Issue 9, 2016

The effect of sequence on the ionization of guanine in DNA

Abstract

The accurate estimation of the ionization energies and understanding the nature of the ionized states of the nucleic acid bases (NABs) are crucial to the understanding of the DNA damage mechanism. The vertical ionization energy (VIE) of guanine is the lowest among the NABs and the ionization energies are strongly affected by the environment, such as solvation and characteristics of nearby NABs. Therefore, we investigate the sequence dependence of the VIEs of guanine in B-DNA. We use the equation of motion coupled cluster method for the estimation of ionization potential with single and double excitations (EOM-IP-CCSD) and density functional theory with dispersion corrected ωB97x-D for the estimation of VIEs. A significant amount of non-additivity or cooperativity, directly proportional to charge delocalization, is noticed in the change in VIE due to the interaction with the nearby NABs. While the change in VIE due to base pairing originates predominantly from charge–dipole interactions, stacking between base pairs is a more complicated balance of dispersion and charge–dipole interactions as well as stabilization due to the delocalization of the positive charge. The long range interactions are however dominated by 1/r3 distance dependence which shows the major role played by charge–dipole interactions. The extent of localization of positive holes on guanine is also estimated for various sequences.

Graphical abstract: The effect of sequence on the ionization of guanine in DNA

Supplementary files

Article information

Article type
Paper
Submitted
17 déc. 2015
Accepted
29 janv. 2016
First published
29 janv. 2016

Phys. Chem. Chem. Phys., 2016,18, 6526-6533

The effect of sequence on the ionization of guanine in DNA

R. Chakraborty and D. Ghosh, Phys. Chem. Chem. Phys., 2016, 18, 6526 DOI: 10.1039/C5CP07804K

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements