559 results about "Cytosine" patented technology

The invention provides structure-oriented excavated cytosine deaminase with high editing activity and no sequence preference and application of the structure-oriented excavated cytosine deaminase. The invention discloses a series of novel cytosine deaminase. The cytosine deaminase disclosed by the invention has enhanced targeted editing performance; the enhanced targeted editing performance includes improved sequence-free preference, improved editing efficiency, reduced off-target effect, and improved targeted specificity.

The instant specification provides for evolved base editors which overcome deficiencies of those in art (including increased efficiency and / or decreased requirement for specific sequence-context at an editing site) and which are obtained a result of a phage-assisted continuous evolution (PACE) system. In particular, the instant specification provides for evolved cytidine base editors (e.g., based on APOBEC1, CDA, or AID cytidine deaminase domains) which overcome deficiencies of those in art (including increased efficiency and / or decreased requirement for specific sequence-context at an editing site) and which are obtained a result of a phage-assisted continuous evolution (PACE) system.

The invention relates to a metabolic marker for diagnosing diabetic secondary osteoporosis and application of the metabolic marker, and belongs to the technical field of biological medicine. The method comprises the following steps: firstly, screening out obviously different metabolites between osteoporosis (DOP) and osteoporosis-free groups (DM) in diabetic patients; and secondly, screening out significant difference metabolites between the primary osteoporosis patient and the healthy control group, and excluding the intersection of the two groups of difference metabolites to obtain metabolites which exclude the influence of the primary osteoporosis. Metabolic markers, namely cytosine nucleotide, ketoglutaric acid and triethylamine, are obtained through further screening, and when the three metabolic markers are independently used, AUCgt; the AUC during combined use is 0.99, so that the limitation that the sensitivity of the traditional bone mineral density detection on the osteoporosis recognition in the diabetic population is insufficient is effectively made up.

The invention belongs to the field of gene engineering, and relates to a DNA binding protein based on TraC effect protein, a fusion protein with a cytosine / adenine base editing function, an editing system and nucleic acid molecules or constructs for encoding the DNA binding protein and the fusion protein. The invention also relates to complexes and kits for gene editing comprising the fusion proteins of the invention or the nucleic acid molecules encoding them. The base editing tool disclosed by the invention can realize efficient, accurate and safe base editing in cells of various eukaryotes such as animals and plants. The unique characteristics of the base editing tool enrich the types of existing base editing tools, and the base editing tool has wide application prospects.

This disclosure describes methods, non-transitory-computer readable media, and systems that can simultaneously determine estimated methylation-level values for cytosine bases and genotype calls for a target genomic sample. The disclosed system can utilize a Bayesian method on a target genomic sample's nucleotide-read data to generate estimated methylation-level values that indicate genomic coordinates at which the target genomic sample comprises a reference cytosine base or a nucleobase that could be called as a cytosine. The disclosed system can estimate methylation-level values based on prior genotype probabilities and observed nucleobases at a genomic coordinate from a read pileup of a target genomic sample. Based on the estimated methylation-level values and base-call-quality metrics, the disclosed system may generate posterior genotype probabilities for the genomic sample at the genomic coordinate. Based on the posterior genotype probabilities, the disclosed system can generate a genotype call for the target genomic sample.

Nucleic acid molecules, compositions, recombinant AAV (rAAV) particles, kits, and methods are described herein for delivering a base editor (or “nucleobase editor”) to cells, e.g., via AAV vectors. In particular, the disclosure provides compositions, methods, and uses for delivery of adenine base editors and cytosine base editors in a single AAV vector (or genome). Further described herein are improved AAV vectors containing size-minimized regulatory components that enable, e.g., the packaging of base editors. Provided herein are methods and compositions for delivering base editor proteins to a cell or tissue in a single recombinant AAV (rAAV) vector. Contemplated herein are improved methods and compositions for delivering these base editors in vivo, in a single rAAV particle. Further provided herein are base editors and compositions and cells comprising these base editors.

Provided herein are systems, compositions, and methods for generating immunogenic peptides or epitopes from tumor associated antigens (e.g., in vivo or ex vivo). Polynucleotides (e.g., genes) encoding the tumor associated antigens may be edited at selected target sites by nucleobase editors comprising a catalytically-inactive Cas9 and a cytosine deaminase, leading to the expression of heteroclitic or cryptic peptides that are more immunogenic than the native peptide derived from the tumor associated antigens. The heteroclitic or cryptic peptide elicit strong tumor-specific immune response (e.g., T-cell response or B-cell response), which inhibits tumor growth and metastasis.

