Fig. 10: Modeled structure of duplex DNA containing an oxoA-G interstrand cross-link.
From: DNA interstrand cross-links induced by the major oxidative adenine lesion 7,8-dihydro-8-oxoadenine
The model was generated by modification of a solution structure containing a G(C2)-G(N2) cross-link in the 5’-CG/GC-5’ sequence context (PDB code: 1S9O [https://doi.org/10.2210/pdb1S9O/pdb]). a Comparison of the oxoA(C2)-G(C2) cross-link with G(C2)-G(N2) cross-link. b Side view of the oxoA-G cross-link-containing DNA. dG and dC that can base pair in non-cross-linked DNA are in green/natural atom. OxoA and dT that can base pair in non-cross-linked DNA are in yellow/natural atom. Note that the dC and dT are flipped out and reside in the minor groove that is widened. The oxoA-G cross-link would adopt a near coplanar geometry and stack well with spatially adjacent base pairs. c Top view of oxoA-G cross-link-containing DNA. d Top view of cross-linked 5’-CoxoA/GT-5’ only. The distance between the dC(C5) and dG(N1) is indicated. Distances between 8-oxo moiety of oxoA and nearby atoms is indicated. Note that N1 of oxoA and N1-H of G can form a hydrogen bond, which can further stabilize the cross-link. OxoA 8-oxoadenine.
