Interaction of the Adenine−Thymine Watson−Crick and Adenine−Adenine Reverse-Hoogsteen DNA Base Pairs with Hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and IIb (Zn2+, Cd2+, Hg2+) Metal Cations:  Absence of the Base Pair Stabilization by Metal-Induced Polarization Effects

1999 ◽  
Vol 103 (13) ◽  
pp. 2528-2534 ◽  
Author(s):  
Jiří Šponer ◽  
Michal Sabat ◽  
Jaroslav V. Burda ◽  
Jerzy Leszczynski ◽  
Pavel Hobza
Keyword(s):  
Base Pair ◽  
Metal Cations ◽  
Induced Polarization ◽  
Base Pairs ◽  
Polarization Effects ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Adenine Thymine

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.

Nonlinear Dynamics of Interconnected Structures: An Application to DNA Dynamics

2005 ◽  
Author(s):  
Amit Shukla
Keyword(s):  
Nonlinear Dynamics ◽  
Base Pair ◽  
Harmonic Excitation ◽  
Dna Dynamics ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Genetic Features ◽  
Nonlinear Potential ◽  
Single Base Pair

Nonlinear dynamics of DNA base-pairs is essential in many of the genetic features and functions of the molecule. The motion of the base-pair is influenced by the nonlinear potential between the two nucleotides as well as the adjacent base-pairs. In this paper nonlinear dynamics of the base-pairs is investigated. A single degree-of-freedom model for the base-pair dynamics as proposed by Peyrard-Bishop-Dauxois is analyzed. First a single base-pair dynamics is investigated using perturbation method. Then a three base-pair model is numerically investigated to understand the nonlinear response of the system to a harmonic excitation. Finally, it is also shown that the effect of interconnection can be minimized by selecting the environment surrounding the DNA molecule.

Covalent Analogues of DNA Base-Pairs and Triplets V. Synthesis of Purine-Purine and Purine-Pyrimidine Conjugates Connected by Diverse Types of Acyclic Carbon Linkages

2002 ◽  
Vol 67 (10) ◽  
pp. 1560-1578 ◽  
Author(s):  
Michal Hocek ◽  
Hana Dvořáková ◽  
Ivana Císařová
Keyword(s):  
Single Crystal ◽  
Crystal Structures ◽  
Base Pair ◽  
Cross Coupling ◽  
X Ray Diffraction ◽  
Base Pairs ◽  
X Ray ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Purine Pyrimidine

The title 1,2-bis(purin-6-yl)acetylenes, -diacetylenes, -ethylenes and -ethanes were prepared as covalent base-pair analogues starting from 6-ethynylpurines and 6-iodopurines by the Sonogashira cross-coupling or oxidative alkyne-dimerization reactions followed by hydrogenations. 6-[(1,3-Dimethyluracil-5-yl)ethynyl]purine (11) was prepared analogously and hydrogenated to the corresponding purine-pyrimidine conjugates linked via vinylene and ethylene linkers. Unlike the cytostatic bis(purin-6-yl)acetylenes and -diacetylenes, the purine-pyrimidine conjugates were inactive. Crystal structures of bis(purin-6-yl)acetylene 6a, -diacetylene 8a and -ethane 5a were determined by single-crystal X-ray diffraction.

Transient proton transfer of base pair hydrogen bonds induced by intense terahertz radiation

2020 ◽  
Vol 22 (17) ◽  
pp. 9316-9321
Author(s):  
Kaicheng Wang ◽  
Lixia Yang ◽  
Shaomeng Wang ◽  
Lianghao Guo ◽  
Jialu Ma ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Terahertz Radiation ◽  
Base Pair ◽  
Quantum Simulation ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs

Intense terahertz radiation was applied to trigger transient proton transfer in DNA base pairs through quantum simulation.

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.

scholarly journals The A·T(rWC)/A·T(H)/A·T(rH) ↔ A·T*(rwWC)/A·T*(wH)/A·T*(rwH) mutagenic tautomerization via sequential proton transfer: a QM/QTAIM study

RSC Advances ◽  
2018 ◽  
Vol 8 (24) ◽  
pp. 13433-13445 ◽  
Author(s):  
Ol'ha O. Brovarets' ◽  
Kostiantyn S. Tsiupa ◽  
Dmytro M. Hovorun
Keyword(s):  
Proton Transfer ◽  
Base Pair ◽  
Building Block ◽  
Genetic Material ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Self Development

We discovered tautomeric wobbling of the classical A·T DNA base pairs. This data evidence, that only a base pair with Watson–Crick architecture can be a building block of the DNA macromolecule as a genetic material, which is able for the evolutionary self-development.

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 Effect of Alkali Metal Cations on Length and Strength of Hydrogen Bonds in DNA Base Pairs

ChemPhysChem ◽  
2020 ◽  
Vol 21 (18) ◽  
pp. 2112-2126
Author(s):  
Olga A. Stasyuk ◽  
Miquel Solà ◽  
Marcel Swart ◽  
Célia Fonseca Guerra ◽  
Tadeusz Marek Krygowski ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Alkali Metal ◽  
Metal Cations ◽  
Alkali Metal Cations ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs
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