A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.
A pyrimidine base that is a fundamental unit of nucleic acids.
The removal of an amino group (NH2) from a chemical compound.
Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.
An enzyme that removes THYMINE and URACIL bases mispaired with GUANINE through hydrolysis of their N-glycosidic bond. These mispaired nucleotides generally occur through the hydrolytic DEAMINATION of 5-METHYLCYTOSINE to thymine.
Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)
An enzyme that catalyzes the transfer of a methyl group from S-ADENOSYLMETHIONINE to the 5-position of CYTOSINE residues in DNA.
Inorganic salts of sulfurous acid.
Thymine is a pyrimidine nucleobase, one of the four nucleobases in the nucleic acid of DNA (the other three being adenine, guanine, and cytosine), where it forms a base pair with adenine.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Osmium. A very hard, gray, toxic, and nearly infusible metal element, atomic number 76, atomic weight 190.2, symbol Os. (From Dorland, 28th ed)
A family of DNA repair enzymes that recognize damaged nucleotide bases and remove them by hydrolyzing the N-glycosidic bond that attaches them to the sugar backbone of the DNA molecule. The process called BASE EXCISION REPAIR can be completed by a DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA.
Methylases that are specific for CYTOSINE residues found on DNA.
5-Hydroxymethyl-6-methyl- 2,4-(1H,3H)-pyrimidinedione. Uracil derivative used in combination with toxic antibiotics to lessen their toxicity; also to stimulate leukopoiesis and immunity. Synonyms: pentoksil; hydroxymethylmethyluracil.
Non-heme iron-containing enzymes that incorporate two atoms of OXYGEN into the substrate. They are important in biosynthesis of FLAVONOIDS; GIBBERELLINS; and HYOSCYAMINE; and for degradation of AROMATIC HYDROCARBONS.
A purine base and a fundamental unit of ADENINE NUCLEOTIDES.
A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.
Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
A group of compounds which consist of a nucleotide molecule to which an additional nucleoside is attached through the phosphate molecule(s). The nucleotide can contain any number of phosphates.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.
Enzymes that are part of the restriction-modification systems. They are responsible for producing a species-characteristic methylation pattern, on either adenine or cytosine residues, in a specific short base sequence in the host cell's own DNA. This methylated sequence will occur many times in the host-cell DNA and remain intact for the lifetime of the cell. Any DNA from another species which gains entry into a living cell and lacks the characteristic methylation pattern will be recognized by the restriction endonucleases of similar specificity and destroyed by cleavage. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms.
A subclass of enzymes of the transferase class that catalyze the transfer of a methyl group from one compound to another. (Dorland, 28th ed) EC 2.1.1.
Small holes of nanometer dimensions in a membrane, that can be used as single molecule detectors. The pores can be biological or synthetic.
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
Deoxycytidine (dihydrogen phosphate). A deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions.
A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent.
Uracil is a nitrogenous base, specifically a pyrimidine derivative, which constitutes one of the four nucleobases in the nucleic acid of RNA (ribonucleic acid), pairing with adenine via hydrogen bonds during base-pairing. (25 words)
An enzyme which catalyzes an endonucleolytic cleavage near PYRIMIDINE DIMERS to produce a 5'-phosphate product. The enzyme acts on the damaged DNA strand, from the 5' side of the damaged site.
The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.
A group of enzymes catalyzing the endonucleolytic cleavage of DNA. They include members of EC 3.1.21.-, EC 3.1.22.-, EC 3.1.23.- (DNA RESTRICTION ENZYMES), EC 3.1.24.- (DNA RESTRICTION ENZYMES), and EC 3.1.25.-.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
Guanine is a purine nucleobase, one of the four nucleobases in the nucleic acid of DNA and RNA, involved in forming hydrogen bonds between complementary base pairs in double-stranded DNA molecules.
One of the Type II site-specific deoxyribonucleases (EC It recognizes and cleaves the sequences C/CGG and GGC/C at the slash. HpaII is from Haemophilus parainfluenzae. Several isoschizomers have been identified. EC 3.1.21.-.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A variant of ADENOMATOUS POLYPOSIS COLI caused by mutation in the APC gene (GENES, APC) on CHROMOSOME 5. It is characterized by not only the presence of multiple colonic polyposis but also extracolonic ADENOMATOUS POLYPS in the UPPER GASTROINTESTINAL TRACT; the EYE; the SKIN; the SKULL; and the FACIAL BONES; as well as malignancy in organs other than the GI tract.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.
The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).
Chemical reactions effected by light.
A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The fertilized OVUM resulting from the fusion of a male and a female gamete.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)

Base pairing of anhydrohexitol nucleosides with 2,6-diaminopurine, 5-methylcytosine and uracil asbase moiety. (1/489)

Hexitol nucleic acids (HNAs) with modified bases (5-methylcytosine, 2,6-diaminopurine or uracil) were synthesized. The introduction of the 5-methylcytosine base demonstrates that N -benzoylated 5-methylcytosyl-hexitol occurs as the imino tautomer. The base pairing systems (G:CMe, U:D, T:D and U:A) obey Watson-Crick rules. Substituting hT for hU, hCMefor hC and hD for hA generally leads to increased duplex stability. In a single case, replacement of hC by hCMedid not result in duplex stabilization. This sequence-specific effect could be explained by the geometry of the model duplex used for carrying out the thermal stability study. Generally, polypurine HNA sequences give more stable duplexes with their RNA complement than polypyrimidine HNA sequences. This observation supports the hypothesis that, besides changes in stacking pattern, the difference in conformational stress between purine and pyrimidine nucleosides may contribute to duplex stability. Introduction of hCMeand hD in HNA sequences further increases the potential of HNA to function as a steric blocking agent.  (+info)

Relationship between amount of esterase and gene copy number in insecticide-resistant Myzus persicae (Sulzer). (2/489)

Overproduction of the insecticide-degrading esterases, E4 and FE4, in peach-potato aphids, Myzus persicae (Sulzer), depends on both gene amplification and transcriptional control, the latter being associated with changes in DNA methylation. The structure and function of the aphid esterase genes have been studied but the determination of their copy number has proved difficult, a common problem with gene amplification. We have now used a combination of pulsed-field gel electrophoresis and quantitative competitive PCR to determine relative esterase gene copy numbers in aphid clones with different levels of insecticide resistance (R1, R2 and R3). There are approx. 4-fold increases between susceptible, R1, R2 and R3 aphids, reaching a maximum of approx. 80 times more genes in R3; this gives proportionate increases in esterase protein relative to susceptible aphids. Thus there is no overexpression of the amplified genes, in contrast with what was thought previously. For E4 genes, the loss of 5-methylcytosine is correlated with a loss of expression, greatly decreasing the amount of enzyme relative to the copy number.  (+info)

DNA methylation is a reversible biological signal. (3/489)

The pattern of DNA methylation plays an important role in regulating different genome functions. To test the hypothesis that DNA methylation is a reversible biochemical process, we purified a DNA demethylase from human cells that catalyzes the cleavage of a methyl residue from 5-methyl cytosine and its release as methanol. We show that similar to DNA methyltransferase, DNA demethylase shows CpG dinucleotide specificity, can demethylate mdCpdG sites in different sequence contexts, and demethylates both fully methylated and hemimethylated DNA. Thus, contrary to the commonly accepted model, DNA methylation is a reversible signal, similar to other physiological biochemical modifications.  (+info)

Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. (4/489)

CpG island methylation has been linked to tumor suppressor gene inactivation in neoplasia and may serve as a useful marker to clone novel cancer-related genes. We have developed a novel PCR-based method, methylated CpG island amplification (MCA), which is useful for both methylation analysis and cloning differentially methylated genes. Using restriction enzymes that have differential sensitivity to 5-methyl-cytosine, followed by adaptor ligation and PCR amplification, methylated CpG rich sequences can be preferentially amplified. In a model experiment using a probe from exon 1 of the p16 gene, signal was detected from MCA products of a colorectal cancer cell line but not in normal colon mucosa. To identify novel CpG islands differentially methylated in colorectal cancer, we have applied MCA coupled with representational difference analysis to the colon cancer cell line Caco2 as a tester and normal colon mucosa as a driver. Using this strategy, we isolated 33 differentially methylated DNA sequences, including fragments identical to several known genes (PAX6, Versican, alpha-tubulin, CSX, OPT, and rRNA gene). The association of hypermethylation of the clones obtained and transcriptional suppression in colorectal cancer was confirmed by examining the Versican gene, which we found to be silenced in methylated cell lines and reactivated by the methylation inhibitor 5-aza-2'-deoxycytidine. We therefore propose that MCA is a useful technique to study methylation and to isolate CpG islands differentially methylated in cancer.  (+info)

Growth phase-dependent regulation of Vsr endonuclease may contribute to 5-methylcytosine mutational hot spots in Escherichia coli. (5/489)

Using rabbit polyclonal antibodies, we have shown that the Dcm cytosine methylase of Escherichia coli is maintained at a constant level during cell growth, while Vsr endonuclease levels are growth phase dependent. Decreased production of Vsr relative to Dcm during the log phase may contribute substantially to the mutability of 5-methylcytosine.  (+info)

Impact of C5-cytosine methylation on the solution structure of d(GAAAACGTTTTC)2. An NMR and molecular modelling investigation. (6/489)

The solution structures of d(GAAAACGTTTTC)2 and of its methylated derivative d(GAAAAMe5CGTTTTC)2 have been determined by NMR and molecular modelling in order to examine the impact of cytosine methylation on the central CpG conformation. Detailed 1H NMR and 31P NMR investigation of the two oligomers includes quantitative NOESY, 2D homonuclear Hartmann-Hahn spectroscopy, double-quantum-filtered COSY and heteronuclear 1H-31P correlation. Back-calculations of NOESY spectra and simulations of double-quantum-filtered COSY patterns were performed to gain accurate information on interproton distances and sugar phase angles. Molecular models under experimental constraints were generated by energy minimization by means of the molecular mechanics program JUMNA. The MORASS software was used to iteratively refine the structures obtained. After methylation, the oligomer still has a B-DNA conformation. However, there are differences in the structural parameters and the thermal stability as compared to the unmethylated molecule. Careful structural analysis shows that after methylation CpG departs from the usual conformation observed in other ACGT tetramers with different surroundings. Subtle displacements of bases, sugars and backbone imposed by the steric interaction of the two methyl groups inside the major groove are accompanied by severe pinching of the minor groove at the C-G residues.  (+info)

The role of the Escherichia coli mug protein in the removal of uracil and 3,N(4)-ethenocytosine from DNA. (7/489)

