scholarly journals Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 241
Author(s):  
Enrique Maciá
Keyword(s):  
Base Pair ◽  
Double Helix ◽  
Three Dimensional ◽  
Dna Molecules ◽  
Analytical Treatment ◽  
Dynamical Equations ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Collective Oscillations ◽  
Triplet Codon

A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment that considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard–Dauxois–Bishop model, we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables corresponding to the bp local scale with those of the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.

scholarly journals Base-Pairs’ Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules

Materials ◽  
2020 ◽  
Vol 13 (22) ◽  
pp. 5119
Author(s):  
Enrique Maciá
Keyword(s):  
Charge Transfer ◽  
Double Helix ◽  
Linear Chain ◽  
Low Frequency ◽  
Dynamical Equations ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Transfer Integrals ◽  
Electronic Parameters ◽  
Collective Oscillations

By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson–Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons’ dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.

Rare internal C4A4 repeats in the micronuclear genome of Oxytricha fallax

1984 ◽  
Vol 4 (12) ◽  
pp. 2661-2667
Author(s):  
D Dawson ◽  
G Herrick
Keyword(s):  
Base Pair ◽  
Full Length ◽  
Dna Molecules ◽  
Base Pairs ◽  
Macronuclear Development ◽  
Structural Relationships

Approximately 20,000 different short, linear, macronuclear DNA molecules are derived from micronuclear sequences of Oxytricha fallax after conjugation. These macronuclear DNAs are terminated at both ends by 20 base pairs of the sequence 5'-dC4A4-3'. Sequences homologous to this repeat (C4A4+) are also abundant in the micronuclear chromosomes, but most reside at their telomeres. Here we show that nontelomeric C4A4 clusters of 20 base pairs or longer exist in only a few hundred copies per micronuclear genome. This demonstrates that nearly none of the 20,000 sequence blocks of micronuclear DNA destined to be macronuclear DNA molecules can be flanked by full-length (20-base pair) C4A4 clusters, and therefore C4A4 repeats must be added to most, if not all, macronuclear telomeres during macronuclear development. Six internal micronuclear C4A4+ loci were cloned, and their structural relationships with macronuclear and micronuclear sequences were examined. The possible origins and functions of these rare, micronuclear internal C4A4 loci are discussed.

scholarly journals Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Shu-ichi Nakano ◽  
Masayuki Fujii ◽  
Naoki Sugimoto
Keyword(s):  
Nucleic Acid ◽  
Base Pair ◽  
Double Helix ◽  
Nucleoside Analogs ◽  
Structural Analog ◽  
Base Pairs ◽  
Nucleic Acid Analogs ◽  
Dna Double Helix ◽  
Nucleic Acid Interactions ◽  
Site Selective

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

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.

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.

scholarly journals DNA information: from digital code to analogue structure

2012 ◽  
Vol 370 (1969) ◽  
pp. 2960-2986 ◽  
Author(s):  
A. A. Travers ◽  
G. Muskhelishvili ◽  
J. M. T. Thompson
Keyword(s):  
Dimensional Space ◽  
Double Helix ◽  
Three Dimensional ◽  
Base Pairs ◽  
Nucleosome Core ◽  
Histone Octamer ◽  
Regulatory Mode ◽  
Sequence Periodicity ◽  
Recent Developments ◽  
Dna Double Helix

The digital linear coding carried by the base pairs in the DNA double helix is now known to have an important component that acts by altering, along its length, the natural shape and stiffness of the molecule. In this way, one region of DNA is structurally distinguished from another, constituting an additional form of encoded information manifest in three-dimensional space. These shape and stiffness variations help in guiding and facilitating the DNA during its three-dimensional spatial interactions. Such interactions with itself allow communication between genes and enhanced wrapping and histone–octamer binding within the nucleosome core particle. Meanwhile, interactions with proteins can have a reduced entropic binding penalty owing to advantageous sequence-dependent bending anisotropy. Sequence periodicity within the DNA, giving a corresponding structural periodicity of shape and stiffness, also influences the supercoiling of the molecule, which, in turn, plays an important facilitating role. In effect, the super-helical density acts as an analogue regulatory mode in contrast to the more commonly acknowledged purely digital mode. Many of these ideas are still poorly understood, and represent a fundamental and outstanding biological question. This review gives an overview of very recent developments, and hopefully identifies promising future lines of enquiry.

Sequencing of large double-stranded DNA using the dideoxy sequencing technique

1982 ◽  
Vol 2 (11) ◽  
pp. 907-912 ◽  
Author(s):  
G. F. Hong
Keyword(s):  
Sequence Analysis ◽  
Direct Sequencing ◽  
Dna Molecules ◽  
Coding Region ◽  
Base Pairs ◽  
Dideoxy Sequencing ◽  
Double Stranded Dna ◽  
Sequencing Technique ◽  
Eukaryotic Dna

The dideoxy sequencing technique has been applied to the direct sequencing of large double-stranded DNA molecules with a small single-stranded primer. For instance, the method was applied to the lambda genome, which contains 48 502 base-pairs (Sanger F, Coulson AR, Hong GF, Hill D & Petersen GB, 1982, J. Mol. Biol., in press), and the coding region for gene W identified. The procedure proves useful in the sequence analysis of a large number of different mutations in a particular region and in the analysis of eukaryotic DNA cloned in plasmids, phages, and cosmids.

Sequence-dependent twist-bend coupling in DNA minicircles

Nanoscale ◽  
2021 ◽  
Author(s):  
Minjung Kim ◽  
Sehui Bae ◽  
Inrok Oh ◽  
Jejoong Yoo ◽  
Jun Soo Kim
Keyword(s):  
Dna Bending ◽  
Dna Molecules ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Sequence Dependent ◽  
Potential Tool

Looping of double-stranded DNA molecules with 100∼200 base pairs into minicircles, catenanes, and rotaxanes has been suggested as a potential tool for DNA nanotechnologies. However, sharp DNA bending into a...

2. Genes as DNA

2014 ◽  
Author(s):  
Jonathan Slack
Keyword(s):  
Molecular Biology ◽  
Double Helix ◽  
Complex Structure ◽  
Genetic Material ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Human Beings ◽  
Base Pairs ◽  
Modern Molecular Biology ◽  
Complete Sequencing

After 1944, a remarkable set of discoveries established the overall shape of modern molecular biology and most famous of all was the discovery of the three dimensional structure of DNA: the famous double helix, which explained how the substance could act as the genetic material. ‘Genes as DNA’ describes the complex structure of genes and explains the terms ‘genome’ and ‘genomics’. In the 1980s and 1990s the complex mechanisms by which genes control embryonic development were discovered. The complete sequencing of a typical human genome was started in the late 1990s and achieved in 2003. It showed that the genome of human beings contains about three billion base pairs of DNA.

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