Synthesis and characterization of non-standard nucleosides and nucleotides bearing the acceptor-donor-donor pyrimidine analog 6-amino-3-methylpyrazin-2(1H)-one

6-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 Warson-Click geometry joined by a non-standard H-bonding pattern. Aspects of the nucleoside chemistry, including syntheses of the beta-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 degrees. 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 beta-pyranosyl form 4 of the 6-aminopyrazin-2(1H)-one nucleoside in its C-4(1) 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.