The human thymine-DNA glycosylase has a sequence homolog in Escherichia coli that is described to excise uracils from U.G mismatches (Gallinari, P., and Jiricny, J. (1996) Nature 383, 735-738) and is named mismatched uracil glycosylase (Mug). It has also been described to remove 3,N(4)-ethenocytosine (epsilonC) from epsilonC.G mismatches (Saparbaev, M., and Laval, J. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 8508-8513). We used a mug mutant to clarify the role of this protein in DNA repair and mutation avoidance. We find that inactivation of mug has no effect on C to T or 5-methylcytosine to T mutations in E. coli and that this contrasts with the effect of ung defect on C to T mutations and of vsr defect on 5-methylcytosine to T mutations. Even under conditions where it is overproduced in cells, Mug has little effect on the frequency of C to T mutations. Because uracil-DNA glycosylase (Ung) and Vsr are known to repair U.G and T.G mismatches, respectively, we conclude that Mug does not repair U.G or T.G mismatches in vivo. A defect in mug also has little effect on forward mutations, suggesting that Mug does not play a role in avoiding mutations due to endogenous damage to DNA in growing E. coli. Cell-free extracts from mug(+) ung cells show very little ability to remove uracil from DNA, but can excise epsilonC. The latter activity is missing in extracts from mug cells, suggesting that Mug may be the only enzyme in E. coli that can remove this mutagenic adduct. Thus, the principal role of Mug in E. coli may be to help repair damage to DNA caused by exogenous chemical agents such as chloroacetaldehyde.  (+info)

5-Methylcytosine distribution and genome organization in triticale before and after treatment with 5-azacytidine. (8/489)

Triticale (2n=6x=42) is a hybrid plant including rye (R) and wheat (A and B) genomes. Using genomic in situ hybridization with rye DNA as a probe, we found the chromosomes of the R genome were not intermixed with the wheat chromosomes in 85% of nuclei. After treatment of seedlings with low doses of the drug 5-azacytidine (5-AC), leading to hypomethylation of the DNA, the chromosomes became intermixed in 60% of nuclei; the next generation showed intermediate organization. These results correlate with previous data showing that expression of R-genome rRNA genes, normally suppressed, is activated by 5-AC treatment and remains partially activated in the next generation. The distribution of 5-methylcytosine (5-mC) was studied using an antibody to 5-mC. Methylation was detected along the lengths of all chromosomes; there were some chromosome regions with enhanced and reduced methylation, but these were not located at consistent positions, nor were there differences between R and wheat genome chromosomes. After 5-AC treatment, lower levels of methylation were detected. After 5-AC treatment, in situ hybridization with rye genomic DNA sometimes showed micronuclei of rye origin and multiple translocations between wheat and rye chromosomes. Genomic DNA was analysed using methylation-sensitive restriction enzymes and, as probes, two rDNA sequences, two tandemly organised DNA sequences from rye (pSc200 and pSc250), and copia and the gypsy group retrotransposon fragments from rye and wheat. DNA extracted immediately after 5-AC treatment was cut more by methylation-sensitive restriction enzymes than DNA from untreated seedlings. Each probe gave a characteristic restriction fragment pattern, but rye- and wheat-origin probes behaved similarly, indicating that hypomethylation was induced in both genomes. In DNA samples from leaves taken 13-41 days after treatment, RFLP (Restriction Fragment Length Polymorphism) patterns were indistinguishable from controls and 5-AC treatments with all probes. Surprising differences in hybridization patterns were seen between DNA from root tips and leaves with the copia-fragment probes.  (+info)

5-Methylcytosine (5mC) is a chemical modification of the nucleotide base cytosine in DNA, where a methyl group (-CH3) is added to the 5th carbon atom of the cytosine ring. This modification is catalyzed by DNA methyltransferase enzymes and plays an essential role in epigenetic regulation of gene expression, genomic imprinting, X-chromosome inactivation, and suppression of transposable elements in eukaryotic cells. Abnormal DNA methylation patterns have been associated with various diseases, including cancer.

Cytosine is one of the four nucleobases in the nucleic acid molecules DNA and RNA, along with adenine, guanine, and thymine (in DNA) or uracil (in RNA). The single-letter abbreviation for cytosine is "C."

Cytosine base pairs specifically with guanine through hydrogen bonding, forming a base pair. In DNA, the double helix consists of two complementary strands of nucleotides held together by these base pairs, such that the sequence of one strand determines the sequence of the other. This property is critical for DNA replication and transcription, processes that are essential for life.

Cytosine residues in DNA can undergo spontaneous deamination to form uracil, which can lead to mutations if not corrected by repair mechanisms. In RNA, cytosine can be methylated at the 5-carbon position to form 5-methylcytosine, a modification that plays a role in regulating gene expression and other cellular processes.

Deamination is a biochemical process that refers to the removal of an amino group (-NH2) from a molecule, especially from an amino acid. This process typically results in the formation of a new functional group and the release of ammonia (NH3). Deamination plays a crucial role in the metabolism of amino acids, as it helps to convert them into forms that can be excreted or used for energy production. In some cases, deamination can also lead to the formation of toxic byproducts, which must be efficiently eliminated from the body to prevent harm.

DNA methylation is a process by which methyl groups (-CH3) are added to the cytosine ring of DNA molecules, often at the 5' position of cytospine phosphate-deoxyguanosine (CpG) dinucleotides. This modification is catalyzed by DNA methyltransferase enzymes and results in the formation of 5-methylcytosine.

DNA methylation plays a crucial role in the regulation of gene expression, genomic imprinting, X chromosome inactivation, and suppression of transposable elements. Abnormal DNA methylation patterns have been associated with various diseases, including cancer, where tumor suppressor genes are often silenced by promoter methylation.

In summary, DNA methylation is a fundamental epigenetic modification that influences gene expression and genome stability, and its dysregulation has important implications for human health and disease.

Thymine DNA Glycosylase (TDG) is an enzyme that plays a crucial role in the process of base excision repair (BER), which is a mechanism for correcting damaged or mismatched bases in DNA. Specifically, TDG is responsible for removing thymine bases that have been improperly incorporated into DNA opposite to guanine, forming a so-called "mismatch" or "lesion." This type of lesion can arise due to errors during DNA replication or from the mutagenic effects of environmental agents such as chemicals and radiation.

TDG recognizes and binds to the thymine-guanine mismatch, then catalyzes the removal of the thymine base by cleaving the N-glycosidic bond that links it to the deoxyribose sugar in the DNA backbone. This creates an abasic site, which is subsequently processed by other enzymes involved in BER to restore the original DNA sequence.

In addition to its role in DNA repair, TDG has been implicated in various cellular processes such as transcriptional regulation and epigenetic modification, due to its ability to interact with other proteins and regulatory elements in the genome. Dysregulation of TDG function has been linked to several human diseases, including cancer and neurological disorders.

Methylation, in the context of genetics and epigenetics, refers to the addition of a methyl group (CH3) to a molecule, usually to the nitrogenous base of DNA or to the side chain of amino acids in proteins. In DNA methylation, this process typically occurs at the 5-carbon position of cytosine residues that precede guanine residues (CpG sites) and is catalyzed by enzymes called DNA methyltransferases (DNMTs).

DNA methylation plays a crucial role in regulating gene expression, genomic imprinting, X-chromosome inactivation, and suppression of repetitive elements. Hypermethylation or hypomethylation of specific genes can lead to altered gene expression patterns, which have been associated with various human diseases, including cancer.

In summary, methylation is a fundamental epigenetic modification that influences genomic stability, gene regulation, and cellular function by introducing methyl groups to DNA or proteins.

Sulfites are a group of chemical compounds that contain the sulfite ion (SO3−2), which consists of one sulfur atom and three oxygen atoms. In medical terms, sulfites are often used as food additives or preservatives, serving to prevent bacterial growth and preserve the color of certain foods and drinks.

Sulfites can be found naturally in some foods, such as wine, dried fruits, and vegetables, but they are also added to a variety of processed products like potato chips, beer, and soft drinks. While sulfites are generally considered safe for most people, they can cause adverse reactions in some individuals, particularly those with asthma or a sensitivity to sulfites.

In the medical field, sulfites may also be used as medications to treat certain conditions. For example, they may be used as a vasodilator to widen blood vessels and improve blood flow during heart surgery or as an antimicrobial agent in some eye drops. However, their use as a medication is relatively limited due to the potential for adverse reactions.

Thymine is a pyrimidine nucleobase that is one of the four nucleobases in the nucleic acid double helix of DNA (the other three being adenine, guanine, and cytosine). It is denoted by the letter T in DNA notation and pairs with adenine via two hydrogen bonds. Thymine is not typically found in RNA, where uracil takes its place pairing with adenine. The structure of thymine consists of a six-membered ring (pyrimidine) fused to a five-membered ring containing two nitrogen atoms and a ketone group.

Deoxyribonucleic acid (DNA) is the genetic material present in the cells of organisms where it is responsible for the storage and transmission of hereditary information. DNA is a long molecule that consists of two strands coiled together to form a double helix. Each strand is made up of a series of four nucleotide bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - that are linked together by phosphate and sugar groups. The sequence of these bases along the length of the molecule encodes genetic information, with A always pairing with T and C always pairing with G. This base-pairing allows for the replication and transcription of DNA, which are essential processes in the functioning and reproduction of all living organisms.

I'm sorry for the confusion, but "Osmium" is not a medical term. It is actually a chemical element with symbol "Os" and atomic number 76. Osmium is a hard, brittle, blue-gray or blue-black transition metal in the platinum group that is found as a minor constituent in some mineral deposits such as placer gold.

It's primarily used in the manufacture of fountain pen tips, electrical contacts, and other specialized applications. Osmium tetroxide, a volatile, pale yellow, water-soluble compound formed by the reaction of osmium with oxygen or chlorine, is used as a fixative and stain in electron microscopy, histology, and in mortuary science for the stabilization and staining of tissues. However, exposure to osmium tetroxide can cause respiratory irritation and damage, so it's handled with great care.

DNA glycosylases are a group of enzymes that play a crucial role in the maintenance of genetic material. They are responsible for initiating the base excision repair (BER) pathway, which is one of the major DNA repair mechanisms in cells.

The function of DNA glycosylases is to remove damaged or mismatched bases from DNA molecules. These enzymes recognize and bind to specific types of damaged or incorrect bases, and then cleave the N-glycosidic bond between the base and the deoxyribose sugar in the DNA backbone. This results in the formation of an apurinic/apyrimidinic (AP) site, which is subsequently processed by other enzymes in the BER pathway.

