47 results about "DNA-binding protein" patented technology

Provided are variant Cas12f4 polypeptides, fusion proteins containing variant Cas12f4 polypeptides, nucleic acids encoding variant Cas12f4 polypeptides and fusion proteins, compositions and methods related to those variant Cas12f4 polypeptides and fusion proteins, and modified host cells comprising the variant Cas12f4 polypeptides and / or encoding nucleic acids. The variant Cas12f4 polypeptides disclosed herein exhibit improved functionality, stability, and / or other desirable properties and may be used in combination with guide Cas12f4 RNAs that can be used in a variety of applications ex vivo, in vitro, and in vivo.

The invention discloses a high-flux and rapid chromatin immunoprecipitation sequencing method based on a HiBiT tag and a Tn5 enzyme, and belongs to the technical field of biology. According to the method, the high affinity characteristic of a HiBiT tag system is combined with a Tn5 enzyme in-situ library building technology, firstly, a DNA binding protein recombinant expression strain containing a HiBiT tag is constructed and subjected to induced expression, after formaldehyde crosslinking and cell lysis, an Anti-HiBiT antibody is used for rapid immunoprecipitation, and a Tn5 enzyme library is constructed; tn5 transposase is directly loaded on the magnetic beads combined with the protein and DNA fragment compound to complete fragmentation and linker connection, so that the construction of a next-generation sequencing library is quickly carried out, and the total consumed time from immunoprecipitation to the completion of library construction is less than or equal to 5 hours. Meanwhile, automatic treatment is realized through a micro experiment board (the reaction system is less than or equal to 200 microliters) and a liquid workstation, the experiment cost and the sample dosage are reduced, 48 transcription factors and 48 control samples can be synchronously treated, the efficiency is greatly improved, and an efficient tool is provided for microbial transcription regulation and control research.

The present disclosure relates to enzymes, compositions and methods for performing conditional homologous recombination of a targeted DNA molecule or genome by using modified proteins comprising nucleic acid DNA binding proteins with protease-conditional recombinase (hereinafter “ProRec”) activity. Namely a new cre recombinase pro enzyme, compositions / kit and sensors comprising the cre recombinase pro enzyme of the present disclosure. Namely, a cre recombinase pro-enzyme, for identifying and quantifying proteolytic activity in a disease or an infection, comprising intein mediated circularization, a flip-excision cassette comprising an output reporter and / or effector protein; a linker sequence cleavable by a protease.

Described herein are engineered proteins and methods of use of such proteins. Also described herein are complexes, compositions, and systems comprising the engineered proteins of the invention, each of the complexes, compositions, and systems can be used to modify and / or edit a target nucleic acid. The engineered proteins of the invention may be enzymes, and / or may be RNA-guided DNA binding proteins.

The invention discloses an HAPP gene and application thereof, and relates to the field of plant genetic engineering, the identified rice HAPP gene can increase the rice plant height and the seed size at the same time, and after the rice HAPP gene is fused with a PANDA gene, the rice plant height and the seed size can be remarkably increased, but the ear number is reduced. Meanwhile, analysis finds that HAPP originates from a Harbinger transposon Myb-like DNA binding protein, interacts with PANDA and is related to a gene expression mode, but has antagonism in function. Therefore, identification of the HAPP gene not only reveals a new function of the transposon-derived gene in regulation and control of rice yield traits, but also provides new theoretical support and practical guidance for rice breeding.

Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and / or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.

The present invention relates to compounds which are suitable for imaging TDP-43 (Transactive response (TAR) DNA binding protein 43 kDa) aggregates. The compounds can be used, for example, for diagnosing a disease, disorder or abnormality associated with TDP-43 aggregates or a TDP-43 proteinopathy, such as amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), Frontotemporal dementia (FTD) and limbic-predominant age-related TDP-43 encephalopathy (LATE).

The present invention belongs to the field of biotechnology. In particular, the present invention relates to a method for detecting chromatin accessibility or DNA binding protein footprint in cells based on a two-enzyme method. More specifically, the present invention relates to a method for converting information on the openness of chromatin into information on mutations in DNA sequences by means of adenine methyltransferase and adenine deaminase, thereby quantitatively determining the chromatin accessibility of DNA molecules and the binding footprint of DNA binding proteins, such as transcription factors.

