DNA: Understanding how nucleobase interactions affect photophysical properties

Research Project, 2021 – 2024

At Chalmers, we share an increasing interest in understanding the base-stacking and -pairing of DNA. Nucleic acid building blocks are modified to influence and understand the weak forces that holds together DNA. Colleagues use fluorescent markers in DNA, sensitive to the local environment, for the analysis. The aim of this theory project is to understand the effects of the local environment on the fluorescence, through first-principle calculations. We will use modern first-principle electronic-structure methods, our recent tool for spatially resolving binding energy contributions, as well as established solvation models to account for the solvent around the DNA. Specifically, we will use our method DF-cx that consistently includes van der Waals interactions on the same level of accuracy as for short-range interactions. This is essential for studying DNA base pair stacking. We will study a set of existing and new modified fluorescent nucleobases both in isolation in a solvent, and when inserted into small (few base pairs) snippets of DNA. The practical use of modified photoactive bases cause a variation of interaction forces between bases, and we will predict and interpret the changes in their absorption/emission spectra.