The invention discloses cytosine deaminase as well as a related biological material and application thereof, and belongs to the technical field of protein. The technical problem to be solved by the invention is to excavate natural cytidine deaminase without sequence preference and improve the base editing efficiency and range. The invention provides a 15th-143rd site protein of which the amino acid sequence is SEQ ID NO.2. The invention also provides a preparation method of the protein. The invention also provides application of the protein and related biological materials thereof in single base editing. According to the application, metagenome big data is utilized, comprehensive and systematic information mining analysis is carried out on novel cytidine deaminase, and a protein L85 which is highly similar to a known DddA protein structure but low in sequence similarity is selected from the novel cytidine deaminase for functional verification. The protein L85 has high catalytic activity as cytidine deaminase, is not limited by target sequence preference, can be widely applied to gene editing in vitro and in cells / tissues, and has good application potential and development value.

The present invention provides for novel methods for regulating and detecting the cytosine methylation status of DNA. The invention is based upon identification of a novel and surprising catalytic activity for the family of TET proteins, namely TET1, TET2, TEM3, and CXXC4. The novel activity is related to the enzymes being capable of converting the cytosine nucleotide 5-methylcytosine into 5-hydroxymethylcytosine by hydroxylation.

The present invention relates to the field of genetic engineering. Specifically, the present invention relates to cytosine deaminase and use thereof in base editing. More specifically, the present invention relates to a base editing system based on a newly identified cytosine deaminase, a method for base editing a target sequence in the genome of an organism (e.g., a plant) using the base editing system, and a genetically modified organism (e.g., a plant) produced by the method and progenies thereof.

The present invention relates to a fusion protein that produces point mutations in cells, its preparation and use. Specifically, the fusion protein provided by the present invention contains a Cas enzyme that lacks cytosine deaminase and nuclease activity and retains helicase activity, or is formed by a Cas enzyme that lacks cytosine deaminase and nuclease activity and retains helicase activity. The present invention also relates to the coding sequence of the fusion protein, a polynucleotide sequence containing the coding sequence, a nucleic acid construct containing the polynucleotide sequence, a corresponding host cell, a method for producing point mutations in a cell, and a kit, etc. By using the present invention, it is possible to achieve site-directed mutagenesis while obtaining high mutation efficiency and a variety of mutation combinations in a specific gene region.

The invention discloses an information storage method based on DNA (deoxyribonucleic acid) coding, which comprises the following steps: converting digital information to be stored into a quaternary code, converting the quaternary code into a DNA sequence consisting of adenine A, cytosine C, guanine G and thymine T according to a preset mapping rule, and expressing an additional information dimension by using a chemical modification state of a nucleotide pair; inserting error detection and correction codes in the DNA sequence every a predetermined number of basic group positions, segmenting the encoded DNA sequence into a plurality of fragments with the length of 100-150bp, and adding a specific recognition sequence and an index marker at two ends of each fragment; a reversible thermosensitive response DNA nanostructure is used as a carrier, DNA fragments are selectively combined to the carrier, and hierarchical storage and rapid retrieval of information are realized through a temperature gradient control system; the DNA storage information density can be remarkably improved, the service life of DNA storage can be remarkably prolonged, and a novel technical path is provided for large-scale, long-term and safe molecular information storage.

The invention provides a non-disease diagnosis purpose 5-hydroxymethylcytosine 5hmC detection method and a non-disease diagnosis purpose 5-hydroxymethylcytosine 5hmC detection kit. The detection method comprises the following steps: S1, glycosylation treatment; s2, carrying out enzyme digestion treatment on the GSREs; s3, carrying out APOBEC deamination treatment; s4, carrying out hydroxymethylation detection; the kit comprises a glycosylation reaction kit, a GSREs enzyme digestion reaction kit, an APOBEC deamination reaction kit and a PCR (Polymerase Chain Reaction) kit. The glycosylation reaction kit comprises a CutSmart buffer solution, UDP-Glucose, a T4-BGT enzyme and nuclease-free water, wherein the CutSmart buffer solution, the UDP-Glucose and the T4-BGT enzyme are used as raw materials; the GSREs enzyme digestion reaction kit comprises a GSREs enzyme, an enzyme digestion reaction buffer solution and nuclease-free water, the APOBEC deamination reaction kit comprises APOBEC, BSA (Bovine Serum Albumin), an APOBEC Reactive buffer solution and nuclease-free water; the PCR kit comprises a PCR reaction solution, a primer and a probe. According to the 5-hydroxymethylcytosine 5hmC detection method and kit for non-disease diagnosis purpose provided by the invention, precise quantification of extremely high specificity of 5hmC is realized, and the detection sensitivity is also improved while the specificity of a detection signal is improved.

