55 results about "DNA Modification" patented technology

The invention discloses a nucleic acid nano structure carrier, a nucleic acid nano structure carrier-precious metal photosensitive contrast agent composite comprising the same, and preparation methods and applications of the carrier and the composite. The nucleic acid nano structure is a random two-dimensional and/or three-dimensional nano structure constructed by a DNA paper-folding technology. The precious metal components are used to carry out DNA modification on the surface of the carrier and selected from one or more of gold nano rods, gold nano shells, silver-coated gold nano rods, and gold nano cages. The provided composite is used as a photo-acoustic imaging probe, is capable of guaranteeing the absorption contrast enhancing effect of the photo-acoustic contrast agent which is coupled to the composite, and moreover can prominently improve the targeting performance of the contrast agent on tumors. Furthermore, the precious metal photosensitive components which are coupled to the carrier are enriched in the inner of tumor tissues, and thus the solved is the problems that conventional contrast agent is distributed over the whole human body or the contrast agent can only stay on the tumor surfaces. The preparation method has the advantages of simple technology, low cost, convenience, and easy application.

The present invention provides compounds and methods for attaching fluorescent labels to biological molecules such as nucleotides. The compounds and methods are useful for biological assays including DNA modification reactions.

A method for analyzing the repair of DNA modifications and base mispairings as well as apurinic and apyrimidinic sites by DNA repair enzymes, comprising the following steps: contacting (a) single- or double-stranded DNA molecules which were covalently coupled to a solid-phase matrix carrying primary or secondary amino groups by reaction with a reactive squaric acid derivative, and which have modifications and/or base mispairings and/or apurinic or apyrimidinic sites, with (b) a composition containing DNA repair enzymes; and determining the elimination of the DNA modifications and/or base mispairings and/or apurinic or apyrimidinic sites. The DNA molecules are covalently coupled to the solid state matrix via a primary or secondary amino group incorporated in the DNA molecule at the 5'-end or at the 3'-end of the DNA or in the 2'-position of at least one deoxyribosyl residue.

Provided herein are methods for a novel bead-based next-generation “X-aptamer” selection scheme that extends aptamer technology to include X-modified bases, thus resulting in X-aptamers, at any position along the sequence because the aptamers are chemically synthesized via a split-pool scheme on individual beads. Also provides are application to a wide range of commonly used DNA modifications, including, but not limited to, monothioate and dithioate backbone substitutions. This new class of aptamer allows chemical modifications introduced to any of the bases in the aptamer sequence as well as the phosphate backbones and can be extended to other carbohydrate-based systems.

The invention relates to high-sensitivity uracil DNA glycosylase (UDG) detection using DNA three-direction section activated hybridization chain reaction. UDG is used as a model to develop an identification mechanism of hairpin reconstruction, and action of DNA modification enzyme on substrate is converted into the triggering process of the hybridization chain reaction so as to cause the self-assembling process of DNA and build a universal DNA nano device. The device can be used for the high-sensitivity detection and inhibitor screening of the DNA modification enzyme (especially the UDG), and has potential application value.

The method includes following steps: (1) carrying out surface activation treatment for Nano carbon tube; (2) carrying out chemical modification or DNA modification of surface functional molecule for Nano carbon tube in order to prepare stable and dispersive suspension liquid of Nano carbon tube; (3) fabricating pattern of electrode couple on surface of silicon piece of containing insulating layer through photo etching; (4) dripping suspension liquid of Nano carbon tube onto surface of electrode couple prepared in step (3) to form even distributed liquid layer; (5) applying DC or AC electric field to implement multiple strips of Nano carbon tube to let them connect to between two kinds of electrodes dividually and in parallel; (6) carrying out irradiation treatment for device of field effect transistor (FET) prepared at step (5) through ultraviolet radiation. The invention can control multiple strips of Nano carbon tube to construct channels for FET or to be as leads for electrodes.

