Effect of phenolic radicals on the geometry and electronic structure of DNA base pairs: computational study

2016 ◽  
Vol 27 (10) ◽  
pp. 1650119 ◽  
Author(s):  
Mohammad Zarei ◽  
Abdolvahab Seif ◽  
Khaled Azizi ◽  
Mohanna Zarei ◽  
Jamil Bahrami
Keyword(s):  
Hydrogen Bond ◽  
Dft Calculations ◽  
Base Pair ◽  
Density Functional ◽  
Base Pairs ◽  
Water Solvent ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Phenoxy Radicals ◽  
Dna Base Pair

In this paper, we show the reaction of a hydroxyl, phenyl and phenoxy radicals with DNA base pairs by the density functional theory (DFT) calculations. The influence of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. The results showed that hydroxyl, phenyl and phenoxy radicals increase the length of the nearest hydrogen bond of adjacent DNA base pair which is accompanied by decrease in the length of furthest hydrogen bond of DNA base pair. Also, hydroxyl, phenyl and phenoxy radicals influenced the dihedral angle between DNA base pairs. According to the results, hydrogen bond lengths between AT and GC base pairs in water solvent are longer than vacuum. All of presented radicals influenced the structure and geometry of AT and GC base pairs, but phenoxy radical showed more influence on geometry and electronic properties of DNA base pairs compared with the phenyl and hydroxyl radicals.

MECHANICAL APPROACH IN THE STUDIES OF DNA BASE PAIR OSCILLATIONS

2011 ◽  
Vol 21 (10) ◽  
pp. 3063-3071 ◽  
Author(s):  
L. V. YAKUSHEVICH ◽  
S. GAPA ◽  
J. AWREJCEWICZ
Keyword(s):  
Base Pair ◽  
Dna Bases ◽  
Lagrange Equations ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Mechanical Approach ◽  
Dna Base Pair ◽  
Angular Displacements ◽  
Rotational Oscillations

The rotational oscillations of the DNA bases around the sugar-phosphate chains make an important contribution to the process of DNA base pairs opening that in turn plays a crucial role in the process of the DNA-protein recognition. As a result, the study of these oscillations helps to understand better the dynamical mechanisms of the biological activity of the DNA molecule. In this work, we study rotational oscillations of two coupled DNA bases that form a base pair: adenine-thymine (AT) or guanine-cytosine (GC). We show that the problem can be reduced to the mechanical problem of two coupled nonsymmetrical nonlinear pendulums oscillating in the horizontal plane. We obtain the Lagrange equations, estimate the values of the coefficients of the equations and use the results of estimations to construct the potential energy surface. We consider in detail the case of small amplitudes of angular displacements, find the general solution of corresponding Lagrange equations and present graphs using Maple 13.

The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance

1999 ◽  
Vol 5 (12) ◽  
pp. 3581-3594 ◽  
Author(s):  
Célia Fonseca Guerra ◽  
F. Matthias Bickelhaupt ◽  
Jaap G. Snijders ◽  
Evert Jan Baerends
Keyword(s):  
Hydrogen Bond ◽  
Charge Transfer ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs

140 Attacking mechanism of H and OH radicals to DNA base pair: DFT calculations in water

2015 ◽  
Vol 33 (sup1) ◽  
pp. 91-92
Author(s):  
Naoko Okutsu ◽  
Eisuke Shimizu ◽  
Victor I. Danilov ◽  
Sergiy Shulga ◽  
Noriyuki Kurita
Keyword(s):  
Dft Calculations ◽  
Base Pair ◽  
Oh Radicals ◽  
Dna Base ◽  
Dna Base Pair

scholarly journals Asymmetric base-pair opening drives helicase unwinding dynamics

2019 ◽  
Vol 116 (45) ◽  
pp. 22471-22477 ◽  
Author(s):  
Francesco Colizzi ◽  
Cibran Perez-Gonzalez ◽  
Remi Fritzen ◽  
Yaakov Levy ◽  
Malcolm F. White ◽  
...  
Keyword(s):  
Base Pair ◽  
Double Helix ◽  
The Other ◽  
Base Pairs ◽  
Dna Helicases ◽  
Cellular Processes ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Opening And Closing ◽  
Base Pair Opening

The opening of a Watson–Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix.

