Bending of Canonical and G/T Mismatched DNAs

J 2021

Bending of Canonical and G/T Mismatched DNAs

BOUCHAL, Tomáš, Ivo DURNÍK a Petr KULHÁNEK

Základní údaje

Originální název

Bending of Canonical and G/T Mismatched DNAs

Autoři

BOUCHAL, Tomáš (203 Česká republika, domácí), Ivo DURNÍK (203 Česká republika, domácí) a Petr KULHÁNEK (203 Česká republika, garant, domácí)

Vydání

Journal of Chemical Information and Modeling, American Chemical Society, 2021, 1549-9596

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10400 1.4 Chemical sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 6.162

Kód RIV

RIV/00216224:14310/21:00123499

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1021/acs.jcim.1c00731

UT WoS

000755141900025

Klíčová slova anglicky

Free energy; Genetics; Chemical structure; Intercalation; Nucleic acid structure

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 14. 3. 2022 10:43, Mgr. Marie Šípková, DiS.

Anotace

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 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.

Návaznosti

LM2018140, projekt VaV

Název: e-Infrastruktura CZ (Akronym: e-INFRA CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

BOUCHAL, Tomáš, Ivo DURNÍK a Petr KULHÁNEK. Bending of Canonical and G/T Mismatched DNAs. Journal of Chemical Information and Modeling. American Chemical Society, 2021, roč. 61, č. 12, s. 6000-6011. ISSN 1549-9596. Dostupné z: https://dx.doi.org/10.1021/acs.jcim.1c00731.

@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 a Petr KULHÁNEK. Bending of Canonical and G/T Mismatched DNAs. \textit{Journal of Chemical Information and Modeling}. American Chemical Society, 2021, roč.~61, č.~12, s.~6000-6011. ISSN~1549-9596. Dostupné z: https://dx.doi.org/10.1021/acs.jcim.1c00731.

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