title: Sequence context effect on the structure of nitrous acid induced DNA interstrand cross-links.
abstract: In the preceding paper in this journal, we described the solution structure of the nitrous acid cross-linked dodecamer duplex [d(GCATCCGGATGC)]2 (the cross-linked guanines are underlined). The structure revealed that the cross-linked guanines form a nearly planar covalently linked 'G:G base pair', with the complementary partner cytidines flipped out of the helix. Here we explore the flanking sequence context effect on the structure of nitrous acid cross-links in [d(CG)]2 and the factors allowing the extrahelical cytidines to adopt such fixed positions in the minor groove. We have used NMR spectroscopy to determine the solution structure of a second cross-linked dodecamer duplex, [d(CGCTACGTAGCG)]2, which shows that the identity of the flanking base pairs significantly alters the stacking patterns and phosphate backbone conformations. The cross-linked guanines are now stacked well on adenines preceding the extrahelical cytidines, illustrating the importance of purine- purine base stacking. Observation of an imino proton resonance at 15.6 p.p.m. provides evidence for hydrogen bonding between the two cross-linked guanines. Preliminary structural studies on the cross-linked duplex [d(CGCGACGTCGCG)]2 show that the extrahelical cytidines are very mobile in this sequence context. We suggest that favorable van der Waals interactions between the cytidine and the adenine 2 bp away from the cross-link localize the cytidines in the previous cross-linked structures.
authors.affiliation: Department of Chemistry, University of Washington, Seattle, WA 98195, USA. fredrik.edfeldt@astrazeneca.com
authors.forename: N B Fredrik
authors.initials: NB
authors.lastname: Edfeldt
authors.forename: Eric A
authors.initials: EA
authors.lastname: Harwood
authors.forename: Snorri Th
authors.initials: ST
authors.lastname: Sigurdsson
authors.forename: Paul B
authors.initials: PB
authors.lastname: Hopkins
authors.forename: Brian R
authors.initials: BR
authors.lastname: Reid
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003432:Cross-Linking Reagents / Q000737:chemistry*; D003562:Cytidine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009038:Motion; D009153:Mutagens / Q000737:chemistry*; D009608:Nitrous Acid / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D011522:Protons
chemical_list: D003432:Cross-Linking Reagents; D009153:Mutagens; D011522:Protons; D003562:Cytidine; D004247:DNA; D009608:Nitrous Acid