title: Structural, energetic and dynamic properties of guanine(C8)-thymine(N3) cross-links in DNA provide insights on susceptibility to nucleotide excision repair.
abstract: The one-electron oxidation of guanine in DNA by carbonate radical anions, a decomposition product of peroxynitrosocarbonate which is associated with the inflammatory response, can lead to the formation of intrastrand cross-links between guanine and thymine bases [Crean et al. (Oxidation of single-stranded oligonucleotides by carbonate radical anions: generating intrastrand cross-links between guanine and thymine bases separated by cytosines. Nucleic Acids Res. 2008; 36: 742-755.)]. These involve covalent bonds between the C8 positions of guanine (G*) and N3 of thymine (T*) in 5'-d(…G*pT*…) and 5'-d(…G*pCpT*…) sequence contexts. We have performed nucleotide excision repair (NER) experiments in human HeLa cell extracts which show that the G*CT* intrastrand cross-link is excised with approximately four times greater efficiency than the G*T* cross-link embedded in 135-mer DNA duplexes. In addition, thermal melting studies reveal that both lesions significantly destabilize duplex DNA, and that the destabilization induced by the G*CT* cross-link is considerably greater. Consistent with this difference in NER, our computations show that both lesions dynamically distort and destabilize duplex DNA. They disturb Watson-Crick base-pairing and base-stacking interactions, and cause untwisting and minor groove opening. These structural perturbations are much more pronounced in the G*CT* than in the G*T* cross-link. Our combined experimental and computational studies provide structural and thermodynamic understanding of the features of the damaged duplexes that produce the most robust NER response.
authors.affiliation: Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA.
authors.forename: Shuang
authors.initials: S
authors.lastname: Ding
authors.forename: Konstantin
authors.initials: K
authors.lastname: Kropachev
authors.forename: Yuqin
authors.initials: Y
authors.lastname: Cai
authors.forename: Marina
authors.initials: M
authors.lastname: Kolbanovskiy
authors.forename: Svetlana A
authors.initials: SA
authors.lastname: Durandina
authors.forename: Zhi
authors.initials: Z
authors.lastname: Liu
authors.forename: Vladimir
authors.initials: V
authors.lastname: Shafirovich
authors.forename: Suse
authors.initials: S
authors.lastname: Broyde
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Geacintov
mesh_terms: D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D004260:DNA Repair; D006147:Guanine / Q000737:chemistry*; D006367:HeLa Cells; D006801:Humans; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry*
chemical_list: D006147:Guanine; D003596:Cytosine; D004247:DNA; D013941:Thymine