A Highly Effective Nonpolar Isostere of Deoxyguanosine: Synthesis, Structure, Stacking, and Base Pairing

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Abstract
We describe the preparation and structure of the deoxyribonucleoside of 4-fluoro-6-methylbenzimidazole, abbreviated dH (8), which acts as a close shape mimic of the nucleoside deoxyguanosine. The nucleoside is prepared from 2-fluoro-4-methylaniline in seven steps. The X-ray crystal structure reveals a (−sc) glycosidic orientation, an S conformation for the deoxyribose moiety, and quite close shape mimicry of guanine by the substituted benzimidazole. Conformational studies by 1H NMR and 1H−1H ROESY experiments reveal an S-type conformation and an anti glycosidic orientation in solution (D2O), essentially the same as that of deoxyguanosine. Base-stacking studies in a “dangling end” context reveal that the benzimidazole base mimic stacks more strongly than all four natural bases, and more strongly than its counterpart guanine by 1.1 kcal/mol. Base-pairing studies in a 12mer DNA duplex show that, like other nonpolar nucleoside isosteres, H is destabilizing and nonselective when paired opposite natural bases. However, when paired opposite another nonpolar isostere, difluorotoluene (F), a mimic of thymine, the pair exhibits stability approaching that of its natural analogue, a G−T (wobble) base pair. The nucleoside analogue dH will be useful in studies of protein−DNA interactions, and the H−F base pair will serve as a structurally and thermodynamically close mimic of G−T in studies of DNA mismatch repair enzymes.