990 results about "Cytosine" patented technology

The present invention provides a polynucleotide that not only has a high RNA interference effect on its target gene, but also has a very small risk of causing RNA interference against a gene unrelated to the target gene. A sequence segment conforming to the following rules (a) to (d) is searched from the base sequences of a target gene for RNA interference and, based on the search results, a polynucleotide capable of causing RNAi is designed, synthesized, etc.:(a) The 3′ end base is adenine, thymine, or uracil,(b) The 5′ end base is guanine or cytosine,(c) A 7-base sequence from the 3′ end is rich in one or more types of bases selected from the group consisting of adenine, thymine, and uracil, and(d) The number of bases is within a range that allows RNA interference to occur without causing cytotoxicity.

A method for the development of gene panels for diagnostic and therapeutic purposes comprising the steps of: (a) isolating at least one biological sample from each of at least two groups of biological material containing mRNA and / or proteins; (b) analyzing the expression level of at least one gene in the at least one biological sample; (c) selecting the gene(s) exhibiting a different expression level between the at least two groups of biological material, whereby a first knowledge base is generated; (d) analyzing the level of cytosine methylation in the methylation relevant regions of at least one gene of at least one of the biological samples of step (a), wherein the gene is selected on the basis of the first knowledge base; (e) selecting the gene(s) exhibiting a different level of cytosine methylation between the at least two groups of biological material, whereby a second knowledge base is generated; and (f) adding selected genes from the second knowledge base to a gene panel.

Provided are compounds represented by: X is O, S or NR6, R1 is H or (CH2)mR5, R2, R2', R3 and R3' are independently NO2, N3 or (CH2)mR5, OH R4 is H, OR6, SR6, NR6R6a, CN, C(O)OR6, C(O)NR6R6a, R6, OR7 or (CH2)nR7, R5 is H, halo, OR6, SR6, NR6R6a, CN, C(O)OR6, C(O)NR6R6a, R6, OR7 or (CH2)mR7, R6 and R6a are individually H, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl or substituted aryl, R7 is: R8 is H, F, SR9 or OR9, R9 is H, alkyl, alkenyl, alkynyl, aryl or hydroxyprotecting group, Y is H, CH3 or (CH2)mR5, Z is O or S W is CH2, CF2, CHF or O, m is 0-4, B is adenine, guanine, cytosine, uracil, thymine, modified purines and pyrimidines substituted pyridines, five membered heterocycles substituted by at least one of amines, substituted amines, amides, substituted amides, esters, halogens, alkyls, ethers; and pharmaceutically acceptable salts thereof and prodrugs thereof. These ring systems may be substituted.

There is disclosed a cancer diagnostic method based upon DNA methylation differences at specific CpG sites. Specifically, the inventive method provides for a bisulfite treatment of DNA, followed by methylation-sensitive single nucleotide primer extension (Ms-SNuPE), for determination of strand-specific methylation status at cytosine residues.

The present invention relates to chemically modified genomic sequences of genes associated with the immune system, to oligonucleotides and / or PNA-oligomers directed against the sequence, for the detection of the methylation status of genes, associated with the immune system as well as to a method for ascertaining genetic and / or epigentic parametres of genes, associated with the immune system.

Methods for amplifying a nucleic acid sample while preserving the methylation status of cytosines are disclosed. In some aspects the amplified methylated sample is modified by methylation sensitive modification and analyzed by hybridization to an array to identify cytosines that were methylated in the starting material and cytosines that were not methylated in the starting material. Methods for detecting methylation status are also disclosed. In one embodiment a DNA methyltransferase activity is included in the amplification reaction and this activity methylates the newly synthesized DNA using the methylated genomic template strand as a guide.

Quinoline derivatives, particularly 4-anilinoquinoline derivatives, are provided. Such quinoline derivatives can be used for modulation of DNA methylation, such as effective inhibition of methylation of cytosine at the C-5 position, for example via selective inhibition of DNA methyltransferase DNMT1. Methods for synthesizing numerous 4-anilinoquinoline derivatives and for modulating DNA methylation are provided. Also provided are methods for formulating and administering these compounds or compositions to treat conditions such as cancer and hematological disorders.

