Synthesis and tautomeric equilibrium of 6-amino-5-benzyl-3-methylpyrazin- 2-one. An acceptor-donor-donor nucleoside base analog

Article abstract of DOI:10.1021/jo00078a038

6-Aminopyrazin-2-one, when incorporated as pyrimidine base analog into an oligonucleotide, might participate in a nonstandard base pair that retains a Watson-Crick geometry but is joined by a nonstandard hydrogen bonding pattern. Such base pairs can, at least in principle, be recognized independently in duplex nucleic acids. To explore the tautomeric properties that govern hydrogen bonding of this heterocycle, 6-amino-5-benzyl-3- methylpyrazin-2-one was synthesized. The equilibrium constant for the interconversion of the keto and hydroxyl tautomeric forms was estimated by comparing its ultraviolet spectrum with those of N- and O-methyl derivatives in water, methanol, ethanol, dioxane, and water-dioxane mixtures. A plot of the logarithm of the tautomeric equilibrium constant versus Dimroth's microscopic dielectric constant (E(T)(30)) was linear. On the basis of an extrapolation of this relationship to the microscopic dielectric of water, 6- amino-5-benzyl-3-methylpyrazin-2-one is expected to favor at equilibrium the keto form over the hydroxyl form by a factor of ca. 2000 under conditions where DNA and RNA polymerases operate. This is substantially better than the tautomeric ratio observed with isoguanosine, where the minor form has been observed to create tautomeric ambiguity with some polymerase systems.