Synthesis and recognition by DNA polymerases of a reactive nucleoside, 1-(2-deoxy-β-d-erythro-pentofuranosyl)-imidazole-4-hydrazide

We report the synthesis of a new nucleoside, 1-(2-deoxy-β-d-erythro-pentofuranosyl)-imidazole-4-hydrazide (dY(NH(2))) as a reactive monomer for DNA diversification. The 5′-triphosphate derivative (dY(NH(2))TP, 1) was evaluated in vitro as a substrate for several DNA polymerases. Primer extension reactions showed that dYNH(2)TP was well tolerated by KF (exo(–)) and Vent (exo–) DNA polymerases. One dYNH(2)MP was incorporated opposite each canonical base with an efficiency depending on the template base (A ≈ T > G > C). Significant elongation after YNH(2) incorporation was observed independently of the YNH(2):N base pair formed. When the nucleobase YNH(2) was incorporated into synthetic oligodeoxynucleotides via the phosphoramidite derivative 11, it directed the insertion of natural bases as well as itself. The mutagenicity of dYNH(2)TP was evaluated by PCR amplification using Vent (exo–) DNA polymerase. The triphosphate dY(NH(2))TP was preferentially incorporated as a dATP or dGTP analogue and led to misincorporations at frequencies of ∼2 × 10(–2) per base per amplification. A high proportion of transversions with a large distribution of all possible mutations was obtained. The reactivity of the nucleobase YNH(2) within a template with several aldehydes was demonstrated.