There are several different types of DNA glycosylases that recognize and remove specific types of damaged or incorrect bases. For example, some DNA glycosylases specialize in removing oxidized bases, while others are responsible for removing mismatched bases or those that have been alkylated or methylated.

Overall, the proper functioning of DNA glycosylases is essential for maintaining genomic stability and preventing the accumulation of mutations that can lead to diseases such as cancer.

DNA cytosine methylases are a type of enzyme that catalyze the transfer of a methyl group (-CH3) to the carbon-5 position of the cytosine ring in DNA, forming 5-methylcytosine. This process is known as DNA methylation and plays an important role in regulating gene expression, genomic imprinting, X-chromosome inactivation, and suppression of transposable elements in eukaryotic organisms.

In mammals, the most well-studied DNA cytosine methylases are members of the DNMT (DNA methyltransferase) family, including DNMT1, DNMT3A, and DNMT3B. DNMT1 is primarily responsible for maintaining existing methylation patterns during DNA replication, while DNMT3A and DNMT3B are involved in establishing new methylation patterns during development and differentiation.

Abnormal DNA methylation patterns have been implicated in various diseases, including cancer, where global hypomethylation and promoter-specific hypermethylation can contribute to genomic instability, chromosomal aberrations, and silencing of tumor suppressor genes.

I'm sorry for any confusion, but "Pentoxyl" doesn't seem to be a recognized term in medical terminology or pharmacology. It's possible that there might be a spelling mistake or it could be a brand name of a drug that is not widely known.

If you meant "Pentoxifylline," however, I can provide a definition. Pentoxifylline is a medication that belongs to a class of drugs known as methylxanthines. It works by improving the flow of blood in the body, particularly in the hands and feet, by decreasing the thickness (viscosity) of the blood. This medication is used to treat conditions such as intermittent claudication (pain in the legs due to poor blood flow) and certain types of Raynaud's phenomenon.

Please make sure that you have the correct spelling when looking for medical information, as it's crucial to have accurate details when researching health-related topics.

Dioxygenases are a class of enzymes that catalyze the incorporation of both atoms of molecular oxygen (O2) into their substrates. They are classified based on the type of reaction they catalyze and the number of iron atoms in their active site. The two main types of dioxygenases are:

1. Intradiol dioxygenases: These enzymes cleave an aromatic ring by inserting both atoms of O2 into a single bond between two carbon atoms, leading to the formation of an unsaturated diol (catechol) intermediate and the release of CO2. They contain a non-heme iron(III) center in their active site.

An example of intradiol dioxygenase is catechol 1,2-dioxygenase, which catalyzes the conversion of catechol to muconic acid.

2. Extradiol dioxygenases: These enzymes cleave an aromatic ring by inserting one atom of O2 at a position adjacent to the hydroxyl group and the other atom at a more distant position, leading to the formation of an unsaturated lactone or cyclic ether intermediate. They contain a non-heme iron(II) center in their active site.

An example of extradiol dioxygenase is homogentisate 1,2-dioxygenase, which catalyzes the conversion of homogentisate to maleylacetoacetate in the tyrosine degradation pathway.

Dioxygenases play important roles in various biological processes, including the metabolism of aromatic compounds, the biosynthesis of hormones and signaling molecules, and the detoxification of xenobiotics.

Adenine is a purine nucleotide base that is a fundamental component of DNA and RNA, the genetic material of living organisms. In DNA, adenine pairs with thymine via double hydrogen bonds, while in RNA, it pairs with uracil. Adenine is essential for the structure and function of nucleic acids, as well as for energy transfer reactions in cells through its role in the formation of adenosine triphosphate (ATP), the primary energy currency of the cell.

N-Glycosyl hydrolases (or N-glycanases) are a class of enzymes that catalyze the hydrolysis of the glycosidic bond between an N-glycosyl group and an aglycon, which is typically another part of a larger molecule such as a protein or lipid. N-Glycosyl groups refer to carbohydrate moieties attached to an nitrogen atom, usually in the side chain of an amino acid such as asparagine (Asn) in proteins.

N-Glycosyl hydrolases play important roles in various biological processes, including the degradation and processing of glycoproteins, the modification of glycolipids, and the breakdown of complex carbohydrates. These enzymes are widely distributed in nature and have been found in many organisms, from bacteria to humans.

The classification and nomenclature of N-Glycosyl hydrolases are based on the type of glycosidic bond they cleave and the stereochemistry of the reaction they catalyze. They are grouped into different families in the Carbohydrate-Active enZymes (CAZy) database, which provides a comprehensive resource for the study of carbohydrate-active enzymes.

It is worth noting that N-Glycosyl hydrolases can have both beneficial and detrimental effects on human health. For example, they are involved in the normal turnover and degradation of glycoproteins in the body, but they can also contribute to the pathogenesis of certain diseases, such as lysosomal storage disorders, where mutations in N-Glycosyl hydrolases lead to the accumulation of undigested glycoconjugates and cellular damage.

CpG islands are defined as short stretches of DNA that are characterized by a higher than expected frequency of CpG dinucleotides. A dinucleotide is a pair of adjacent nucleotides, and in the case of CpG, C represents cytosine and G represents guanine. These islands are typically found in the promoter regions of genes, where they play important roles in regulating gene expression.

Under normal circumstances, the cytosine residue in a CpG dinucleotide is often methylated, meaning that a methyl group (-CH3) is added to the cytosine base. However, in CpG islands, methylation is usually avoided, and these regions tend to be unmethylated. This has important implications for gene expression because methylation of CpG dinucleotides in promoter regions can lead to the silencing of genes.

CpG islands are also often targets for transcription factors, which bind to specific DNA sequences and help regulate gene expression. The unmethylated state of CpG islands is thought to be important for maintaining the accessibility of these regions to transcription factors and other regulatory proteins.

Abnormal methylation patterns in CpG islands have been associated with various diseases, including cancer. In many cancers, CpG islands become aberrantly methylated, leading to the silencing of tumor suppressor genes and contributing to the development and progression of the disease.

A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.

DNA restriction enzymes, also known as restriction endonucleases, are a type of enzyme that cut double-stranded DNA at specific recognition sites. These enzymes are produced by bacteria and archaea as a defense mechanism against foreign DNA, such as that found in bacteriophages (viruses that infect bacteria).

Restriction enzymes recognize specific sequences of nucleotides (the building blocks of DNA) and cleave the phosphodiester bonds between them. The recognition sites for these enzymes are usually palindromic, meaning that the sequence reads the same in both directions when facing the opposite strands of DNA.

Restriction enzymes are widely used in molecular biology research for various applications such as genetic engineering, genome mapping, and DNA fingerprinting. They allow scientists to cut DNA at specific sites, creating precise fragments that can be manipulated and analyzed. The use of restriction enzymes has been instrumental in the development of recombinant DNA technology and the Human Genome Project.

Dinucleoside phosphates are the chemical compounds that result from the linkage of two nucleosides through a phosphate group. Nucleosides themselves consist of a sugar molecule (ribose or deoxyribose) and a nitrogenous base (adenine, guanine, cytosine, thymine, or uracil). When two nucleosides are joined together by an ester bond between the phosphate group and the 5'-hydroxyl group of the sugar moiety, they form a dinucleoside phosphate.

These compounds play crucial roles in various biological processes, particularly in the context of DNA and RNA synthesis and repair. For instance, dinucleoside phosphates serve as building blocks for the formation of longer nucleic acid chains during replication and transcription. They are also involved in signaling pathways and energy transfer within cells.

It is worth noting that the term "dinucleotides" is sometimes used interchangeably with dinucleoside phosphates, although technically, dinucleotides refer to compounds formed by joining two nucleotides (nucleosides plus one or more phosphate groups) rather than just two nucleosides.

Oligodeoxyribonucleotides (ODNs) are relatively short, synthetic single-stranded DNA molecules. They typically contain 15 to 30 nucleotides, but can range from 2 to several hundred nucleotides in length. ODNs are often used as tools in molecular biology research for various applications such as:

1. Nucleic acid detection and quantification (e.g., real-time PCR)
2. Gene regulation (antisense, RNA interference)
3. Gene editing (CRISPR-Cas systems)
4. Vaccine development
5. Diagnostic purposes

Due to their specificity and affinity towards complementary DNA or RNA sequences, ODNs can be designed to target a particular gene or sequence of interest. This makes them valuable tools in understanding gene function, regulation, and interaction with other molecules within the cell.

Epigenetics is the study of heritable changes in gene function that occur without a change in the underlying DNA sequence. These changes can be caused by various mechanisms such as DNA methylation, histone modification, and non-coding RNA molecules. Epigenetic changes can be influenced by various factors including age, environment, lifestyle, and disease state.

Genetic epigenesis specifically refers to the study of how genetic factors influence these epigenetic modifications. Genetic variations between individuals can lead to differences in epigenetic patterns, which in turn can contribute to phenotypic variation and susceptibility to diseases. For example, certain genetic variants may predispose an individual to develop cancer, and environmental factors such as smoking or exposure to chemicals can interact with these genetic variants to trigger epigenetic changes that promote tumor growth.

Overall, the field of genetic epigenesis aims to understand how genetic and environmental factors interact to regulate gene expression and contribute to disease susceptibility.

DNA modification methylases are a type of enzyme that catalyze the transfer of methyl groups (-CH3) to specific nucleotides in DNA, usually cytosine or adenine residues. This process is known as DNA methylation and is an important epigenetic mechanism that regulates gene expression, genome stability, and other cellular processes.

There are several types of DNA modification methylases, including:

1. Cytosine-5 methyltransferases (CNMTs or DNMTs): These enzymes catalyze the transfer of a methyl group to the fifth carbon atom of cytosine residues in DNA, forming 5-methylcytosine (5mC). This is the most common type of DNA methylation and plays a crucial role in gene silencing, X-chromosome inactivation, and genomic imprinting.
2. N6-adenine methyltransferases (MTases): These enzymes catalyze the transfer of a methyl group to the sixth nitrogen atom of adenine residues in DNA, forming N6-methyladenine (6mA). This type of DNA methylation is less common than 5mC but has been found to be involved in various cellular processes, such as transcriptional regulation and DNA repair.
3. GpC methyltransferases: These enzymes catalyze the transfer of a methyl group to the second carbon atom of guanine residues in DNA, forming N4-methylcytosine (4mC). This type of DNA methylation is relatively rare and has been found mainly in prokaryotic genomes.

Dysregulation of DNA modification methylases has been implicated in various diseases, including cancer, neurological disorders, and immunological diseases. Therefore, understanding the function and regulation of these enzymes is essential for developing novel therapeutic strategies to treat these conditions.

