The hybridisation properties of synthetic oligonucleotides are crucial for almost all applications. Optimisation of base pairing, and subsequent duplex stabilisation, is therefore desirable. C-5 Methyl pyrimidine nucleosides are known to stabilise duplexes relative to the non- methylated bases. Therefore the use of 5-Me-dC-CE Phosphoramidite (available either as N-Bz or N-Ac )⁽¹⁾ rather than dC results in enhanced binding (a similar comparison can be made between thymidine and 2'-deoxyuridine). This increase in duplex stabilisation is attributed to the hydrophobic nature of the methyl groups that helps eliminate water molecules from the duplex. We also offer a 5-Me-dC CPG for modification at the 3'-end. The stabilisation properties of Me-dC make this a suitable modification for stabilisation of triplex strands, where its presence raises the melting temperature of the third strand.

Ref:

1. Effect of 5-methylcytosine on the stability of triple-stranded DNA-a thermodynamic study, L.E. Xodo, G. Manzini, F. Quadrifoglio, G.A. van der Marel and J.H. van Boom, Nucleic Acids Research, 19, 5625-5631, 1991.