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@proceedings{1843902,
author = {Bouchal, Tomáš and Durník, Ivo and Kulhánek, Petr},
booktitle = {XXVI. Annual Congress of Czech and Slovak Societies for Biochemistry and Molecular Biology with cooperation of Austrian and German Biochemical Section, 2021.},
keywords = {mismatched DNA; bending; biased MD simulations},
language = {eng},
isbn = {978-80-907779-1-0},
title = {Bending of Canonical and G/T Mismatched DNAs},
year = {2021}
}
TY - CONF
ID - 1843902
AU - Bouchal, Tomáš - Durník, Ivo - Kulhánek, Petr
PY - 2021
TI - Bending of Canonical and G/T Mismatched DNAs
SN - 9788090777910
KW - mismatched DNA
KW - bending
KW - biased MD simulations
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 towards 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 only without any effect on mismatch discrimination.
ER -
BOUCHAL, Tomáš, Ivo DURNÍK a Petr KULHÁNEK. Bending of Canonical and G/T Mismatched DNAs. In \textit{XXVI. Annual Congress of Czech and Slovak Societies for Biochemistry and Molecular Biology with cooperation of Austrian and German Biochemical Section, 2021.}. 2021. ISBN~978-80-907779-1-0.
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