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Nucleic Acids Research, 2003, Vol. 31, No. 21 6227-6234
© 2003 Oxford University Press

Groove-binding unsymmetrical cyanine dyes for staining of DNA: syntheses and characterization of the DNA-binding

H. Jonas Karlsson, Maja Eriksson, Erik Perzon, Björn Åkerman, Per Lincoln and Gunnar Westman*

Department of Chemistry and Bioscience, Chalmers University of Technology, S-412 96 Gothenburg, Sweden

*To whom correspondence should be addressed. Tel: +46 31 772 3072; Fax: +46 31 772 3657; Email: westman{at}oc.chalmers.se
Correspondence may also be addressed to H. J. Karlsson. Tel: +46 31 772 8213; Fax: +46 31 772 3657; Email: karjo{at}oc.chalmers.se

Two new crescent-shaped unsymmetrical cyanine dyes have been synthesised and their interactions with DNA have been investigated by different spectroscopic methods. These dyes are analogues to a minor groove binding unsymmetrical cyanine dye, BEBO, recently reported by us. In this dye, the structure of the known intercalating cyanine dye BO was extended with a benzothiazole substituent. To investigate how the identity of the extending heterocycle affects the binding to DNA, the new dyes BETO and BOXTO have a benzothiazole group and a benzoxazole moiety, respectively. Whereas BEBO showed a heterogeneous binding to calf thymus DNA, linear and circular dichroism studies of BOXTO indicate a high preference for minor groove binding. BETO also binds in the minor groove to mixed sequence DNA but has a contribution of non-ordered and non-emissive species present. A non-intercalative binding mode of the new dyes, as well as for BEBO, is further supported by electrophoresis unwinding assays. These dyes, having comparable spectral properties as the intercalating cyanine dyes, but bind in the minor groove instead, might be useful complements for staining of DNA. In particular, the benzoxazole substituted dye BOXTO has attractive fluorescence properties with a quantum yield of 0.52 when bound to mixed sequence DNA and a 300-fold increase in fluorescence intensity upon binding.


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M. Eriksson, H. J. Karlsson, G. Westman, and B. Akerman
Groove-binding unsymmetrical cyanine dyes for staining of DNA: dissociation rates in free solution and electrophoresis gels
Nucleic Acids Res., November 1, 2003; 31(21): 6235 - 6242.
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