Molecular recognition of PNA-containing hybrids: Spontaneous assembly of helical cyanine dye aggregates on PNA templates

Symmetrical cyanine dyes containing benzothiazole groups have been shown to bind with high affinity to a variety of PNA-containing hybrids, including PNA/DNA duplexes, a PNA/PNA duplex, and a bisPNA/DNA tripler. Binding of a dicarbocyanine dye results in a 114 nm hypsochromic shift of the main visib le absorption band. Circular dichroism spectropolarimetry reveals exciton c oupling between multiple chromophores bound to the same PNA/DNA or PNA/PNA duplex, demonstrating binding of the dye as an aggregate. A continuous vari ations experiment indicates that the dye binds as a 6(+/-1):1 complex with a 12 base pair PNA/DNA duplex. The dye aggregate forms in a highly cooperat ive manner and exhibits a temperature-dependent self-assembly behavior whic h is independent of the PNA/DNA hybridization event. Experiments with misma tched and parallel duplexes demonstrate a strong preference for a continuou s, antiparallel helix as a template on which to assemble the helical dye ag gregate. Successful binding of the dye to the duplex and tripler indicates that dyes associate with one another in the minor groove of the template. T he 114 nm shift in absorption causes an instantaneous visible color change from blue to purple, providing a convenient method for detecting PNA hybrid ization with its complementary target sequence.