Methyltransferases are a class of enzymes that catalyze the transfer of a methyl group (-CH3) from a donor molecule to an acceptor molecule, which is often a protein, DNA, or RNA. This transfer of a methyl group can modify the chemical and physical properties of the acceptor molecule, playing a crucial role in various cellular processes such as gene expression, signal transduction, and DNA repair.

In biochemistry, methyltransferases are classified based on the type of donor molecule they use for the transfer of the methyl group. The most common methyl donor is S-adenosylmethionine (SAM), a universal methyl group donor found in many organisms. Methyltransferases that utilize SAM as a cofactor are called SAM-dependent methyltransferases.

Abnormal regulation or function of methyltransferases has been implicated in several diseases, including cancer and neurological disorders. Therefore, understanding the structure, function, and regulation of these enzymes is essential for developing targeted therapies to treat these conditions.

A nanopore is a tiny, narrow opening or passage at the molecular level, with a diameter typically measured in nanometers (nm). In the context of medicine and biology, nanopores are often used to describe protein structures that form water-filled channels across lipid membranes. These nanopores allow for the selective transport of ions, small molecules, or RNA/DNA strands between intracellular and extracellular spaces.

Nanopore technology has gained significant attention in medical research due to its potential applications in single-molecule analysis, diagnostics, and targeted drug delivery. For instance, nanopores can be used for rapid DNA sequencing by threading individual DNA strands through the pore and detecting changes in ionic current as nucleotides pass through. This information can then be translated into a sequence of bases, providing valuable insights into genetic makeup and potential disease markers.

Nucleic acid denaturation is the process of separating the two strands of a double-stranded DNA molecule, or unwinding the helical structure of an RNA molecule, by disrupting the hydrogen bonds that hold the strands together. This process is typically caused by exposure to high temperatures, changes in pH, or the presence of chemicals called denaturants.

Denaturation can also cause changes in the shape and function of nucleic acids. For example, it can disrupt the secondary and tertiary structures of RNA molecules, which can affect their ability to bind to other molecules and carry out their functions within the cell.

In molecular biology, nucleic acid denaturation is often used as a tool for studying the structure and function of nucleic acids. For example, it can be used to separate the two strands of a DNA molecule for sequencing or amplification, or to study the interactions between nucleic acids and other molecules.

It's important to note that denaturation is a reversible process, and under the right conditions, the double-stranded structure of DNA can be restored through a process called renaturation or annealing.

Deoxycytidine monophosphate (dCMP) is a nucleotide that is a building block of DNA. It consists of the sugar deoxyribose, the base cytosine, and one phosphate group. Nucleotides like dCMP are linked together through the phosphate groups to form long chains of DNA. In this way, dCMP plays an essential role in the structure and function of DNA, including the storage and transmission of genetic information.

Azacitidine is a medication that is primarily used to treat myelodysplastic syndrome (MDS), a type of cancer where the bone marrow does not produce enough healthy blood cells. It is also used to treat acute myeloid leukemia (AML) in some cases.

Azacitidine is a type of drug known as a hypomethylating agent, which means that it works by modifying the way that genes are expressed in cancer cells. Specifically, azacitidine inhibits the activity of an enzyme called DNA methyltransferase, which adds methyl groups to the DNA molecule and can silence the expression of certain genes. By inhibiting this enzyme, azacitidine can help to restore the normal function of genes that have been silenced in cancer cells.

Azacitidine is typically given as a series of subcutaneous (under the skin) or intravenous (into a vein) injections over a period of several days, followed by a rest period of several weeks before the next cycle of treatment. The specific dosage and schedule may vary depending on the individual patient's needs and response to treatment.

Like all medications, azacitidine can have side effects, which may include nausea, vomiting, diarrhea, constipation, fatigue, fever, and decreased appetite. More serious side effects are possible, but relatively rare, and may include bone marrow suppression, infections, and liver damage. Patients receiving azacitidine should be closely monitored by their healthcare provider to manage any side effects that may occur.

Uracil is not a medical term, but it is a biological molecule. Medically or biologically, uracil can be defined as one of the four nucleobases in the nucleic acid of RNA (ribonucleic acid) that is linked to a ribose sugar by an N-glycosidic bond. It forms base pairs with adenine in double-stranded RNA and DNA. Uracil is a pyrimidine derivative, similar to thymine found in DNA, but it lacks the methyl group (-CH3) that thymine has at the 5 position of its ring.

Epigenomics is the study of the epigenome, which refers to all of the chemical modifications and protein interactions that occur on top of a person's genetic material (DNA). These modifications do not change the underlying DNA sequence but can affect gene expression, or how much a particular gene is turned on or off.

Examples of epigenetic modifications include DNA methylation, histone modification, and non-coding RNA molecules. These modifications can be influenced by various factors such as age, environment, lifestyle, and disease state. Epigenomic changes have been implicated in the development and progression of many diseases, including cancer, and are an active area of research in molecular biology and genomics.

Endodeoxyribonucleases are a type of enzyme that cleave, or cut, phosphodiester bonds within the backbone of DNA molecules. These enzymes are also known as restriction endonucleases or simply restriction enzymes. They are called "restriction" enzymes because they were first discovered in bacteria, where they function to protect the organism from foreign DNA by cleaving and destroying invading viral DNA.

Endodeoxyribonucleases recognize specific sequences of nucleotides within the DNA molecule, known as recognition sites or restriction sites, and cut the phosphodiester bonds at specific locations within these sites. The cuts made by endodeoxyribonucleases can be either "sticky" or "blunt," depending on whether the enzyme leaves single-stranded overhangs or creates blunt ends at the site of cleavage, respectively.

Endodeoxyribonucleases are widely used in molecular biology research for various applications, including DNA cloning, genome mapping, and genetic engineering. They allow researchers to cut DNA molecules at specific sites, creating defined fragments that can be manipulated and recombined in a variety of ways.

DNA repair is the process by which cells identify and correct damage to the DNA molecules that encode their genome. DNA can be damaged by a variety of internal and external factors, such as radiation, chemicals, and metabolic byproducts. If left unrepaired, this damage can lead to mutations, which may in turn lead to cancer and other diseases.

There are several different mechanisms for repairing DNA damage, including:

1. Base excision repair (BER): This process repairs damage to a single base in the DNA molecule. An enzyme called a glycosylase removes the damaged base, leaving a gap that is then filled in by other enzymes.
2. Nucleotide excision repair (NER): This process repairs more severe damage, such as bulky adducts or crosslinks between the two strands of the DNA molecule. An enzyme cuts out a section of the damaged DNA, and the gap is then filled in by other enzymes.
3. Mismatch repair (MMR): This process repairs errors that occur during DNA replication, such as mismatched bases or small insertions or deletions. Specialized enzymes recognize the error and remove a section of the newly synthesized strand, which is then replaced by new nucleotides.
4. Double-strand break repair (DSBR): This process repairs breaks in both strands of the DNA molecule. There are two main pathways for DSBR: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ directly rejoins the broken ends, while HR uses a template from a sister chromatid to repair the break.

Overall, DNA repair is a crucial process that helps maintain genome stability and prevent the development of diseases caused by genetic mutations.

Guanine is not a medical term per se, but it is a biological molecule that plays a crucial role in the body. Guanine is one of the four nucleobases found in the nucleic acids DNA and RNA, along with adenine, cytosine, and thymine (in DNA) or uracil (in RNA). Specifically, guanine pairs with cytosine via hydrogen bonds to form a base pair.

Guanine is a purine derivative, which means it has a double-ring structure. It is formed through the synthesis of simpler molecules in the body and is an essential component of genetic material. Guanine's chemical formula is C5H5N5O.

While guanine itself is not a medical term, abnormalities or mutations in genes that contain guanine nucleotides can lead to various medical conditions, including genetic disorders and cancer.

Deoxyribonuclease HpaII, also known as HpaII endonuclease or simply HpaII, is an enzyme that cleaves double-stranded DNA at the recognition site 5'-CCGG-3'. It is a type of restriction endonuclease that is isolated from the bacterium Haemophilus parainfluenzae. The 'H' and the 'pa' in HpaII stand for Haemophilus parainfluenzae, and the Roman numeral II indicates that it was the second such enzyme to be discovered from this bacterial species.

The HpaII enzyme cuts the DNA strand between the two Gs in the recognition site, leaving a 5'-overhang of two unpaired cytosines on the 3'-end of each cleaved strand. This specificity makes it useful for various molecular biology techniques, such as genetic fingerprinting, genome mapping, and DNA sequencing.

It is worth noting that HpaII is sensitive to methylation at the internal cytosine residue within its recognition site. If the inner cytosine in the 5'-CCGG-3' sequence is methylated (i.e., 5-methylcytosine), HpaII will not cut the DNA at that site, which can be exploited for epigenetic studies and DNA methylation analysis.

Substrate specificity in the context of medical biochemistry and enzymology refers to the ability of an enzyme to selectively bind and catalyze a chemical reaction with a particular substrate (or a group of similar substrates) while discriminating against other molecules that are not substrates. This specificity arises from the three-dimensional structure of the enzyme, which has evolved to match the shape, charge distribution, and functional groups of its physiological substrate(s).

Substrate specificity is a fundamental property of enzymes that enables them to carry out highly selective chemical transformations in the complex cellular environment. The active site of an enzyme, where the catalysis takes place, has a unique conformation that complements the shape and charge distribution of its substrate(s). This ensures efficient recognition, binding, and conversion of the substrate into the desired product while minimizing unwanted side reactions with other molecules.

Substrate specificity can be categorized as:

1. Absolute specificity: An enzyme that can only act on a single substrate or a very narrow group of structurally related substrates, showing no activity towards any other molecule.
2. Group specificity: An enzyme that prefers to act on a particular functional group or class of compounds but can still accommodate minor structural variations within the substrate.
3. Broad or promiscuous specificity: An enzyme that can act on a wide range of structurally diverse substrates, albeit with varying catalytic efficiencies.

Understanding substrate specificity is crucial for elucidating enzymatic mechanisms, designing drugs that target specific enzymes or pathways, and developing biotechnological applications that rely on the controlled manipulation of enzyme activities.

Gardner Syndrome is a rare inherited condition associated with a mutation in the APC gene, which also causes Familial Adenomatous Polyposis (FAP). This syndrome is characterized by the development of multiple benign tumors called adenomas in the colon and rectum. Additionally, individuals with Gardner Syndrome often develop various types of non-cancerous growths outside the gastrointestinal tract, such as osteomas (benign bone tumors), dental abnormalities, and epidermoid cysts on the skin.

