Fluorescence quenching by intercalation of a pyrene group tethered to an N4-modified cytosine in duplex DNA

Abstract

A series of duplex DNA oligomers was prepared that contain a pyrene chromophore linked by a trimethylene chain (-(CH2)3-) to N4 of a cytosine. The pyrene group stabilizes the DNA as evidenced by an increase in melting temperature. The absorption spectrum of the linked pyrene chromophore shows a temperature-dependent shift and there is also a strong induced circular dichroism spectrum attributed to the pyrene group. The fluorescence of the pyrene chromophore is strongly quenched at room temperature by linkage to the DNA, but it increases above the melting temperature. We attribute these observations to intramolecular intercalation of the pyrene group at a base pair adjacent to its linkage site at cytosine. The self-organizing and scaffolding properties of DNA are often used to assemble complex structures. We describe duplex DNA oligomers that contain a pyrene chromophore linked by a trimethylene chain to N4 of cytosine. Intercalation of the pyrene group stabilizes the duplex and causes efficient quenching of pyrene's fluorescence. © 2012 The American Society of Photobiology.