Nonstandard Hydrogen Bonding in Duplex Oligonucleotides. The Base Pair between an Acceptor-Donor-Donor Pyrimidine Analog and a Donor-Acceptor-Acceptor Purine Analog

Abstract

In its most general form, the Watson-Crick base pair joins a six-membered heterocyclic ring (in natural oligonucleotides, a pyrimidine) with a five-six fused ring system (in natural oligonucleotides, a purine) via three hydrogen bonds, one that joins the two central ring nitrogens of the paired heterocycles, and two that join flanking exocyclic functional groups (Figure 1). To hold the pair together, hydrogen bond donors in one heterocycle must face hydrogen bond acceptors in the other. With three hydrogen bonds, eight (Z3) hydrogen-bonding patterns and 16 independently replicatable bases are conceivable within the Watson-Crick geometry. Six hydrogen-bonding patterns, or 12 independently replicatable bases, are readily accessible using amino and carbonyl functionality (Figure l).lJ Pyrimidine analogs presenting acceptor-donor-donor and donordonor-acceptor hydrogen-bonding patterns have proven to be the most difficult to obtain.1sJ First, to be aromatic and therefore able to stack, the ring system must be joined to the sugar by a carbon4arbon bond (a ’C-nucleoside”). Further, the 6-aminopyrid-2sne structure, which formally presents the correct hydrogen bonding pattern, is evidently readily ~xidized.~ Adding a ring nitrogen to yield the aminopyrimidone pseudocytidine decreases susceptibility to oxidation, but creates an unacceptable tautomeric ambiguity? We report here that the 6-aminopyrazin-2-one ring system (trivially designated V) as the aglycon in an oligoribonucleotide forms a base pair as an acceptor-donor-donor pyrimidine analog with the donor-acceptor-acceptor purine analog 2‘-deoxy-5-aza7-deazaisoguanosine (trivially designated J) in an RNA-DNA duplex. The 2’-deoxyriboside of the donor-acceptor-acceptor purine analog6 was protected and converted into a phosphoramidite suitable for incorporation into a DNA strand by automated synthesis (Figure 2): The riboside 3’,5’-bis(phosphate) (pVp)