Rationalizing Sequence and Conformational Effects on the Guanine Oxidation in Different DNA Conformations

Overview

Journal J Phys Chem B

Publisher American Chemical Society

Specialty Chemistry

Date 2022 Jun 7

PMID 35671051

Authors

Alessandro Nicola Nardi

Alessio Olivieri

Marco DAbramo

Affiliations

Soon will be listed here.

Abstract

The effect of the environment on the guanine redox potential is studied by means of a theoretical-computational approach. Our data, in agreement with previous experimental findings, clearly show that the presence of consecutive guanine bases in both single- and double-stranded DNA oligomers lowers their reduction potential. Such an effect is even more marked when a G-rich quadruplex is considered, where the oxidized form of guanine is particularly stabilized. To the best of our knowledge, this is the first computational study reporting on a quantitative estimate of the dependence of the guanine redox potential on sequence and conformational effects in complex DNA molecules, ranging from single-stranded DNA to G-quadruplex.

Citing Articles

Selective 8-oxo-rG stalling occurs in the catalytic core of polynucleotide phosphorylase (PNPase) during degradation.

Miller L, Kim W, Schowe S, Taylor K, Han R, Jain V Proc Natl Acad Sci U S A. 2024; 121(46):e2317865121.

PMID: 39495922 PMC: 11572968. DOI: 10.1073/pnas.2317865121.

What tunes guanine ionization potential in a nucleosome? An all-in-one systematic QM/MM assessment.

Kermarrec M, Dumont E, Gillet N Biophys J. 2024; 123(18):3100-3106.

PMID: 38988071 PMC: 11427773. DOI: 10.1016/j.bpj.2024.07.009.

One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA.

Lucia-Tamudo J, Alcami M, Diaz-Tendero S, Nogueira J Biochemistry. 2023; 62(22):3312-3322.

PMID: 37923303 PMC: 10666269. DOI: 10.1021/acs.biochem.3c00324.

Theoretical Evaluation of Sulfur-Based Reactions as a Model for Biological Antioxidant Defense.

De Sciscio M, DAnnibale V, DAbramo M Int J Mol Sci. 2022; 23(23).

PMID: 36498842 PMC: 9741100. DOI: 10.3390/ijms232314515.

PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method.

Chen C, Nardi A, Amadei A, DAbramo M J Chem Theory Comput. 2022; 19(1):33-41.

PMID: 36378163 PMC: 9835827. DOI: 10.1021/acs.jctc.2c00767.

References

Cauet E . Unique hole-trapping property of the human telomere sequence. J Biomol Struct Dyn. 2011; 29(3):557-61. DOI: 10.1080/07391102.2011.10507405. View

Slavicek P, Winter B, Faubel M, Bradforth S, Jungwirth P . Ionization energies of aqueous nucleic acids: photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations. J Am Chem Soc. 2009; 131(18):6460-7. DOI: 10.1021/ja8091246. View

Kumar A, Sevilla M . Density functional theory studies of the extent of hole delocalization in one-electron oxidized adenine and guanine base stacks. J Phys Chem B. 2011; 115(17):4990-5000. PMC: 3084348. DOI: 10.1021/jp200537t. View

STEEL G . From targets to genes: a brief history of radiosensitivity. Phys Med Biol. 1996; 41(2):205-22. DOI: 10.1088/0031-9155/41/2/001. View

Pluharrova E, Jungwirth P, Bradforth S, Slavicek P . Ionization of purine tautomers in nucleobases, nucleosides, and nucleotides: from the gas phase to the aqueous environment. J Phys Chem B. 2011; 115(5):1294-305. DOI: 10.1021/jp110388v. View

Bussi G, Donadio D, Parrinello M . Canonical sampling through velocity rescaling. J Chem Phys. 2007; 126(1):014101. DOI: 10.1063/1.2408420. View

Li K, Yatsunyk L, Neidle S . Water spines and networks in G-quadruplex structures. Nucleic Acids Res. 2020; 49(1):519-528. PMC: 7797044. DOI: 10.1093/nar/gkaa1177. View

Kawanishi S, Hiraku Y, Oikawa S . Mechanism of guanine-specific DNA damage by oxidative stress and its role in carcinogenesis and aging. Mutat Res. 2001; 488(1):65-76. DOI: 10.1016/s1383-5742(00)00059-4. View

Amadei A, Daidone I, Aschi M . A general theoretical model for electron transfer reactions in complex systems. Phys Chem Chem Phys. 2011; 14(4):1360-70. DOI: 10.1039/c1cp22309g. View

10.

Conwell E, Basko D . Hole traps in DNA. J Am Chem Soc. 2001; 123(46):11441-5. DOI: 10.1021/ja015947v. View

11.

Jin Y, Ru X, Su N, Mei Y, Beratan D, Zhang P . Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections. J Phys Chem B. 2020; 124(16):3428-3435. PMC: 7456463. DOI: 10.1021/acs.jpcb.0c03112. View

12.

Bravaya K, Epifanovsky E, Krylov A . Four Bases Score a Run: Ab Initio Calculations Quantify a Cooperative Effect of H-Bonding and π-Stacking on the Ionization Energy of Adenine in the AATT Tetramer. J Phys Chem Lett. 2015; 3(18):2726-32. DOI: 10.1021/jz3011139. View

13.

Thapa B, Schlegel H . Calculations of pKa's and redox potentials of nucleobases with explicit waters and polarizable continuum solvation. J Phys Chem A. 2014; 119(21):5134-44. DOI: 10.1021/jp5088866. View

14.

De Bont R, Van Larebeke N . Endogenous DNA damage in humans: a review of quantitative data. Mutagenesis. 2004; 19(3):169-85. DOI: 10.1093/mutage/geh025. View

15.

Kumar A, Adhikary A, Sevilla M, Close D . One-electron oxidation of ds(5'-GGG-3') and ds(5'-G(8OG)G-3') and the nature of hole distribution: a density functional theory (DFT) study. Phys Chem Chem Phys. 2020; 22(9):5078-5089. PMC: 7058519. DOI: 10.1039/c9cp06244k. View

16.

Isse A, Gennaro A . Absolute potential of the standard hydrogen electrode and the problem of interconversion of potentials in different solvents. J Phys Chem B. 2010; 114(23):7894-9. DOI: 10.1021/jp100402x. View

17.

Aidas K, Angeli C, Bak K, Bakken V, Bast R, Boman L . The Dalton quantum chemistry program system. Wiley Interdiscip Rev Comput Mol Sci. 2014; 4(3):269-284. PMC: 4171759. DOI: 10.1002/wcms.1172. View

18.

Paukku Y, Hill G . Theoretical determination of one-electron redox potentials for DNA bases, base pairs, and stacks. J Phys Chem A. 2011; 115(18):4804-10. DOI: 10.1021/jp201281t. View

19.

Psciuk B, Lord R, Munk B, Schlegel H . Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases. J Chem Theory Comput. 2015; 8(12):5107-23. DOI: 10.1021/ct300550x. View

20.

DAnnibale V, Nardi A, Amadei A, DAbramo M . Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution. J Chem Theory Comput. 2021; 17(3):1301-1307. PMC: 8028051. DOI: 10.1021/acs.jctc.0c00728. View