46 results about "Dna interaction" patented technology

System and methods for detection and measurement of interactions in microarrays or within a human body are described. The system includes a CMOS sensor which can be placed in a fluidic environment, and is capable of measuring DNA interactions and protein binding kinetics, as well as cellular interactions and signals within the body. The sensor can be placed in close proximity with the sample and eliminates the need for optics, and in some embodiments is a wireless device.

The invention belongs to a method of preparing deoxyribonucleic acid (DNA) electrochemical nano sensor. It fixes the nano gold crystal on the surface of the gold electrode, uses the property that nano gold crystal and mercapto functional group containing DNA can interact to fix sequence- known target single-string DNA (ssDNA) on the surface of the gold electrode. The nano silver crystal labeled compensatory DNA and the target ssDNA make cross reaction. In an acidic medium, oxidize and release the nano silver crystal to make the nano silver crystal exist in the solution in an ion state. It detects the quantity of silver ions by electrochemical method, thus detecting that of the target DNA. The sensor has very strong selectivity and very high sensitivity.

The invention belongs to the field of pharmaceutical chemistry, and particularly discloses 7-fluoro-substituted Isaindigotone derivatives. The structural formula of the derivatives is disclosed as Formula (I) or Formula (II), wherein X is C or N; R1 is hydrogen, amino, substituted amino, orpenta- or hexa-heterocyclic radical; R2 is hydrogen, hydroxy, amino, C1-C8 alkyl, or C1-C8 alkoxy or halo; R3, R5 and R6 are defined the same as R2; and R4 is hydrogen, hydroxy, amino, phenyl, C1-C8 cycloalkyl, C1-C8 alkyl, C1-C8 alkoxy, C1-C6 alkyl acyloxy, C1-C6 alkynyl, halo, or penta- or hexa-heterocyclic radical. The fluoro-substituted Isaindigotone derivatives can bebondedwith NM23-H2 protein and block the interaction between the NM23-H2 protein and c-myc G-quadruplex DNA, thereby causing the reduction of protooncogene c-myc transcription and translation, and inhibiting the proliferation of multiple tumor cell strains. The fluoro-substituted Isaindigotone derivatives have wide antitumor effects. The fluoro-substituted Isaindigotone derivatives are a novel NM23-H2-protein-targeted transcription regulation blocker, and have wide application space in preparing anticancer drugs.

Provided is a method for specifically isolating any genomic region while maintaining interaction of the genomic region with its interacting molecule(s). According to the method comprising the following steps 1 to 5:

Step 1:

• • preparing a cell in which a DNA fragment having a recognition sequence(s) for an exogenous DNA-binding molecule is inserted in genomic DNA of a genomic region to be isolated;

Step 2:

bringing genomic DNA of the cell into contact with an exogenous molecule at least having a DNA-binding domain of the exogenous DNA-binding molecule;

Step 3:

performing a treatment for maintaining interaction of the genomic DNA of the cell with a molecule(s) interacting with the genomic DNA;

Step 4:

performing a treatment for fragmenting the genomic DNA; and

Step 5:

allowing a complex to be formed by binding of a molecule capable of specifically binding to the exogenous molecule, and then collecting the complex,

specific genomic regions can be specifically isolated while kept interacting with their interacting molecules.

The present invention provides a method for globally mapping a genome for its protein-binding pattern. A computer system useful for this purpose is also described.

The invention provides a targeting transposon complex with an oligonucleotide tag and application of the targeting transposon complex to research of interaction of multiple-target molecule-DNA.

The invention relates to a method for determining a transcriptional control complex, and belongs to the field of molecular biology. The method for determining the transcriptional control complex includes the following steps: preparation of a bait DNA sequence, preparation of a DNA sequence for encoding a bar code protein, construction of a bar code protein library, screening of the transcriptional control complex, and in situ adjacent connection capture of the transcriptional control complex, and the identification of the transcriptional control complex. The invention combines cDNA display technology and the adjacent connection technology to establish a novel method for determining the transcriptional control complex; the determination of transcriptional control complex involves simultaneous determination of a variety of interaction effects of protein-protein and protein-DNA; and the method can realize simultaneous determination of a variety of interaction effects of protein-protein and protein-DNA in a same experimental system, and effectively solve the incompatibility of the determination methods for the protein-protein interaction and protein-DNA interaction in the same experimental system in the prior art.

The invention provides a screening assay for selecting inhibitors of NFAT:Transcription factor interactions. The invention also provides compositions and methods for inhibiting immune response in a subject.

