Methylation
 

biomers.net offers modified oligonucleotides with 5-Methyl-2'deoxycytidine (5-Me-dC)- as well as 5-Hydroxymethyl-2'deoxycytidine (5-hm-dC).
 

5-Methyl-2’-desoxycytidine (5-Me-dC)

Methylation on cytosine bases is a common mechanism in eukaryotic cells for the regulation of chromosomal activity; the most prominent example in this regard is surely the "silencing" of whole chromosoms.

The research area "Epigenetic" studies such mechanisms by which genetic information is regulated and controlled beyond the plain sequence.
The methylation state of the DNA is carefully controlled by the cells and has important influence on their activity and behaviour.

Particularly in tumor research the methylation state of genome has a prominent position, as findings indicated differences in the methylation pattern of tumor cells and normal cells. This different pattern accounts for different genetic activities, which play a crucial role in tumor development and progression.

To analyse the exact regulative processes, often the exact position of the methylation is required, best directly accessible. This may be achieved with oligonucleotides bearing a methylated cytosine in the required position.

5-Hydroxymethyl-2’-desoxycytidine (5-hm-dC)

Already in 1952 Wyatt and Cohen succeeded in isolating 5-hydroxymethylcytosin from bacteriophage DNA¹. However, recently this socalled "sixth base" moved into the focus of epigenetic research when significant amounts of 5-hm-dC were found in different cell tissue DNA (brain, liver)^2,3.

Apparently it is not possible to differentiate between 5-Me-dC and 5-hm-dC by the usual "bisulfite sequencing" which is frequently used for methylation studies⁴. Accordingly there is a need for new technologies to (re)evaluate  the grade of DNA methylation in detail. So, for example, 5-hm-dC can be selectively glycosylated by enzymatic reactions^5,6, or oxidized under mild conditions as recently described by Booth et al.⁷. Both procedures allow to distinguish between 5-hm-dC and 5-Me-dC in further analytical analysis steps.
 

Literature:

1. A new pyrimidine base from bacteriophage nucleic acids. Wyatt GR, Cohen SS; Nature (1952), 170: 1072. 

2. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Kriaucionis S, Heintz N; Science (2009), 324: 929. 

3. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Roa A; Science (2009), 324: 930. 

4. Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Nester C, Ruzov A, Meehan RR, Dunican DD, BioTechniques (2010), 48, 317. 

5. A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA. Robertson AB, Dahl JA, Vagbo CB, Tripathi P, Krokan HE, Klungland A, Nucleic Acids Research (2011), 39, e55. 

6. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, Li Y, Chen C, Zhang W, Jian X, Wang J, Zhang L, Looney TJ, Zhang B, Godley LA, Hicks LM, Lahn BT, Jin P, He C, Nature Biotechnology (2011), 29, 68. 

7. Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution. Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S; Science (2012), 336, 934.