Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: Crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one

Abstract

The incorporation of the bicyclic cytosine analogue 7,8-dihydropyrido[2,3-d]pyrimidin-2-one (X) into DNA duplexes results in a significant enhancement of their stability (3-4 K per modification). To establish the effects of X on the local hydrogen-bonding and base stacking interactions and the overall DNA conformation, and to obtain insights into the correlation between the structure and stability of X-containing DNA duplexes, the crystal structures of [d(CGCGAATT-X-GCG)]2 and [d(CGCGAAT-X-CGCG)]2 have been determined at 1.9-2.9 Å resolutions. In all of the structures, the analogue X base pairs with the purine bases on the opposite strands through Watson-Crick and/or wobble type hydrogen bonds. The additional ring of the X base is stacked on the thymine bases at the 5′-side and overall exhibits greatly enhanced stacking interactions suggesting that this is a major contribution to duplex stabilization. © The Author(s) 2010. Published by Oxford University Press.