Competition between stacked and hydrogen bonded structures of cytosine aggregates

Abstract

The four bases of DNA constitute what is known as the “alphabet of life”. Their combination of proton-donor and acceptor groups and aromatic rings allows them to form stacking structures and at the same time establish hydrogen bonds with their counterparts, resulting in the formation of the well-known double-helix structure of DNA. Here we explore the aggregation preferences of cytosine in supersonic expansions, using a combination of laser spectroscopic techniques and computations. The data obtained from the experiments carried out in the cold and isolated environment of the expansion allowed us to establish which are the leading interactions behind aggregation of cytosine molecules. The results obtained demonstrated that ribbon-like structures held together by hydrogen bonds are the preferred conformations in the small clusters, but once the tetramer was reached, the stacking structures became enthalpically more stable. Stacking is further favoured when cytosine is replaced by its 1′-methylated version, as demonstrated by quantum-mechanical calculations performed using the same level that reproduced the experimental results obtained for cytosine aggregates. A discussion on the biological implications that such observations may have is also offered.