Modulation of the Directionality of Hole Transfer between the Base and the Sugar-Phosphate Backbone in DNA with the Number of Sulfur Atoms in the Phosphate Group

2022 ◽  
Author(s):  
Sergey A. Denisov ◽  
Samuel Ward ◽  
Viacheslav Shcherbakov ◽  
Alexander D. Stark ◽  
Renata Kaczmarek ◽  
...  
Keyword(s):  
Phosphate Group ◽  
Sugar Phosphate ◽  
Hole Transfer ◽  
Phosphate Backbone

The interaction of the 2′-OH group with the vicinal phosphate in ribonucleoside 3′-ethylphosphate drives the sugar-phosphate backbone into unique (S,ω−) conformational state

Tetrahedron ◽  
1995 ◽  
Vol 51 (43) ◽  
pp. 11775-11792 ◽  
Author(s):  
J. Plavec ◽  
C. Thibaudeau ◽  
G. Viswanadham ◽  
C. Sund ◽  
A. Sandström ◽  
...  
Keyword(s):  
Conformational State ◽  
Sugar Phosphate ◽  
Phosphate Backbone

scholarly journals Theoretical modelling of epigenetically modified DNA sequences

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 52 ◽  
Author(s):  
Alexandra Teresa Pires Carvalho ◽  
Maria Leonor Gouveia ◽  
Charan Raju Kanna ◽  
Sebastian K. T. S. Wärmländer ◽  
Jamie Platts ◽  
...  
Keyword(s):  
Molecular Mechanics ◽  
Dna Sequences ◽  
Base Pair ◽  
Density Functional ◽  
Epigenetic Modifications ◽  
Theoretical Modelling ◽  
Sugar Phosphate ◽  
Base Pairs ◽  
Phosphate Backbone ◽  
Modified Dna

We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.

The Effects of Split Valence Basis Sets on Muon Hyperfine Interaction in Guanine Nucleobase and Nucleotide Structures

2019 ◽  
Vol 966 ◽  
pp. 222-228 ◽  
Author(s):  
Wan Nurfadhilah Zaharim ◽  
Shukri Sulaiman ◽  
Siti Nuramira Abu Bakar ◽  
Nur Eliana Ismail ◽  
Harison Rozak ◽  
...  
Keyword(s):  
Total Energy ◽  
Hyperfine Interactions ◽  
Phosphate Group ◽  
Basis Set ◽  
Basis Sets ◽  
Cluster Method ◽  
Sugar Phosphate ◽  
Atomic Orbitals ◽  
Fermi Contact ◽  
Triple Zeta

The DFT cluster method was employed to investigate the electronic structures and muonium hyperfine interactions in guanine nucleobase and nucleotide using three different basis sets. The total energy and Fermi contact values were calculated for muon trapped at carbon '8'. The three basis sets, 6-31G, 6-311G and 6-311G(d,p), were used in tandem with the B3LYP functional. There are significant quantitative differences in the calculated total energy. 6-311G(d,p) produced the lowest total energy as compared to the other basis sets. The lowering of the total energy is due to the increase in the number of basis functions to describe the atomic orbitals, which is consistent with the postulate on basis set completeness. The 6-31G basis set produced the muon Fermi contact value that is the closest to the experimental value. The calculated Fermi contact values for the nucleobase and nucleotide are significantly lowered in going from the double-zeta to the triple-zeta basis set by 5% and 4% respectively. The lowering of the Fermi contact value can be attributed to the extension of the triple-zeta basis set in describing the valence atomic orbitals. The presence of the sugar phosphate group in the nucleotide instead of the methyl group tends to lower the Fermi contact value. Thus, the sugar phosphate group should be taken into consideration when designing a calculation model.

scholarly journals Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

2008 ◽  
Vol 112 (27) ◽  
pp. 8188-8197 ◽  
Author(s):  
Daniel Svozil ◽  
Judit E. Šponer ◽  
Ivan Marchan ◽  
Alberto Pérez ◽  
Thomas E. Cheatham ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Nucleic Acids ◽  
Sugar Phosphate ◽  
Phosphate Backbone
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