The invention discloses novel nanoparticles with core-shell structures. A preparation method comprises the following steps: (1) adding CTAB solution into a container, adding HAuCl4 solution, and then adding NaBH4 solution to obtain seed crystal; adding the CTAB solution into another container, sequentially adding the HAuCl4 solution, silver nitrate solution, L-AA solution and the seed crystal to prepare gold nanorods; (2) carrying out DNA modification on the gold nanorods to obtain gold nanorods stably protected by thiolated DNA; and (3) centrifuging the gold nanorods, dissolving the gold nanorods in the CTAB solution, sequentially adding SDS solution, the silver nitrate solution and the L-AA solution, and standing to obtain the novel nanoparticles with the core-shell structures. The nanoparticles disclosed by the invention are high in stability, thin silver covers the two ends of each core-shell structure, most of each connected DNA single strand is exposed outside, and each tip part has a higher surface plasma effect; and the nanoparticles have a high application value in the fields of bio-optoelectronics, biological nanometer detection and the like.

The invention relates to a single-molecule analysis method for detecting methylated DNA. According to the method, in an electrolytic tank containing a tetramethyl ammonium salt electrolyte or a tetraethyl ammonium salt electrolyte or a tetrapropyl ammonium salt electrolyte or a tetrabutyl ammonium salt electrolyte, a nanopore sensor distinguishes and detects DNA of different methylation levels through current electrochemical signals, wherein DNA of different methylation levels includes un-methylated DNA, mono-methylated DNA and multi-methylated DNA, and the structural forms of DNA include a single-stranded structural form, a double-stranded structural form and a hairpin structural form. According to the single-molecule analysis method for detecting methylated DNA, the quantity of needed samples is small, sensitivity is high, and single-base resolution is achieved; nanopore and DNA modification, DNA amplification and marking are not needed, operation is easy, and high applicability is achieved.

The invention discloses an iodine dissociation type gene cloning method based on sulfo-modifiers. According to the method, phosphodiester bonds between the positions of 1-15, 16, 17, 18, 19 or 20 of the 5' ends of primers of a target gene and a plasmid vector are amplified into the sulfo-modifiers; a base sequence at the positions of 1-15, 16, 17, 18, 19 or 20 of the 5' ends of forward primers of the target gene and the plasmid vector and a base sequence at the positions of 1-15, 16, 17, 18, 19 or 20 of the 5' ends of reverse primers of the target gene and the plasmid vector are matched in a supplementary mode; after the target gene and the plasmid vector are subjected to PCR amplification, a PCR product is purified; iodine selectively breaks the phosphodiester bonds of the sulfo-modifiers, and under the combined action of existence of the sulfo-modifiers at the positions of 1-15, 16, 17, 18, 19 or 20 of the 5' ends and iodine heat treatment, DNA will generate a 3' single-link protruding end where 20 nucleotides grow. Through the method, cloning of the target gene does not rely on restriction endonuclease, DNA ligase or any other DNA modification enzyme, operation flux is large, and the method can be applied to large-scale gene cloning.

A method of site-specific modification of an endogenous target DNA of a eukaryotic cell is provided. The method includes contacting the endogenous target DNA having an intended modification site with (i) a gene editing system configured to introduce a double strand break in the endogenous target DNA at or near the intended modification site, and (ii) a donor DNA repair template comprising a plurality of tandem repeat sequences. In the method, each of the plurality of tandem repeat sequences comprises an exogenous donor DNA sequence flanked by a donor 5′ flanking sequence and a donor 3′ flanking sequence. The donor 5′ flanking sequence and the donor 3′ flanking sequence are homologous to a continuous DNA sequence on either side of the intended modification site in the endogenous target DNA.

The invention belongs to the field of high-throughput sequencing library building, and particularly relates to an epigenetic DAP-seq sequencing library building method. The sequencing library buildingmethod provided by the invention mainly comprises the processes of vector building, TF in-vitro expression pre-experiment, DAP-seq library building and the like. According to the sequencing library building method provided by the invention, the genome DNA extracted from cells can be directly combined with target TF, so that genome DNA modification can be reserved, and compared with the prior art,the sequencing library building method is closer to an in-vivo test.

The present invention relates to application of DNA three-way regulation activation based hybridization chain reaction to high sensitivity detection of DNA methyltransferase. The present invention uses DNA methyltransferase M.SssI as a model to develop an enzyme protection cleavage recognition mechanism, which converts the effect of enzyme on a substrate into a trigger process of a hybridization chain reaction, thereby causing a DNA self-assembly process and achieving construction of a universal DNA nanodevice. The device can be applied to high sensitivity detection of DNA modification enzyme (especially DNA methyltransferase) and inhibitor screening, and has potential application value.

