual RNA-DNA (Ribonucleic Acid-Deoxyribose Nucleic Acid) interaction omics analysis and detection method for a trace sample. An F (ab ') 2 fragment is coupled with an oligonucleotide fragment modified by biotin and NH2 to generate F (ab') 2-oligo, the F (ab ') 2-oligo is adapted to single-cell light guide equipment on the market, cells are operated in a microcavity, a buffer solution system is replaced, and temperature control is carried out, so that micro-cell-level visual operation is realized, RNA-DNA interaction in a specific action mode and mediated by specific RNA can be enriched, and the application range of the F (ab') 2-oligo is widened. And a high-quality sequencing library is formed for next sequencing analysis, so that the requirement of researching RNA-DNA interaction heterogeneity of different cell subpopulations is met, and a new technical method is provided for precise medical research and diagnosis and treatment practice of diseases.

The invention discloses a method for detecting chromatin modification and whole genome information based on single molecule sequencing and application of the method. The invention provides a single molecule long read sequencing platform and a sequencing technology capable of researching protein-DNA interaction under single cell resolution, and the method can accurately analyze epigenetic information such as chromatin modification and the like in a single cell. Comprising histone covalent modification and a binding distribution mode of chromatin binding protein in a genome. According to the construction method of the long-read sequencing library and the single-molecule long-read sequencing data obtained by single-molecule sequencing based on the library, the data can be applied to analysis of repetitive sequences of each copy in a genome and chromatin modification of a'blacklist 'region by analyzing the data.

The invention discloses an in-vivo protein-DNA interaction analysis method based on methylated DNA immunoprecipitation, and belongs to the technical field of molecular biology. According to the method, an instantaneous protein binding event is recorded as stable 6mA, MeIP captures interaction which cannot be detected by ChIP, and meanwhile, the sequence background limitation of DamID is avoided. The compatibility with qPCR and sequencing enables the experiment scale to be flexibly adjusted, and the simple implementation of the method enables the method to be very suitable for researching related proteins interacting with chromatin in organisms lacking endogenous DNA methylation. The invention also discloses the transient but critical localization of a kinase at the centromere, and emphasizes the necessity of capturing a dynamic chromatin event for understanding genome regulation. The MeIP technology can be applied to a mammalian cell system, and a powerful tool is provided for researching instantaneous chromatin regulation events in higher eukaryotes.

The present disclosure provides novel compounds of formula (A) or a pharmaceutically acceptable salt, solvate, prodrug or stereoisomer thereof. The compounds may be used as inhibitors of PBX1-DNA interaction and for treatment of disease associated with inhibition of PBX1-DNA interaction.

The invention discloses a PLAG-Tn5 fusion protein as well as a preparation method and application thereof. According to the fusion protein, dominant immunoglobulin binding structural domains of Protein L, Protein A and Protein G are functionally fused with Tn5 transposase, so that IgG antibodies of various genus sources such as mice, rats and rabbits can be efficiently recognized in a broad-spectrum manner, and the problem of existing CUTamp is thoroughly solved; and the problems of poor antibody compatibility, need of using a second antibody, low signal-to-noise ratio and the like caused by insufficient PA / PG-Tn5 affinity in a Tag technology are solved. The invention also provides a low-cost and high-yield preparation method of the fusion protein and a matched preparation process of low-cost and high-efficiency carboxyl nucleic acid purification magnetic beads. The fusion protein and the magnetic beads jointly form the CUTamp which is low in cost, high in efficiency and high in sensitivity. A Tag research system is especially suitable for protein-DNA interaction research of precious low-amount clinical samples such as primary cells and PBMC, and popularization and clinical transformation of the technology are powerfully promoted.