Individuals with this syndrome have an increased risk of developing colorectal cancer at a young age, typically before 40 years old, if not monitored and treated appropriately. Other cancers that may develop in association with Gardner Syndrome include duodenal cancer, thyroid cancer, brain tumors (particularly cerebellar medulloblastomas), and adrenal gland tumors.

Regular surveillance through colonoscopies and other diagnostic tests is crucial for early detection and management of potential malignancies in individuals with Gardner Syndrome.

A genome is the complete set of genetic material (DNA, or in some viruses, RNA) present in a single cell of an organism. It includes all of the genes, both coding and noncoding, as well as other regulatory elements that together determine the unique characteristics of that organism. The human genome, for example, contains approximately 3 billion base pairs and about 20,000-25,000 protein-coding genes.

The term "genome" was first coined by Hans Winkler in 1920, derived from the word "gene" and the suffix "-ome," which refers to a complete set of something. The study of genomes is known as genomics.

Understanding the genome can provide valuable insights into the genetic basis of diseases, evolution, and other biological processes. With advancements in sequencing technologies, it has become possible to determine the entire genomic sequence of many organisms, including humans, and use this information for various applications such as personalized medicine, gene therapy, and biotechnology.

Cytidine is a nucleoside, which consists of the sugar ribose and the nitrogenous base cytosine. It is an important component of RNA (ribonucleic acid), where it pairs with guanosine via hydrogen bonding to form a base pair. Cytidine can also be found in some DNA (deoxyribonucleic acid) sequences, particularly in viral DNA and in mitochondrial DNA.

Cytidine can be phosphorylated to form cytidine monophosphate (CMP), which is a nucleotide that plays a role in various biochemical reactions in the body. CMP can be further phosphorylated to form cytidine diphosphate (CDP) and cytidine triphosphate (CTP), which are involved in the synthesis of lipids, glycogen, and other molecules.

Cytidine is also available as a dietary supplement and has been studied for its potential benefits in treating various health conditions, such as liver disease and cancer. However, more research is needed to confirm these potential benefits and establish safe and effective dosages.

A base pair mismatch is a type of mutation that occurs during the replication or repair of DNA, where two incompatible nucleotides pair up instead of the usual complementary bases (adenine-thymine or cytosine-guanine). This can result in the substitution of one base pair for another and may lead to changes in the genetic code, potentially causing errors in protein synthesis and possibly contributing to genetic disorders or diseases, including cancer.

Photochemical processes refer to chemical reactions that are initiated or driven by the absorption of light. In these reactions, photons (light particles) interact with molecules, causing electrons in the molecules to become excited and leading to the formation of new chemical bonds or the breaking of existing ones. This results in the creation of different molecular structures or products.

In the context of human health and medicine, photochemical processes can occur both naturally and artificially. For instance, the body uses light-dependent reactions in the process of vision, where light is absorbed by rhodopsin in the retina, triggering a series of chemical events that ultimately lead to visual perception.

Additionally, photochemotherapy is a medical treatment that utilizes photochemical processes to achieve therapeutic effects. In this approach, a photosensitizing agent is administered to a patient, and then exposed to specific wavelengths of light. The light causes the photosensitizer to react with oxygen, generating reactive oxygen species that can destroy targeted cells or tissues, such as cancer cells or bacteria.

Overall, photochemical processes play an essential role in various biological and medical contexts, enabling critical functions like vision and offering promising therapeutic avenues for a range of conditions.

Oxidation-Reduction (redox) reactions are a type of chemical reaction involving a transfer of electrons between two species. The substance that loses electrons in the reaction is oxidized, and the substance that gains electrons is reduced. Oxidation and reduction always occur together in a redox reaction, hence the term "oxidation-reduction."

In biological systems, redox reactions play a crucial role in many cellular processes, including energy production, metabolism, and signaling. The transfer of electrons in these reactions is often facilitated by specialized molecules called electron carriers, such as nicotinamide adenine dinucleotide (NAD+/NADH) and flavin adenine dinucleotide (FAD/FADH2).

The oxidation state of an element in a compound is a measure of the number of electrons that have been gained or lost relative to its neutral state. In redox reactions, the oxidation state of one or more elements changes as they gain or lose electrons. The substance that is oxidized has a higher oxidation state, while the substance that is reduced has a lower oxidation state.

Overall, oxidation-reduction reactions are fundamental to the functioning of living organisms and are involved in many important biological processes.

DNA-binding proteins are a type of protein that have the ability to bind to DNA (deoxyribonucleic acid), the genetic material of organisms. These proteins play crucial roles in various biological processes, such as regulation of gene expression, DNA replication, repair and recombination.

The binding of DNA-binding proteins to specific DNA sequences is mediated by non-covalent interactions, including electrostatic, hydrogen bonding, and van der Waals forces. The specificity of binding is determined by the recognition of particular nucleotide sequences or structural features of the DNA molecule.

DNA-binding proteins can be classified into several categories based on their structure and function, such as transcription factors, histones, and restriction enzymes. Transcription factors are a major class of DNA-binding proteins that regulate gene expression by binding to specific DNA sequences in the promoter region of genes and recruiting other proteins to modulate transcription. Histones are DNA-binding proteins that package DNA into nucleosomes, the basic unit of chromatin structure. Restriction enzymes are DNA-binding proteins that recognize and cleave specific DNA sequences, and are widely used in molecular biology research and biotechnology applications.

Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.

A zygote is the initial cell formed when a sperm fertilizes an egg, also known as an oocyte. This occurs in the process of human reproduction and marks the beginning of a new genetic identity, containing 46 chromosomes - 23 from the sperm and 23 from the egg. The zygote starts the journey of cell division and growth, eventually developing into a blastocyst, then an embryo, and finally a fetus over the course of pregnancy.

Oligonucleotides are short sequences of nucleotides, the building blocks of DNA and RNA. They typically contain fewer than 100 nucleotides, and can be synthesized chemically to have specific sequences. Oligonucleotides are used in a variety of applications in molecular biology, including as probes for detecting specific DNA or RNA sequences, as inhibitors of gene expression, and as components of diagnostic tests and therapies. They can also be used in the study of protein-nucleic acid interactions and in the development of new drugs.

