Comparison of TT–AA base pairs in SP-containing and non-SP-containing structures. (a) Stick renderings of superimposed non-SP TT–AA (purple) and SP tt–AA dinucleotide steps are shown. The hydrogen-bonding distances are shown for N6 of A11 and O4 of T6 for both base pairs in the dinucleotide step. For the non-SP-containing structure this hydrogen bond is very long at 3.31 Å, while in the SP-containing structure it is 2.76 Å. The hydrogen bonds between the same atoms in A10 and T7 are very similar. (b) Stick renderings of the SP-containing dinucleotide step in this work (C, green; N, blue; O, red; P, orange) and a mimic lacking the linking phosphate complexed with B. stearothermophilus DNA polymerase I (Heil et al., 2011; pink) are shown superimposed. The structures are very similar despite the fact that the mimic lacks the linking phosphate. Hydrogen-bonding distances are shown for both base pairs of the SP structure and indicate strong hydrogen bonding of the SP lesion to complementary adenines.