Molecular Recognition of PNA-Containing Hybrids: Spontaneous Assembly of Helical Cyanine Dye Aggregates on PNA Templates

Abstract

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 triplex. Binding of a dicarbocyanine dye results in a 114 nm hypsochromic shift of the main visible absorption band. Circular dichroism spectropolarimetry reveals exciton coupling between multiple chromophores bound to the same PNA/DNA or PNA/PNA duplex, demonstrating binding of the dye as an aggregate. A continuous variations 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 cooperative manner and exhibits a temperature-dependent self-assembly behavior which is independent of the PNA/DNA hybridization event. Experiments with mismatched and parallel duplexes demonstrate a strong preference for a continuous, antiparallel helix as a template on which to assemble the helical dye aggregate. Successful binding of the dye to the d...