The invention belongs to the technical field of second generation gene sequencing, in particular to a quantitative sequencing method for genome DNA modifications (such as 5-hydroxymethylcytosine (namely 5hmC), 5-methylation cytosine (namely 5mC), 5-carboxyl cytosine (namely 5caC), 5-formoxyl cytosine (namely 5fC) and the like) in a full genome range. Specific sequence tags (namely Barcode) are respectively added to multiple to-be-detected samples by adopting a tag method, and the samples are mixed together for DNA fragment immuno-precipitation) of corresponding modifications, so that quantitative sequencing of the genome DNA modifications in the full genome range is realized. The method comprises the following steps of: extraction of genome DNA, preparation of Barcode samples, DNA fragment immuno-precipitation experiments of the corresponding modifications, polymerase chain reaction (PCR) amplification of specific products, and sequencing on an illumina GA ll platform. The method can be used for quantitatively comparing the DNA of the corresponding modifications in multiple samples at the same time in the full genome range and accurately positioning the content difference of the DNA of different areas and different modifications.

The invention provides a preparation method of high-strength responsive DNA hydrogel with a macroporous structure. According to the preparation method, a polymer monomer and a DNA chain with a modification group at a 5' end are concentrated into a micro-liquid phase around an ice crystal under a freezing condition, and polymerization is conducted under the action of an initiator; i.e., DNA is grafted to a polymer chain through a polymerization reaction between DNA modification groups and a polymer monomer; due to interaction between DNA chains, two or more DNA chains can be connected together,so the DNA serves as a cross-linking unit to connect polymer chains into a polymer network, and the DNA hydrogel is formed; the ice crystal functions as a pore-foaming agent, and after the reaction is finished, temperature is raised, so the ice crystals are melted, and the interconnected macroporous structure is left; and in the process, a freezing polymerization method is introduced into preparation of the DNA hydrogel, the obtained DNA hydrogel is good in mechanical property and high in response speed, and the application field of the DNA hydrogel is widened.

The invention relates to a method for detecting thrombin by virtue of an SERS enhanced controllable chain-shaped assembly, belonging to the field of nano-sensing detection. According to the method, DNA molecules of two aptamers of the thrombin are respectively modified to the surfaces of an Au@ nano-particle and an Ag nano-particle, an alternate-arrayed chain-shaped structure is formed between thetwo nano-particles by controlling the DNA modification amounts of the surfaces of the nano-particles through the combination between assembly molecules and the thrombin when the thrombin exists, anda relatively strong Raman signal enhancement effect is achieved; and when the content of the thrombin is higher, the chain structure is longer, and the Raman signal strength is stronger, and the quantitative determination of the thrombin can be realized according to the corresponding relation between the content of the thrombin and the Raman signal strength. The method is simple in operation and high in sensitivity, and the thrombin in a serum sample can be detected; and by utilizing the nano-structure assembly, an important theoretical foundation is provided for detection of other target objects taking the aptamers as recognition molecules.

The invention relates to a new monomolecular nucleotide microarray chip with high density and distinguishability. A plurality of polymer high molecule containing nucleotide fragment of this chip can randomly fix on a solid base-plate and can form a monomolecular nucleotide microarray with high density, and can make every array point contain one polymer high molecule, in which the said polymer high molecule contains some similar copies of nucleotide fragment. This chip can be assembled to many kinds of chips used for functional genom study, testing order of complete gene of special types, gene transferring and expression efficiency testing, and testing of kinds of genom DNA modification chart(such as DNA methylation chart). This chip will have great value in the fields of molecular mechanism study in human being life process, genom DNA information decoding, individualized medicine, disease predicting and precaution, medicine developing and individuation.

The invention provides a preparation method of a biosensor for ctDNA detection, which comprises the following steps: preparing gold nanoparticles: mixing and heating chloroauric acid and ultrapure water, then adding a sodium citrate solution, continuously conducting heating and reacting, conducting cooling to room temperature after the reaction is finished, conducting filtering to obtain the gold nanoparticles, and conducting preserving at low temperature for later use; and conducting DNA modification: carrying out annealing treatment on DNA, then uniformly mixing the DNA subjected to annealing treatment with the prepared gold nanoparticles, carrying out standing treatment, then adding a sodium citrate solution, then adding a phosphate buffer solution, carrying out standing, finally adding water, and carrying out centrifugal washing, thus obtaining the biosensor for ctDNA detection.