scholarly journals Quantum Surprises from the Watson-Crick and Hoogsteen G·C Nucleobase Pairs: A Comprehensive QM/QTAIM Investigation

2021 ◽  
Author(s):  
Ol’ha O. Brovarets ◽  
Alona Muradova ◽  
Dmytro M. Hovorun
Keyword(s):  
Base Pair ◽  
Ion Pairs ◽  
Reaction Pathways ◽  
Proton Acceptor ◽  
Future Research ◽  
Base Pairs ◽  
Dna Base ◽  
Physico Chemical ◽  
Intermolecular Proton Transfer ◽  
Necessary And Sufficient

Abstract In this study at the MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory in the isolated state it was revealed 14 novel physico-chemical mechanisms of the tautomerization of the G·C nucleotide base pairs in the Watson-Crick G·C(WC) / G*·C*(WC), reverse Watson-Crick G*·C*(rWC) / G·C*O2(rWC), Hoogsteen G*t·C*(H) / G*N7·C(H) or reverse Hoogsteen G*t·C*(rH) / G*tN7·C(rH) configurations into the wobble (wWC, wH) and reverse wobble (rwWC, rwН) base pairs: 1. G·C(WC)↔G·C*(rwWC), 2./3. G*·C*(WC)↔G·C*(rwWC)/G*N2·C*(rwWC), 4. G*·C*(rWC)↔G*·C(wWC), 5. G·C*O2(rWC)↔G·C*(wWC); 6./7./8./9. G*t·C*(H)↔G*t·C(rwН)/G*t·C*O2(wH)/G*t·C*O2(rwН)/G*tN7·C*(rwН)↔G*t·C*O2(rwН), 10. G*N7·C(H)↔G*t·C(wH) amino, 11./12. G*t·C*(rH)↔G*N7·C*(wН)/G*t·C(wН), 13. G*tN7·C(rH)↔G*tN7·C*(wН)↔G*t·C(wН) and 14. G*N7·C*(rwH)↔G*N7·C*(rwH) perp↔G-·C+(wH)↔G*t·C(rwН) reaction pathways. It was established that the presence in the base pair of the two anti-parallel neighboring H-bonds is a necessary and sufficient condition for the implementation of such transformations, since it enables intermolecular proton transfer between the bases inside the base pair. It was found out that these tautomeric transitions are controlled by the TSs with quasi-orthogonal structure, which are tight G+·C-/G-·C+ ion pairs, joined by at least two parallel intermolecular H-bonds, connected on a common negatively charged endocyclic N-/C- atoms – proton acceptor. All reaction pathways have been reliably confirmed. These transitions are accompanied by the changing of the mutual cis-orientation of the N9H and N1H glycosidic bonds of the bases on the trans-orientation and vice versa. These data complement the reported earlier mechanisms of the tautomerisations of the classical A·T and G·C DNA base pairs. Experimental verification of the novel G·C nucleobase pairs is looking as an attractive task for the future research.

Nucleosome structure

1978 ◽  
Vol 283 (997) ◽  
pp. 241-258 ◽  
Keyword(s):  
Dynamic Structure ◽  
Histone H2a ◽  
Electron Microscopic ◽  
Base Pairs ◽  
Compact Structure ◽  
Nucleosome Structure ◽  
Dna Base ◽  
Open Structures ◽  
Dna 2 ◽  
Necessary And Sufficient

Electron microscopic and biochemical results are presented supporting the following conclusions: (1) Two molecules of each histone H2A, H2B, H3 and H4 are necessary and sufficient to form a nucleosome with a diameter of 12.5± 1 nm and containing about 200 base pairs of DNA. (2) H3 plus H4 alone can compact 129 ± 8 DNA base pairs into a sub-nucleosomal particle with a diameter of 8 ± 1 nm. In such a particle the DNA duplex is under a constraint equivalent to negative superhelicity. (3) Chromatin should be viewed as a dynamic structure, oscillating between a compact structure (the nucleosome) and more open structures, depending on the environmental conditions.

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.

