Electronic interactions in helical stacked arrays of the modified DNA base pyrrolocytosine

The thermal stability and ultraviolet and circular dichroism spectra of nine synthetic DNA hairpins possessing one or more (P)C-G base pairs ((P)C = pyrrolocytosine) have been investigated. One group of hairpins possess 1-5 sequential (P)C-G base pairs while another group possess two (P)C-G base pairs separated by 1-3 A-T base pairs. The first group displays a nearly linear dependence of UV and exciton-coupled circular dichroism (EC-CD) band intensity upon the number of neighboring chromophores, whereas the second group shows weak EC-CD only at the shortest distances between non-neighboring chromophores. This result stands in marked contrast to the exciton coupling seen between stilbene chromophores separated by as many as a dozen base pairs. The weak exciton coupling between non-neighboring (P)C chromophores, like that of the natural nucelobases, is attributed to their relatively weak electronic transition dipoles.