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Article

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

Supporting Info

Jeffrey O. Smith, Darren A. Olson, and Bruce A. Armitage*

Contribution from the Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213

J. Am. Chem. Soc., 1999, 121 (12), pp 2686–2695

DOI: 10.1021/ja9837553

Publication Date (Web): March 13, 1999

To whom correspondence should be addressed. E-mail: army@ cyrus.andrew.cmu.edu.

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 duplex and triplex indicates that dyes associate with one another in the minor groove of the template. The 114 nm shift in absorption causes an instantaneous visible color change from blue to purple, providing a convenient method for detecting PNA hybridization with its complementary target sequence.

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