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  4. Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations
 
research article

Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

Diamantis, Polydefkis  
•
Tavernelli, Ivano  
•
Rothlisberger, Ursula  
October 13, 2020
Journal of Chemical Theory and Computation

The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. The quantum region of the native fragment comprised 3 G-C base pairs, while one G was replaced by an 8oxoG in the defect fragment. The calculated values for the redox free energy are 6.55 +/- 0.28 eV and 5.62 +/- 0.30 eV for the native and the 8oxoG-containing fragment, respectively. The respective estimates for the reorganization free energy are 1.25 +/- 0.18 eV and 1.00 +/- 0.18 eV. Both reactions follow the Marcus theory for electron transfer. The large difference in redox potential between the two fragments shows that replacement of a G by an 8oxoG renders the DNA more easily oxidizable. This finding is in agreement with the suggestion that DNA fragments containing an 8oxoG defect can act as sinks of oxidative damage that protect the rest of the genome from assault. In addition, the difference in redox potential between the native and the defect DNA fragment indicates that a charge transfer-based mechanism for the recognition of DNA defects might be feasible, in line with recent suggestions based on experimental observations.

  • Details
  • Metrics
Type
research article
DOI
10.1021/acs.jctc.0c00568
Web of Science ID

WOS:000580954000061

Author(s)
Diamantis, Polydefkis  
Tavernelli, Ivano  
Rothlisberger, Ursula  
Date Issued

2020-10-13

Publisher

AMER CHEMICAL SOC

Published in
Journal of Chemical Theory and Computation
Volume

16

Issue

10

Start page

6690

End page

6701

Subjects

Chemistry, Physical

•

Physics, Atomic, Molecular & Chemical

•

Chemistry

•

Physics

•

electron-transfer reactions

•

nucleic-acid bases

•

vertical ionization energies

•

charge-transport

•

duplex dna

•

photoemission-spectroscopy

•

theoretical determination

•

adenine-thymine

•

rna nucleobases

•

singlet oxygen

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCBC  
Available on Infoscience
November 24, 2020
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/173469
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