The method for testing of substances for hormonal effects, especially for androgenic or anti-androgenic effects, includes exposing cells transfected with two vectors to the substances, wherein one vector contains a DNA, which codes for a nuclear receptor protein, or a fragment thereof, especially a human nuclear receptor protein, or a fragment thereof, and the other vector contains a DNA, which codes for the HSRNAAM co-modulator, or a fragment thereof; and measuring transcription activity, which the nuclear receptor protein, or its fragment, activates or releases in the presence of the HSRNAAM co-modulator, or its fragment, and/or measuring the influence of the substance on the interaction between the nuclear receptor protein, or its fragment, and the HSRNAAM co-modulator, or its fragment, by protein-protein interaction or by protein-protein-DNA interaction. Also a method for determining interference in the co-modulation mechanism between androgen receptor protein and HSRNAAM co-modulator is described.

According to particular exemplary aspects, DNA target site binding and cleavage properties of native, variant or modified homing endonucleases (HE) (e.g., LAGLIDAG (LHE), HNH, His-Cys Box, GIY-YIG, I-SspI-type, and fusions, muteins or variants thereof) in solution are recapitulated on the cell surface (e.g., as assessed by flow cytometric analysis) to provide for novel cells expressing one or more cell surface HEs (e.g., expressing one or more HE binding and/or cleavage specificities), novel cell libraries, and high-throughput methods for assessing target site binding, target site cleavage. The rapid analysis of HE and LHE-DNA interactions on the cell surface with concurrent sorting options provides for high-throughput library screening affording rapid identification, analysis and isolation of novel HEs or LHEs having novel sequence specificities. Such novel sequence specificities, obtained by said methods provide novel methods for introducing targeted DNA-strand cleavage events, and novel chromatin immunoprecipitation methods (CHIP methods).

The invention discloses a kit for detecting the interaction between proteins and DNA, wherein the kit at least includes an exogenous histone antigen. The invention also discloses an application of thekit in detecting the interaction between a small number of proteins and the DNA, and the required sample amount can be as low as 1000 cells. The invention also discloses a method for detecting the interaction between the proteins and the DNA and an application thereof. According to the technical scheme provided by the invention, sample loss is reduced and the efficiency of immunoprecipitation reaction is improved by additionally adding a corresponding antigen of histone requiring to be researched and interacting with DNA into a small number of initial samples. The kit has the following advantages: 1, the minimum required sample number is 1000 cells, and the kit is more suitable for detection and analysis of the interaction of a small number of proteins and DNA from the samples; and 2, a ChIP experiment does not require specific kits and experimental equipment, the cost is low, and the kit has high universal applicability.

Targeting uncontrolled cell proliferation and resistance to DNA damaging chemotherapeutics with at least one reagent has significant potential in cancer treatment. Replication Protein A, the eukaryotic single-strand (ss) DNA binding protein, is essential for genomic maintenance and stability via roles in both DNA replication and repair. Reported herein are small molecules that inhibit the in vitro, in vivo, and cellular ssDNA binding activity of RPA, thereby disrupting the eukaryotic cell cycle, inducing cytotoxicity and increasing the efficacy of chemotherapeutic agents damage DNA, and/or disrupt its replication and/or function. These results provide new insights into the mechanism of RPA-ssDNA interactions in chromosome maintenance and stability. This represents a molecularly targeted eukaryotic DNA binding inhibitor and demonstrates the utility of targeting a protein-DNA interaction as a means of studying the cell cycle and providing a therapeutic strategy for cancer treatment.

A method for screening the effect of a segment A (chemical species A) on a substance (for example, a cell) containing DNA or RNA by using artificial chemical species. Namely, a method of detecting or identifying the function of a chemical species A on a substance containing DNA or RNA by using one or more chemical species represented by the following general formula (I) which are capable of recognizing a DNA base sequence; a kit therefor; and a plate to be used therein: B-L-A (I) wherein B represents a chemical structure containing an non-natural base capable of recognizing a DNA base sequence; A represents a chemical structure having an interaction with DNA; and L represents a linker whereby the chemical structures A and B can be linked together.

The invention discloses a fluorescent sensor formed on the basis of DNA combining terbium ion, and an application thereof for distinguishing and detecting metal ions, wherein distinguish and detectionon large-scale metal ions are achieved by means of a time resolution fluorescent method. A method includes the steps of: screening three single-chain DNAs, which are rich in guanine (G) and thymine (T) and are in different lengths, as ligands, and forming the fluorescent sensor (DNA/Tb) by sensitizing the terbium through an antenna effect; then dissolving the DNA/Tb in a buffer solution and adding 49 metal ions, comprising alkali metal ions, alkaline-earth metal ions, transition/late-transition metal ions, and rare earth metal ions, wherein the antenna effect is influenced due to interactionbetween the metal ions and DNA, so that the DNA/Tb can acquire different time resolution fluorescent signals and fluorescent service life under different metal ion conditions; finally performing principal component analysis (PCA) to analyze the fluorescent signals and fluorescent service life to achieve the distinguish and detection on metal ions. The method also achieves semi-quantitative detection on metal in river water.

