52 results about "DNA Binding Motif" patented technology

The present invention relates to a viral gene therapy vector for removing hepatitis B viruses, a preparation method therefor, and the use thereof, aiming to solve the problem in which existing viral gene therapy vectors can only inhibit the replication of hepatitis B viruses, but cannot remove virus cccDNA. The vector comprises a promoter, an intron, an enhancer, a nuclear localization signal (NLS) functional domain encoding gene of PGLYRP2 protein, an HBV DNA binding domain encoding gene of the PGLYRP2 protein, a secretory signal peptide functional domain encoding gene of the PGLYRP2 protein, an HBV nucleocapsid-binding functional domain encoding gene of the PGLYRP2 protein, and an IRES fragment. The viral gene therapy vector can remarkably promote the removal of HBVs in the liver of mice and is used for treatment of hepatitis B virus infection.

Provided herein is a base editor system for editing the SBDS gene comprising a base editor protein and a guide polynucleotide, wherein the base editor protein comprises a polynucleotide programmable DNA binding domain and a cytosine deaminase domain. Methods, edited cells, and compositions thereof are also described herein.

The invention provides a retrotransposase, which comprises a target DNA binding structural domain containing a zinc finger binding motif, a reverse transcriptase structural domain and an endonuclease structural domain, and can be used for reversely transcribing RNA (Ribonucleic Acid) into DNA. The amino acid sequence of the retrotransposase is shown as any one of SEQ ID No.1 to 6 or SEQ ID No.32 to 43 or SEQ ID No.68 to 71 or has at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% and 99% identity with the amino acid sequence of any one of SEQ ID No.1 to 6 or SEQ ID No.32 to 43 or SEQ ID No.68 to 71. The invention also relates to a system for modifying DNA. The system comprises the retrotransposase provided by the invention or a nucleic acid encoding the retrotransposase provided by the invention; and a donor RNA or a nucleic acid encoding the donor RNA, the donor RNA comprising: a sequence that binds to the retrotransposase and a heterologous sequence.

Constructs comprising transactivation domains (TADs) for activating gene expression are disclosed herein, along with methods of using the same. Nucleotides encoding the same and vectors for the delivery of the nucleotides are also disclosed. In particular, synthetic transcription factors comprising a TAD fused to a heterologous DNA binding domain, and methods of using thereof are provided.

The present invention provides a method of identifying the amino acid position of a DNA modifying enzyme for insertion into a heterologous DNA binding domain (DBD), the method comprising the steps of: providing a library of DNA modifying enzymes wherein members of the library comprise heterologous amino acid sequence insertion throughout the DNA modifying enzyme; identifying those DNA modifying enzymes in the library that have DNA modifying activity; and determining insertion positions in those DNA modifying enzymes identified in the previous step. The invention also relates to a method of preparing a DNA modifying enzyme comprising an inserted heterologous DBD, a method of modifying a nucleic acid sequence in a cell, and a method of evolving a DNA binding domain for a desired target sequence. The invention also provides nucleic acid sequences encoding such DNA modifying enzymes and DNA binding domains, corresponding vectors and host cells.

The present invention relates to chimeric receptors that can be used in whole-cell sensors for detecting analytes of interest. The inventors showed that the DNA binding domains and downstream gene expression can be activated via dimerization of an artificial dimerization composed of a single chain variable domain. They demonstrated for the first time that an artificial bacterial receptor using an antibody-like domain can be activated and produce a transcriptional output upon ligand-binding. In particular, the present invention relates to a chimeric receptor polypeptide comprising: i) a first DNA binding domain, ii) at least one binding domain selected from the group consisting of heavy chain variable domain, camelid VHHs, or antibody mimetics having specificity for an analyte, and iii) a linker between the DNA binding domain and the binding domain.

To provide methods of using base editors comprising adenosine deaminase variants for altering mutations associated with Glycogen Storage Disease Type 1a (GSD1a).SOLUTION: The present invention provides a method of editing a glucose-6-phosphatase (G6PC) polynucleotide comprising a single nucleotide polymorphism (SNP) associated with Glycogen Storage Disease Type 1a (GSD1a). The method comprises contacting the G6PC polynucleotide with an adenosine deaminase base editor 8 (ABE8) in a complex with one or more guide polynucleotides, wherein the adenosine deaminase base editor 8 (ABE8) comprises a polynucleotide programmable DNA binding domain and an adenosine deaminase domain, and wherein the one or more of guide polynucleotides target the base editor to effect an A T to G C alteration of the SNP associated with the GSD1a.SELECTED DRAWING: None

