Abstract
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 - 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.
Highlights
In physiological conditions, the DNA double helix exhibits a full-fledged three-dimensional (3D) geometry, where every two consecutive Watson–Crick base pairs stand nearly parallel to each other, and they are twisted by a certain angle (θ0 ' 36◦ in equilibrium conditions) around the helix axis
In order to analyze the interplay between the double-stranded DNA (dsDNA) low frequency bps’ dynamics and charge transfer (CT) efficiency, we will study the coupling between the oscillations of complementary bases along the transversal direction and the twisting motion of each bp as a whole through the helical sugar-phosphate backbone structure, explicitly taking into account its characteristic helical geometry, which has been shown to be very important in biological processes, such as denaturation and transcription [17]
The π and π ∗ molecular orbitals are formed throughout the π-stacking, so that the resulting electronic transfer integrals values explicitly depend by the C, N, and O atomic pz orbitals perpendicular to the bps and∗ pointing along the helical axis, on the dynamical degrees of freedom ρn, ρn±1 and θn,n±1
Summary
The DNA double helix exhibits a full-fledged three-dimensional (3D) geometry, where every two consecutive Watson–Crick base pairs (bps) stand nearly parallel to each other, and they are twisted by a certain angle (θ0 ' 36◦ in equilibrium conditions) around the helix axis. In order to analyze the interplay between the dsDNA low frequency bps’ dynamics and CT efficiency, we will study the coupling between the oscillations of complementary bases along the transversal direction and the twisting motion of each bp as a whole through the helical sugar-phosphate backbone structure, explicitly taking into account its characteristic helical geometry, which has been shown to be very important in biological processes, such as denaturation and transcription [17] To this end, we will explicitly take into account the stacking interaction, mediated by the orbital overlapping between adjacent bps along the helix, as well as hydrogen bond stretch motions, as described in the Peyrard–Dauxois–Bishop (PDB) model [18,19,20], in the phonon dynamical equations.
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