Abstract
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.
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