Provided herein are techniques relating to the identification of binding sites of DNA binding proteins, and in particular, but not exclusively, to methods, systems and kits for simultaneous mapping of binding sites of multiple proteins in the same cell using affinity reagent specific barcodes.

The present disclosure relates to cell penetrating anti-DNA binding proteins. Compositions comprising these binding proteins may be may be useful for delivering agents to cells and treating diseases such as cancer.

The present invention relates to a base editing system having the activity of correcting (A-to-G) a G11778A mutation in the mitochondrial DNA of LHON patients. Preferably, the base editing system of the present invention uses a base editor comprising a programmable DNA binding protein, a cytosine deaminase, and an adenine deaminase, or a nucleic acid encoding these proteins, wherein the cytosine deaminase is a double-stranded DNA-specific cytosine deaminase derived from Ruminococcus.

A kind of PLS DNA polymerase constructed by DNA polymerase-DNA binding protein and its application in DNA information storage belong to the technical field of biochemistry and molecular biology.The present application connects Sso7d DNA binding protein to the C-terminal of 9°N DNA polymerase by flexible short peptide to construct fusion protein PLS DNA polymerase.The codon-optimized PLS DNA polymerase gene is chemically synthesized, and high-purity PLS DNA polymerase is prepared by purification;the enzymatic properties of the PLS DNA polymerase and its application effects in in vitro DNA information storage addressing and in vivo DNA information storage assembling DNA active block are systematically evaluated.The results show that after fusing DNA binding protein, the performance of PLS DNA polymerase such as continuous synthesis ability, fidelity and PCR efficiency is significantly improved, and specific files can be recovered from mixed file pool to realize random addressing.

The present invention is in the field of trans-activation responsive DNA binding proteins (TARDB or also referred to as TDP-43) having a molecular weight of 43 kDa. The present invention relates to TDP-43 specific binding molecules, in particular to anti-TDP-43 antibodies or antigen binding fragments or derivatives thereof, and uses thereof. The present invention provides means and methods for diagnosing, preventing, ameliorating, and / or treating diseases, disorders, and / or abnormalities associated with TDP-43 aggregates, including, but not limited to, frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD), chronic traumatic encephalopathy (CTE), and edge dominant age-related TDP-43 encephalopathy (LATE).

We described herein are click edits, which are a series of genome editing methods that combine DNA nicking enzymes, including but not limited to RNA programmable CRISPR nicking enzymes, with DNA ligases or DNA polymerases to perform many different genome edits. Edits of interest are encoded on nucleic acid templates or substrates (optionally'click nucleic acids' (clkNA) or'click DNA '(clkDNA) as described herein) that can be provided in trans form or recruited preferentially to a target site via a variety of nucleic acid telomere methods (optionally HUH family endonucleases (HUHe), telomere binding proteins (TBP), or DNA binding proteins or RNA binding proteins).

The invention belongs to the technical field of biological medicine, a novel gene editing system is successfully created through humanized application of a sequence-specific double-chain DNA binding protein (DDB) from microorganisms, a homologous repair template is collected at a DNA double-chain breakage position in a high-specificity manner through the DDB, the precise gene editing efficiency is greatly improved, and the gene editing efficiency is greatly improved. The efficiency short plate of a traditional gene editing tool is broken through, the spCas9-mediated eukaryotic genome precise editing efficiency is remarkably improved, and a new tool is provided for development of gene therapy and cell therapy.

The present invention is in the field of transactive response DNA binding protein with a molecular weight of 43 kDa (TARDB or also TDP-43). The invention relates to TDP-43 specific binding molecules, in particular to anti-TDP-43 antibodies or antigen-binding fragments or a derivative thereof, vectors delivering nucleic acid encoding antibodies of the invention, and uses thereof. The present invention provides means and methods to diagnose, prevent, alleviate and / or treat a disease, disorder and / or abnormality associated with TDP-43 aggregates including but not limited to Frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD), Chronic Traumatic Encephalopathy (CTE), and limbic-predominant age-related TDP-43 encephalopathy (LATE).

Compositions and methods for single reaction and multiplexed profiling of histone modifications. Compositions include a binding domain and adaptor or a nucleosome binding conjugate comprising a binding domain conjugated to an adapter. Methods include analyzing a plurality of nucleosomes comprising (i) contacting a plurality of substrates comprising a binding domain and adaptor composition with a solution comprising the plurality of nucleosomes, wherein a nucleosome comprising a histone modification or DNA binding protein binds to the binding domain; (ii) ligating an adapter with the nucleic acid barcode to the target DNA of the nucleosome comprising the histone modification or DNA binding protein; (iii) introducing universal sequences for amplifying the target DNA; (iv) amplifying the barcoded target DNA; and (v) analyzing the amplified barcoded target DNA by sequencing.