To provide methods for producing and identifying Paenibacillus sp. strains with enhanced fungicidal activity and processability.SOLUTION: The present invention provides a composition comprising a biologically pure culture of a Paenibacillus sp. strain comprising a mutant DegU lacking a functional receiver domain or a functional DNA binding domain and / or a mutant DegS lacking a functional single binding domain or a functional ATPase domain with decreased viscosity in a liquid culture. Also provided is a method of identifying a Paenibacillus sp. mutant derivative strain with decreased viscosity in a liquid culture compared to a Paenibacillus sp. parental strain with a visual screen for mutant with a non-mucoid morphology.SELECTED DRAWING: Figure 1

The disclosure pertains to methods and compositions for the rapid and efficient transformation of plants. The disclosure further provides methods for producing a transgenic plant, comprising (a) transforming a cell of an explant with an expression construct comprising (i) a nucleotide sequence encoding a WUS / WOX homeobox polypeptide; (ii) a nucleotide sequence encoding a polypeptide comprising two AP2-DNA binding domains; or (iii) a combination of (i) and (ii); and (b) allowing expression of the polypeptide of (a) in each transformed cell to form a regenerable plant structure in the absence of exogenous cytokinin, wherein no callus is formed; and (c) germinating the regenerable plant structure to form the transgenic plant. This abstract is intended as a scanning tool for purposes of searching in the particular art and is not intended to be limiting of the present disclosure.

The application discloses a mutant of a photosensitive protein BphP1. The application also provides a kind of optogenetic system, which comprises the fusion protein of the BphP1 mutant and the transcription activation domain (AD) of Gal4, the fusion protein of the photosensitive protein PpsR2 and the DNA binding domain (DBD) of Gal4, and the expression vector for expressing target genes through Gal1 promoter, wherein the PpsR2 can be wild type truncated variant Q-PpsR2. The induction intensity of the optimized optogenetic system of the application is 2.99 times that of the original light induction system.

The present invention relates to methods and compositions for modifying target sites in the genome of a cell. Fusion proteins are provided, which include one or more DNA binding domains and one or more heterologous domains, such as DNA modification domains, connected by improved linker sequences. Codon-optimized polynucleotides are provided, which encode fusion proteins including one or more DNA binding domains and one or more heterologous domains connected by improved linker sequences.

A recombinant prion protein (PRNP) gene-specific epigenetic editor is disclosed, comprising an unmethylated H3K4meO peptide, a DNMT3 methyltransferase-binding domain, and a PRNP gene-specific DNA binding domain. Expression of the epigenetic editor is non-toxic, and effective at silencing prion gene (PRNP) expression through DNA methylation (DNAme) at CpG sites within the PRNP promoter region. The PRNP-specific epigenetic editor should provide an AAV gene therapy approach for the treatment of prion diseases.

The present invention provides a composition comprising a biologically pure culture of a Paenibacillus sp. strain comprising a mutant DegU lacking a functional receiver domain or a functional DNA binding domain and / or a mutant DegS lacking a functional single binding domain or a functional ATPase domain with decreased viscosity in a liquid culture. Also provided is a method of identifying a Paenibacillus sp. mutant derivative strain with decreased viscosity in a liquid culture compared to a Paenibacillus sp. parental strain with a visual screen for mutant isolates with a non-mucoid morphology.

To provide an improved form of genome editing that is more efficient and with far fewer undesired products such as stochastic insertions or deletions (indels) or translocations, which edits HBB polynucleotide including single nucleotide polymorphism (SNP) associated with sickle cell disease.SOLUTION: Provided is a method including bringing HBB polynucleotide into contact with a base editor forming one or more guide polynucleotides and a complex, wherein the base editor includes a polynucleotide programmable DNA binding domain and an adenosine deaminase domain, and the one or more guide polynucleotides target the base editor to effect an AT to GC alteration of SNP associated with sickle cell disease.SELECTED DRAWING: Figure 5

A composition for editing the PCSK9 gene comprises: (i) an mRNA encoding a protein comprising a programmable DNA binding domain; and (ii) a guide polynucleotide, wherein the guide polynucleotide compr

The present invention is inter alia directed to a fusion protein comprising (i) an adenosine deaminase 2 (ADA2) domain and (ii) a DNA binding domain, wherein the DNA binding domain is capable of binding to a target DNA sequence; a pharmaceutical composition comprising adenosine deaminase 2 (ADA2) or a functional variant thereof and at least one pharmaceutically suitable excipient, wherein the pharmaceutical composition is targeted to the lysosome; and a pharmaceutical composition comprising adenosine deaminase 2 (ADA2) or a functional variant thereof and at least one pharmaceutically suitable excipient, wherein the pharmaceutical composition is targeted to a macrophage.