The invention belongs to the technical field of protein engineering, and specifically relates to an optimum design method of a structure-based CRISPR protein. The optimum design method comprises the following steps: carrying out analysis and comparison based on an analyzed CRISPR protein structure, so as to find out an amino acid site greatly influencing a certain function of Cas9; and optimizinga Protein-DNA interaction interface of the Cas9 through combination with Rosetta, finally carrying out designing to successfully obtain a novel mutant yCas9. The mutant has shearing activities equal to xCas9: the mutant has a wide PAM recognition range, is capable of recognizing NGG, NGA, NGT, NGC, GAA and GAT and is low in missing rate during gene editing. Therefore, the yCas9 functionally keepspace with the xCas9 and is a gene editing tool with a potential application value, thereby proving the validity and practicability of the design method.

The invention discloses a method for predicting protein-RNA interaction sites. Multiple kinds of characteristic data of a protein-RNA compound are combined for forming a complicated multidimensional characteristic set. Then an effective characteristic with high weight is selected through a characteristic selecting algorithm. Finally a protein-RNA interaction site is predicted through a machine learning algorithm. Compared with the prior art, the method is advantageous in that more and more effective characteristics are fused; a more advanced algorithm is used; the more effective characteristics are selected; and besides consideration of prediction of the protein-RNA interaction sites which are proved by experiments, more data can be integrated, such as protein-DNA interaction sides. According to the method of the invention, through fusing more effective algorithm and more characteristic data, the protein-RNA interaction sites can be more accurately predicted than previous technology. Furthermore multiple pairs of protein-RNA interaction sites can be predicted in one time in a large scale manner, thereby effectively settling problems of blindness and high cost of a biological experiment method.

In accordance with one or more embodiments, the present invention provides a compound of formulas I, II, and III, for use in methods of inhibition of PBX1-DNA interaction in a mammalian cell or population of cells, and for use in the treatment of medical conditions including but not limited to cancers, developmental disorders, inflammatory disorders, autoimmune diseases, or neuro-degenerative disorders.

The invention discloses a method for detecting saxitoxin on the basis of embedded dye and DNA interaction. The method comprises the following specific steps: dissolving DNA in a buffer solution at first, then adding the saxitoxin in the buffer solution, carrying out interaction on the saxitoxin and DNA for 25-35 minutes, when interaction time is up, adding the embedded dye in the buffer solution, waiting for 25-35 minutes, then carrying out fluorescence spectrometry, and calculating the concentration of the saxitoxin through the peak value of the measured spectrum according to a standard curve. The concentration of the saxitoxin can be measured quantitatively through measurement to fluorescent light, complicated instruments and construction of a detecting platform are not required, the detection mode is simple, rapid and accurate, therefore, the technological difficulty that traditional measurement depends on complicated and high-cost instruments is avoided, and complexity on fixing of DNA and construction of the detecting platform is avoided.

Methods of screening for compounds which are, for example, capable of modulating amino acid-DNA interaction, modulating DNA replication, modulating cell proliferation, and for identifying compounds which inhibit cellular proliferation caused by cancer, are provided.

Fluorescent dyes with affinity for nucleic acids and related methods are provided. Dielectric or semiconducting films including fluorescent dyes with affinity for nucleic acids and related methods are also provided. Coumarin-based surfactants conjugated to the fluorescent dyes with affinity for nucleic acids and related methods are provided. Fluorescent compounds capable of interacting with DNA can be used for a variety of applications.

The invention discloses a method for separating a specific protein-DNA (Deoxyribose Nucleic Acid) complex in a living body, a fusion protein and a preparation method thereof, and relates to the technical field of bioengineering. The key point of the invention is that a nano antibody of a tag binds the same tag in a target protein, micrococcus nuclease is brought to a binding site between the target protein and chromatin, and the chromatin is cleaved through activation of nuclease, so that the protein-DNA complex is released, and DNA can be sequenced after the protein is digested, so as to determine the binding site. The method can be applied to research of protein-DNA interaction, when studying the protein specific binding DNA sequence, an antigen-specific antibody does not need to be additionally provided, the steps are simple, and a new technical means is provided for searching for the in-vivo chromatin binding sequence of different proteins containing the same tag.