In 5-methylcytosine, a methyl group is attached to the 5th atom in the 6-atom ring, counting counterclockwise from the NH- ... In plants, 5-methylcytosine occurs at CpG, CpHpG and CpHpH sequences (where H = A, C or T). In fungi and animals, 5- ... methylcytosine predominantly occurs at CpG dinucleotides. Most eukaryotes methylate only a small percentage of these sites, but ... 5-Methylcytosine is a methylated form of the DNA base cytosine (C) that regulates gene transcription and takes several other ...
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The Discovery of 5-Methyl-Cytosine in Tuberculinic Acid, the Nucleic Acid of the Tubercle Bacillus". Journal of the American ... Together with R. D. Coghill, Johnson was the first to discover the existence of 5-methylcytosine in nature, from tuberculinic ... Wyatt, G. R. (1950). "Occurrence of 5-Methyl-Cytosine in Nucleic Acids". Nature. 166 (4214): 237-238. Bibcode:1950Natur.166.. ...
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86 (5): 432-440. doi:10.1111/cge.12465. PMID 25060537. S2CID 8499325. He Z, Zhang R, Jiang F, Zhang H, Zhao A, Xu B, et al. ( ... 71 (5): 865-73. doi:10.1016/0092-8674(92)90561-P. PMID 1423634. S2CID 5995820. Chuang LS, Ian HI, Koh TW, Ng HH, Xu G, Li BF ( ... 302 (1): 5-18. doi:10.1002/jez.b.20002. PMID 14760651. Alvarez-Buylla ER, Chaos A, Aldana M, Benítez M, Cortes-Poza Y, Espinosa ... 128 (4): 641-5. doi:10.1016/j.cell.2007.02.007. PMID 17320501. S2CID 6928707. Zaidi SK, Lian JB, van Wijnen A, Stein JL, Stein ...
... is a modified nucleoside derived from 5-methylcytosine. It is found in ribonucleic acids of animal, plant, and ... Dunn, D. B. (1960). "Isolation of 5-methylcytidine from ribonucleic acid". Biochimica et Biophysica Acta. 38: 176-178. doi: ...
... (5fC) is a pyrimidine nitrogen base derived from cytosine. In the context of nucleic acid chemistry and ... "5-Formylcytosine". pubchem.ncbi.nlm.nih.gov. Retrieved 2020-07-26. Wu, Xiaoji; Zhang, Yi (2017). "TET-mediated active DNA ... In mammals, 5fC is formed by oxidation of 5-Hydroxymethylcytosine (5hmC) a reaction mediated by TET enzymes. Its molecular ... Dubini, Romeo C. A.; Schön, Alexander; Müller, Markus; Carell, Thomas; Rovó, Petra (2020). "Impact of 5-formylcytosine on the ...
This can occur in vitro through the use of bisulfite, which deaminates cytosine, but not 5-methylcytosine. This property has ... A DNA polymerase may perform this replacement via nick translation, a terminal excision reaction by its 5'⟶3' exonuclease ... Spontaneous deamination of 5-methylcytosine results in thymine and ammonia. This is the most common single nucleotide mutation ...
... may be especially important in the central nervous system, as it is found in very high levels there. ... 5-Hydroxymethylcytosine was originally observed in mammals in 1972 by R. Yura, but this initial finding is dubious. Yura found ... 5-Hydroxymethylcytosine was observed by Skirmantas Kriaucionis, an associate at the Heintz lab, who was looking for levels of 5 ... methylcytosine in two different neuron types. He discovered a significant amount of an unknown substance instead, and after ...
6 (5): 836-43. doi:10.1016/j.celrep.2014.01.031. PMC 4010117. PMID 24582957. Kanfi Y, Naiman S, Amir G, Peshti V, Zinman G, ... 134 (5-6): 261-9. doi:10.1016/j.mad.2013.03.006. PMID 23562424. S2CID 25146054. Theil AF, Nonnekens J, Steurer B, Mari PO, de ... 5 (5): 503-9. doi:10.1038/sj.embor.7400127. PMC 1299048. PMID 15105825. Reiling E, Dollé ME, Youssef SA, Lee M, Nagarajah B, ... 37 (5): 1043-53. doi:10.1016/j.biocel.2004.10.006. PMID 15743677. MacRae SL, Croken MM, Calder RB, Aliper A, Milholland B, ...
5-methylcytosine (5-mC) also commonly occurs in various RNA molecules. Recent data strongly suggest that m6A and 5-mC RNA ... 480 (7378): 490-5. doi:10.1038/nature11086. PMID 22170606. Rotondo JC, Selvatici R, Di Domenico M, Marci R, Vesce F, Tognon M, ... 5 (19): 19. doi:10.1186/1472-6807-5-19. PMC 1282579. PMID 16225687. Fustin, J.M.; Ye, S.; Rakers, C.; Kaneko, K.; Fukumoto, K ... This 5-O-methylation affects the flavonoid's water solubility. Examples are 5-O-methylgenistein, 5-O-methylmyricetin or 5-O- ...
The Figure in this section indicates the central roles of ten-eleven translocation methylcytosine dioxygenases (TETs) in the ... 32 (5): 645-655. doi:10.1038/emboj.2012.357. PMC 3590984. PMID 23353889. Zhou X, Zhuang Z, Wang W, He L, Wu H, Cao Y, et al. ( ... 131 (5): 861-872. doi:10.1016/j.cell.2007.11.019. hdl:2433/49782. PMID 18035408. S2CID 8531539. David L, Polo JM (May 2014). " ... TET2 does not have an affinity for 5-methylcytosine in DNA. The CXXC domain of the full-length TET3, which is the predominant ...
This usually occurs in the DNA sequence CpG, changing the DNA at the CpG site from CpG to 5-mCpG. Methylation of cytosines in ... 80 (5): 1387-1391. Bibcode:1983PNAS...80.1387B. doi:10.1073/pnas.80.5.1387. ISSN 0027-8424. PMC 393602. PMID 6572396. Ohno M, ... The mutation frequencies for cells in different stages of gametogenesis are about 5 to 10-fold lower than in somatic cells both ... Yamaguchi S, Hong K, Liu R, Inoue A, Shen L, Zhang K, Zhang Y (March 2013). "Dynamics of 5-methylcytosine and 5- ...
"Role of 5' mRNA and 5' U snRNA cap structures in regulation of gene expression" - Research - Retrieved 13 December 2010. Nguyen ... In DNA, the most common modified base is 5-methylcytosine (m5C). In RNA, there are many modified bases, including those ... "Some viruses thwart bacterial defenses with a unique genetic alphabet". 5 May 2021. Berg JM, Tymoczko JL, Stryer L. "Section ...
These are a ten-eleven translocation methylcytosine dioxygenase (TET) and thymine-DNA glycosylase (TDG). One particular TET ... by ten-eleven translocation methylcytosine dioxygenases (TET enzymes). The molecular steps of this initial demethylation are ... In short patch repair, 5′ dRP lyase trims the 5′ dRP end to form a phosphorylated 5′ end. This is followed by DNA polymerase β ... The human genome contains about 28 million CpG sites, and roughly 60% of the CpG sites are methylated at the 5 position of the ...
"TET methylcytosine oxidases: new insights from a decade of research". Journal of Biosciences. 45 (1): 21. doi:10.1007/s12038- ... replacement of 5-methylcytosine by cytosine. At the La Jolla Institute, her lab demonstrated the importance of TET enzymes in ... "Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1". Science. 324 (5929): 930-935. ... "Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2". Nature. 468 (7325): 839-843. Bibcode:2010Natur ...
49 (6): 380-5. doi:10.1136/jmedgenet-2011-100686. PMC 4771841. PMID 22577224. "Body weight data for Nsun2". Wellcome Trust ... v t e (Articles with short description, Short description matches Wikidata, Genes on human chromosome 5, Human proteins, Genes ... The protein is a methyltransferase that catalyzes the methylation of cytosine to 5-methylcytosine (m5C) at position 34 of ... July 2019). "NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs". Nucleic Acids Research. 47 (16): 8720-8733. ...
... 6-Methylcytosine Cytosine Nucleic acid analogue This set index article lists chemical compounds articles ... Methylcytosine may refer to: 5-Methylcytosine 1-Methylcytosine, a nucleic acid in Hachimoji DNA N(4)- ...
14 (13): 2921-5. doi:10.1021/bi00684a020. PMID 1148185. Zhou W, Sherwood B, Ji Z, Xue Y, Du F, Bai J, Ying M, Ji H (October ... 7 (6): 461-5. doi:10.1038/nmeth.1459. PMC 2879396. PMID 20453866. Yang Y, Scott SA (2017). "DNA Methylation Profiling Using ... 403 (6765): 41-5. Bibcode:2000Natur.403...41S. doi:10.1038/47412. PMID 10638745. S2CID 4418993. Sedighi M, Sengupta AM ( ... In eukaryotes, methylation is most commonly found on the carbon 5 position of cytosine residues (5mC) adjacent to guanine, ...
In 5-methylcytosine, a methyl group is attached to the 5th atom in the 6-atom ring, counting counterclockwise from the NH- ... In plants, 5-methylcytosine occurs at CpG, CpHpG and CpHpH sequences (where H = A, C or T). In fungi and animals, 5- ... methylcytosine predominantly occurs at CpG dinucleotides. Most eukaryotes methylate only a small percentage of these sites, but ... 5-Methylcytosine is a methylated form of the DNA base cytosine (C) that regulates gene transcription and takes several other ...
Moreover, repeats with selectivity for 5-methylcytosine (5mC) and its oxidized derivatives can be designed for analytical ... Figure 5. Engineered TALE scaffolds enable genomic 5mC detection with enhanced selectivity by affinity enrichment. (a) Workflow ... 2b and a single C or 5mC at position 5. Lane 1 and Lane 2/3 of the WT gel are individually cropped from the same gel with same ... The solution was added to wells of the 96 well plate and incubated at 37 °C and 5% CO2 for 48 hr. Each well was then washed ...
The naturally occurring nucleobase 5-methylcytosine (mC) and its oxidized derivatives 5-hydroxymethylcytosine (hmC), 5- ... formylcytosine (fC), and 5-carboxylcytosine (caC) play important roles in epig... ... Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange. Nucleic Acids Research 2020, 48 (15) , ... Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA. *Paul J. Sanstead. ...
DNA and RNA methylation dynamics have been linked to a variety of cellular processes such as development, differentiation, and the maintenance of genome integrity. The correct deposition and removal of methylated cytosine and its oxidized analogues is pivotal for cellular homeostasis, rapid responses to exogenous stimuli, and regulated gene expression. Uncoordinated expression of DNA/RNA methyltransferases and demethylase enzymes has been linked to genome instability and consequently to cancer progression. Furthermore, accumulating evidence indicates that post-transcriptional DNA/RNA modifications are important features in DNA/RNA function, regulating the timely recruitment of modification-specific reader proteins. Understanding the biological processes that lead to tumorigenesis or somatic reprogramming has attracted a lot of attention from the scientific community. This work has revealed extensive crosstalk between epigenetic and epitranscriptomic pathways, adding a new layer of complexity to our
NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. Nucleic Acids Res. 2019 Sep 19;47(16):8720-8733. doi: ... Cytosine-5 methylation (m5C) has been detected in mitochondrial transcriptome, however its biogenesis has not been investigated ...
Uracil is selected over cytosine by a pattern of specific hydrogen bonds, and thymine is excluded by steric clash of its 5- ... This enzyme may offer a new approach for discriminating between cytosine and 5-methylcytosine. ... distinguishes between cytosine and methylcytosine. Uracil DNA glycosylase (UDG) efficiently removes uracil from DNA in a ... In contrast no cleavage is observed with any substrates that contain 5-methylcytosine. ...
Identification of Sequence Specificity of 5-Methylcytosine Oxidation by Tet1 Protein with High-Throughput Sequencing ... Identification of Sequence Specificity of 5-Methylcytosine Oxidation by Tet1 Protein with High-Throughput Sequencing ...
5-methylcytosine (m5C); RNA methylation modification; oral squamous cell carcinoma; prognosis; tumor immune microenvironment ... The RNA Methylation Modification 5-Methylcytosine Impacts Immunity Characteristics, Progno The RNA Methylation Modification 5- ... Methylcytosine Impacts Immunity Characteristics, Prognosis and Progression of Oral Squamous Cell Carcinoma by Bioinformatics ... Disorders pertaining to 5-methylcytosine (m5C) modifications are involved in the pathological process of many diseases. However ...
An Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcytosine and its Oxidized Derivatives ... BiQ Analyzer HiMod: An Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcytosine and its ... Latex : {BiQ} Analyzer {HiMod}: An Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcytosine ... An Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcytosine and its Oxidized Derivatives. ...
5-methylcytosine; Ogt, O-GlcNAc transferase; PUGNAc, O-(2-acetamido-Precipitation; KD, knockdown; 5mC, 5-methylcytosine; Ogt, O ... 5-methylcytosine; Ogt,. Post date. July 30, 2023. Post last updated dateUpdated July 30, 2023. Post read time. 2 min read Post ... Ihbxnj on Precipitation; KD, knockdown; 5mC, 5-methylcytosine; Ogt, O-GlcNAc transferase; PUGNAc, O-(2-acetamido-Precipitation ... PatrickBed on Precipitation; KD, knockdown; 5mC, 5-methylcytosine; Ogt, O-GlcNAc transferase; PUGNAc, O-(2-acetamido- ...
Tet methylcytosine dioxygenase 1 (TET1) catalyses the sequential oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine ... Tet methylcytosine dioxygenase 1 (TET1) catalyses the sequential oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine ...
In this work, we showed that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 ... important epigenetic control mechanism in a wide array of eukaryotic organisms and generally carried out by proteins of the C-5 ... Figure 5. Enrichment (X) of Leishmania DNA in artificial mixtures of Leishmania promastigote DNA and human DNA, with the ... Figure 5. Enrichment (X) of Leishmania DNA in artificial mixtures of Leishmania promastigote DNA and human DNA, with the ...
Deposition of 5-methylcytosine on enhancer RNAs enables the coactivator function of PGC-1α. Cell Rep. 14, 479-492 (2016). ...
5.. Bernardes de Jesus B, et al: Telomerase gene therapy in adult and old mice delays aging and increases longevity without ... Mazin A: Genome loses all 5-methylcytosine a life span. How is this connected with accumulation of mutations during aging? (in ... Mazin A: Loss of total 5-methylcytosine from the genome during cell culture aging coincides with the Hayflick limit (in Russian ... Within the DNA molecule, cytosine can accept a methyl group to form 5-methylcytosine, and this suppresses transcription locally ...
Journal Article] NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA(Met)2016. *. Author(s). ... Journal Article] Accurate estimation of 5-methylcytosine in mammalian mitochondrial DNA2018. *. Author(s). Matsuda, S., * ... Presentation] Biogenesis and physiological role of 5-formylcytidine in human mitochondrial tRNA2016. *. Author(s). Tsutomu ... Journal Article] 5-Hydroxymethylcytosine Plays a Critical Role in Glioblastomagenesis by Recruiting the CHTOP-Methylosome ...
Methylcytosine and Its Oxidized Derivatives. 21-Feb-2013. ... Deamination, Oxidation, and C−C Bond Cleavage Reactivity of 5‑ ... Proteins, 2013, DOI: 10.1002/prot.24233, Volume 81, Issue 5, pages 774-787 published on 15.01.2013. Proteins, online ablage ... Sci., 2013, DOI: 10.1039/C3SC52228H, 5, 1158-1167 published on 21.11.2013. Chem. Sci., online article ... Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC), and 5-carboxylcytosine (caC). The ...
5-formyl cytosine undergoes deamination in bisulfite treatment, which allows distinguishing between the two. We investigated ... The experimental part of the thesis studies selective oxidation of 5-hydroxymethyl cytosine to 5-formyl cytosine. In addition ... A class of epigenetic modification involves the methylation and hydroxymethylation of the 5-carbon of cytosine. The modified ... In addition, we synthesized a protected 5-hydroxymethyl-2-deoxycytidine that could further be used for synthesis of 5- ...
The EpiMark 5-hmC and 5-mC Analysis Kit is a robust method for the identification & quantitation of 5-hydroxymethylcytosine (5- ... hmC) and 5-methylcytosine (5-mC) within a specific DNA locus. ... 5-hmC Detection & Analysis * Kit Components Kit Components. The ... 5´- CA GTG AAG TTG GCA GAC TGA GC -3´ REV Primer Sequence 5´- CTG ACT TGC CAC CTA TAG ACA GC -3´ This product is related to the ... Presence of 5-hmC and 5-mC can be determined by PCR analysis.. Figure 1b: Experimental Overview. The DNA of interest is ...
These sites which contain methyl cytosine are known as hot spots (Lutsenko and Bhagwat, 1999). Another important point in this ... The reported results showed that approximately 1% of bases in a somatic human genome are methyl-cytosines which equates to 70- ... These genomic regions contain both the fifth base methyl cytosine and the other four coding bases. Methylated and non ... Gethylomes are specific regions on the chromosomes which contain methyl cytosine and refer to specific interactive part(s) of ...
5 Heterogeneity of glucocorticoid receptor messenger RNA is tissue specific: differential regulation of variant transcripts by ... Developmental regulation of the 5-HT7 serotonin receptor and transcription factor NGFI-A in the fetal guinea-pig limbic system ... A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. ... Influence of life stress on depression: moderation by a polymorphism in the 5-HTT gene. ...
Chapter 5 Functional Modulators Linking Inflow with Outflow of Aqueous HumorCoca‐Prados M, Ghosh S. Chapter 5 Functional ... Enzymatic analysis of 5-methylcytosine content in eukaryotic DNA. Study of intracellular Simian Virus 40 DNA.Ford J, Coca- ... Prados M, Hsu M. Enzymatic analysis of 5-methylcytosine content in eukaryotic DNA. Study of intracellular Simian Virus 40 DNA. ... PMID: 9392872, DOI: 10.1002/(sici)1097-010x(19971201)279:5. 3.0.co;2-4. ...
Among authors: braukmann f. EMBO J. 2021 Mar 1;40(5):e105565. doi: 10.15252/embj.2020105565. Epub 2021 Feb 3. EMBO J. 2021. ... Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans. Navarro IC, Tuorto F, ...
These changes are characterized by a globally hypomethylated genome with focal hypermethylation of numerous 5-cytosine- ... These changes are characterised by a globally hypomethylated genome with focal hypermethylation of numerous 5-cytosine- ... The 5-hydroxymethylcytosine (5-hmC) epigenetic mark, which is mostly confined to embryonic stem cells and to an extent brain ... Huang, Y., Pastor, W. A., Shen, Y., Tahiliani, M., Liu, D. R., Rao, A. (2010). The behaviour of 5-hydroxymethylcytosine in ...
Characterization of 5-methylcytosine dioxygenase Tet2 and rescue of mutant Tet2 activity by using turbo co-substrate  ... Regulation of epigenetic transcription mediated by 5-methylcytosine (5mC) plays a critical role in eukaryotic development. ...
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A "Conversion of 5- ... methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.." Science. 2009;324(5929):930-935. Pubmed PMID ... In particular, the Tet-Eleven-Translocation (TET) DNA dioxygenases erase DNA methylation by reiterative oxidation of 5- ... methylcytosine via 5-hydroxymethylcytosine. Our current studies examine the nuanced and long-term developmental impact of DNA ...
Medical Physic 42 (5), 2311-2316. (Article publié). * Benoit Paquette. (2015). Triple Negative Breast Cancer. Encyclopedia of ... Photochemistry and photobiology 84 (5), 1182-6. (Article publié). * Paquette, B.*, Lemay, R., Pépin, C., Tremblay, L. and ... International Journal of Radiation Biology 87 (5), 472-482. (Article publié). * Paquette B**, Therriault H*, Desmarais G*, ... International Journal Radiation Biology 93 (5), 507-516. (Article publié). * Gina Bouchard*, Hélène Therriault*, Sameh Geha, ...
They introduce a non-destructive 5-methylcytosine sequencing method (SEM-seq) utilizing a newly identified DNA deaminase. ...
Back in the 80s, scientists threw another base into the mix: 5-methylcytosine (mC). As the name suggests, mC is cytosine with ...
  • The function of this chemical varies significantly among species: In bacteria, 5-methylcytosine can be found at a variety of sites, and is often used as a marker to protect DNA from being cut by native methylation-sensitive restriction enzymes. (wikipedia.org)
  • Actually DNA methylation is the covalent addition of a methyl group to the 5 position of cytosine within CpG dinucleotides and is a fundamental process that not only modulates gene expression, but is also key to regulating chromosomal stability. (nih.gov)
  • We now show, for several previously identified genomic sites, that the loss of DNA methylation during the differentiation of primary, post-proliferative human monocytes into dendritic cells is preceded by the local appearance of 5-hydroxymethylcytosine. (biomedcentral.com)
  • In particular, the Tet-Eleven-Translocation (TET) DNA dioxygenases erase DNA methylation by reiterative oxidation of 5-methylcytosine via 5-hydroxymethylcytosine. (bcm.edu)
  • In order to identify the genome-wide effects of DNA methylation in E. histolytica , we used a short oligonucleotide microarray representing 9,435 genes (~95% of all annotated amebic genes) and compared the expression profile of E. histolytica HM-1:IMSS parasites with those treated with 23 μM 5-AzaC for up to one week. (biomedcentral.com)
  • i) genes that were endogenously silenced by genomic DNA methylation and for which 5-AzaC treatment induced transcriptional de-repression, and (ii) genes that have genomic DNA methylation, but which were not endogenously silenced by the methylation. (biomedcentral.com)
  • DNA methylation is also responsible for maintenance of chromatin structure [ 4 ] and inactivation of chromosome X in female mammals [ 5 ]. (biomedcentral.com)
  • As well as, HIF-1α overexpression elevated TET2 expression, 5-hmC stage and cyclin-dependent kinase inhibitor 2B [p15(INK4B)] gene demethylation in contrast with the HIF-1α non-overexpression group in KG-1 cells detected by reverse transcription-quantitative PCR, western blotting, 5-hydroxymethylcytosine detection kits and methylation-specific PCR, respectively. (ncbcs.org)
  • DNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and significant epigenetic modification. (salk.edu)
  • lnterphase nuclei of G. nigrocaulis and of related species with small genomes, G. aurea (133 Mbp, 2n 104) and G. pygmaea (179 Mbp, 2n = 80), are hallmarked by intensely DAPI -stained chromocenters, carrying typical heterochromatin-associated methylation marks (5-methylcytosine, H3K9me2), while in G. hispidula and surprisingly also in the small genome of G. margaretae (184 Mbp, 2n = 38) the heterochromatin marks are more evenly distributed. (muni.cz)
  • In ANIMALS , the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. (nih.gov)
  • The spiked APC DNA contained either no methylation (DNA), 5-methylcytosine methylation (5-mC) or 5-hydroxymethylcytosine methylation (5-hmC). (activemotif.jp)
  • 5-Methylcytosine is a methylated form of the DNA base cytosine (C) that regulates gene transcription and takes several other biological roles. (wikipedia.org)
  • This methyl group distinguishes 5-methylcytosine from cytosine. (wikipedia.org)
  • While spontaneous deamination of cytosine forms uracil, which is recognized and removed by DNA repair enzymes, deamination of 5-methylcytosine forms thymine. (wikipedia.org)
  • In addition, active enzymatic deamination of cytosine or 5-methylcytosine by the APOBEC family of cytosine deaminases could have beneficial implications on various cellular processes as well as on organismal evolution. (wikipedia.org)
  • 5-methylcytosine is resistant to deamination by bisulfite treatment, which deaminates cytosine residues. (wikipedia.org)
  • In addition, using the positive and negative mode of the mass spectrometer we have developed an improved and highly sensitive positive/negative ion-switching-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) method that can separate and quantify modified cytosine bases produced by TET-family 5-methylcytosine dioxygenases. (umsystem.edu)
