title: Synthesis and DNA binding studies of a new asymmetric cyanine dye binding in the minor groove of [poly(dA-dT)]2.
abstract: A new asymmetric cyanine dye has been synthesised and its interaction with different DNA has been investigated. In this dye, BEBO, the structure of the known intercalating cyanine dye BO has been extended with a benzothiazole substituent. The resulting crescent-shape of the molecule is similar to that of the well-known minor groove binder Hoechst 33258. Indeed, comparative studies of BO illustrate a considerable change in binding mode induced by this structural modification. Linear and circular dichroism studies indicate that BEBO binds in the minor groove to [poly (dA-dT)](2), but that the binding to calf thymus DNA is heterogeneous, although still with a significant contribution of minor groove binding. Similar to other DNA binding asymmetric cyanine dyes, BEBO has a large increase in fluorescence intensity upon binding and a relatively large quantum yield when bound. The minor groove binding of BEBO to [poly (dA-dT)](2) affords roughly a 180-fold increase in intensity, which is larger than to that of the commonly used minor groove binding probes DAPI and Hoechst 33258.
authors.affiliation: Department of Chemistry and Bioscience, Chalmers University of Technology, Kemivägen 10, S-41296 Göteborg, Sweden.
authors.forename: H Jonas
authors.initials: HJ
authors.lastname: Karlsson
authors.forename: Per
authors.initials: P
authors.lastname: Lincoln
authors.forename: Gunnar
authors.initials: G
authors.lastname: Westman
mesh_terms: D000818:Animals; D006690:Bisbenzimidazole; D002232:Carbocyanines / Q000138:chemical synthesis*; D002417:Cattle; D002942:Circular Dichroism; D004396:Coloring Agents / Q000138:chemical synthesis*; D004247:DNA / Q000378:metabolism*; D005453:Fluorescence; D005456:Fluorescent Dyes; D007202:Indicators and Reagents; D007211:Indoles; D011067:Poly dA-dT / Q000378:metabolism*; D011119:Polynucleotides / Q000737:chemistry
chemical_list: C478828:BEBO cyanine dye; D002232:Carbocyanines; D004396:Coloring Agents; D005456:Fluorescent Dyes; D007202:Indicators and Reagents; D007211:Indoles; D011119:Polynucleotides; D011067:Poly dA-dT; C007293:DAPI; D004247:DNA; D006690:Bisbenzimidazole