The invention discloses a GAL4-TEAD4 fusion protein, a YAP activation level detection kit and application of the GAL4-TEAD4 fusion protein and the YAP activation level detection kit, the GAL4-TEAD4 fusion protein comprises a GAL4 DNA binding structural domain and a TEAD4 YAP binding structural domain, and endogenous interference is eliminated by deleting the DNA binding structural domain of TEAD4; the kit comprises a GAL4-TEAD4 expression plasmid, a UAS-luciferase reporter plasmid and a luciferase detection reagent, and during detection, mammalian cells are co-transfected, a GAL4-UAS reporter system is utilized, and the YAP activity is directly quantified through a luciferase activity value. The system is high in sensitivity, can accurately capture activity change caused by YAP overexpression or siRNA knock-down, and is suitable for YAP activity detection and screening of small molecule compounds targeting YAP-TEAD interaction.

Provided are chimeric high mobility group (HMG) transcription factor polypeptides. In some aspects, provided are chimeric polypeptides comprising an N-terminal effector domain of a first HMG transcription factor and an HMG DNA binding domain and a C-terminal effector domain, wherein the HMG DNA binding domain or C-terminal effector domain is of a second HMG transcription factor. Also provided are cells (e.g., immune effector cells) that express a chimeric HMG transcription factor polypeptide of the present disclosure. In some instances, such cells (e.g., T cells) exhibit enhanced function relative to cells expressing only native wild-type HMG transcription factors. Also provided are methods of using such cells to treat a condition (e.g., cancer, infection, and / or the like) in a subject in need thereof.

Provided herein are polypeptides, compositions comprising the polypeptides and methods for genome editing and gene regulation (e.g., activation and / or repression) using the polypeptides or the compositions comprising the polypeptides, such as, DNA binding domains derived from the genus of Legionella. These DNA binding proteins include a fragment of N-cap sequence and / or a C-cap sequence of a DNA binding protein derived from the genus of Legionella.

Provided are directed to compositions, methods, and systems for epigenetic editing of antigen presentation mechanism (APM) -related genes in a cancer cell. In some embodiments, provided are directed to methods of modulating methylation at a methylation site in an APM-related gene in a cancer cell. In some embodiments, the site-specific demethylation systems comprise a fusion protein or a nucleic acid encoding the fusion protein, wherein the fusion protein comprises a site-specific DNA binding domain and an effector domain having demethylation activity. In some embodiments, provided are directed to such methods, wherein recruitment of the site-specific demethylation system to a target site results in demethylation at the methylation site. Also provided herein are nucleic acids encoding the polypeptides described herein, systems comprising additional components useful for editing, such as gRNA, methods of treating cancer, and kits directed to practicing the methods described herein.

The invention discloses a transcriptional activation type RUBY visual virus infection system as well as a method and application thereof. The system is based on a betacyanin biosynthesis pathway, a transcriptional activation system is utilized, and a yeast GAL4 DNA binding domain (BD) and a herpes virus VP16 transcriptional activation domain (AD) are fused and constructed in a virus vector; when the virus infects expressed transgenic tobacco, the expression of the RUBY whole gene can be activated, so that a red signal is generated. The construction method of the system is clear, complex instruments are not needed, an efficient and convenient tool platform is provided for protein function analysis, host factor screening and infection mechanism exploration in virology research, and good expandability is achieved.

The present invention provides a method of identifying an amino acid position of a DNA modifying enzyme for insertion of a heterologous DNA binding domain (DBD), the method comprising the steps of providing a library of DNA modifying enzymes, wherein the members of the library comprise heterologous amino acid sequence insertions throughout the DNA modifying enzyme; identifying those DNA modifying enzymes of the library that have DNA modifying activity; and identifying the position of the insertion in those DNA modifying enzymes identified in the previous step. The present invention further pertains to methods of producing DNA modifying enzymes comprising an inserted heterologous DBD, to methods for modifying a nucleic acid sequence in a cell, and to methods for evolving a DNA binding domain on desired target sequences. Further provided are nucleic acid sequences encoding such DNA modifying enzymes and DNA binding domains, respective vectors and host cells.

