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Pré-Publication, Document De Travail Année : 2022

Electrodynamic forces driving DNA-enzyme interaction at a large distance

Résumé

In the present paper we address a model of DNA-protein selective interaction. The biochemical model is chosen on the basis of existing literature, both theoretical and experimental. This consists of a restriction enzyme, EcoRI, binding selectively to a 6 base-pair subsequence of an oligonucleotide to cleave it. A signature of the specific partnership of the two molecules is first obtained by applying the so-called Resonant Recognition Model. Then the same system is investigated by means of a model inspired to the standard Davydov and Holstein-Fröhlich models describing the electron motion along a biomolecule. Starting with a model Hamiltonian written in second quantization, the Time Dependent Variational Principle is used to work out the dynamical equations of the system. The time-Fourier spectra of the electron currents numerically computed for the DNA fragment and for the EcoRI enzyme, respectively, are multiplied to get a crossspectrum which displays a sharp peak of co-resonance. The remarkable result is the replacement of this sharp peak with a broad and noisy frequency pattern when the recognition sequence GAATTC on the DNA is randomized. This sequence-dependent charge transfer phenomenology is suggestive of a potentially rich variety of selective electrodynamic interactions of DNA molecules and transcription factors under the action of electron excitation.
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Dates et versions

hal-03679348 , version 1 (26-05-2022)

Identifiants

  • HAL Id : hal-03679348 , version 1

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Elham Faraji, Philip Kurian, Roberto Franzosi, Stefano Mancini, Irena Cosic, et al.. Electrodynamic forces driving DNA-enzyme interaction at a large distance. 2022. ⟨hal-03679348⟩
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