title: New aspects of the interaction of the antibiotic coralyne with RNA: coralyne induces triple helix formation in poly(rA)*poly(rU).
abstract: The interaction of coralyne with poly(A)*poly(U), poly(A)*2poly(U), poly(A) and poly(A)*poly(A) is analysed using spectrophotometric, spectrofluorometric, circular dichroism (CD), viscometric, stopped-flow and temperature-jump techniques. It is shown for the first time that coralyne induces disproportionation of poly(A)*poly(U) to triplex poly(A)*2poly(U) and single-stranded poly(A) under suitable values of the [dye]/[polymer] ratio (C(D)/C(P)). Kinetic, CD and spectrofluorometric experiments reveal that this process requires that coralyne (D) binds to duplex. The resulting complex (AUD) reacts with free duplex giving triplex (UAUD) and free poly(A); moreover, ligand exchange between duplex and triplex occurs. A reaction mechanism is proposed and the reaction parameters are evaluated. For C(D)/C(P)> 0.8 poly(A)*poly(U) does not disproportionate at 25 degrees C and dye intercalation into AU to give AUD is the only observed process. Melting experiments as well show that coralyne induces the duplex disproportionation. Effects of temperature, ionic strength and ethanol content are investigated. One concludes that triplex formation requires coralyne be only partially intercalated into AUD. Under suitable concentration conditions, this feature favours the interaction of free AU with AUD to give the AUDAU intermediate which evolves into triplex UAUD and single-stranded poly(A). Duplex poly(A)*poly(A) undergoes aggregation as well, but only at much higher polymer concentrations compared to poly(A)*poly(U).
authors.affiliation: University of Pisa, Chemistry and Industrial Chemistry Department, 56126 Pisa, Italy.
authors.forename: Tarita
authors.initials: T
authors.lastname: Biver
authors.forename: Alessia
authors.initials: A
authors.lastname: Boggioni
authors.forename: Begoña
authors.initials: B
authors.lastname: García
authors.forename: José M
authors.initials: JM
authors.lastname: Leal
authors.forename: Rebeca
authors.initials: R
authors.lastname: Ruiz
authors.forename: Fernando
authors.initials: F
authors.lastname: Secco
authors.forename: Marcella
authors.initials: M
authors.lastname: Venturini
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry*; D001600:Berberine Alkaloids / Q000737:chemistry*; D002942:Circular Dichroism; D000431:Ethanol / Q000737:chemistry; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011061:Poly A / Q000737:chemistry; D011063:Poly A-U / Q000737:chemistry*; D012965:Sodium Chloride / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013057:Spectrum Analysis; D013816:Thermodynamics; D014783:Viscosity
chemical_list: D000900:Anti-Bacterial Agents; D001600:Berberine Alkaloids; D011063:Poly A-U; D011061:Poly A; D000431:Ethanol; D012965:Sodium Chloride; C000666:coralyne