Conformations of Nicked and Gapped DNA Structures by NMR and Molecular Dynamic Simulations in Water

• Published in: Biochemistry (Easton) Vol. 37; no. 12; pp. 4059 - 4070
• Main Authors: Roll, Claus, Ketterlé, Christophe, Faibis, Valérie, Fazakerley, G. Victor, Boulard, Yves
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 24.03.1998
• Subjects: Base Composition; DNA - chemistry; DNA Damage; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes; Protons; Temperature; Thermodynamics; Water
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi972377w

We have analyzed and compared the molecular structures and dynamics of DNA duplexes containing a nick or a gap of one nucleotide where the base in front of the gap is a guanine. The continuous strand has the sequence 5‘(CAGAGTCXCTGGCTC) where the residue X is absent for the nick, 14-mer, and where it is a G residue for the gap. Duplexes were formed with the two corresponding 7-mers. Neither of these is phosphorylated adjacent at the nick site, but it is a good model for a single strand break. For the nick structure, the quantitative NMR data show that the global conformation is very close to canonical B-form DNA, but it displays enhanced local flexibility. For the gap structure, we observe only one species in which the extra G is well stacked into the helix. The two half-helices around this residue also show a B-form conformation. As with the nick duplex, the adjacent G imino protons show enhanced exchange with solvent. The gap does not close completely. Using distance constraints, MD calculations show that the nick conformation is very close to a duplex with no lesion but is indeed more flexible in the central part. The gapped structure shows two families of conformations. One is close to B-DNA, the other is significantly kinked at the gap which reduces the size of the cavity. We observe a spine of hydration within the cavities, similar, but of different geometry in the two cases.