A novel nucleotide derivative, in case of existing as a member of a single-stranded sequence, undergoing a change in the fluorescent signal intendity depending on the corresponding base type in the partner strand with which the single-stranded sequence is hybridized, and which is a thymin / uracil derivative (1) emitting light most intensely when a confronting base in the partner strand with which the single-stranded nucleotide sequence is hybridized is adenine; a cytosine derivative (2) emitting light most intensely when the confronting base is guanine; an adenine derivative (3) emitting light most intensely when the confronting base is cytosine; a guanine derivative (4) emitting light most intensely when the confronting base is cytosine or thymine / uracil; and an adrnine derivative (5) emitting light most intensely when the confronting base is thymine / uracil / .

Methods of analyzing DNA to determine the methylation status of a plurality of cytosines are disclosed. In one aspect genomic DNA is fragmented, fragments are circularized, the circles are treated with a methylation sensitive enzyme to enrich for circles with methylated sites or with a methylation dependent enzyme to enrich for circles with unmethylated sites, and the circles are amplified. The amplified product is fragmented, labeled and hybridized to an array of probes. The array of probes may be a tiling array or an array of junction probes. The hybridization pattern is analyzed to determine methylation status of cytosines.

A reliable and highly sensitive method is provided for detecting methylation status of CpG-containing nucleic acids by nucleic acid amplification and melting curve analysis of amplification products. The methods and compositions employs a novel design of primers. CpG-containing methylation-independent oligonucleotide primers, wherein both unmethylated and methylated alleles of a CpG-containing nucleic acid can be detected by use of only one set of primers after the CpG-containing nucleic acid has been subjected to cytosine to thymine conversion of unmethylated Cytosine. The method is useful for detection of methylation status in for example cancer genes and other disease related genes, wherein methylation influences gene expression.

Quinoline derivatives, particularly 4-anilinoquinoline derivatives, are provided. Such quinoline derivatives can be used for modulation of DNA methylation, such as effective inhibition of methylation of cytosine at the C-5 position, for example via selective inhibition of DNA methyltransferase DNMT1. Methods for synthesizing numerous 4-anilinoquinoline derivatives and for modulating DNA methylation are provided. Also provided are methods for formulating and administering these compounds or compositions to treat conditions such as cancer and hematological disorders.

This invention provides a nucleotide analogue comprising (i) a base selected from the group consisting of adenine, guanine, cytosine, thymine and uracil, (ii) a deoxyribose, (iii) an allyl moiety bound to the 3′-oxygen of the deoxyribose and (iv) a fluorophore bound to the base via an allyl linker, and methods of nucleic acid sequencing employing the nucleotide analogue.

Quinoline derivatives, particularly 4-anilinoquinoline derivatives, are provided. Such quinoline derivatives can be used for modulation of DNA methylation, such as effective inhibition of methylation of cytosine at the C-5 position, for example via selective inhibition of DNA methyltransferase DNMT1. Methods for synthesizing numerous 4-anilinoquinoline derivatives and for modulating DNA methylation are provided. Also provided are methods for formulating and administering these compounds or compositions to treat conditions such as cancer and hematological disorders.

Described is a method for methylation detection in a DNA sample. An isolated genomic DNA sample is treated in a manner capable of distinguishing methylated from unmethylated cytosine bases. The pretreated DNA is amplified using at least one oligonucleotide primer, a polymerase and a set of nucleotides of which at least one is labeled with a first type of label. A sequence-specific oligonucleotide probe, marked with a second type of label, hybridizes to the amplification product and a FRET reaction occurs if a labeled oligonucleotide is present in close proximity in the amplification product. The method determines the level of methylation of a sample by measuring the extent of fluorescence resonance energy transfer (FRET) between the donor and acceptor fluorophore.

A method for preparing a nucleic acid probe is provided. The method comprises forming an activated cytosine or cytidine by a bisulfite catalyzed reaction; and covalently linking a reporter molecule to the activated cytosine or cytidine, wherein said activating step, said covalently linking step, or both are conducted in the presence of microwave energy. Also provided by the invention are nucleic acid probes.