The invention provides a perovskite solar cell, a preparation method thereof and a photovoltaic module. The perovskite solar cell comprises a first electrode, a hole transport layer, a perovskite layer, an electron transport layer and a second electrode which are stacked in sequence. The material of the hole transport layer comprises a biomolecular material which is fixed on a self-assembly monomolecular layer material through an intermolecular force, and the biomolecular material comprises one or more of guanine, adenine, thymine, uracil, cytosine, hydroxymethylcytosine, xanthine, hypoxanthine, 6-mercaptopurine and corrin. According to the perovskite cell provided by the invention, the biomolecular material with a plurality of nitrogen heterocyclic structures and amino groups is added to generate multipoint hydrogen-bond interaction and pi-pi accumulation with the tail end of the SAM, so that the orderliness of molecular arrangement is improved, and the dipole direction and strength of the whole interface are regulated and controlled; and a coordination bond or hydrogen bond network is formed by the coordination compound and uncoordinated cations or anions in perovskite, so that interface defects are effectively passivated, and the thermal stability and the humid and hot life of a device are enhanced.

Provided is an improved cytosine base editing system with reduced genome-wide off-target effects and a narrow editing window, the system comprising a base editing fusion protein comprising an APOBEC3B deaminase or an APOBEC3B deaminase mutant fused to a CRISPR effector protein.

The invention relates to the field of genetic engineering in biotechnology, in particular to a high-precision base editor capable of expanding the editing range and improving the editing efficiency. According to the editor, the Cas9 variant SpRY which is not limited by PAM and cytosine deaminase CDA1 with different truncation lengths are fused, the CDA1 delta-SpRY-BE3 high-precision editor which is wider in editing range and higher in editing efficiency is constructed, and the editor can effectively edit any cytosine on a genome while keeping high editing precision. Tests in yeast and rice cells show that compared with an existing standard editor CDA1-SpRY-BE3, the editor has the advantages that the editing efficiency is remarkably improved on multiple target spots, the application value of the editor in higher eukaryotes is proved, and a more efficient and accurate tool is provided for genetic disease treatment and crop breeding.

The invention discloses a genetically engineered bacterium for producing pseudouridine and a construction method of the genetically engineered bacterium, escherichia coli W3110 is used as a starting strain, the supply of precursor substances including aspartic acid, carbamyl phosphoric acid, glutamine and 5 '-phosphoribosyl pyrophosphate prpp is enhanced, pyrimidine nucleoside synthesis operon from bacillus subtilis is introduced, and the pseudouridine is produced. The invention discloses a pseudouridine-5 '-phosphosidase gene psuG and a preparation method thereof, and relates to the field of microorganisms, the field of genetic engineering and the field of fermentation engineering. The pseudouridine-5'-phosphosidase gene psuG is expressed by using high-copy plasmids, and the application of the pseudouridine-5 '-phosphosidase gene psuG to preparation of the pseudouridine-5'-phosphosidase gene psuG is provided. The strain is fermented in a 50L fermentation tank for 60h, the yield of pseudouridine reaches 50.8 g / L, the conversion rate is 18%, which is the highest value reported at present, and the strain has high industrial production value.

Described herein are methods, compositions, and kits for removing false positive uracils due to the deamination of unmethylated cytosines in assays using engineered cytosine deaminases to deaminate methylated cytosines. The methods, compositions, and kits utilize a dual enzymatic process. After cytidine deaminase treatment, the DNA is first incubated with Uracil DNA Glycosylase (UDG), which generates abasic sites where dC to dU conversions have occurred. The DNA is then incubated with a high-fidelity polymerase supplemented with a deoxycytidyl transferase, such as Rev1, to repair the lesion with the installation of a cytidine.

The present invention discloses a recombinant glycosylase base editing system and its application. The recombinant glycosylase base editing system of the present invention is an APOBEC-nCas9-Ung1 or APOBEC(R33A)-nCas9-Rad51-Ung1 base editing system; the base editing system APOBEC-nCas9-Ung1 includes cytosine deaminase APOBEC, nuclease nCas9 and uracil DNA glycosylase Ung1; the base editing system APOBEC(R33A)-nCas9-Rad51-Ung1 includes cytosine deaminase APOBEC(R33A), nuclease nCas9, single-stranded DNA binding protein Rad51 and uracil DNA glycosylase Ung1. Experiments have shown that the recombinant glycosylase base editing system of the present invention can improve the editing efficiency of base C to base G in the genome sequence of an organism or a biological cell and the purity of the editing product.

