Berry & Associates - Fluorous Purification of Oligonucleotides

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)

PY 7635 5-Methyl-2'-deoxycytidine Hydrochloride
PY 7637 5-Methylcytidine

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)

PY 7599 5-Formylcytidine
PY 7589 5-Formyl-2'-deoxycytidine
BA 0367 Masked 5-formyl-dC CEP

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