Bending of Canonical and G/T Mismatched DNAs

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Authors

BOUCHAL Tomáš DURNÍK Ivo KULHÁNEK Petr

Year of publication 2021
Type Article in Periodical
Magazine / Source Journal of Chemical Information and Modeling
MU Faculty or unit

Faculty of Science

Citation
Web https://pubs.acs.org/doi/10.1021/acs.jcim.1c00731
Doi http://dx.doi.org/10.1021/acs.jcim.1c00731
Keywords Free energy; Genetics; Chemical structure; Intercalation; Nucleic acid structure
Description 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.
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