Immunostimulatory compositions described as CpG-like nucleic acids are provided, including nucleic acids having immunostimulatory characteristics of CpG nucleic acid, despite certain substitutions of C, G, or C and G of the CpG dinucleotide. The substitutions can include, among others, exchange of methylated C for C, inosine for G, and ZpY for CpG, where Z is cytosine or dSpacer and Y is inosine, 2-aminopurine, nebularine, or dSpacer. Also provided are methods for inducing an immune response in a subject using the CpG-like nucleic acids. The methods are useful in the treatment of a subject that has or is at risk of developing an infectious disease, allergy, asthma, cancer, anemia, thrombocytopenia, or neutropenia.

The present invention provides pharmaceutical formulations of cytidine analogs and derivatives, such as 5-azacytidine, 5-aza-2′-deoxy-2′,2′-difluorocytidine, 5-aza-2′-deoxy-2′-fluorocytidine, 2′-deoxy-2′,2′-difluorocytidine, and cytosine 1-β-D-arabinofuranoside, as well as methods of manufacturing the formulations. In particular, the cytidine analog or derivative is formulated with a cyclodextrin compound to stabilize and / or enhance solubility of the drug. Kits and methods for using the pharmaceutical formulations are also provided, including methods of administering the cytidine analog or derivative to treat conditions or diseases, such as cancer and hematological disorders.

The invention discloses a construction method and an application of a high-throughout sequencing library. The construction method of the high-throughout sequencing library comprises the following steps: fragmenting genome DNA (deoxyribonucleic acid); repairing terminals of DNA fragments; adding a base A to 3' terminals of the DNA fragments with the repaired terminals; connecting the DNA fragments with sticky ends A to methylation linkers; carrying out hybrid capture on connecting products by using a specificity probe so as to obtain target fragments; carrying out bisulfite treatment on the target fragments so as to convert non-methylated cytosine in the target fragments to uracil; carrying out PCR (polymerase chain reaction) amplification on the converted target fragments; separating and purifying amplification products which form the high-throughout sequencing library. According to the method and application of the high-throughout sequencing library, the high-throughout sequencing library of a genome specific zone of a sample can be conveniently and efficiently constructed.

The invention provides a construction method and application of a genome-wide methylation high-throughput sequencing library. The construction method of the genome-wide methylation high-throughput sequencing library comprises steps of: conducting digestion on a genome DNA with Msp I and a second restriction endonuclease; conducting end repair on DNA fragments; adding a basic group A on a 3'terminal of the DNA fragment subjected to end repair; connecting a DNA fragment with a cohesive end A to a methylation joint; conducting fragment selection on the connect products with the methylation joint, in order to obtain a target fragment; subjecting the target fragment to a bisulfite treatment, in order to convert unmethylated cytosine in the target fragment to uracil; subjecting the converted target fragment to PCR amplification; and separating and purifying the amplification products, wherein the amplification products form the genome-wide methylation high-throughput sequencing library. The construction method and application of the genome-wide methylation high-throughput sequencing library provided by the invention can conveniently and effectively construct the genome-wide methylation high-throughput sequencing library of the genome DNA sample.

Short deoxyribonucleic acid molecules that are partially single-stranded, dumbbell-shaped, and covalently closed, which contain one or more unmethylated cytosine guanosine motif (CpG motif) and exhibit immunomodifying effects. Such molecules can be used for immunostimulation applications in humans or vertebrates.

Quinoline derivatives, particularly 4-anilinoquinoline derivatives, are provided. Such quinoline derivatives can be used for modulation of DNA methylation, such as effective inhibition of methylation of cytosine at the C-5 position, for example via selective inhibition of DNA methyltransferase DNMT1. Methods for synthesizing numerous 4-anilinoquinoline derivatives and for modulating DNA methylation are provided. Also provided are methods for formulating and administering these compounds or compositions to treat conditions such as cancer and hematological disorders.

Oligonucleotide analogues are provided that incorporate 5-aza-cytosine in the oligonucleotide sequence, e.g., in the form of 5-aza-2′-deoxycytidine (decitabine) or 5-aza-cytidine. In particular, oligonucleotide analogues rich in decitabine-deoxyguanosine islets (DpG and GpD) are provided to target the CpG islets in the human genome, especially in the promoter regions of genes susceptible to aberrant hypermethylation. Such analogues can be used for modulation of DNA methylation, such as effective inhibition of methylation of cytosine at the C-5 position. Methods for synthesizing these oligonucleotide analogues and for modulating nucleic acid methylation are provided. Also provided are phosphoramidite building blocks for synthesizing the oligonucleotide analogues, methods for synthesizing, formulating and administering these compounds or compositions to treat conditions, such as cancer and hematological disorders.

