The synthesis and stability of oligodeoxyribonucleotides containing the deoxyadenosine mimic 1-(2'-deoxy-β-D-ribofuranosyl)imidazole-4-carboxamide

Abstract

Oligodeoxyribonucleotides containing the nucleoside analog 1-(2'-deoxy-β-D-ribofuranosyl) imidazole-4-carboxamide (1) were synthesized by solid phase phosphoramidite technology. Nucleoside 1, which contains a reactive exocyclic amide moiety, was incorporated into synthetic oligodeoxyribonucleotides with the use of a benzoyl protecting group. The corresponding oligodeoxyribonucleotides with dI or dA in the same position in the sequence were synthesized for UV comparison of helix-coil transitions. The thermal melting studies indicate that 1, which could conceptually adopt either a dA- or a dI-like hydrogen bond configuration, pairs with significantly higher affinity to T than to dC. Nucleoside 1 further resembles dA in the relative order of its base pairing preferences (T > dG > dA > dC), but may be less discriminating than dA in its bias for base pairing with T over dG.