Dideoxycytosine (ddC) is a dideoxyribonucleoside, and is a synthetic analog of deoxycytosine. The difference between the two is that, in ddC, both the 2- and 3-positions of the ribose have a hydrogen (-H) group substituted for the OH group, whereas in dC, only the 2-position is so substituted.
ddC is generally used in two applications. First, to block the 3-end of oligonucleotides to prevent their extension by a polymerase in a PCR reaction or PCR-based assay. For example, 3-ddC-blocked oligos have been used in microarray-based DNA re-sequencing (1). ddC is also used to block the 3-end of 5-adenylated oligos (5-App) that are used as adapters in miRNA library generation. Blocking the 3-end in this manner prevents the oligo from either circularization (by self-ligation) or concatemerization to other 5-App oligos (2).
1. Sram, J., Sommer, S.S., Liu, Q. Microarray-based DNA re-sequencing using 3 blocked primers. Anal. Biochem. (2008), 3744: 41-47.
2. Lau, N.C., Lim, L.P., Weinstein, E.G., Bartel, D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.Science (2001), 294: 858-862.