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Usage

Uses

Used in Biotechnology and Molecular Biology:
5-METHYLCYTOSINE is used as a marker to protect DNA from being cut by native methylation-sensitive restriction enzymes. This application is essential in studying gene expression, regulation, and epigenetic modifications, as it helps researchers understand the role of DNA methylation in various biological processes.
Used in Chemical Synthesis:
In the field of chemical synthesis, 5-METHYLCYTOSINE is employed in the production of 4-amino-5-hydroxy-5-methyl-2-oxo-2,5-dihydro-imidazole-1-carbaldehyde. 5-METHYLCYTOSINE serves as an intermediate in the synthesis of various biologically active molecules, contributing to the development of new drugs and therapeutic agents.
Used in Epigenetic Research:
5-METHYLCYTOSINE is a key player in epigenetic research, as it is involved in the regulation of gene expression without altering the DNA sequence. It is used to study the role of DNA methylation in various diseases, including cancer, neurological disorders, and developmental abnormalities. Understanding the function of 5-METHYLCYTOSINE in these contexts can lead to the development of targeted therapies and personalized medicine approaches.
Used in Diagnostics:
5-METHYLCYTOSINE can be utilized in the development of diagnostic tools and tests for various diseases. By detecting the presence or absence of specific methylation patterns, these tools can help identify early signs of disease, monitor disease progression, and assess the effectiveness of treatments.
Used in Drug Development:
The unique properties of 5-METHYLCYTOSINE make it a valuable compound in the development of new drugs. It can be used as a starting material or a building block for the synthesis of novel therapeutic agents, particularly those targeting epigenetic modifications and gene regulation.

Purification Methods

Crystallise it from water (solubility is 3.4%). The hydrochloride has m 299-301o (sintering at 280o) (from aqueous HCl/Me2CO). [Hitchings et al. J Biol Chem 177 537 1949, Cohn J Am Chem Soc 73 1539 1951, Beilstein 25 II 183, 25 III/IV 3727.]

InChI:InChI=1/C5H7N3O.ClH/c1-3-2-7-5(9)8-4(3)6;/h2H,1H3,(H3,6,7,8,9);1H

Upstream product

• 7390-56-9 4-amino-5-methyl-1H-pyrimidine-2-thione 
• 54410-87-6 2-ethylsulfanyl-5-methyl-pyrimidin-4-ylamine 
• 25902-89-0 4-methoxy-5-methyl-pyrimidin-2(1H)-one 
• 838-07-3 5-methyldeoxycytidine 
• 2140-61-6 5-methylcytidine 
• 50-89-5 thymidine 
• 64-17-5 ethanol 
• 7722-84-1 dihydrogen peroxide 
• 7087-68-5 N-ethyl-N,N-diisopropylamine 
• 13480-96-1 4-chloro-2-ethylsulfanyl-5-methyl-pyrimidine 
• 71-30-7 Cytosine 
• 6217-61-4 5-methylthio-2-thiouracil 
• 144782-14-9 5-methyl-4-(1,2,4-triazol-1-yl)-pyrimidin-2-(1H)-one 
• 65-71-4 thymin 

Downstream Products

• 126354-30-1 N-(5-methyl-2-oxo-1H-pyrimidin-4-yl)benzamide 
• 134419-40-2 4-Amino-1-formyl-5-hydroxy-5-methyl-1H-imidazol-2(5H)-one 
• 65-71-4 thymin 
• 32865-88-6 2'-O,N⁴-bis-trimethylsilyl-5-methylcytosine 
• 116-09-6 hydroxy-2-propanone 
• 65-71-4 2,4-dihydroxy-5-methylpyrimidine 
• 911110-79-7 N-benzoyl-5-methyl-[2'-O-(2-trifluoroacetamido)ethyl-β-D-ribofuranosyl]cytosine 
• 911110-77-5 N-benzoyl-5-methyl-[3',5'-di-O-acetyl-2'-O-(2-trifluoroacetamido)ethyl-β-D-ribofuranosyl]cytosine 
• 911110-80-0 N-benzoyl-5-methyl-[5'-O-(4,4'-dimethoxytrityl)-2'-O-(2-trifluoroacetamido)ethyl-β-D-ribofuranosyl]cytosine 
• 4160-72-9 1-methylthymine 
• 17634-60-5 1,5-dimethylcytosine 
• 3650-93-9 5-carboxylcytosine 
• 1123-95-1 5-hydroxymethylcytosine 
• 1123-95-1 5-hydroxymethylcytosine 

Relevant academic research and scientific papers

Preparation of carbocyclic phosphonate nucleosides

A versatile and high-yielding synthesis of racemic carbocyclic phosphonate nucleosides of adenine, hypoxanthine, guanine, cytosine, uracil, and thymine has been developed. These newly prepared compounds are isosteric (and isoelectronic) with (carbo)cyclic 2′,3′-dideoxy- and 2′,3′-dideoxy-2′,3′-didehydronucleoside monophosphates.

