Figure 1.

(A) A model depicting the RNase H primer grip residues and their proposed contacts with a DNA/RNA hybrid, based on the structure of Sarafianos et al. (5). Amino acids are presented in single letter format and the DNA and RNA strands are in blue and red, respectively. (B) Experimental strategy for methylphosphonate substitution. In the model DNA/RNA hybrid, the analog is substituted at positions −10 through −20 either as singlet, doublet or triplets in an overlapping manner. Filled circles represent the DNA phosphates proposed to interact with the RNase H primer grip residues. The open shaded RNA phosphate is the scissile bond. For reference, protein contacts from the polymerase domain (template grip and translocation track), and RNase H active center are also shown. (C) Chemical structure methylphosphonate Rp and Sp stereoisomers, where a methyl group replaces one oxygen of the phosphate.