QUANTUM MECHANICAL DESCRIPTION OF THE INTERACTIONS BETWEEN DNA AND 9,10-ANTHRAQUINONE

2008 ◽  
Vol 07 (03) ◽  
pp. 317-329 ◽  
Author(s):  
SIAVASH RIAHI ◽  
MOHAMMAD REZA GANJALI ◽  
PARVIZ NOROUZI
Keyword(s):  
Base Pair ◽  
Dft Method ◽  
Base Pairs ◽  
Dispersion Energy ◽  
Charge Delocalization ◽  
Dna Base ◽  
Quantum Mechanical Description ◽  
London Dispersion ◽  
Dna Base Pair ◽  
The Stability

Molecular geometries of the 9,10-anthraquinone (AQ) and DNA bases (Adenine, Guanine, Cytosine, and Thymine) were optimized using B3LYP/6-31G** method. Properties of isolated intercalator (9,10-anthraquinone) and their stacking interactions with adenine ⋯ thymine (AT) and guanine ⋯ cytosine (GC) nucleic acid base pairs were investigated by means of DFTB method. DFTB method, an approximate version of the DFT method, was extended to cover London dispersion energy. AQ exhibits a large charge delocalization and it has no site with dominant charge. This intercalator has a large polarizability and is a good electron acceptor, while base pairs are good electron donors. B3LYP/6-31G** stabilization energies of intercalator ⋯ base pair complexes are large (-18.83 kcal/mol for AT ⋯ AQ and -15.69 kcal/mol for GC ⋯ AQ). It is concluded that, the dispersion energy predominantly contributes to the stability of intercalator ⋯ DNA base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation. The results showed that AQ changes the structure of DNA on bond length, bond angle, torsion angle, and charges.

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.

An electrochemical study based on thymine–Hg–thymine DNA base pair mediated charge transfer processes

RSC Advances ◽  
2015 ◽  
Vol 5 (61) ◽  
pp. 49819-49823 ◽  
Author(s):  
Ensheng Xu ◽  
Yanqin Lv ◽  
Jifeng Liu ◽  
Xiaohong Gu ◽  
Shuqiu Zhang
Keyword(s):  
Charge Transfer ◽  
Base Pair ◽  
Electrochemical Study ◽  
Base Pairs ◽  
Transfer Processes ◽  
Dna Base ◽  
Dna Base Pair

The (TT)n might have more π-overlapping than the corresponding matched base pairs, and the intercalation of Hg(ii) into TT may further increase this overlapping, causing faster CT kinetics.

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.

scholarly journals Where Quantum Biochemistry Meets Structural Bioinformatics: Excited Conformationally-Tautomeric States of the Classical A·T DNA Base Pair

2021 ◽  
Author(s):  
Ol’ha O. Brovarets’ ◽  
Kostiantyn S. Tsiupa ◽  
Dmytro M. Hovorun
Keyword(s):  
Base Pair ◽  
Biological Significance ◽  
Structural Bioinformatics ◽  
The Novel ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pair ◽  
First Time ◽  
Energy Hypersurface ◽  
Shed Light

This Chapter summarizes recent quantum-chemical (QM) investigations of the novel conformational and tautomeric states on the potential energy hypersurface of the classical A·T/A·U nucleobase pairs. For the first time, it was observed 28 local minima for each base pair excluding enantiomers - planar, non-planar base pairs and structures with wobble geometry. Considered excited conformationally-tautomeric states of the classical A·T DNA base pair have been revealed in the Nucleic Acid Database by structural bioinformatics. These data shed light on the biological significance of the unusual A·T/A·U nucleobase pairs for the functioning of the nucleic acids at the quantum level.

scholarly journals Solvent effects on the excited state characteristics of adenine–thymine base pairs

RSC Advances ◽  
2017 ◽  
Vol 7 (53) ◽  
pp. 33426-33440 ◽  
Author(s):  
S. Saha ◽  
H. M. Quiney
Keyword(s):  
Excited State ◽  
Solvent Effects ◽  
Base Pair ◽  
Base Pairs ◽  
Systematic Analysis ◽  
Dna Base ◽  
Dna Base Pair ◽  
Adenine Thymine ◽  
Hydrogen Bonded

A systematic analysis of the excited state characteristics of the DNA base pair adenine–thymine in stacked and Watson–Crick hydrogen bonded configurations has been carried out in this study.

On the change of the order od stability of DNA base pairs as a result of the methylation of guanine

1988 ◽  
Vol 53 (9) ◽  
pp. 1943-1945
Author(s):  
Pavel Hobza ◽  
Camille Sandorfy
Keyword(s):  
Ab Initio ◽  
Base Pairs ◽  
Dispersion Energy ◽  
Dna Base ◽  
Dna Base Pairs

The interaction of the 6-O methylguanine cation with cytosine and thymine was studied using the ab initio SCF method in combination with a London type expression for dispersion energy. The structure of the complex formed with cytosine differs from that found previously with guanine itself.

Varying DNA Base-Pair Size in Subangstrom Increments:  Evidence for a Loose, Not Large, Active Site in Low-Fidelity Dpo4 Polymerase

Biochemistry ◽  
2006 ◽  
Vol 45 (9) ◽  
pp. 2772-2778 ◽  
Author(s):  
Shin Mizukami ◽  
Tae Woo Kim ◽  
Sandra A. Helquist ◽  
Eric T. Kool
Keyword(s):  
Active Site ◽  
Base Pair ◽  
Dna Base ◽  
Dna Base Pair

scholarly journals A rhodium(III) complex for high-affinity DNA base-pair mismatch recognition

2003 ◽  
Vol 100 (7) ◽  
pp. 3737-3742 ◽  
Author(s):  
H. Junicke ◽  
J. R. Hart ◽  
J. Kisko ◽  
O. Glebov ◽  
I. R. Kirsch ◽  
...  
Keyword(s):  
Base Pair ◽  
High Affinity ◽  
Base Pair Mismatch ◽  
Dna Base ◽  
Mismatch Recognition ◽  
Dna Base Pair
Sign in / Sign up

Export Citation Format

Share Document