A TDDFT study of the excited states of DNA bases and their assemblies

TL;DR

This study uses TDDFT to analyze the optical absorption spectra of DNA bases and their assemblies, revealing how hydrogen bonding and stacking influence spectral features and providing insights into structural characterization.

Contribution

It demonstrates the reliability of TDDFT in modeling nucleobase spectra and explores the effects of molecular interactions on optical properties for DNA assemblies.

Findings

Hydrogen bonding and stacking significantly affect UV absorption spectra.

Hypochromicity depends on light polarization and interaction type.

Blue shift observed in spectra of base assemblies compared to isolated bases.

Abstract

We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional: Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and $\pi$-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.