New aspects of the interaction of the antibiotic coralyne with RNA: coralyne induces triple helix formation in poly(rA) poly(rU)

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 dispropo...

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Bibliographic Details
Published in:Nucleic acids research 2010-03, Vol.38 (5), p.1697-1710
Main Authors: Biver, Tarita, Boggioni, Alessia, García, Begoña, Leal, José M, Ruiz, Rebeca, Secco, Fernando, Venturini, Marcella
Format: Article
Language:English
Subjects:
Anti-Bacterial Agents - chemistry
Berberine Alkaloids - chemistry
Circular Dichroism
Ethanol - chemistry
Kinetics
Nucleic Acid Conformation
Nucleic Acid Denaturation
Poly A - chemistry
Poly A-U - chemistry
RNA
Sodium Chloride - chemistry
Spectrometry, Fluorescence
Spectrum Analysis
Thermodynamics
Viscosity
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Summary: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 (CD/CP). 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 CD/CP> 0.8 poly(A) poly(U) does not disproportionate at 25°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).
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkp1146