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.

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 Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

Collective oscillations in bubble clouds

2011 ◽  
Vol 680 ◽  
pp. 114-149 ◽  
Author(s):  
ZORANA ZERAVCIC ◽  
DETLEF LOHSE ◽  
WIM VAN SAARLOOS
Keyword(s):  
Frequency Response ◽  
Acoustic Field ◽  
Low Frequency ◽  
Acoustic Energy ◽  
Viscous Damping ◽  
Edge States ◽  
Bubble Cloud ◽  
Collective Oscillations ◽  
The Individual ◽  
Bubble Oscillations

In this paper the collective oscillations of a bubble cloud in an acoustic field are theoretically analysed with concepts and techniques of condensed matter physics. More specifically, we will calculate the eigenmodes and their excitabilities, eigenfrequencies, densities of states, responses, absorption and participation ratios to better understand the collective dynamics of coupled bubbles and address the question of possible localization of acoustic energy in the bubble cloud. The radial oscillations of the individual bubbles in the acoustic field are described by coupled linearized Rayleigh–Plesset equations. We explore the effects of viscous damping, distance between bubbles, polydispersity, geometric disorder, size of the bubbles and size of the cloud. For large enough clusters, the collective response is often very different from that of a typical mode, as the frequency response of each mode is sufficiently wide that many modes are excited when the cloud is driven by ultrasound. The reason is the strong effect of viscosity on the collective mode response, which is surprising, as viscous damping effects are small for single-bubble oscillations in water. Localization of acoustic energy is only found in the case of substantial bubble size polydispersity or geometric disorder. The lack of localization for a weak disorder is traced back to the long-range 1/r interaction potential between the individual bubbles. The results of the present paper are connected to recent experimental observations of collective bubble oscillations in a two-dimensional bubble cloud, where pronounced edge states and a pronounced low-frequency response had been observed, both consistent with the present theoretical findings. Finally, an outlook to future possible experiments is given.

scholarly journals Base pairing structure in the poly d(G-T) double helix: wobble base pairs

1978 ◽  
Vol 5 (6) ◽  
pp. 1955-1970 ◽  
Author(s):  
Thomas A. Early ◽  
John Olmsted ◽  
David R. Kearns ◽  
Axel G. Lezius
Keyword(s):  
Double Helix ◽  
Base Pairing ◽  
Base Pairs

scholarly journals Hoogsteen Base Pairs Increase the Susceptibility of Double-Stranded DNA to Cytotoxic Damage

2021 ◽  
Vol 120 (3) ◽  
pp. 9a
Author(s):  
Akanksha Manghrani ◽  
Yu Xu ◽  
Emily Cannistraci ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Base Pairs ◽  
Double Stranded Dna

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

scholarly journals Intermolecular Charge-Transfer-Induced Strong Optical Emission from Herringbone H-Aggregates

2021 ◽  
Author(s):  
Qi Sun ◽  
Jiajun Ren ◽  
Tong Jiang ◽  
Qian Peng ◽  
Qi Ou ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Optical Emission ◽  
Light Emitting ◽  
High Charge ◽  
Organic Light ◽  
Intermolecular Charge Transfer ◽  
Transfer Integrals ◽  
Strong Luminescence ◽  
Theoretical Finding ◽  
Three State Model

Superior organic light-emitting transistors (OLETs) materials require two conventionally exclusive properties: strong luminescence and high charge mobilities. We propose a three-state model through localized diabatization to quantitative analyze excited state structures for various herringbone (HB) H-aggregates and demonstrate that for some investigated systems, the low-lying intermolecular charge-transfer (CT) state couples with the bright Frenkel exciton (FE) and forms a dipole-allowed S<sub>1</sub> that lies below the dark state, proceeding strong luminescence. Specifically, such conversion in luminescence properties occurs when the electron- and hole-transfer integrals ( and ) are of the same sign and is notably larger than the excitonic coupling (<i>J</i>), i.e., . This theoretical finding can not only explain and rationalize recent experimental results on DPA and dNaAnt, both with OLET property, but also unravel an exciting scenario where strong luminescence and high charge mobilities are compatible, which will considerably broaden the aperture of novel OLET design.

Intrinsic charge transfer in the mixed halide PtCl«I−« linear chain solids

1993 ◽  
Vol 56 (2-3) ◽  
pp. 3449-3455 ◽  
Author(s):  
X.Z. Huang ◽  
A. Saxena ◽  
A.R. Bishop ◽  
B.L. Scott ◽  
B.I. Swanson
Keyword(s):  
Charge Transfer ◽  
Linear Chain

The unique structure of A-tracts and intrinsic DNA bending

2009 ◽  
Vol 42 (1) ◽  
pp. 41-81 ◽  
Author(s):  
Tali E. Haran ◽  
Udayan Mohanty
Keyword(s):  
Current Knowledge ◽  
Double Helix ◽  
Dna Bending ◽  
Helical Axis ◽  
Base Pairs ◽  
Regulatory Regions ◽  
Unique Structure ◽  
Distinct Structure ◽  
Global Curvature ◽  
Dna Double Helix

AbstractShort runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.

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