305 results about "Cytosine" patented technology

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.

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 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 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.

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.

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.

The invention discloses a Cg12n-v4.6 nuclease. The amino acid sequence of the nuclease is as shown in SEQ ID No. 12. The invention also discloses a preparation method of the nuclease. The Cg12n-v4.6 nuclease mutant with increased activity and improved editing efficiency is developed, and the editing efficiency of the Cg12n-v4.6 nuclease mutant is up to 70% or above. Meanwhile, through engineering modification of corresponding sgRNA of Cas12n, the size of the sgRNA skeleton is reduced. An enhanced Cas12n gene editing tool, namely an eCg12n gene editing system, is developed by combining an engineered Cg12n-v4.6 nuclease mutant and a simplified sgRNA skeleton. Meanwhile, by fusing deaminase, a compact cytosine base editor and a compact adenine base editor are constructed, and the cytosine base editor is applied to edit and induce disease genes to generate early termination codons, so that safe knockout of the genes is realized. Compared with an original wild type editing system, the Cg12n-v4.6 nuclease mutant and a compact eCg12n gene editing system derived from the Cg12n-v4.6 nuclease mutant have the advantages that the editing efficiency is improved, the system size is further simplified, and the Cg12n-v4.6 nuclease mutant and the compact eCg12n gene editing system derived from the Cg12n-v4.6 nuclease mutant are more suitable for gene editing application.

The invention provides an efficient double-base editing system without PAM (Pulse Amplitude Modulation) limitation. According to the technology, different point mutations are introduced into SpRY, the SpRY is fused with efficient adenine deaminase and cytosine deaminase to construct a double-base editor, and efficient PAM-limitation-free double-base editing is achieved in the rice protoplast. According to the plant basic group editing method, efficient and PAM-less double basic group editing can be achieved, and the plant basic group editing technology is wider in target range, higher in efficiency and higher in double basic group editing product proportion.

A method of detecting the level of 5-hydroxymethylcytosines (5-hmc) in a DNA molecule of a cell having a 5-hmc prevalence lower than 0.002% of total DNA bases is provided. The method comprising:(a) attaching a 5-hmc labeling agent to the DNA molecule; and(b) subjecting the DNA molecule to an imaging method suitable for detecting the labeling agent, thereby detecting the level of 5-hmc in the DNA molecule. Also provided is a method of diagnosing cancer in a subject in need thereof, the method comprising:(a) providing a DNA sample of a cell of the subject;(b) detecting the level of 5-hmc in the DNA sample as described herein; wherein a significant decrease in the level of 5-hmc in the DNA sample, as compared to a control DNA sample from a healthy subject is indicative that the subject has cancer.

The present invention belongs to the technical field of genetic engineering. Provided are a single-base editor, a deaminase used therein, and the use thereof. The technical problems to be solved are to identify a naturally occurring cytosine deaminase without sequence preference, construct a base editor, and improve the efficiency and scope of base editing. In order to solve the technical problems above, a cytosine base editor is provided. The cytosine base editor is a fusion protein, wherein the fusion protein is a protein containing a cytidine deaminase, a Cas protein and a uracil-DNA glycosylase inhibitor, and the cytidine deaminase is a protein having an amino acid sequence of positions 28-164 of SEQ ID NO. 2. Further provided is the use of the fusion protein above and a biomaterial related thereto in plant single-base editing. The single-base editor can improve the efficiency of cytosine base editing and accurately mediate the base mutation of a target, and is widely applicable in the cells of maize and even other plants.

Methods of predicting a chromatin state metric associated with a genomic region in a sample are provided. The methods comprise: receiving sequence data comprising genetic data and epigenetic data indicative of the presence of one or more epigenetic bases including methylated cytosine and hydroxymethylated cytosine at one or more genomic positions, the one or more epigenetic bases, the genetic data and epigenetic data obtained from a single assay; and predicting for each base or set of bases of the genomic region and using the sequence data associated with the genomic region, a value of the chromatin state metric, wherein the predicting is performed using a machine learning model.

