Influence of solvating water molecules on the attacking mechanisms of OH-radical to DNA base pairs: DFT calculations in explicit waters

Shimamura, Kanako; Okutsu, Naoko; Shimizu, Eisuke; Shulga, Sergiy; Blume, Ya. B.; Danilov, V.I.; Kurita, Noriyuki

doi:10.1007/s11224-016-0800-3

Cited by 4 publications

(2 citation statements)

References 24 publications

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“…Many computational studies of the guanine (or G.C pair)···HO • interaction have been reported. − However, a theoretical comparison of three HO • additions to dR-Gua (to C(4), C(5), and C(8)) has not been made so far. Also, it has not been examined whether and how three OH adducts undergo the ring cleavage.…”

Section: Introductionmentioning

confidence: 99%

DFT Study of the Hydroxyl Radical Addition to 2′-Deoxyguanosine and the Guanine Base in Four Double-Stranded B-Form Dimers

2020

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Density functional theory (DFT) calculations of reactions between 2′-deoxyguanosine (dR-Gua) and hydroxyl radical (HO • ) with water molecules (H 2 O) n , n = 0, 1, and 2, were carried out. The HO • addition to three carbon sites, C(4), C(5), and C(8), and the subsequent ring cleavage of the three HO adducts were investigated. The addition to C( 5) is of the smallest activation energy according to the largest lobe of the dR-Gua highest occupied molecular orbital (HOMO) at C(5). However, its adduct has small stability, and the C(8) adduct has the largest one. The C(8) adduct and the ring-opened amide have similar stability, which would lead to the apparent small yield of the former. Calculations were also performed on HO • additions to the C(4) and C(8) sites of the guanine moiety of four dimer sequence models of B-form DNA with nucleotide moieties (a) 5′-GA-3′, (b) 5′-GG-3′, (c) 5′-GT-3′, and (d) 5′-GC-3′. For instance, the (a) 5′-GA-3′ model has a molecular formula C 39 H 50 N 15 Na 2 O 21 P 2 . The HO • attack to C(4) is ruled out owing to the reinforced deformation of the parallel stacking of base pairs. The clear selectivity that the (b) 5′-GG-3′ sequence is most reactive was found with the inclusion of the water dimer.

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Section: Introductionmentioning

confidence: 99%

DFT Study of the Hydroxyl Radical Addition to 2′-Deoxyguanosine and the Guanine Base in Four Double-Stranded B-Form Dimers

2020

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“…Sadr et al [ 11 , 12 , 13 , 14 ] have used the DFT to study the fragmentation of cytosine, adenine, guanine, and uracil bases. Okutsu et al [ 15 , 16 ] investigated the attacking mechanisms of radicals to base pairs in water, and Santosh and Abolfath [ 17 ], the relation of the molecule charge with the bond dissociation and fragmentation behavior of DNA bases. However, no time-dependent calculation was carried out by these authors, nor did they study the dynamics of the collision.…”

Section: Introductionmentioning

confidence: 99%

A TD-DFT-Based Study on the Attack of the OH· Radical on a Guanine Nucleotide

Santiago

Faria

San-Miguel

et al. 2022

IJMS

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Heavy charged particles induce severe damage in DNA, which is a radiobiological advantage when treating radioresistant tumors. However, these particles can also induce cancer in humans exposed to them, such as astronauts in space missions. This damage can be directly induced by the radiation or indirectly by the attack of free radicals mainly produced by water radiolysis. We previously studied the impact of a proton on a DNA base pair, using the Time Dependent-Density Functional Theory (TD-DFT). In this work, we go a step further and study the attack of the OH· radical on the Guanine nucleotide to unveil how this molecule subsequently dissociates. The OH· attack on the H1′, H2′, H3′, and H5′ atoms in the guanine was investigated using the Ehrenfest dynamics within the TD-DFT framework. In all cases, the hydrogen abstraction succeeded, and the subsequent base pair dissociation was observed. The DNA dissociates in three major fragments: the phosphate group, the deoxyribose sugar, and the nitrogenous base, with slight differences, no matter which hydrogen atom was attacked. Hydrogen abstraction occurs at about 6 fs, and the nucleotide dissociation at about 100 fs, which agrees with our previous result for the direct proton impact on the DNA. These calculations may be a reference for adjusting reactive force fields so that more complex DNA structures can be studied using classical molecular dynamics, including both direct and indirect DNA damage.

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Interplay of thermochemistry and Structural Chemistry, the journal (Volume 27, 2016, Issues 5 and 6) and the discipline

2017

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Influence of solvating water molecules on the attacking mechanisms of OH-radical to DNA base pairs: DFT calculations in explicit waters

Cited by 4 publications

References 24 publications

DFT Study of the Hydroxyl Radical Addition to 2′-Deoxyguanosine and the Guanine Base in Four Double-Stranded B-Form Dimers

DFT Study of the Hydroxyl Radical Addition to 2′-Deoxyguanosine and the Guanine Base in Four Double-Stranded B-Form Dimers

A TD-DFT-Based Study on the Attack of the OH· Radical on a Guanine Nucleotide

Interplay of thermochemistry and Structural Chemistry, the journal (Volume 27, 2016, Issues 5 and 6) and the discipline

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