150 results about "DNA-binding protein" patented technology

Disclosed herein are methods for designing DNA binding proteins comprising a plurality of zinc fingers and methods for binding the proteins to target nucleotide sequences in cells.

Chimeric proteins containing composite DNA-binding regions are disclosed together with DNA constructs encoding them, compositions containing them and applications in which they are useful.

This invention provides improved polyamides comprising a positive patch for contacting the phosphate backbone or major groove of a DNA molecule. As such, the improved polyamides are capable of inhibiting the function or binding of a DNA-binding protein to a DNA molecule. The improved polyamide provides for more efficient function of the polyamide.

The present invention is directed to a method for localizing, in chromatin or DNA, the binding loci of a chromatin or DNA binding protein comprising the following steps:a) tethering, directly or indirectly, an enzyme with regulatable activity to said chromatin binding protein,b) transiently activating the regulatable enzymatic activity bound to the targeted chromatin andc) mapping the enzymatically-modified genomic sites introduced by the enzyme into the chromatin.According to an embodiment of the invention, the regulatable enzyme is a regulatable protease. The mapping step may be carried out on specific DNA fragments, or on a chromosome-wide scale or a genome-wide scale.The present invention is also directed to kits for carrying out the methods of the invention.

The invention provides a microarray and methods for producing a protein microarray. The array comprises multiple nucleic acid molecules immobilized on a substrate, each comprising (i) a protein-binding domain and (ii) a nucleic acid sequence encoding a fusion protein comprising a polypeptide of interest and a DNA-binding protein that binds the protein-binding domain, and one or more fusion proteins produced from the multiple nucleic acid molecules. Each fusion protein is immobilized on the substrate via binding to a nucleic acid sequence comprising the protein-binding domain present on the nucleic acid molecule from which the fusion protein is produced or on the substrate. The invention also provides a method of analyzing protein interactions with, for example, other proteins, lipids and drugs.

The invention belongs to microarray chip based DNA binding protein detection technology, and in particular relates to high-sensitivity high-flux DNA binding protein detection technology by a microarray chip. Double-stranded or single-stranded oligonucleotides are fixed on the chip, and a cell crude extract to be screened and the chip are directly incubated; then exonuclease is put into the system for incubation; and finally, a circular probe is added into the system for rolling circle amplification. Specific lattice sequences of the chip capable of combining a target protein can be taken as an extension primer for the rolling circle amplification; and sequences not combined with the protein are digested by the exonuclease, and cannot perform the rolling circle amplification, and finally amplified products and universal fluorescent probes are hybridized. The existence of the DNA binding protein can be detected according to the existence of specific array dot signals on the chip; and the intensity of the lattice fluorescence can quantitatively detect the content of the target protein. The chip can realize the detection of the DNA binding protein with super sensitivity, low cost, high specificity and high flux, and can be widely applied to scientific research and clinical detection and diagnosis.

The invention discloses nearly 474 novel phosphorylation sites identified in signal transduction proteins and pathways underlying human carcinoma, and provides phosphorylation-site specific antibodies and heavy-isotope labeled peptides (AQUA peptides) for the selective detection and quantification of these phosphorylated sites / proteins, as well as methods of using the reagents for such purpose. Among the phosphorylation sites identified are sites occurring in the following protein types: Kinase, Adaptor / Scaffold proteins, Phosphatase, G protein Regulator / Guanine Nucleotide Exchange Factors / GTPase Activating Proteins, Cytoskeleton Proteins, DNA Binding Proteins, Phospholipase, Receptor Proteins, Enzymes, DNA Repair / Replication Proteins, Adhesion Proteins, and Proteases, as well as other protein types.

Some aspects of this disclosure provide a fusion protein comprising a guide nucleotide sequence-programmable DNA binding protein domain (e.g., a nuclease-inactive variant of Cas9 such as dCas9), an optional linker, and a recombinase catalytic domain (e.g., a tyrosine recombinase catalytic domain or a serine recombinase catalytic domain such as a Gin recombinase catalytic domain). This fusion protein can recombine DNA sites containing a minimal recombinase core site flanked by guide RNA-specified sequences. The instant disclosure represents a step toward programmable, scarless genome editing inunmodified cells that is independent of endogenous cellular machinery or cell state.

The present invention relates to a method of identifying a region (one or more) of a genome of a cell to which a protein of interest binds. In the methods described herein, DNA binding protein of a cell is linked (e.g., covalently crosslinked) to genomic DNA of a cell. The genomic DNA to which the DNA binding protein is linked is removed and combined or contacted with DNA comprising a sequence complementary to genomic DNA of the cell under conditions in which hybridization between the identified genomic DNA and the sequence complementary to genomic DNA occurs. Region(s) of hybridization are region(s) of the genome of the cell to which the protein of binds. A method of identifying a set of genes where cell cycle regulator binding correlates with gene expression and of identifying genomic targets of cell cycle transcription activators in living cells is also encompassed.

