Fig. 6

Conformation of the models around the orphaned nucleotide. a, glycosidic angle of the orphaned A⁽⁰⁾ nucleotide in the Aa models. b, overlay of structures from two snapshots at 6 ns (PRN-GLU-Aa model, carbons colored green; PRO-GLH-Aa model, cyan, the same structure as in Panel J but slightly turned for a clearer view) showing the central three bases (the non-damaged strand) and Arg109. The hydrogen bond between N6[A⁽⁰⁾] and O2P[A⁽⁺¹⁾] in the PRO-GLH-Aa model and stacking between the partially extrahelical A⁽⁰⁾ and Arg109 in the PRN-GLU-Aa model are shown. c, structures from an 8-ns snapshot (PRO-GLH-As model) showing the central four base pairs and Arg109. The non-damaged DNA strand is colored. Note the hydrogen bonds formed by the orphaned A base with other nucleotides and Arg109