Cyanine dye-DNA interactions: Intercalation, groove binding, and aggregation

The cyanine dyes are among the oldest classes of synthetic compounds but continue to find applications in a variety of fields. In many cases, the dyes act as fluorescent labels for biomolecules, and can interact with the biomolecule either through covalent or noncovalent bonding. One particularly important application involves dyes that bind to double helical DNA by intercalation and exhibit large fluorescence enhancements upon binding. This chapter describes recent investigations of the noncovalent binding modes by which cyanine dyes recognize DNA, with special emphasis placed on relationships between the dye structure and DNA binding mode. In addition to simple binding of the dye as a monomer, several dyes form well-defined helical aggregates using DNA as a template. While these dyes are typically achiral, the aggregates exhibit induced chirality due to the right-handed helical structure of the underlying DNA template. Spectroscopic methods for characterizing these supramolecular assemblies as well as the monomeric complexes are described.