The invention relates to a T7RNA polymerase-guided bacillus subtilis cytosine base editor and application thereof, and belongs to the technical field of gene editing. A T7RNAP guided cytosine base editor is developed in bacillus subtilis, four kinds of cytidine deaminase from different sources are selected to be fused with T7RNAP, the cytidine deaminase is fused at the N end of the T7RNAP, and a fusion body with the highest mutation activity is obtained through screening; the cytosine base editor is used for evolving a global transcriptional regulatory factor CodY, in-situ evolution of genome protein is achieved, and the expression level of bovine-derived beta-lactoglobulin (beta-Lg) is improved. According to the cytosine base editor, the operable range of the cytosine base editor on a genome is widened, multi-site base (C-T) editing can be realized, and an editing window is large.

Disclosed are methods of preparing a composition of non-naturally occurring DNA, comprising: (a) extracting DNA from a sample of a subject; (b) contacting the extracted DNA or its derivative with a panel of oligonucleotide probes designed to hybridize to a plurality of preselected genomic regions, thereby generating selected DNA, wherein at least 50% of the preselected genomic regions are CpG regions that each comprises at least 3 CpG sites and a CpG density of at least 0.02 CpG / bp, wherein the preselected genomic regions cover 10-500 Mb of sequence space in human genome, wherein the extracted DNA or its derivative or the selected DNA or its derivative is further treated with an agent or a combination of agents that discriminates between methylated and unmethylated cytosines; and (c) performing high-throughput sequencing on the selected DNA or its derivative and generating sequencing reads.

The invention discloses a high-efficiency wide-targeting-range C-to-G double-enzyme synergistic base editor and application thereof, and belongs to the technical field of gene editing. The editor is a fusion protein comprising a Cas protein having reduced or lost endonuclease activity, a cytosine deaminase (CDA), and a cytosine DNA glycosylase (CDG). In order to solve the problems that an existing C-to-G editor is low in efficiency and limited in targeting range, the C-to-G editor synergistically and efficiently generates a base removal (AP) site on a target DNA through the dual effects of CDA and CDG, so that C-to-G base transversion is promoted. According to the editor, the C-to-G editing efficiency is remarkably improved, an editing window can be effectively expanded or moved, the targeting flexibility is greatly enhanced, meanwhile, high genome specificity is kept, and the editor shows strong application potential in various organisms such as yeast and plants.

Provided are siRNA compositions comprising gemcitabine (GEM) substituted for cytosine moieties in siRNAs. Provided are pharmaceutical compositions containing these siRNA molecules, and methods of using these compositions to treat diseases, such as cancer.

The application discloses cytosine deaminase and related biological materials and applications thereof, and belongs to the technical field of proteins. The technical problem to be solved by the application is to mine natural sequence-unpreferred cytosine deaminase, and to improve base editing efficiency and range. The application provides a protein with amino acid sequence of SEQ ID NO. 2 at positions 15-143. The application also provides application of the above protein and related biological materials thereof in single base editing. The application uses macro-genome big data, performs comprehensive and systematic bioinformatics mining analysis on novel cytosine deaminase, and selects a protein L85 highly similar to known DddA protein structure but with low sequence similarity for function verification. The protein L85 has high catalytic activity as cytosine deaminase, and has no target sequence preference restriction, and can be widely applied to in-vitro and in-cell / tissue gene editing, and has good application potential and development value.

The invention relates to the technical field of dye separation, and discloses a loose nanofiltration membrane and a preparation method and application thereof, the loose nanofiltration membrane comprises a porous support membrane, and a polyesteramide separation layer formed on the porous support membrane through one-step interfacial polymerization of nucleoside monomers and multi-acyl chloride monomers. The nucleoside monomer is one or more than two of adenosine, guanosine and cytidine nucleoside. The nucleoside monomer with a long-chain structure, a branched-chain structure, a rigid twisted structure and a plurality of hydrophilic reaction sites is selected as an interfacial polymerization water-phase monomer, so that the loose nanofiltration membrane is endowed with excellent permeation and separation performance. The membrane has a high rejection rate on dye molecules such as Congo red and methyl blue, also has high water permeability and extremely high dye / inorganic salt separation selectivity, and shows good application potential in the aspects of dye production and purification and dye wastewater recovery.

