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Nucleic Acids Research, 1993, Vol. 21, No. 24 5720-5726
© 1993

CHEMISTRY

Heterodimeric DNA-binding dyes designed for energy transfer: stability and applications of the DNA complexes

Scott C. Benson, Richard A. Mathies and Alexander N. Glazer*

Department of Molecular and Cell Biology, 229 Stanley Hall, University of California Berkeley, CA 94720, USA

*To whom correspondence should be addressed

Received August 12, 1993. Revised November 11, 1993. Accepted November 11, 1993.

Spectroscopic studies of the complexes of doublestranded (ds) DNA with the polymethylene - amine linked heterodimers thiazole orange - thiazole blue, thiazole orange-ethidium, and fluorescein - ethidium, in each case show efficient energy transfer from donor to acceptor chromophores (Benson,S.C., Singh,P. and Glazer,A.N. (1993) accompanying manuscript). A quantitative assay of the stability of such complexes during gel electrophoresis is presented. The off-rate of dye from complexes formed at an initial dsDNA bp:dye ratio greater double equals10:1 follows strict first-order kinetics. The t0.5 values for the dissociation of a series of related dyes provide a quantitative criterion for the design of DNAbinding fluorophores. Complexes of dsDNA with the monomeric propidium and cyanine dyes, [1-(9-amino- 4,7-diazanonyl)-3,8-diamino-6-phenyl-phenanthridinium bromide trihydrobromide] and (N,N'-tetramethyl-1,3- propanediamino)propyl thiazole orange [4-[3-methyl- 2,3-dihydro-(benzo-1,3-thiazole)-2-methylidenyl]-1 - (4,4,8-trimethyl-4,8-diazanonyl)-quinolinium diiodide], are much more stable than those with their widely used counterparts, ethidium and thiazole orange. Applications of the new dyes in post-staining of gels and in the multiplex detection of DNA restriction fragments are presented.


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