Modelling the nanoscale patterning of nucleic acid base pairs deposited on graphite

Abstract

Interactions between graphite and nucleic-acid base pairs are investigated. An existing polarizable potential that uses distributed multipoles up to and including quadrupoles is extended to describe the graphite surface and the nucleic-acid bases cytosine and guanine. Adsorption energies and structures calculated with this potential are compared with data obtained using electronic structure theory. Structures of co-adsorbed cytosine and guanine layers are optimised and two competing arrangements, the ‘dimer-row’ and ‘quartet-row’ patterns, are compared with experimental scanning tunnelling microscopy images. We include two factors not considered in previous studies: the presence of the graphite surface and the inter-row packing. However, our findings agree with previous calculations in that the ‘quartet-row’ is energetically preferred, despite STM experiments suggesting the ‘dimer-row’ structure is observed.

Keywords:

• interactions
• DNA
• surfaces
• nanoscale

Acknowledgements

The author gratefully acknowledges the computing facilities of the Centre for Scientific Computing, University of Warwick.