A simple, non-nucleosidic base surrogate increases the duplex stability of DNA containing an abasic site

Abasic sites represent a common type of lesion in DNA. If not repaired, they can lead to mutations during replication or to cell death. Due to their biological importance, there is a strong interest in methods of recognizing abasic sites in DNA both for diagnostic and also for potential pharmaceutical applications. Extended aromatic residues can have a substantial positive influence on the stability of double-stranded DNA containing abasic sites. We report here the use of a simple, non-nucleosidic phenanthrene as a base surrogate, which effectively enhances the duplex stability of DNA with an abasic site. The influence of the linker length on the stability of the duplex is investigated. Data and model considerations indicate that stabilization is a result of stacking interactions between the phenanthrene and DNA base pairs.