To provide a molecule capable of recognizing a cytosine-cytosine mismatch in DNA.SOLUTION: A solution of FcDANP represented by the chemical formula below, and three solutions each obtained by mixing FcDANP with one of three DNAs having different base sequences, are measured using an ultraviolet-visible spectrophotometer. In the wavelength range of approximately 375-400 nm, the sample containing FcDANP and the DNA having a C-C mismatch exhibits a significantly higher absorption intensity than the other samples.SELECTED DRAWING: Figure 1

The invention includes improved methods and compositions for reduction of a C5-C6 double bond of a cytosine. In particular, the improved methods and compositions for reduction of a C5-C6 double bond of a cytosine is via enzymatic means, not via chemical means. In particular, the disclosure is directed to methods of converting 5,6-dihydro-fC (fC) and / or 5,6-dihydro-caC to 5,6-dihydro-U (DHU). In particular, the disclosure is directed to methods of converting 5fC and / or 5caC to DHU. In addition, the disclosure is directed to methods for detection of epigenetic cytosine modification, particularly cytosine methylation, using ene reductases to reduce the C5-C6 double bond of cytosine.

The present invention relates to a modified mitochondrial comprising, on the outer membrane of the mitochondrial, an antibody that binds to a cancer cell-specific protein and a cytosine deaminase. It is proved that when the mitochondria and 5-FC are jointly used for treating a pancreatic cancer cell line, the cytotoxicity induced by 5-FC treatment is remarkably enhanced. The effect is proved as follows: 5-FC is converted into 5-FU by cytosine deaminase expressed on a mitochondrial outer membrane, so that pancreatic cancer cells are induced to generate apoptosis. Therefore, the modified mitochondria according to the present invention can be effectively used in anticancer therapy using 5-FC as an anticancer agent.

The present invention provides technology for inhibiting or suppressing proliferation of cells. Disclosed herein is a double-stranded RNA that has a first strand and a second strand which is complementary to the first strand, wherein the first strand has a main sequence which comprises 19-23 bases and in which a base at the 5'-end is guanine (G) or cytosine (C) and an additional sequence which comprises 2-4 bases and which is added to the 3'-end side of the main sequence. The main sequence is a portion of a base sequence that encodes semaphorin-3A, the portion including at least a portion of a base sequence that encodes a signal peptide region of the semaphorin-3A.

Provided are compositions, methods, and systems for DNA pyrimidine-base editing. In some embodiments, provided are engineered thymine-modifying polypeptides or engineered cytosine-modifying polypeptides comprising a variant of a uracil-DNA glycosylate (UNG). In some embodiments, provided are such engineered polypeptides and a DNA recognition domain, which are configured to target a nucleic acid for excision. Also provided herein are nucleic acid encoding the polypeptides described herein, additional components useful for editing, such as sgRNA, kits, medicines, composition, and method of use thereof.

The present invention is directed to improved materials and methods related to cytosine and adenosine base editing of genomic DNA.

The present invention relates to the field of data storage, and discloses a DNA-based dynamic balancing system, a data storage method, and a decoding method. During the process of encoding the first data to obtain a DNA molecular chain, various constraints are added to the first address and the second address, enabling the encoded data to be read efficiently and accurately. For example, the Hamming distance between the first address and the second address is greater than or equal to half of the length of the first address, reducing the possibility of address selection errors during reading; the prefix of the first address is different from the prefix of the second address and the suffix of the second address, avoiding the possibility of matching errors during the reading process; the content of guanine and cytosine in the prefix of each primer accounts for a preset ratio of the total content of guanine, cytosine, adenine, and thymine contained in the primer, resulting in high accuracy when sequencing is required to read the encoded data in advance.

Described herein are methods of modifying or editing a target nucleic acid such as methods that edit adenine to cytosine, thymine, or guanine. Compositions and systems for modifying or editing a target nucleic acid are also described. Methods, compositions and systems described herein may be used for generating allelic diversity.