Exploiting structurally diverse nucleoside analogs as probes of reverse transcription complexes

Crystal structures of HIV-1 reverse transcriptase (RT) in complex with either duplex DNA or an RNA/DNA hybrid have provided significant insights into the manner in which this highly versatile enzyme accommodates the conformationally-distinct nucleic acid substrates encountered during the reverse transcription cycle. Biochemical data likewise suggest that unique structural features of the nucleic acid substrates contribute towards recognition by their cognate RT. While site-directed mutagenesis of catalytically- and structurally-critical protein motifs is relatively facile, understanding how nucleic acid structure contributes to its recognition presents a greater challenge. The relative ease with which large DNA and RNA fragments can now be chemically synthesized, in conjunction with the increased availability of ribo- and deoxyribonucleoside analogs, allows nucleic acid structure to be examined with respect to the role of hydrogen bonding, nucleobase stacking, sugar ring geometry and charge of the phosphodiester backbone. This review summarizes our use of nucleoside analogs to understand how the structure of cis-acting regulatory signals mediates their recognition by structurally diverse retroviral and retrotransposon enzymes.