Biomimetic Iron Complex Achieves TET Enzyme Reactivity**

The epigenetic marker 5-methyl-2′-deoxycytidine (5mdC) is the most prevalent modification to DNA. It is removed inter alia via an active demethylation pathway: oxidation by Ten-Eleven Translocation 5-methyl cytosine dioxygenase (TET) and subsequent removal via base excision repair or direct demodification. Recently, we have shown that the synthetic iron(IV)-oxo complex [FeIV(O)(Py5Me2H)]2+ (1) can serve as a biomimetic model for TET by oxidizing the nucleobase 5-methyl cytosine (5mC) to its natural metabolites. In this work, we demonstrate that nucleosides and even short oligonucleotide strands can also serve as substrates, using a range of HPLC and MS techniques. We found that the 5-position of 5mC is oxidized preferably by 1, with side reactions occurring only at the strand ends of the used oligonucleotides. A detailed study of the reactivity of 1 towards nucleosides confirms our results; that oxidation of the anomeric center (1′) is the most common side reaction.

Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase

5-Methylcytosine (mC) is an epigenetic mark that is written by methyltransferases, erased through passive and active mechanisms, and impacts transcription, development, diseases including cancer, and aging. Active DNA demethylation involves TET-mediated stepwise oxidation of mC to 5-hydroxymethylcytosine, 5-formylcytosine (fC), or 5-carboxylcytosine (caC), excision of fC or caC by thymine DNA glycosylase (TDG), and subsequent base excision repair. Many elements of this essential process are poorly defined, including TDG excision of caC. To address this problem, we solved high-resolution structures of human TDG bound to DNA with cadC (5-carboxyl-2′-deoxycytidine) flipped into its active site. The structures unveil detailed enzyme-substrate interactions that mediate recognition and removal of caC, many involving water molecules. Importantly, two water molecules contact a carboxylate oxygen of caC and are poised to facilitate acid-catalyzed caC excision. Moreover, a substrate-dependent conformational change in TDG modulates the hydrogen bond interactions for one of these waters, enabling productive interaction with caC. An Asn residue (N191) that is critical for caC excision is found to contact N3 and N4 of caC, suggesting a mechanism for acid-catalyzed base excision that features an N3-protonated form of caC but would be ineffective for C, mC, or hmC. We also investigated another Asn residue (N140) that is catalytically essential and strictly conserved in the TDG-MUG enzyme family. A structure of N140A-TDG bound to cadC DNA provides the first high-resolution insight into how enzyme-substrate interactions, including water molecules, are impacted by depleting the conserved Asn, informing its role in binding and addition of the nucleophilic water molecule.

Opened-ring adducts of 5-methylcytosine and 1,5-dimethylcytosine with amines and water and evidence for an opened-ring hydrate of 2′- deoxycytidine

A variety of nucleic acid components and related compounds undergo photoreaction with water to form so-called photohydrates (e.g. uracil forms 6-hydroxy-5,6-dihydrouracil). However, the corresponding hydrates of 5-methylcytosine (a minor nucleobase in eukaryotic DNA) and related compounds have not been characterized. We report the preparation of opened-ring forms of such products for 5-methylcytosine (m5C) and 1,5-dimethylcytosine (DMC). This was accomplished via thermal reaction of ring-opened amine adducts (e.g. N-carbamoyl-3-amino-2-methylacrylamidine (IVa) or N-(N′-methylcarbamoyl)- 3-amino-2-methylacrylamidine (IVb)) produced by photo-induced reactions of m5C with ammonia or methylamine. When these adducts were treated with dilute trifluoroacetic acid, the amino group at the 3-position was replaced with a hydroxyl group; with IVa, N-carbamoyl-3-hydroxy-2-methylacrylamidine (Va) was formed, while reaction of IVb led to N-(N′-methylcarbamoyl)-3-hydroxy-2- methylacrylamidine (Vb). These compounds are ring-opened isomers of 5,6-dihydro-6-hydroxy-5-methylcytosine (Ia and IIa) and 5,6-dihydro-6-hydroxy-1, 5-dimethylcytosine (Ib and IIb). Compounds Va and Vb each undergo thermal ring closure reactions to form two unstable compounds with chemical and UV spectral properties expected for Ia and IIa (or Ib and IIb). The latter compounds have been identified as minor products in UV-irradiated aqueous solutions of m5C and DMC. Evidence is also presented that the 2′-deoxycytidine photohydrates coexist with an opened-ring form, possibly similar in nature to Vb. The nucleobase 5-methylcytosine (m5C) reacts photochemically with ammonia to form an opened-ring adduct (IVa); similar reactions occur with 1,5-dimethylcytosine and with methylamine. Subjection of such adducts to hydrolysis in dilute acid (e.g. 0.1% trifluoracetic acid) produces opened-ring hydrates of m5C (Va) and DMC. Photoreaction of the nucleoside 2′-deoxycytidine in water results in formation of closed-ring hydrates that equilibrate thermally with a compound that has the UV spectral properties expected for an adduct similar in nature to Va.