  • Spontaneous or induced deamination of cytosine, adenine, guanine or 5-methylcytosine converts these bases to the miscoding uracil, hypoxanthine, xanthine and thymine, respectively. (asbmb.org)
  • Methods: % 5-methylcytosine (5-mC) and % 5-hydroxymethyl-cytosine (5-hmC) levels were measured by capture and detection antibodies followed by colorimetric quantification. (cdc.gov)
  • In mammalian DNA, cytosine occurs in several chemical forms, including unmodified cytosine (C), 5-methylcytosine (5 mC), 5-hydroxymethylcytosine (5 hmC), 5-formylcytosine (5 fC), and 5-carboxylcytosine (5 caC). (rcsb.org)
  • Additionally, absolute levels of 5-formylcytosine (fC) in adult individuals and cytosine modification levels in sorted neurons were quantified. (cipsm.de)
  • The disorder-causing mutation is the amplification of a cytosine-guanine-guanine (CGG) repeat in the 5' untranslated region of FMR1 located at Xq27.3 1 . (cdc.gov)
  • However, the precise 5-methylcytosine (5mC) dynamics and its relationship with the generation of 5-hydroxymethylcytosine (5hmC) are not clear. (ca.gov)
  • Bisulfite sequencing has been the gold standard for mapping DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) for decades1-4. (ox.ac.uk)
  • TAPS combines ten-eleven translocation (TET) oxidation of 5mC and 5hmC to 5-carboxylcytosine (5caC) with pyridine borane reduction of 5caC to dihydrouracil (DHU). (ox.ac.uk)
  • Tet1 knockdown embryonic stem cells (ESCs), we show that in vitro PGC (iPGC) formation and genome-wide DNA demethylation are unaffected by the absence of Tet1 and Tet2, and thus 5-hydroxymethylcytosine (5hmC). (nih.gov)
  • TET proteins are Fe(II) and alpha-ketoglutarate-dependent dioxygenases that oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and beyond, thereby facilitating DNA demethylation. (nih.gov)
  • DNA (25 pg) derived from the promoter of the APC gene was spiked into 500 ng of human genomic DNA and subjected to the MeDIP procedure using 2 μg of 5-Hydroxymethylcytosine antibody (5hmC, maroon bars) or 2 μg of control rabbit IgG (IgG, blue bars). (activemotif.jp)
  • The work described here provides definite evidence that TET2-mediated conversion of 5-methylcytosine to 5-hydroxymethylcytosine initiates targeted, active DNA demethylation in a mature postmitotic myeloid cell type. (biomedcentral.com)
  • mutations high frequency of IDH1/2 mutations in oligodendrogliomas, astrocytomas and in alteRations in the RB1 pathway in The TET2 gene encodes the -KG- secondary glioblastomas derived thereof low-gRade diffuse gliomas lacking dependent enzyme that catalyses suggests that these tumours share a common genetic alteRations the conversion of 5-methylcytosine to common progenitor cell population. (who.int)
  • To study the functional analysis of TET-family 5-methylcytosine dioxygenases in non-CpG DNA demethylation, efficient purification of enzymatically active untagged human TET2 and His-Tagged mouse TET1 using cation exchange chromatography and affinity chromatography was established. (umsystem.edu)
  • The role of the 5-methylcytosine (5mC) dioxygenases Tet1 and Tet2 in the initial genome-wide DNA demethylation process has not been examined directly. (nih.gov)
  • As an essential DNA hydroxymethylase and a tumor suppressor gene, the expression regulating mechanism of Tet methylcytosine dioxygenase 2 (TET2) stays unclear. (ncbcs.org)
  • [ 5-7 ] 60-90% of CpG dinucleotides are methylated in the adult vertebrate genome, and this modification results in the spontaneous deamination of 5-methylcytosine to thymine. (medscape.com)
  • Thymine, thymidine and thymidine 5'-monophosphate studied by femtosecond fluorescence upconversion spectroscopy T . Gustavsson, A. Sharonov, D. Markovitsi, Chem. (cea.fr)
  • In plants, 5-methylcytosine occurs at CpG, CpHpG and CpHpH sequences (where H = A, C or T). In fungi and animals, 5-methylcytosine predominantly occurs at CpG dinucleotides. (wikipedia.org)
  • This study was performed to determine whether the repair of DNA damage formed preferentially at CpG dinucleotides is sensitive to 5-methylcytosine substitutions. (uzh.ch)
  • These results raise the possibility that 5-methylcytosines in CpG dinucleotides modulate not only the distribution of bulky DNA lesions but, at least in some cases, also the kinetics of subsequent excision repair reactions. (uzh.ch)
  • One of the most widely studied epigenetic marks in DNA is 5-methylcytosine (5mC). (umsystem.edu)
  • 5 mC is a major epigenetic signal that acts to regulate gene expression. (rcsb.org)
  • 5 hmC, 5 fC, and 5 caC are oxidized derivatives that might also act as distinct epigenetic signals. (rcsb.org)
  • Monocytes were found to express the methylcytosine dioxygenase Ten-Eleven Translocation (TET) 2, which is frequently mutated in myeloid malignancies. (biomedcentral.com)
  • The major 5-methylcytosine modulators, including NSUN2, NSUN5 , and Aly/REF , which represented the major parameters related to the abnormal m5C modification level, were observed up-regulating in AAA tissues at both protein and mRNA levels. (imrpress.com)
  • NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. (nih.gov)
  • It remains largely unclear about the function of 5-methylcytosine (m5C) RNA modification in the context of abdominal aortic aneurysm (AAA). (imrpress.com)
  • In eukaryotes, the primary modification of DNA is found in cytosines (C), where DNA Methyltransferases mediate the transfer of a methyl group to cytosines, converting them to 5-methylcytosine (5-mC), minor modifications with broad implications for the activity of the DNA. (epigenie.com)
  • The implications of deamination on 5-hydroxymethylcytosine, on the other hand, remains less understood. (wikipedia.org)
  • Dual functions of TET1 in germ layer lineage bifurcation distinguished by genomic context and dependence on 5-methylcytosine oxidation. (bcm.edu)
  • Dr Kasuya Motomura amplification bias, we assessed genome secondary events reflecting progressive wide chromosomal imbalance by array genomic instability, a hallmark of CGH (Agilant 105K) in DNA from 2-5 glioblastomas. (who.int)
  • In mammalian cells, clusters of CpG at the 5' ends of genes are termed CpG islands. (wikipedia.org)
  • In 5-methylcytosine, a methyl group is attached to the 5th atom in the 6-atom ring, counting counterclockwise from the NH-bonded nitrogen at the six o'clock position. (wikipedia.org)
  • S-Adenosylmethionine then donates a methyl group to carbon 5. (wikipedia.org)
  • 5-Hydroxymethylcytosine (5-hmC) antibody tested by Methyl DNA immunoprecipitation. (activemotif.jp)
  • In addition to this monoclonal, Active Motif offers two polyclonal antibodies that recognize 5-hydroxymethylcytosine, a whole serum version ( 39769 ) and a purified IgG version ( 39791 ).All are validated for use in methyl DNA immunoprecipitation (MeDIP). (activemotif.jp)
  • Research has indicated that in the mammalian genome around 5-6% of all cytosines are methylated (5mC), with a strong preference for the CpG dinucleotide context. (umsystem.edu)
  • While this treatment effectively deaminates cytosines to uracils, leaving most 5-methylcytosines intact, it also introduces abasic sites that generate a significant number of single-strand breaks in DNA. (nih.gov)
  • Solvent effect on the singlet excited state lifetimes of nucleic acid bases: a computational study of 5-fluorouracil and uracil in acetonitrile and water F. Santoro, V. Barone, T. Gustavsson, R. Improta, J. Am. Chem. (cea.fr)
  • We identified among the genes down regulated by 5-AzaC treatment a cysteine proteinase (2.m00545) and lysozyme (52.m00148) both of which have known roles in amebic pathogenesis. (biomedcentral.com)
  • Decreased expression of these genes in the 5-AzaC treated E. histolytica may account in part for the parasites reduced cytolytic abilities. (biomedcentral.com)
  • Thus the aim of our study was to assess the potential association between current rotating night shift work and levels of 5-methylcytosine in the promoter regions of selected suppressor genes. (bmj.com)
  • The analysis did not reveal any statistically significant associations between current rotating night work and level of 5-methylcytosine within promoter regions of the studied genes. (bmj.com)
  • The results show that 5-hydroxymethylcytosine is enriched primarily in the coding regions of genes, rather than in the gene promoter or regulatory regions. (activemotif.jp)
  • Both displayed high affinity for the sequence when C or 5 mC was present and much reduced affinity when 5 hmC or 5 fC was present, indicating that they differentiate primarily oxidized C from unoxidized C, rather than methylated C from unmethylated C. 5 caC affected the two proteins differently, abolishing binding by Egr1 but not by WT1. (rcsb.org)
  • This 5-Hydroxymethylcytosine antibody was raised against 5-hydroxymethylcytosine conjugated to KLH and recognizes 5-hydroxymethylcytosine. (activemotif.jp)
  • 5-Hydroxymethylcytosine (5-hmC) antibody (mAb) - 100 µg (Cat. (activemotif.jp)
  • hMeDIP-chip performed on human brain DNA using 5-Hydroxymethylcytosine (5-hmC) antibody. (activemotif.jp)
  • Human brain DNA (2 µg) was immunoprecipitated with 10 µg of 5-Hydroxymethylcytosine antibody. (activemotif.jp)
  • 5-Hydroxymethylcytosine (5-hmC) antibody (mAb) tested by dot blot analysis. (activemotif.jp)
  • DNA samples were spotted (indicated in ng on the left) on to a positively charged nylon membrane and blotted with 5-Hydroxymethylcytosine antibody at a 0.2 µg/ml dilution. (activemotif.jp)
  • Dot blot analysis was used to confirm the specificity of 5-Hydroxymethylcytosine antibody for 5-hydroxymethylcytosine. (activemotif.jp)
  • Solvent effect on the singlet excited state dynamics of 5-fluorouracil in acetonitrile as compared to water T. Gustavsson, N. Sarkar, E. Lazzarotto, D. Markovitsi, V. Barone, R. Improta, J. Phys. (cea.fr)
  • Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. (ox.ac.uk)
  • Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. (nature.com)
  • Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming. (ca.gov)
  • However, this harsh chemical treatment degrades the majority of the DNA and generates sequencing libraries with low complexity2,5,6. (ox.ac.uk)
  • In the protozoan parasite Entamoeba histolytica , a DNA methyltransferase has been identified and treatment with 5-azacytidine (5-AzaC), a potent inhibitor of DNA methyltransferase, has been reported to attenuate parasite virulence. (biomedcentral.com)
  • Importantly E. histolytica strain HM-1:IMSS grown with 5-azacytidine (5-AzaC), a potent inhibitor of DNA methyltransferase, had been shown to have significantly reduced virulence in vitro and in vivo [ 15 ]. (biomedcentral.com)
  • A base in the DNMT enzyme deprotonates the residual hydrogen on carbon 5 restoring the double bond between carbon 5 and 6 in the ring, producing the 5-methylcytosine base pair. (wikipedia.org)
  • En las PLANTAS, la secuencia metilada es CpNpGp, donde N puede ser una base. (bvsalud.org)
  • Repair reactions in human cell extracts suggested that 5-methylcytosines modulate local repair efficiency in a seemingly unpredictable manner. (uzh.ch)
  • The absolute levels of 5-hydroxymethylcytosine (hmC) and 5-methylcytosine (mC) in human brain tissues at various ages were determined. (cipsm.de)
  • 5 Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892-8132. (nih.gov)
  • 5. Department of Clinical Laboratory, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China. (jcancer.org)
  • Results: The Spearman's correlation coefficient for 5-mC and 5-hmC levels was 0.32 (p - value = 0.03) at visit 1 and 0.54 (p - value (cdc.gov)