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Updated: May 29, 2026

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes
Published on: July 6, 2016
Noncovalent binding and fluorogenic response of cyanine dyes to DNA homoquadruplex and PNA-DNA heteroquadruplex
Halimatu S Mohammed1, Junriz O Delos Santos, Bruce A Armitage
1Department of Chemistry and Center for Nucleic Acids Science and Technology; Carnegie Mellon University; Pittsburgh, PA USA.
Abstract:
Two symmetrical cyanine dyes based on benzothiazole heterocycles and a trimethine bridge were found to bind to a parallel-stranded DNA guanine quadruplex based on the MYC oncogene promoter sequence with high nanomolar affinity and 1:1 stoichiometry. The dyes exhibited substantial fluorescence enhancements upon binding. In the presence of homologous guanine-rich peptide nucleic acid oligomers, PNA-DNA heteroquadruplexes were formed. The dyes retained their ability to bind to the heteroquadruplexes at low micromolar concentrations and with varying fluorescence enhancements, although indeterminate stoichiometries preclude quantitative comparison of the affinities with the DNA homoquadruplex precursor. The difference in fluorescence enhancement between DNA homoquadruplex and PNA-DNA heteroquadruplex allows the dyes to be used as fluorogenic indicators of hybridization in a facile method for determining PNA-DNA stoichiometry.
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