Halogenated Hypoxanthine 2'-Deoxyribonucleosides With Pyrazolo[3,4-d]Pyrimidine Skeleton: Synthesis, Crystal Structures, Physical Properties, and Impact on Watson-Crick and Purine-Purine Base Pairs.

Syntheses and base pairing properties of halogenated and nonhalogenated hypoxanthine nucleosides with 8-aza-7-deazapurine skeleton (dI*) are reported. Modified hypoxanthine nucleosides were accessed from 6-alkoxy precursors. Single-crystal X-ray analyses disclosed unit cells consisting of two conformers adopting high-anti conformation around the glycosylic bond with N-type C3'-endo (3T2) or E-type, O4'-endo (0E) sugar puckering. Crystal packing is stabilized by inosine/inosine wobble base pairs as well as intermolecular and intramolecular hydrogen bonds. Hirshfeld surface analyses confirmed these findings. Halogenated and nonhalogenated dI* nucleosides were converted to phosphoramidites and applied to solid-phase oligonucleotide synthesis. Single and consecutive incorporations were accomplished and Watson-Crick and purine-purine base pairing was investigated. Single incorporations opposite to canonical nucleosides afforded stable duplexes in all cases. Tm values revealed the following order of stability dI*-dC = dI*-dA > dI*-dT > dI*-dG. Consecutive incorporations furnished more distinguished results. Double helices with halogenated dI*-dC base pairs were the most stable ones, whereas hybridization for dI* opposite to dT was hindered. Halogenated dI*-dG and dI*-dA purine-purine base pairs gave stable duplexes, whereas hybridization of nonhalogenated dI*-dA pairs failed. From CD spectra, helical changes for duplexes with three dI*-dG purine-purine base pairs were detected. All other duplexes showed the typical shape of a B-DNA.