Tandem 5′-GA:GA-3′ mismatches account for the high stability of the fold-back structures formed by the centromeric Drosophila dodeca-satellite

Abstract

The centromeric dodeca-satellite of Drosophila forms unusual DNA structures in which its purine-rich strand (GTACGGGACCGA)n folds into very stable intramolecular hairpins. These intramolecular hairpins contain groups of tandem 5′-GA:GA-3′ mismatches that, as judged by gel electrophoresis analysis and UV-melting studies, have a determinant contribution to their stability. Duplexes of the dodeca-satellite purine-rich strand, carrying tandem 5′-GA:GA-3′ mismatches, are as stable as equivalent fully Watson-Crick duplexes containing tandem 5′-TA:TA-3′ Watson-Crick pairs in place of the non-Watson-Crick G·A pairs. On the other hand, duplexes carrying any of the other three possible tandem combinations of purine·purine mismatches, including G·A pairs on the opposite orientation 5′-AG:AG-3′, are very unstable. The high stability of the dodeca-satellite hairplus suggests that the tandem G·A pairs are on the sheared configuration although they are found within the less favourable 5′-G-(G-A)-C-3′ sequence context. Other centromeres DNA sequences, including the AAGAG satellite of Drosophila and the mammalian CENP-B box sequence, have the potential of forming intramolecular hairpins stabilised by similar purine·purine interactions.