The relative ease with which large DNA and RNA fragments can be chemically synthesized, combined with increased availability of ribo- and deoxyribonucleoside analogs as phosphoramidites, 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 via targeted insertion of nucleoside analogs. The unique properties of fluorinated, non-hydrogen-bonding pyrimidine isosteres have also allowed us to study nucleic acid structure by ¹⁹F NMR spectroscopy. We have combined these high-resolution strategies to investigate features of the polypurine tract primer of plus-strand DNA synthesis in retroviruses and long terminal repeat-containing retrotransposons of Saccharomyces cerevisiae that dictate selection by their cognate reverse transcriptase.

The illustration provides a recent example of the power of nucleoside analog interference mapping (NAIM), where we have examined structural features of single-stranded DNA that contribute to its recognition and deamination by the host antiviral protein APOBEC3G. Modifications depicted here were introduced to examine contributions from the phosphodiester backbone (phosphotriester linkages, gold), nucleobase (abasic lesion, white), and deoxyribose (2'-O-methyl substitution, red) to APOBEC3G specificity. Additional details of this study can be found in the manuscript of Rausch et al. (J. Biol. Chem. 284: 7047-7058, 2009).

Last modified: 23 March 2009