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Oligo Modifications List | Oligo Modifications Reference Category
Modification : ddC-3'
Reference Catalog Number 26-6337
Category End Blockers
Modification Code ddC-3
5 Prime N
3 Prime Y
Internal N
Molecular Weight (mw) 273.19
Extinction Coeficient (ec) 7.4
Technical Info (pdf) PS26-6337.pdf
Catalog NoScalePrice
26-6337-0550 nmol$195.00
26-6337-02200 nmol$195.00
26-6337-011 umol$292.00
26-6337-032 umol$438.50
26-6337-1010 umol$2,336.00
26-6337-1515 umol$2,920.00
Related Modifications
3'-O methyl bases
Spacer C3

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.

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