The present invention relates to a base editing method for plant DNA, the method comprising a step of expressing a base editing composition in a target plant, plant cell or protoplast, the base editing composition comprising one or more DNA binding proteins and one or more zymoproteins, or comprising a polynucleotide encoding said proteins. The invention is used for editing bases in nuclear DNA or organelle DNA of plants, especially for editing bases in organelle DNA of plants such as chloroplast or mitochondria. The base editing composition can be used for realizing targeted editing from adenine (A) base to guanine (G), targeted editing from cytosine (C) base to thymine (T) base or a method for realizing the two editing methods at the same time in plant DNA (Deoxyribose Nucleic Acid). In addition, the present invention relates to a plant cell, plant or seed implementing such base editing.

The present application relates to the technical field of biological detection, in particular to a one-tube pathogen detection method based on PAM-Disruptor regulated CRISPR-Cas12a system, the detection method comprising: constructing a PAM regulated CRISPR-Cas system; mixing and incubating PAM-Disruptor with LbCas12a effector protein, guide RNA, fluorescent reporter, F-primer, R-primer, recombinase, single-stranded DNA binding protein (SSB), DNA polymerase and reaction buffer solution to prepare a premixed reaction solution, and then performing reaction and judgment. The present application realizes light control and non-light control dual-mode one-tube detection, effectively avoids the problems of complicated operation, cross contamination, aerosol pollution and the like caused by step-by-step reaction, and provides a new strategy for one-tube detection of pathogens.

The invention discloses a method and a system for identifying DNA (Deoxyribose Nucleic Acid) binding protein. The method comprises the following steps: acquiring a DBPs data set, wherein the DBPs data set comprises a positive sample and a negative sample; dividing the DBPs data set into a training set and an independent test set; a CNNCaps-DBP model is constructed, and the training process comprises the steps that protein sequences in a training set are input into an ESM C module to be used for coding the protein sequences and extracting sequence features, and the protein sequence features are obtained; inputting the protein sequence features into two attention enhancement convolution modules connected in sequence for capturing local and global information of the protein sequence to obtain high-dimensional features; inputting the high-dimensional features into a capsule network, capturing the mutual relation between the high-dimensional features through the capsule network, and inputting the output of the capsule network into a multi-layer perceptron to obtain a prediction result; and evaluating the model. According to the method, DBPs prediction with high speed, low cost and high accuracy can be realized.

Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and / or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.

The application discloses a method for efficiently detecting the distribution and abundance of DNA binding proteins at the whole genome level of fungi. The application provides a method for detecting the distribution and abundance of target proteins in the whole genome of a test organism, characterized in that the organism is fungi, and the target protein is a DNA binding protein in the test fungi; the method for detecting the distribution and abundance of target proteins in the whole genome of a test organism provided by the application is fungal CUT&Tag; compared with traditional CUT&Tag, the difference of the fungal CUT&Tag lies in that the following step is added before adsorbing the cell nucleus: taking fungal hyphae, performing formaldehyde cross-linking, and then preparing protoplasts; the following step is added between fragmentation and library amplification: removing formaldehyde cross-linking. The application first realizes the application of the CUT&Tag technology to the detection of the distribution and abundance of DNA binding proteins of filamentous fungi at the genome level, and provides an important means for the research on fungal DNA binding proteins.

The present invention relates to the field of medical imaging technology, and in particular to an in vivo base editing system using magnetic navigation, comprising: a magnetic navigation module, used to provide a magnetic navigation electromagnetic selection field and a magnetic navigation electromagnetic excitation field for an experimental subject; a receiving signal acquisition module, arranged on the magnetic navigation module, used to receive a magnetic induction signal of the experimental subject in the magnetic navigation module; an in vivo gene editing module, using pcDNA3.1 as a plasmid vector, DNA binding protein Cas9 and cytidine deaminase or IS621mRNA as a base editor, wherein the base editor is used to realize gene expression including a dTtomato sequence, an EPG sequence and an hAPOBE3A sequence; and a control module, which controls the magnetic navigation module and the receiving signal acquisition module through an FPGA board and a PC.

