Synthesis and Characterization of Non‐standard Nucleosides and Nucleotides Bearing the Acceptor‐Donor‐Donor Pyrimidine Analog 6‐Amino‐3‐methylpyrazin‐2(1H)‐one

Abstract

Abstract6‐Aminopyrazin‐2(1H)‐one, when incorporated as a pyrimidine‐base analog into an oligonucleotide chain, presents a H‐bond acceptor‐donor‐donor pattern to a complementary purine analog. When paired with the corresponding donor‐acceptor‐acceptor purine in oligonucleotides, the heterocycle selectively contributes to the stability of the duplex, presumably by forming a base pair of Watson‐Crick geometry joined by a non‐standard H‐bonding pattern. Aspects of the nucleoside chemistry, including syntheses of the β‐furanosyl ribonucleoside 1, the ribonucleoside triphosphate 2 and the ribonucleoside bisphosphate 3 of 6‐aminopyrazin‐2(1H)‐one are reported here. In aqueous solution, the ribonucleoside 1 was found to undergo acid‐ and base‐catalyzed rearrangement with an apparent half‐life of ca. 63 h at neutral pH and 30°. The rearrangement appears to be specific acid‐ and base‐catalyzed. The thermodynamically most stable compound formed during this rearrangement reaction was isolated by HPLC and shown to be the β‐pyranosyl form 4 of the 6‐aminopyrazin‐2(1H)‐one nucleoside in its 4C1 chair conformation. This reactivity of 1 under physiological conditions may explain why Nature does not use this particular heterocyclic system to implement an acceptor‐donor‐donor H‐bonding pattern in the genetic alphabet.