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@article{1730407, author = {Bouchal, Tomáš and Durník, Ivo and Illík, Viktor and Réblová, Kamila and Kulhánek, Petr}, article_number = {20}, doi = {http://dx.doi.org/10.1093/nar/gkaa896}, keywords = {mismatch repair; MutS/DNA; adaptive biasing force; free energy; simple base-pair parameters}, language = {eng}, issn = {0305-1048}, journal = {Nucleic Acids Research}, title = {Importance of base-pair opening for mismatch recognition}, url = {https://doi.org/10.1093/nar/gkaa896}, volume = {48}, year = {2020} }
TY - JOUR ID - 1730407 AU - Bouchal, Tomáš - Durník, Ivo - Illík, Viktor - Réblová, Kamila - Kulhánek, Petr PY - 2020 TI - Importance of base-pair opening for mismatch recognition JF - Nucleic Acids Research VL - 48 IS - 20 SP - 11322-11334 EP - 11322-11334 PB - Oxford University Press SN - 03051048 KW - mismatch repair KW - MutS/DNA KW - adaptive biasing force KW - free energy KW - simple base-pair parameters UR - https://doi.org/10.1093/nar/gkaa896 L2 - https://doi.org/10.1093/nar/gkaa896 N2 - Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs. ER -
BOUCHAL, Tomáš, Ivo DURNÍK, Viktor ILLÍK, Kamila RÉBLOVÁ a Petr KULHÁNEK. Importance of base-pair opening for mismatch recognition. \textit{Nucleic Acids Research}. Oxford University Press, 2020, roč.~48, č.~20, s.~11322-11334. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaa896.
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