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Assessing the Sequence Dependence of Pyrimidine-Pyrimidone (6-4) Photoproduct in a Duplex Double-Stranded DNA: A Challenge for Microsecond Range Simulation

preprint
submitted on 17.12.2020, 18:23 and posted on 18.12.2020, 12:07 by Natacha Gillet, Alessio Bartocci, Elise Dumont
Sequence dependence of the (6-4)photoproduct dynamics when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing a different upstream and downstream flexibilities. Moreover, REST2 simulations allow to probe structures possibly important for damaged DNA recognition.

Funding

Genci Idris 2020-A0070800609

LABEX PRIMES (ANR-11-LABX-0063)

History

Email Address of Submitting Author

natacha.gillet@ens-lyon.fr

Institution

Laboratoire de Chimie ENS de Lyon UMR5182

Country

France

ORCID For Submitting Author

0000-0002-7657-6861

Declaration of Conflict of Interest

no conflict of interest

Version Notes

The following article has been submitted to Journal of Chemical Physics

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