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@article{1816729,
author = {Bouchal, Tomáš and Durník, Ivo and Kulhánek, Petr},
article_number = {12},
doi = {http://dx.doi.org/10.1021/acs.jcim.1c00731},
keywords = {Free energy; Genetics; Chemical structure; Intercalation; Nucleic acid structure},
language = {eng},
issn = {1549-9596},
journal = {Journal of Chemical Information and Modeling},
title = {Bending of Canonical and G/T Mismatched DNAs},
url = {https://pubs.acs.org/doi/10.1021/acs.jcim.1c00731},
volume = {61},
year = {2021}
}
TY - JOUR
ID - 1816729
AU - Bouchal, Tomáš - Durník, Ivo - Kulhánek, Petr
PY - 2021
TI - Bending of Canonical and G/T Mismatched DNAs
JF - Journal of Chemical Information and Modeling
VL - 61
IS - 12
SP - 6000-6011
EP - 6000-6011
PB - American Chemical Society
SN - 15499596
KW - Free energy
KW - Genetics
KW - Chemical structure
KW - Intercalation
KW - Nucleic acid structure
UR - https://pubs.acs.org/doi/10.1021/acs.jcim.1c00731
N2 - Mismatched base pairs alter the flexibility and intrinsic curvature of DNA. The role of such DNA features is not fully understood in the mismatch repair pathway. MutS/DNA complexes exhibit DNA bending, PHE intercalation, and changes of base-pair parameters near the mismatch. Recently, we have shown that base-pair opening in the absence of MutS can discriminate mismatches from canonical base pairs better than DNA bending. However, DNA bending in the absence of MutS was found to be rather challenging to describe correctly. Here, we present a computational study on the DNA bending of canonical and G/T mismatched DNAs. Five types of geometric parameters covering template-based bending toward the experimental DNA structure, global, and local geometry parameters were employed in biased molecular dynamics in the absence of MutS. None of these parameters showed higher discrimination than the base-pair opening. Only roll could induce a sharply localized bending of DNA as observed in the experimental MutS/DNA structure. Further, we demonstrated that the intercalation of benzene mimicking PHE decreases the energetic cost of DNA bending without any effect on mismatch discrimination.
ER -
BOUCHAL, Tomáš, Ivo DURNÍK and Petr KULHÁNEK. Bending of Canonical and G/T Mismatched DNAs. \textit{Journal of Chemical Information and Modeling}. American Chemical Society, 2021, vol.~61, No~12, p.~6000-6011. ISSN~1549-9596. Available from: https://dx.doi.org/10.1021/acs.jcim.1c00731.
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