Provided herein are polypeptides, compositions comprising the polypeptides and methods for genome editing and gene regulation (e.g., activation and / or repression) using the polypeptides or the compositions comprising the polypeptides, such as, DNA binding domains derived from the genus of Ralstonia. Also disclosed are DNA binding proteins that include a fragment of N-cap sequence of a TALE protein, such as, a Xanthomonas TALE protein. Also disclosed are DNA binding proteins that include a fragment of N-cap sequence of a DNA binding protein derived from bacteria of the genus Ralstonia.

Provided is a retrotransposase which comprises a target DNA binding domain comprising a zinc finger binding motif, a reverse transcriptase domain, and an endonuclease domain, and which is capable of reverse transcription of RNA to DNA. The invention also relates to a system for modifying DNA. The system comprises the retrotransposase or a nucleic acid encoding the retrotransposase; and a donor RNA or a nucleic acid encoding the donor RNA, the donor RNA comprising: a sequence that binds to the retrotransposase and a heterologous sequence.

The invention discloses a functional module for regulating drought and salt stress response of plants and application of the functional module. The functional module comprises a micro RNA member TaMIR7762, a target gene TaCML31 of the micro RNA member TaMIR7762 and a downstream MYB member TaMYB77 of the micro RNA member TaMIR7762. A precursor sequence of the micro RNA member TaMIR7762 is a sequence obtained by replacing T in SEQ ID NO: 1 with U, and a mature region sequence of the micro RNA member TaMIR7762 is a sequence obtained by replacing T in SEQ ID NO: 2 with U; the target gene TaCML31 is used for coding calmodulin protein, and the sequence of the target gene TaCML31 is shown as SEQ ID NO: 3; the sequence of the MYB transcription factor TaMYB77 is as shown in SEQ ID NO: 4, the expression of TaCML31 is negatively regulated through transcriptional cutting of the micro RNA member TaMIR7762, and the TaCML31 interacts with a DNA (Deoxyribose Nucleic Acid) binding structural domain in MYB of the TaMYB77 through an EF-Hand structural domain to jointly regulate the expression of a downstream stress defense gene. The invention shows that by silencing or inhibiting or reducing or knocking out the TaMIR7762 and overexpressing the target gene TaCML31 of the TaMIR7762 and the downstream MYB member TaMYB77, the drought tolerance and salt tolerance of wheat growth can be realized, so that the yield of wheat is greatly increased.

Provided are designed proteins, derived from OCT4 and SOX2, which have enhanced stability and binding affinity for one another compared to the wild-type equivalents. These designed proteins are species-agnostic. Specifically provided are isolated SOX2 proteins having an artificial SOX2 DNA binding domain and isolated OCT4 proteins having an artificial OCT4 DNA binding domain. Also provided are uses of these proteins to generate induced pluripotent stem cells, vectors, and host cells containing these proteins.

This invention provides a technology that can improve the proliferation rate of cells in cultures using microcarriers. [Solution] The cell line is established by introducing the following four genes: CDK4(R24C), TERT, CCND1, and p53 lacking the DNA binding domain into bovine progenitor cells.

The present invention relates to methods and compositions for modifying a target site in the genome of a cell. Fusion proteins including one or more DNA binding domains and one or more heterologous domains, such as DNA modifying domains, connected by improved linker sequences are provided. Codon optimized polynucleotides encoding fusion proteins including one or more DNA binding domains and one or more heterologous domains connected by improved linker sequences are provided.

The present invention belongs to the field of biomedicine, and specifically relates to a gene delivery method based on exosomes and polypeptides containing nuclear localization sequences. Specifically, the present invention provides a method for increasing the expression of exogenous genes in target cells through exosomes, the method comprising the steps of mixing exosomes with exogenous genes and co-electroporating them with cells; the method also comprises mixing and incubating the exogenous genes with auxiliary polypeptides and / or KK58 before electroporation, wherein the auxiliary polypeptides are composed of nuclear localization signals, nuclear localization signals and DNA binding domains.

Provided herein are compositions, systems, and methods for the generation, identification, and characterization of effector domains for activating and silencing gene expression. In particular, synthetic transcription factors comprising one or more transcriptional activator domains, one or more transcriptional repressor domains, or a combination thereof fused to a heterologous DNA binding domain, and methods of using thereof are provided.