2′-O-aminoethyl oligoribonucleotides containing novel base analogues: Synthesis and triple-helix formation at pyrimidine/purine inversion sites

The synthesis of a common sugar intermediate for the 2′-aminoethyl- ribonucleoside synthesis in 9 steps and an overall yield of 33 % starting from D-ribose is described. This intermediate was successfully used for the synthesis of the 2′-aminoethyl-ribonucleosides containing the bases thymine (t), 5-methylcytosine (c), 5-methyl-2-pyrimidinone (x), 2-aminopurine (ap) and guanine (g). These were subsequently transformed into the corresponding cyanoethyl phosphoramidite building blocks for oligonucleotide synthesis. 2′-Aminoethyl oligonucleotide 15-mers were prepared with a DNA synthesizer, and an optimized post-synthetic deprotection protocol has been developed which prevents cyanoethylation of the 2′-amino side chains during conventional ammonia deprotection. A series of fully modified, triplex forming 2′-aminoethyl oligoribonucleotides (2′AE-TFOs) were prepared in which x was designed to bind to CG inversion sites and ap as well as g to TA inversion sites on a double-helical DNA target. The affinity of x-CG base-triple formation in different sequence contexts was assessed by UV- and CD melting analysis. It was found that TFO 15-mers containing up to 5 x residues still form stable triplexes even in the case where all x residues are consecutively arranged in the TFO. The nearest neighbor properties of x have been probed and it was found that triplex stability decreases in the local sequence order -txt- > -txc- ? -cxc-. TFOs containing ap and g were found to bind to their DNA targets with TA inversion sites with less affinity and less selectivity compared to TFOs containing the corresponding deoxyribonucleosides, irrespective whether they were incorporated in TFOs with a DNA or a 2′-AE-RNA backbone. The obtained data suggest that guanine-TA or aminopurine-TA base-triple formation is strongly sensitive to TFO conformation and more efficient in TFOs with a DNA than an RNA backbone. Wiley-VCH Verlag GmbH & Co. KGaA, 2006.

Compounds and methods for the characterization of oligonucleotides

The present invention relates to oligonucleotide synthesis. In particular, the present invention provides methods for characterizing samples useful for making oligonucleotides.

Cycloalkltriols containing cyclic substituents, processes and intermediate products for their preparation and their use as antiviral and antiparasitic agents

Cycloalkyltriols containing heterocyclic substituents, in particular cyclopentyl- and cyclohexyltriols containing heterocyclic substituents Compounds of the formulae I and II STR1 in which the substituents A, R1, R2 and R3 and n have the meanings given, have an antiviral and antiparasitic action.

Preparation of oligonucleotides containing 5-bromouracil and 5-methylcytidine

A previously described side reaction on 5-bromouracil during standard oligonucleotide deprotection conditions has been studied in detail. The side product, 5-amino-2′-deoxyuridine, is isolated and characterized. The use of several 5-methylcytidine protected derivatives for the preparation of oligonucleotides containing 5-bromouracil and 5-methylcytidine free of 5-amino-2′-deoxyuridine is discussed.

Process for the preparation of 5-substituted cytosines and other 4,5-disubstituted pyrimidin-2(1H)-ones, and intermediates arising in the course of this

Process for the preparation of 5-substituted cytosines and other 4,5-disubstituted pyrimidin-2(1H)-ones, and intermediates arising in the course of this The process for the preparation of compounds of the formula I, STR1 wherein compounds of the formula II STR2 are converted into an azole derivative of the formula III or an azine derivative of the formula IV STR3 which can subsequently be converted into a compound of the formula I using a nucleophile XH.

Oxidation of Cytosine and 5-Methylcytosine Nucleosides and 5-Methyl-2'-deoxycytidine 5'-Monophosphate with Peroxosulfate Ions

Reaction of 5-methylcytosine nucleosides and nucleotide with Na2S2O8 resulted in an oxidation of the 5-methyl group, while treatment of them and cytosine nucleosides with KHSO5 gave the corresponding N3-oxides.