Fluorescence energy-transfer cyanine heterodimers with high affinity for double-stranded DNA. I. Synthesis and spectroscopic properties.

We have designed, synthesized, and characterized fluorescent cyanine heterodimers that exploit resonance energy transfer to achieve strong emission above 650 nm with 488-nm excitation. Thiazole orange serves as the common fluorescence donor in these dyes and thiazole-indolenine, thiazole blue, or symmetric thiazole blue as acceptors. The donor and acceptor chromophores are linked by a polymethylene linker containing quaternary amino groups. These heterodimers have a high affinity for double-stranded DNA (dsDNA). The donor emission in the dsDNA-bound dyes is quenched by over 85%. The affinity for dsDNA and the quenching of donor fluorescence were optimized by varying the length of the linker between the donor and acceptor. Complexes of dsDNA fragments with such optimized dyes dissociated very slowly (t(0.5) > 300 min) during agarose gel electrophoresis.