The invention relates to a characteristic extraction and classification method and device for DNA (Deoxyribo-Nucleic Acid) binding protein sequence information. The method comprises the following steps that: firstly, carrying out theory argumentation, and analyzing and arranging collected data to obtain a reliable dataset with a biological meaning and a statistical meaning; then, extracting effective protein sequence data characteristic parameters from a complex protein three-dimensional structure as a key link which is a way of converting sequence character information into digital characteristic information, designing a reasonable classification algorithm for extracted characteristic data, and screening the characteristics favorable for classification for realizing target classification;and finally, adopting a reasonable and fair evaluation system, including testing methods, checking means, evaluation index selection and the like, for classification performance. By use of the method, requirements on high-flux protein sequencing function annotation can be met, automated DNA binding protein sequence function annotation can be realized, and meanwhile, the characteristics which areput forward can assist biologists in carrying out experimental analysis and research on the DNA binding protein sequence.

A chip for the non-label detection of DNA bindin has the dual-chain oligonucleotide probes designed according to the specific DNA recognizing sequence for the DNA bindin to be detected. The probe A is fixed to the substrate, and a label is introduced to the probe B. The probe B and the solution of the DNA bindin are inculated together and then hybridized with chip. If DNA bindin exists, the probes A and B have very high binding efficiency and the label of probe B can be detected at the position of probe A.

The present invention discloses high-temperature-resistant Pyrolobus polymerase and efficient expression plasmid and application thereof. The Pyrolobus polymerase is YP_004780419.1 protein, and Sso7dDNA binding protein connected through a linker sequence GGSG exits at the carbon end of the Pyrolobus polymerase, wherein the sequence of the Pyrolobus polymerase is shown as Sequence 1 in the sequence table. The present invention improves the efficiency of polymerase by connecting DNA binding protein to the end of the polymerase, and synthetizes and recombines Pyrolobus polymerase with DNA modified through in vitro synthesis suitable to express in colibacillus. The enzyme has the same polymerase activity as products in the markets, and can synthetize large segments of DNA more effectively. In addition, the Pyrolobus polymerase has strong high-temperature resistance, and is still active even after being processed for 5h at 98 DEG C. The enzyme will be widely applied to the fields of DNA synthesis, sequencing, labeled probe synthesis and the like.

The invention belongs to the field of bioscience, and particularly relates to transmembrane Dps (starvation-induced DNA binding protein) and an application. By means of rational design of a protein nanocage derived from prokaryotes, the protein nanocage is enabled to be an antioxidant protein nanomaterial which can be applied to mammalian cells. The protein nanomaterial is characterized in that transportation across mammalian cell membranes of Dps is realized by fused expression of His-tag and Avitag (LNDIFEAQKIEWHE) at the N-terminal of Dps; the cells can be protected from being damaged by ROS (Reactive Oxygen Species); meanwhile, the protein nanomaterial is good in biocompatibility, simple to design, easy to prepare, high in yield and suitable for large-scale production.

Methods for delivering non-mitochondrial proteins to mitochondria are provided. Also provided are nucleic acid constructs comprising a coding sequence encoding a DNA-binding polypeptide, fused to a mitochondrial targeting sequence (MTS) and a nuclear export signal (NES), and the encoded proteins. The construct successfully delivers DNA binding proteins to the mitochondrion. A chimeric methylase based on the above construct is successfully delivered to mitochondria, resulting in modification of mtDNA.

The invention discloses a method for detecting DNA (deoxyribonucleic acid) binding protein. The method comprises the following steps: providing a sample solution of the DNA binding protein to be detected, and carrying out digestion reaction under the condition that Exo III exists, thus obtaining a digestive juice after complete reaction; adding the digestive juice in an amplification system, carrying out isothermal amplification reaction under the condition that a polymerase, an incision enzyme and an amplification template exist to obtain an amplification solution; mixing a gold nanoparticle solution with a solution containing a first detection probe and a second detection probe and then carrying out incubation to obtain a nano gold detection probe solution; mixing the amplification solution with the nano gold detection probe solution and then detecting a mixed solution to complete the detection for the DNA binding protein. The first detection probe and the second detection probe are combined with a target DNA in an amplification product so that gold nanoparticles of the detection probes gather to cause that the color of the mixed solution changes, thus the method is visual in phenomenon and high in sensitivity.