91 results about "DNA-binding protein" patented technology

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. The disclosure provides fusion proteins of nucleic acid programmable DNA binding proteins (napDNAbp), e.g., Cas9 or variants thereof, and nucleic acid editing proteins such as cytidine deaminase domains (e.g., novel cytidine deaminases generated by ancestral sequence reconstruction), and adenosine deaminases that deaminate adenine in DNA. Aspects of the disclosure relate to fusion proteins (e.g., base editors) that have improved expression and / or localize efficiently to the nucleus. In some embodiments, base editors are codon optimized for expression in mammalian cells. In some embodiments, base editors include multiple nuclear localization sequences (e.g., bipartite NLSs), e.g., at least two NLSs. In some embodiments, methods for targeted nucleic acid editing are provided.

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.

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 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 humanized TDP-43 specific binding molecules, in particular to humanized anti-TDP-43 antibodies or antigen-binding fragment or a derivative thereof 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 using programmable DNA binding proteins to increase the efficiency and / or specificity of targeted genome modification or to facilitate the detection of specific genomic loci in eukaryotic cells.

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 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.

The invention relates to a method for inducing pichia pastoris to express human alpha-lactalbumin by using ethanol, and belongs to the technical field of genetic engineering. Recombinant pichia pastoris using ethanol as an inducer for heterologous expression of human alpha-lactalbumin is constructed, three different expression vectors are used in the construction process, the first expression vector uses an ethanol inducible promoter to express fusion polypeptide of DNA binding protein and a transcription activator, and the second expression vector uses an ethanol inducible promoter to express fusion polypeptide of human alpha-lactalbumin. The second expression vector sequentially expresses a protein binding sequence, a methanol inducible promoter, an alpha signal peptide and human alpha-lactalbumin, the third expression vector overexpresses a signal recognition particle subunit participating in a protein targeting endoplasmic reticulum, and the yield of the constructed recombinant pichia pastoris shake flask fermentation human alpha-lactalbumin is 23.3 mg / L; the yield of the human alpha-lactalbumin reaches 1.1 g / L in a 3L fermentation tank, and methanol is not required to be added as an inducer in the fermentation process, so that the problems of toxicity and safety possibly caused by methanol are avoided, and efficient production of the human alpha-lactalbumin is realized.

The invention provides for a composition, which in particular comprising a fusion molecule comprising a least one DNA binding protein and at least one modulator of gene expression, wherein the fusion molecule is targeted to a genomic region near a VEGF gene and / or within a VEGF regulatory element and the at least one modulator of gene expression provides a modification of at least one nucleotide near the VEGF gene and / or within a VEGF regulatory element. The invention also provides methods of reduction or elimination of VEGF gene products in vivo and uses thereof.

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 relates to the technical field of medical imaging, in particular to a magnetic navigation in-vivo basic group editing system, which comprises a magnetic navigation module, a magnetic navigation module, an in-vivo basic group editing module and an in-vivo basic group editing module, and is characterized in that the magnetic navigation module is used for providing a magnetic navigation electromagnetic selection field and a magnetic navigation electromagnetic excitation field; the receiving signal acquisition module is arranged on the magnetic navigation module and is used for receiving the magnetic induction signal of the experimental object in the magnetic navigation module; the in-vivo gene editing module adopts pcDNA3.1 as a plasmid vector, DNA binding protein Cas9 and cytidine deaminase or IS621mRNA as a base editor, and the base editor is used for realizing gene expression and comprises a dTtomato sequence, an EPG sequence and an hAPOBE3A sequence; and the control module is used for controlling the magnetic navigation module and the received signal acquisition module through an FPGA (Field Programmable Gate Array) board and a PC (Personal Computer) terminal.

Compositions and methods for reducing complement activation by introducing one or more alterations into a complement factor B (CFB) polynucleotide in a cell. In particular embodiments, the invention of the disclosure features a base editor system (e.g., a fusion protein or complex comprising a programmable DNA binding protein, a nucleobase editor, and gRNA) for modifying a CFB polynucleotide, where the modification is associated with reduced expression, and / or reduced activity of the CFB polypeptide encoded by the polynucleotide.

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 the field of antisense oligonucleotides used to reduce expression of the transactive response DNA binding protein 43 (TARDBP) gene which encodes the protein TAR DNA-binding protein 43 (TDP43). The present invention also relates to the field of antisense oligonucleotides used to prevent the subsequent downregulation of stathmin-2. The invention also provides pharmaceutical compositions and methods to treat the effects of a disease associated with TDP43 proteinopathy by administration of antisense oligonucleotides and therapeutic compositions comprising AONs targeted to TARDBP and AONs targeted to STMN2.

Compositions and methods for single reaction and multiplex analysis of histone modification. Compositions include a binding domain and a linker or a nucleosome binding conjugate comprising a binding domain bound to the linker. The method comprises analyzing a plurality of nucleosomes, comprising: (i) contacting a plurality of matrices comprising a binding domain and a linker composition with a solution comprising a plurality of nucleosomes wherein nucleosomes comprising a histone modification or DNA binding protein are bound to the binding domain; (ii) attaching a linker carrying a nucleic acid barcode to a target DNA of a nucleosome comprising a histone modification or DNA binding protein; (iii) introducing a universal sequence for amplifying the target DNA; (iv) amplifying the barcode labeled target DNA; and (v) analyzing the amplified barcode-labeled target DNA by sequencing.

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 invention belongs to the field of transactivation-responsive DNA binding protein with a molecular weight of 43 kDa (TARDB or also known as TDP-43). The present invention relates to TDP-43 specific binding molecules, in particular anti-TDP-43 antibodies or antigen-binding fragments or derivatives thereof and their uses. The present invention provides means and methods for diagnosing, preventing, alleviating 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 limbic-dominant age-related TDP-43 encephalopathy (LATE).

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 provides a gene editing system based on an sgRNA-donor DNA chimera. Specifically, the present invention provides a gene editing system, comprising: (i) a nucleic acid programmable DNA binding protein; and (ii) an sgRNA-donor DNA chimera. The sgRNA-donor DNA chimera is of a single-chain structure and comprises sgRNA and donor DNA that are linked. In the gene editing system based on the sgRNA-donor DNA chimera provided in the present invention, crRNA, tracrRNA, and the donor DNA are covalently linked, for achieving multiple types of gene editing.

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 present disclosure relates to nuclear penetrating conjugates comprising anti-DNA binding proteins and methods of use thereof in applications such as cancer therapy.

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.