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  4. Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach
 
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research article

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Johnson, Sophia  
•
Rothlisberger, Ursula  
April 1, 2024
Chimia

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to explain the high detection rate in the face of numerous, small lesions. The viability of CT DNA defect detection is explored via hybrid QM/MM computational studies that leverage the accuracy of quantum mechanics (QM) for a region of interest and the descriptive power of molecular mechanics (MM) for the remainder of the system. We find that the presence of an oxidative lesion lowers the redox free energy of oxidation by approximately 1.0 eV regardless of DNA compaction (free DNA versus packed DNA in nucleosome core particles) and damage location indicating the high feasibility of a CT-based process for defect detection in DNA.

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Type
research article
DOI
10.2533/chimia.2024.243
Web of Science ID

WOS:001222129700002

Author(s)
Johnson, Sophia  
•
Rothlisberger, Ursula  
Date Issued

2024-04-01

Publisher

Swiss Chemical Soc

Published in
Chimia
Volume

78

Issue

4

Start page

243

End page

250

Subjects

Physical Sciences

•

Chromatin

•

Dna

•

Molecular Dynamics

•

Oxidative Damage

•

Qm/Mm

Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
ISIC  
LCBC  
FunderGrant Number

Partnership for Advanced Computing in Europe (PRACE)

2019204961

Swiss National Science Foundation

200020-185092

CSCS

s1157

Available on Infoscience
June 5, 2024
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/208352
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