Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons
Abstract
:1. Introduction
2. Dynamical DNA Model Hamiltonian
3. Dynamical Equations of Motion
3.1. General Expressions
3.2. Dynamics of Homopolymer dsDNA Chains
3.3. Dynamics of Poly(XX’)-Poly(X’X) dsDNA Molecules
3.4. Dynamics of Poly(XYX)-Poly(X’Y’X’) dsDNA Molecules
4. Helical Waves Related Dispersion Relations
5. Orchestrated Codon Oscillations
6. Environmental Effects in the DNA Dynamics
7. Conclusions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
dsDNA | double-stranded DNA |
bp | base pair |
A | adenine |
C | cytosine |
G | guanine |
T | thymine |
PDB | Peyrard–Dauxois–Bishop |
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Geometrical | Dynamical | Potential |
---|---|---|
rad | amu | Å [15,30] |
nm | Å [14,30,31] | |
nm | eV [21,30,31] | |
nm | amu | eV Å [21] |
nm | amu | eV Å [30] |
Oscillation | Codon | ( rad s) | (THz) | (ps) | |
---|---|---|---|---|---|
Twist | |||||
Stacking | |||||
Stretching | |||||
Twist-Stacking | X’XX’ | ||||
YXY | |||||
XXX | |||||
XYX | |||||
XX’X | |||||
Twist-Stretching | XXX | ||||
Twist-Stacking-Stretching | XX’X | ||||
XYX | |||||
YXY | |||||
X’XX’ | |||||
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Maciá, E. Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons. Symmetry 2021, 13, 241. https://doi.org/10.3390/sym13020241
Maciá E. Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons. Symmetry. 2021; 13(2):241. https://doi.org/10.3390/sym13020241
Chicago/Turabian StyleMaciá, Enrique. 2021. "Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons" Symmetry 13, no. 2: 241. https://doi.org/10.3390/sym13020241