Epigenetics Collection: 5-Hydroxymethyl Deoxycytidine Tools
The 5-methylation of 2'-deoxycytidine is an important and well studied modification of DNA. This methylation does not impact base pairing but it alters DNA in ways that affect the binding of tran-scription factors and subsequent gene expression. Therefore, cytosine methylation is an important epigenetic marker. The widespread 5-hydroxymethylation of cytosine in DNA of brain tissue has also been documented.1 The exact function of this new "sixth base" is the subject of much current research. As shown in Scheme 1, DNA methyltransferases (DNMT) catalyze the in vivo conversion of dC to mC and subsequent oxidation by ten-to-eleven translocation oxidases (TET) affords hmC. It has been further postulated that a complete cycle involving further oxidation to fC and then to caC followed by decarboxylation to dC could exist in vivo.2 Recently, fC has been discovered in embryonic stem cells with concentrations decreasing as cell differentiation proceeds.3
Scheme 1: Cytosine methylation cycle and associated Berry & Associates products.
Our Our collection of epigenetic tools includes representative analogs of each of the important structures in the proposed cytosine methylation cycle.4-7 We hope that you will find these tools useful for your research.References 1. a) Kriaucionis, S.; Heintz, N. Science, 2009, 324, 929-930. b) Tahiliani, M.; Koh, K.P.; Shen, Y.H.; Pastor, W.A.; Bandukwala, H.; Brundo, Y.; Agrawal, S.; Iyer, l.M.; Liu, D.R.; Aravind, L.; Rao, A. Science, 2009, 324, 930-935. c) Munzel, M.; Globisch, D.; Bruckl, T.; Wagner, M.; Welzmiller, V.; Michalakis, S.; Muller, M.; Biel, M.; Carell, T. Angew. Chem. Int. Ed. 2010, 49, 5375-5377. d) Szwagierczak, A.; Bultmann, S.; Schmidt, C.S.; Spada, F.; Leonhardt, H. Nucleic Acids Res. 2010, 38, e181. 2. Munzel, M.; Globisch, D.; Carell, T. Angew. Chem. Int. Ed. 2010, 50, 6460-6468. 3. Pfaffeneder, T.; Hackner, B.; Trub, M.; Munzel, M.; Muller, M.; Deiml, C.A.; Hagemeier, C.; Carell, T, Angew. Chem. Int. Ed.2011, 50, 7008-7012. 4. Tardy-Planechaud, S.; Fujimoto, J.; Lin, S.S.; Sowers, L.C. Nucleic Acids Res. 1997, 25, 553-558. 5. Munzel, M.; Globisch, D.; Trindler, C.; Carell, T. Org. Lett. 2010, 12 (24), 5671-5673. 6. Karino, N.; Ueno, Y.; Matsuda, A. Nucleic Acids Research. 2001, 29 (12), 2456-2463. 7. Sumino, M.; Ohkubo, A.; Taguchi, H.; Seio, K.; Sekine, M. Bioorg. & Med. Chem. Lett. 2008, 18, 274-277.
5-Methyl Cytidine Tools (mC tools)
Hydroxymethyl Tools (5hmC or mC Tools)
- PY 7587 5-[(2-Cyanoethoxy)methyl]-2'-deoxycytidine
- PY 7594 5-Hydroxymethyl-2'-deoxycytidine cyclic carbamate
- PY 7588 5-Hydroxymethyl-2'-deoxycytidine
- PY 7596 5-Hydroxymethylcytidine
- BA 0371 5-Hydroxymethyl-dC cyclic carbamate CEP
- BA 0338 N-Benzoyl-5-((2-cyanoethoxy)methyl)-2'-deoxycytidine CEP
Formyl Cytidine Tools (fC Tools)
Carboxy Cytidine Tools (caC Tools)
- PY 7598 Cytidine-5-carboxylic acid, sodium salt
- PY 7593 2'-Deoxycytidine-5-carboxylic acid, sodium salt
- PY 7586 Cytidin-5-yl-methanesulfonate sodium salt hydrate
- BA 0363 5-Carboethoxy dC CEP
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