Figure 2. Phosphate contacts made in the specific EcoRV-DNA recognition complex.

(a) Specific DNA substrate used for all thermodynamic experiments. The specific recognition sequence GATATC (bold) is embedded in a 24 bp parent oligonucleotide. All P_Me substitutions were made symmetrically in both DNA strands. (b) Comparison of anionic prochiral phosphodiester (left) with uncharged chiral methylphosphonates (P_Me). By IUPAC convention, replacement of the pro-S (O1P) non-bridging phosphoryl oxygen with a methyl group results in an Rp-P_Me diastereomer; replacement of the pro-R (O2P) phosphoryl oxygen results in an Sp-P_Me diastereomer. (c) Phosphate contacts made to one strand of the specific EcoRV-bound DNA, based on 10 crystal structures of EcoRV-DNA ternary complexes. The base sequence is that used in our thermodynamic experiments. Hydrogen bonds (<3.5Å) to the phosphoryl oxygens from polar side chains and water molecules (black circles) are shown as dotted lines; Coulombic interactions (≤4.3Å) with cationic sidechains are denoted by arrows. Most contacts are symmetrical with respect to protein subunits and DNA strands; those contacts made to only one DNA chain are denoted by # or *; these correspond to chains C and D in PDB ID: 1B94. Sidechains that contact phosphoryl oxygens within the GATATC recognition site are in blue; those making contact outside the GATATC site are in green.