Helical Parameters, Fluctuations, Alternative Hydrogen Bonding, and Bending in Oligonucleotides Containing a Mistmatched Base-pair by NOESY Distance Restrained and Distance Free Molecular Dynamics

• Published in: Journal of molecular biology 1995, Vol.246 (1), p.209-226
• Main Authors: Cognet, J.A.H., Boulard, Y., Fazakerley, G.V.
• Format: Article
• Language: English
• Subjects: Base Sequence; DNA - chemistry; DNA bending; flexibility; Genes, ras - genetics; Hydrogen Bonding; Magnetic Resonance Spectroscopy; molecular dynamics; Molecular Sequence Data; Molecular Structure; NMR of DNA mismatches; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes - chemistry; Oligodeoxyribonucleotides - chemical synthesis; Oligodeoxyribonucleotides - chemistry; three centered hydrogen bonds
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.1994.0077

We have analysed and compared the molecular structures and dynamics of the DNA duplex, that corresponds to the sequence 29 to 39 of the K- rasgene, where the central base-pair is the normal C·G base or a mismatch base-pair C·A, C·A +, A·G and A +·G. Molecular dynamics runs of 100 picoseconds without or with distance restraints derived from NOE measurements are analysed and compared in all cases. (1) The EMBO convention of helical parameters for nucleic acids is extended to account for the construction and the description of any DNA mismatched base-pair. (2) Both types of MD runs reproduce very well and NMR data, except the H 8H 2′inter-residue distances where ageeement is not as good. (3) Average parameter values and fluctuations are in good agreement with results from persistence lengh and torsion modulus measurements. (4) Our molecular dynamics suggest the presence, in certain cases, of three-centred hydrogen bonds, which should be viewed as an equilibrium between hydrogen-bonding alternatives. In the case of the C·A mismatch, we observe the correlation between transient DNA bending and possible hydrogen bonding between the base and its 5′ neighbour on the opposite strand in the sequence CCA. (5) These molecular dynamics analyses and observations provide a coherent view for the results obtained from recent DNA crystal structures and for results derived from other techniques such as gel electrophroesis at C·A steps.