title: Influence of cyanine dye structure on self-aggregation and interaction with nucleic acids: a kinetic approach to TO and BO binding.
abstract: Kinetics and equilibria of cyanine dyes thiazole orange (TO) and benzothiazole orange (BO) self-aggregation and binding to CT-DNA are investigated in aqueous solution at 25 degrees C and pH 7. Absorbance spectra and T-jump experiments reveal that BO forms J-aggregates while TO forms more stable H-aggregates. Fluorescence and absorbance titrations show that TO binds to DNA more tightly than BO. TO stacks externally to DNA for low polymer-to-dye concentration ratios (C(P)/C(D)) while dye intercalation occurs for high values of C(P)/C(D). T-jump and stopped-flow experiments performed at high C(P)/C(D) agree with reaction scheme D+S <=> D,S <=> DS(I) <=> DS(II) where the precursor complex D,S evolves to a partially intercalated complex DS(I) which converts to the more stable intercalate DS(II). Non-electrostatic forces play a major role in D,S stabilization. Last step is similar for both dyes suggesting accommodation of the common benzothiazole residue between base pairs. Experiments using poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC) confirm base pair preference for TO.
authors.affiliation: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy. tarita@dcci.unipi.it
authors.forename: Tarita
authors.initials: T
authors.lastname: Biver
authors.forename: Alessia
authors.initials: A
authors.lastname: Boggioni
authors.forename: Fernando
authors.initials: F
authors.lastname: Secco
authors.forename: Elisa
authors.initials: E
authors.lastname: Turriani
authors.forename: Marcella
authors.initials: M
authors.lastname: Venturini
authors.forename: Sergiy
authors.initials: S
authors.lastname: Yarmoluk
mesh_terms: D052160:Benzothiazoles / Q000737:chemistry*; D001665:Binding Sites; D002232:Carbocyanines / Q000737:chemistry*; D003198:Computer Simulation; D003460:Crystallization / Q000379:methods; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D005456:Fluorescent Dyes / Q000737:chemistry; D007364:Intercalating Agents / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D011804:Quinolines / Q000737:chemistry*
chemical_list: D052160:Benzothiazoles; D002232:Carbocyanines; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D011804:Quinolines; C051000:thiazole orange; D004247:DNA; C427203:calf thymus DNA