DNA Base Identification by Electron Microscopy

2012 ◽  
Vol 18 (5) ◽  
pp. 1049-1053 ◽  
Author(s):  
David C. Bell ◽  
W. Kelley Thomas ◽  
Katelyn M. Murtagh ◽  
Cheryl A. Dionne ◽  
Adam C. Graham ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Base Pair ◽  
Heavy Atom ◽  
Genomic Research ◽  
Biological Research ◽  
Template Molecule ◽  
Dna Molecules ◽  
Base Pairs ◽  
Dna Molecule ◽  
Dna Base

AbstractAdvances in DNA sequencing, based on fluorescent microscopy, have transformed many areas of biological research. However, only relatively short molecules can be sequenced by these technologies. Dramatic improvements in genomic research will require accurate sequencing of long (>10,000 base-pairs), intact DNA molecules. Our approach directly visualizes the sequence of DNA molecules using electron microscopy. This report represents the first identification of DNA base pairs within intact DNA molecules by electron microscopy. By enzymatically incorporating modified bases, which contain atoms of increased atomic number, direct visualization and identification of individually labeled bases within a synthetic 3,272 base-pair DNA molecule and a 7,249 base-pair viral genome have been accomplished. This proof of principle is made possible by the use of a dUTP nucleotide, substituted with a single mercury atom attached to the nitrogenous base. One of these contrast-enhanced, heavy-atom-labeled bases is paired with each adenosine base in the template molecule and then built into a double-stranded DNA molecule by a template-directed DNA polymerase enzyme. This modification is small enough to allow very long molecules with labels at each A-U position. Image contrast is further enhanced by using annular dark-field scanning transmission electron microscopy (ADF-STEM). Further refinements to identify additional base types and more precisely determine the location of identified bases would allow full sequencing of long, intact DNA molecules, significantly improving the pace of complex genomic discoveries.

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.

scholarly journals A Quantum-Mechanical Looking Behind the Scene of the Classic G·C Nucleobase Pairs Tautomerization

2020 ◽  
Vol 8 ◽  
Author(s):  
Ol'ha O. Brovarets' ◽  
Alona Muradova ◽  
Dmytro M. Hovorun
Keyword(s):  
Base Pair ◽  
Double Helix ◽  
Ion Pairs ◽  
Electronic Energy ◽  
Tautomeric Equilibrium ◽  
Chemical Mechanism ◽  
Hydroxyl Group ◽  
Quantum Mechanical ◽  
Base Pairs ◽  
Tautomeric Forms

For the first time, at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory, a comprehensive quantum-mechanical investigation of the physico-chemical mechanism of the tautomeric wobblization of the four biologically-important G·C nucleobase pairs by the participation of the monomers in rare, in particular mutagenic, tautomeric forms (marked with an asterisk) was provided. These novel tautomeric transformations (wobblization or shifting of the bases within the pair) are intrinsically inherent properties of the G·C nucleobase pairs. In this study, we have obtained intriguing results, lying far beyond the existing representations. Thus, it was shown that Löwdin's G*·C*(WC) base pair does not tautomerize according to the wobblization mechanism. Tautomeric wobblization of the G*·C*(rWC) (relative Gibbs free energy ΔG = 0.00/relative electronic energy ΔE = 0.00 kcal·mol−1) (“r”—means the configuration of the base pair in reverse position; “WC”—the classic Watson-Crick configuration) and G*t·C*(H) (ΔG = −0.19/ΔE = 0.29 kcal·mol−1) (“H”—Hoogsteen configuration;”t” denotes the O6H hydroxyl group in the trans position) base pairs are preceded by the stages of the base pairs tautomerization by the single proton transfer (SPT). It was established that the G*t·C*(rH) (ΔG = 2.21/ΔE = 2.81 kcal·mol−1) base pair can be wobbled through two different pathways via the traditional one-stage mechanism through the TSs, which are tight G+·C− ion pairs, stabilized by the participation of only two intermolecular H-bonds. It was found out that the G·C base pair is most likely incorporated into the DNA/RNA double helix with parallel strands in the G*·C*(rWC), G·C*(rwwc), and G*·C(rwwc) (“w”—wobble configuration of the pair) tautomeric forms, which are in rapid tautomeric equilibrium with each other. It was proven that the G*·C*(rWC) nucleobase pair is also in rapid tautomeric equilibrium with the eight tautomeric forms of the so-called Levitt base pair. It was revealed that a few cases of tautomerization via the DPT of the nucleobase pairs by the participation of the C8H group of the guanine had occurred. The biological role of the obtained results was also made apparent.

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.

Sign in / Sign up

Export Citation Format

Share Document