DFT/TDDFT STUDY ON DNA-BINDING AND SPECTRAL PROPERTIES OF "LIGHT SWITCH" COMPLEX [Ru(phen)2 (taptp)]2+ IN AQUEOUS SOLUTION

2008 ◽  
Vol 07 (06) ◽  
pp. 1147-1158 ◽  
Author(s):  
JUN LI ◽  
LIAN-CAI XU ◽  
SI-YAN LIAO ◽  
KANG-CHENG ZHENG ◽  
LIANG-NIAN JI
Keyword(s):  
Aqueous Solution ◽  
Dna Binding ◽  
Solvent Effect ◽  
Spectral Properties ◽  
Density Functional ◽  
Frontier Molecular Orbital ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Planar Area

The theoretical studies on the electronic structure, DNA-binding, and absorption-spectral properties of "light switch" complex [ Ru ( phen )2( taptp )]2+ (phen = 1,10-phenanthroline; taptp = 4,5,9,18-tetraazaphenanthreno-[9,10-b]triphenylene) in aqueous solution have been carried out using density functional theory (DFT) and time-dependent DFT (TDDFT) methods. The results show the following: (i) The solvent effect makes all the frontier molecular orbital energies of complex to increase to a certain extent; however, the energies (ε LUMO + x) of some frontier unoccupied molecular orbitals (MOs) in aqueous solution are still negative and rather lower than those of the energies (ε HOMO - x) of some frontier-occupied MOs of DNA-base pairs, and thus the complex in aqueous solution is still an excellent electron-acceptor in its DNA-binding. (ii) The solvent effect further shows that simply increasing the conjugative planar area of intercalative ligand may be ineffective on the improvement of DNA-binding of the resulting complex because of going along with the increase in the LUMO (and LUMO + x) energy. It is the reason why the DNA-binding affinity of "light switch" complex [ Ru ( phen )2( taptp )]2+ is not better than that of the well-known complex [ Ru ( phen )2( dppz )]2+ yet. (iii) The three main experimental bands (~450 nm, ~360 nm, and ~290 nm) of the studied complex in aqueous solution were further well calculated, simulated, and explained by the TDDFT computations.

scholarly journals Mechanisms and Parameters of the Binding of Amitozinoberamid to DNA in the Aqueous Solution

2018 ◽  
Vol 63 (8) ◽  
pp. 709 ◽  
Author(s):  
S. Yu. Kutovyy ◽  
R. S. Savchuk ◽  
N. V. Bashmakova ◽  
D. M. Hovorun ◽  
L. A. Zaika
Keyword(s):  
Aqueous Solution ◽  
Density Functional ◽  
Spectral Characteristics ◽  
Dna Interaction ◽  
Base Pairs ◽  
Electron Absorption ◽  
Dna Base ◽  
The Density Functional Theory ◽  
Dna Base Pairs ◽  
The One

The interaction between the amitozinoberamid preparation (thiotepa-alkylated berberine) and a DNA macromolecule in the aqueous solution has been studied, by using the optical spectroscopy methods: electron absorption and fluorescence. The dependence of spectral characteristics on the concentration ratio N/c between the DNA base pairs and the ligand molecules is plotted. Using the system of modified Scatchard and McGhee–von Hippel equations, the parameters of the binding of amitozinoberamid to DNA are determined. A comparative analysis of the DNA interaction with amitozinoberamid, on the one hand, and berberine and sanguinarine alkaloids, on the other hand, is carried out. The structure and the spectra of electron absorption of thiotepa, berberine, and amitozinoberamid molecules are calculated in the framework of the density functional theory at the DFT B3LYP/6-31G(d,p) level.

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