Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water.
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.
Roll
C
C
CEA, Service de Biochimie et de Génétique Moléculaire, Département de Biologie Cellulaire et Moléculaire, Gif-sur-Yvette, France.
Ketterlé
C
C
Faibis
V
V
Fazakerley
G V
GV
Boulard
Y
Y
D001482:Base Composition; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes; D011522:Protons; D013696:Temperature; D013816:Thermodynamics; D014867:Water
D009692:Nucleic Acid Heteroduplexes; D011522:Protons; D014867:Water; D004247:DNA