Table 3.

van der Waals overlap between the base pair containing 8-oxo-G or Fapy·G and the base pair on the 3′-side computed using structures developed by molecular modeling in the active site of pol β^a

	anti-8-oxo-G:dCTP	anti-Fapy·G:dCTP
5′-TGT	10.50 (3.35)	10.66 (3.21)
5′-TGA	9.28 (3.06)	10.99 (4.94)

	syn-8-oxo-G:dATP	syn-Fapy·G:dATP
5′-TGT	7.03 (4.27)	11.86 (4.87)
5′-TGA	4.13 (1.45)	5.96 (0.61)

^aThe X-ray structure of anti-8-oxo-G:dCTP in the active site of pol β was used as the starting point to construct models for each of the indicated base pairs in the 5′-TGT sequence context used in the mutagenesis study (Materials and Methods). Thereafter, a MD run was conducted with water and counter ions. The lowest energy structure from the MD run was used to compute the van der Waals overlap area (Materials and Methods) between the 8-oxo-G:dCTP base pair and T:A base pair on the 3′-side; the value reported in the table is in units of Angstroms squared. The van der Waals overlap areas were computed for all-atoms and endocyclic (aromatic) atoms (parentheses) in each base using 3DNA.