title: A kinetic analysis of cyanine selectivity: CCyan2 and Cyan40 intercalation into poly(dA-dT) x poly(dA-dT) and poly(dG-dC) x poly(dG-dC).
abstract: A T-jump investigation of the binding of Cyan40 [3-methyl-2-(1,2,6-trimethyl-4(1H)pyridinylidenmethyl)-benzothiazolium ion] and CCyan2 [3-methyl-2-[2-methyl-3-(3-methyl-2(3H)-benzothiazolylidene)-1-propenyl]-benzothiazolium ion] with poly(dA-dT) x poly(dA-dT) and poly(dG-dC) x poly(dG-dC) is performed at I = 0.1M (NaCl), 25 degrees C and pH 7. Two kinetic effects are observed for both systems. The binding process is discussed in terms of the sequence D + P <==> P,D <==> PD(I) <==> PD(II), which leads first to fast formation of a precursor complex P,D and then to a partially intercalated complex PD(I) which converts to the fully intercalate complex PD(II). Concerning CCyan2 the rate parameters depend on the polymer nature and their analysis shows that in the case of poly(dG-dC) x poly(dG-dC) the most stable bound form is the fully intercalated complex PD(II), whereas in the case of poly(dA-dT) x poly(dA-dT) the partially intercalated complex PD(I) is the most stable species. Concerning Cyan40, the rate parameters remain unchanged on going from A-T to G-C indicating that this dye is unselective.
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: Marco
authors.initials: M
authors.lastname: Pulzonetti
authors.forename: Fernando
authors.initials: F
authors.lastname: Secco
authors.forename: Marcella
authors.initials: M
authors.lastname: Venturini
authors.forename: Sergiy
authors.initials: S
authors.lastname: Yarmoluk
mesh_terms: D001483:Base Sequence; D002232:Carbocyanines / Q000737:chemistry* / Q000494:pharmacology*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D005456:Fluorescent Dyes / Q000494:pharmacology*; D006863:Hydrogen-Ion Concentration; D007364:Intercalating Agents / Q000494:pharmacology*; D007477:Ions; D007700:Kinetics; D015394:Molecular Structure; D011067:Poly dA-dT / Q000737:chemistry; D011108:Polymers / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics
chemical_list: D002232:Carbocyanines; C467363:Cyan 40; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D007477:Ions; D011108:Polymers; D011067:Poly dA-dT; D004247:DNA