The invention relates to the technical field of biotechnology and plant genetic engineering, in particular to a rice two-way single-base edited co-transcription unit gene ABE-CBE system and application of the rice two-way single-base edited co-transcription unit gene ABE-CBE system. The rice bidirectional single base edited co-transcription unit gene ABE-CBE system provided by the invention comprises a co-transcription unit gene ABE-CBE, and the co-transcription unit gene ABE-CBE comprises an encoding gene ABE8e of adenine deaminase and an encoding gene Sdd7 of cytosine deaminase, and the coding gene ABE8e and the coding gene Sdd7 in the co-transcription gene ABE-CBE are constructed in the same expression vector. Through the designed ABE-CBE system, the two editors can be mediated at the same site to play a role at the same time, generation of unexpected base substitution can be further reduced, the editing efficiency of the base editors is improved, and wide application value is achieved.

The invention relates to the field of gene engineering. In particular, the present invention relates to cytosine deaminases and their use in base editing. More specifically, the invention relates to a method for screening and identifying a deaminase, a base editing system based on a newly identified cytosine deaminase, a method for editing a target sequence in a genome of an organism (such as a plant) by using the base editing system, and a method for screening and identifying the target sequence. As well as genetically modified organisms (e.g., plants) and progeny thereof produced by the method.

Aspects of the present disclosure are directed to methods, compositions, and kits for detection and analysis of DNA and RNA cytosine methylation. Certain aspects include methods, compositions and kits useful in bisulfite sequencing of methylated nucleic acids, including methylated nucleic acids from low-input samples such as cell-free DNA and cell-free RNA. Also disclosed are methods and compositions for detection and quantification of 5-hydroxymethylcytosine in DNA.

The invention comprises a process for the production of a linear P-linked oligonucleotide bearing an alkyl phosphonate group at 5′-terminus of the formula Iwherein R1 is a C1-4-alkyl group, R2 is fluoro, hydroxyl or C1-4-alkoxy, X is sulfur or oxygen, the term Nucleobase stands for an optionally modified adenine, cytosine, guanine or uracil and the term oligo strand stands for the remaining P-linked oligo nucleotide strand, and wherein the oligo strand comprises at least one uracil nucleobase.The process is performed under conditions that the level of alkyl transfer impurities and the level of cyanoethyl (CNET) impurities in the linear P-linked oligonucleotide of formula I, is substantially reduced.

Described herein are nucleic acid molecules, compositions, recombinant AAV (rAAV) particles, kits, and methods for delivering a base editor (or a "nucleobase editor") to a cell, for example via an AAV vector. In particular, the present disclosure provides compositions, methods and uses for delivery of adenine base editors and cytosine base editors in a single AAV vector (or genome). Further described herein are improved AAV vectors comprising a minimised size regulatory component, for example, a regulatory component that can enable packaging of a base editor. Provided herein are methods and compositions for delivering a base editor protein to a cell or tissue in a single recombinant AAV (rAAV) vector. Improved methods and compositions for in vivo delivery of these base editors in a single rAAV particle are contemplated herein. Further provided herein are base editors, and compositions and cells comprising these base editors.

The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and / or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and / or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.

The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and / or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and / or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.

Compositions and methods comprising artificial poly (A) sequences having at least one cytosine and at least one uridine and / or guanosine are provided.

The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and / or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and / or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.

The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and / or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and / or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.

Transgene-free genome editing of plants in T0 generation is highly desirable but challenging, especially in perennials and vegetatively propagated plants. Here is provided a co-editing strategy for generating transgene-free, gene-edited plants via Agrobacterium-mediated transient expression of cytosine base editor (CBE) / gRNA-Cas 12a / crRNA-GFP in plants. Specifically, CBE / gRNA was used to base edit the AES gene to confer resistance to herbicide chlorsulfuron as a selection marker, which has no negative effects on plant phenotypes; Casl2a / crRNA was used for editing genes(s) of interest; GFP was used for selecting transgene-free transformants. Using this approach, transgene- free genome-edited plants were efficiently generated for various genes (either individual or multiplex) in tomato, tobacco, potato, and citrus in the T0 generation. The biallelic / homozygous transgene-free mutation rates for target genes among herbicide-resistant transformants ranged from 8% to 50%. Whole genome sequencing further confirmed transgene-free and absence of off- target mutations in the edited plants. The co-editing strategy is efficient for generating transgene- free, genome-edited plants in the T0 generation, thus being a potent tool for plant genetic improvement.