The invention belongs to the technical field of bioengineering and in particular relates to a gene site-directed mutation vector as well as a construction method and application thereof. The invention provides the gene site-directed mutation vector due to lots of optimizations, cytosine deaminase is guided to be close to cytosine through a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system, the cytosine is changed into uracil, then uracil is changed into thymine through self-repair in plant cells, and finally, site-specific mutagenesis from C to T is realized in plants so as to generate resistance to herbicides. In addition, point mutation can be produced in a non-sgRNA targeted area, and novel herbicide-resistant great agronomic traits are brought.

The invention provides a fluorescently-labeled gene multiplex amplification technology for detecting sources of goat, sheep, pig and duck meat simultaneously. A method comprises the steps that mitochondria 16S rRNA (ribosomal Robonucleic Acid) and Cyt (Cytosine) b genes of a goat, sheep, a pig and a duck serve as target genes, and are subjected to PCR (Polymerase Chain Reaction) multiplex amplification by two pairs of fluorescently-labeled primers; PCR amplification products are detected by a 3730xl full automatic gene analysis meter; and species identification is performed according to 16S rRNA gene amplified fragment length polymorphism. The method fills in a gap of a detection method of the four kinds of meat.

The invention belongs to the field of molecular biology, specifically belongs to the technical field of DNA storage, more specifically an artificially synthesized DNA storage medium with coding information, a storage reading method for the information, and applications. Discarding DNA storage technology depended on a mature binary code or a ternary code in the prior art, the invention creatively discloses a DNA storage mode capable of coding directly. Through using storage method capable of coding directly, especially tetragenous basic group coding, the obtained DNA chain storing digit information is short in entire sequence and average content of guanine and cytosine in the sequence is relatively balanced. The method of the invention is in favour of synthesizing, convenient for decoding, and could reduce error rate. The method of the invention can be used for covering a plurality of character types such as English, figure, Chinese and punctuation marks with wide application range.

Oligonucleotide analogues are provided that incorporate 5-aza-cytosine in the oligonucleotide sequence, e.g., in the form of 5-aza-2′-deoxycytidine (decitabine) or 5-aza-cytidine. In particular, oligonucleotide analogues rich in decitabine-deoxyguanosine islets (DpG and GpD) are provided to target the CpG islets in the human genome, especially in the promoter regions of genes susceptible to aberrant hypermethylation. Such analogues can be used for modulation of DNA methylation, such as effective inhibition of methylation of cytosine at the C-5 position. Methods for synthesizing these oligonucleotide analogues and for modulating nucleic acid methylation are provided. Also provided are phosphoramidite building blocks for synthesizing the oligonucleotide analogues, methods for synthesizing, formulating and administering these compounds or compositions to treat conditions, such as cancer and hematological disorders.

The invention provides a gene base editor, in particular relates to fusion protein. The fusion protein is characterized by comprising two fragments. The first fragment comprises APOBEC3A and the second fragment comprises CRISPR-related Cas protein. The base editor is capable of performing base edition in DNA and performing deamination on cytosine to be uracil, and the base editor still has higherediting efficiency even if cytosine is located at a GpC site or in a hypermethylated state.

Methods and kits of characterizing a GC rich region of a nucleic acid of interest are provided. One method is effected by (a) contacting the nucleic acid of interest with an agent that modifies cytosine or guanine residues into residues complementary to adenine or thymine for obtaining a modified nucleic acid in which the cytosine or guanine residues are replaced by the residues complementary to adenine or thymine; (b) amplifying the modified nucleic acid by amplification primers being hybridizable with the modified nucleic acid and being designed for directing amplification of at least a portion of the modified nucleic acid, for obtaining an amplification product corresponding to the GC rich region; and (c) determining the size of the amplification product, thereby characterizing the GC rich region of the nucleic acid of interest.