Bending of Canonical and G/T Mismatched DNAs

a 2021

Bending of Canonical and G/T Mismatched DNAs

BOUCHAL, Tomáš, Ivo DURNÍK and Petr KULHÁNEK

Basic information

Original name

Bending of Canonical and G/T Mismatched DNAs

Authors

BOUCHAL, Tomáš, Ivo DURNÍK and Petr KULHÁNEK

Edition

XXVI. Annual Congress of Czech and Slovak Societies for Biochemistry and Molecular Biology with cooperation of Austrian and German Biochemical Section, 2021. 2021

Other information

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Organization unit

Faculty of Science

ISBN

978-80-907779-1-0

Keywords in English

mismatched DNA; bending; biased MD simulations

Změněno: 5/4/2022 14:41, Mgr. Pavla Foltynová, Ph.D.

Abstract

V originále

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.

Links

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

BOUCHAL, Tomáš, Ivo DURNÍK and Petr KULHÁNEK. Bending of Canonical and G/T Mismatched DNAs. In 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.

@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 and 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.

Detailed Information on Publication Record