Contribution of Opening and Bending Dynamics to Specific Recognition of DNA Damage

• Published in: Journal of molecular biology Vol. 330; no. 4; pp. 687 - 703
• Main Authors: Seibert, Eleanore, Ross, J.B.Alexander, Osman, Roman
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 18-07-2003
• Subjects: Base Pair Mismatch; base-pair opening; Computer Simulation; DNA - chemistry; DNA bending; DNA Damage; Hydrogen Bonding; Kinetics; mismatch DNA; Models, Molecular; Models, Statistical; molecular dynamics; Nucleic Acid Conformation; potential of mean force; Protein Conformation; Time Factors; MD, molecular dynamics; TDG, thymine DNA glycosylase; potential of mean force; base-pair opening; PMF, potential of mean force; 6MI, 6-methylisoxanthopterin; mismatch DNA; molecular dynamics; 2AP, 2-aminopurine; UDG, uracil DNA glycosylase; DNA bending
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/S0022-2836(03)00598-9

Guanine-uracil (G·U) wobble base-pairs are a detrimental lesion in DNA. Previous investigations have shown that such wobble base-pairs are more prone to base-opening than the normal G·C base-pairs. To investigate the sequence-dependence of base-pair opening we have performed 5
ns molecular dynamics simulations on G·U wobble base-pairs in two different sequence contexts, TGT/AUA and CGC/GUG. Furthermore, we have investigated the effect of replacing the guanine base in each sequence with a fluorescent guanine analogue, 6-methylisoxanthopterin (6MI). Our results indicate that each sequence opens spontaneously towards the major groove in the course of the simulations. The TGT/AUA sequence has a greater proportion of structures in the open state than the CGC/GUG sequence. Incorporation of 6MI yields wobble base-pairs that open more readily than their guanine counterparts. In order of increasing open population, the sequences are ordered as CGC<TGT<CMC<TMT, where M represents 6MI. Both members of the base-pair open towards the major groove in a symmetrically coupled motion. Opening results in breakage of the H3(U)–O6(G/6MI) hydrogen bond, and distortion of the H1(G/6MI)–O2(U) hydrogen bond. Structural consequences of the opening include the formation of the H21(G/6MI)–O2(U) hydrogen bond and a change in local solvation in the grooves and particularly near N3–H3 of uracil. Additionally, DNA flexibility is reduced in the open state for bending towards the major groove generating two nearly discrete states: closed unbent and open bent. The observed differences in the local structural and dynamical properties of the G·U base-pair may play an important role in the activity of DNA repair enzymes that initiate base excision by distorting the DNA and flipping the target base from inside the DNA helix.