Excited states in DNA, from single nucleobases to base pairs, double helix and beyond: computational modelling of dynamics, spectroscopy, and environmental effects

A photochemical understanding of DNA is of fundamental relevance to life, due to damage of the genetic code by UV light, and the photoprotection mechanisms inherent in DNA that attempt to prevent this. Additionally, due to the unique and complex electronic behaviour of each of the nucleobases, and their ability to form a number of different multi-chromophoric structures, DNA provides a challenging playground for the development of methods that can be applied to related fields such as photosynthesis, optoelectronics, and biomedical devices. In this seminar, I will describe how a recently developed theoretical method to parameterise model Hamiltonians, in combination with quantum and classical dynamics calculations, can help elucidate photochemical behaviour in a range of DNA structures. At the single nucleobase level, the effect that ultrafast internal conversions have on the absorption spectrum lineshape will be demonstrated [1]. Then, the competition between these intra-base internal conversions and inter-base energy/charge transfer processes for the Guanine-Cytosine (GC) [2] and Adenine-Thymine (AT) [3] Watson-Crick base pairs will be shown. For the GC pair, initial work on including solvent effect on the quantum dynamics will be presented, with a view to accurately reproducing experimental conditions in time-resolved spectroscopy measurements. Then, towards modelling the double helix, stacking effects and the competition between single-strand and inter-strand processes will be shown for model GCGC tetrads. Finally, if time allows, an excitonic modelling simulation of the electronic circular dichroism spectrum of a non-canonical DNA structure, a Guanine-Quadruplex, will be shown, demonstrating the influence of charge transfer states and thermal fluctuations of the bases on the spectral shape [4][5].

[1] J. A. Green, M. Yaghoubi Jouybari, D. Aranda, R. Improta, & F. Santoro, “Nonadiabatic absorption spectra and ultrafast dynamics of DNA and RNA photoexcited nucleobases”, Molecules, 2021, 26, 1743 [2] J. A. Green, M. Yaghoubi Jouybari, H. Asha, F. Santoro, & R. Improta, “Fragment diabatization linear vibronic coupling model for quantum dynamics of multichromophoric systems: population of the charge transfer state in the photoexcited guanine–cytosine pair”, J. Chem. Theory. Comput., 2021, 17, 4660
[3] M. Yaghoubi Jouybari, J. A. Green, R. Improta, & F. Santoro, “The ultrafast quantum dynamics of photoexcited adenine thymine basepair investigated with a fragment based diabatisation and a linear vibronic coupling model.”, J. Phys. Chem. A, 2021, 125, 8912
[4] J. A. Green, H. Asha, F. Santoro, & R. Improta “Excitonic model for strongly coupled multichromophoric systems: the electronic circular dichroism spectra of guanine quadruplexes as test cases”, J. Chem. Theory. Comput., 2021, 17, 405
[5] H. Asha, J. A. Green, L. Martinez-Fernandez, L. Esposito, & R. Improta, “Electronic circular dichroism spectra of DNA quadruple helices studied by molecular dynamics simulations and excitonic calculations including charge transfer states”, Molecules, 2021, 26, 4789