The present disclosure provides a novel prime editer guide RNA for prime editing, a construct for prime editing, and a method of using the same. Additionally, the present disclosure provides a composition and a method for performing prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of nucleotide changes and / or targeted mutagenic agents (e.g., insertions or deletions). Nucleotide changes may include single-nucleotide changes (e.g., any transition or any conversion), the insertion of one or more nucleotides, or the deletion of one or more nucleotides. More particularly, the present disclosure provides a fusion protein comprising a nucleic acid programmable DNA binding protein (napDNAbp) and a polymerase (e.g., a reverse transcriptase) that is guided to a specific DNA sequence by a prime editer RNA (PEgRNA). Prime editer guide RNA comprises an extension arm that provides a DNA synthesis template sequence encoding a single-stranded DNA flap that is homologous to the endogenous DNA sequence but contains one or more desired nucleotide changes and is incorporated into a target DNA molecule after synthesis by a polymerase (e.g., reverse transcriptionase).

The present disclosure provides compositions and methods for prime editing of target DNA molecules (e.g., genomes) that enables incorporation of nucleotide changes and / or targeted mutagenesis. Nucleotide changes can include single nucleotide changes (e.g., any transition or any transversion), one or more nucleotide insertions, or one or more nucleotide deletions. More specifically, the present disclosure provides fusion proteins comprising a nucleic acid programmable DNA binding protein (napDNAbp) and a polymerase (e.g., a reverse transcriptase) that are guided to a specific DNA sequence by a modified guide RNA (termed a PEgRNA). The PEgRNA (relative to a standard guide RNA) has been altered to comprise an extension portion that provides a DNA synthesis template sequence encoding a single-stranded DNA flap that is homologous to a strand of the targeted endogenous DNA sequence to be edited but comprises a desired nucleotide change(s) and is incorporated into the target DNA molecule after synthesis by a polymerase (e.g., a reverse transcriptase). Also disclosed herein are various methods of utilizing prime editing, including treating trinucleotide repeat contraction diseases, installing targeted peptide tags, treating prion diseases by installing protective mutations, manipulating RNA coding genes to install RNA tags for controlling RNA function and expression, using prime editing to construct complex gene libraries, using prime editing to insert immunogenic epitopes into proteins, using prime editing to insert inducible dimerization domains into protein targets, and delivery methods, among others.

The present disclosure discloses a base editor and the use thereof. The present disclosure provides a nucleic acid base editor, specifically a base editor which is not based on CRISPR technology. The base editor comprises a sequence-specific DNA binding protein, a nickase, an exonuclease and a base-specific deaminase. This base editor is single-strand-specific, and as compared with conventional base editors, the base editor of the present disclosure has wide applicability in cells and is capable of functioning in the nucleus as well as in mitochondrial DNA and / or chloroplast DNA. This base editor has the characteristics of achieving base editing products with high purity and resulting in few indel byproducts while realizing efficient base editing, which is conducive to being used as an efficient and safe gene editing tool.

This disclosure relates generally to proteinaceous molecules that bind to pathological transactive response DNA binding protein of 43 kDa (TDP-43), such as a TDP-43 aggregate, and their use for determining the presence of pathological TDP-43 in the brain of a subject. More particularly, this disclosure relates to proteinaceous molecules and conjugates comprising such proteinaceous molecules and a labelling moiety that bind to pathological TDP-43 and their use for determining if a subject has a neurodegenerative disease associated with TDP-43 pathology and, optionally, further treating said subject for the neurodegenerative disease.

Provided herein are guide nucleic acid-guided DNA binding proteins and derivatives and uses thereof and methods of using the same.

The present disclosure provides methods and compositions for modulating expression of a target gene in a cell by reducing binding of an endogenous transcription factor to a regulatory sequence of the target gene. The method includes introducing into the cell a DNA binding polypeptide (DBF) that binds a sequence in regulatory region of a target gene bound by a transcription factor (TF), thereby displacing the TF and modulating expression of the target gene. The DBF may be designed to bind a sequence comprising the binding site for the TF and additional nucleotides present on one or both sides of the sequence. Accordingly, the DBF specifically binds to binding site for the TF in the target gene but not in other genes that are also regulated by binding of the TF but do not include the nucleotides present on one or both sides of the sequence.