Doxorubicin binds to duplex RNA with higher affinity than ctDNA and favours the isothermal denaturation of triplex RNA

• Published in: RSC advances Vol. 6; no. 13; pp. 11142 - 11152
• Main Authors: Rubio, Ana R, Busto, Natalia, Leal, José M, García, Begoña
• Format: Journal Article
• Language: English
• Published: 01.01.2016
• Subjects: Affinity; Binding; Denaturation; Doxorubicin; Fluorescence; Grooves; Ribonucleic acids; Viscometry
• ISSN: 2046-2069; 2046-2069
• DOI: 10.1039/c6ra21387a

The interaction of doxorubicin (DOX) with triplex, duplex and single RNA helices has been studied by fluorimetric, circular dichroism, viscometry, DSC, ITC, T-jump kinetic relaxation technique and fluorescence lifetime measurements in near physiological conditions (pH = 7, I = 0.1 M and 25 °C). DOX binds to the groove of poly(rA)·2poly(rU), while it intercalates into poly(rA)·poly(rU) and forms external complex with poly(rA) and poly(rU). Fluorescence lifetime measurements have shown that all the RNA/DOX complexes are non-fluorescent. The affinity with the duplex is some 15 times greater than with the triplex; this behaviour favours the isothermal denaturation of the triplex/DOX complex according to reaction poly(rA)·2poly(rU)/DOX + DOX poly(rA)·poly(rU)/DOX + poly(rU)/DOX, that is, the reaction shifts to right upon increasing the DOX content. ITC measurements have revealed that, under the same conditions, the affinity of DOX with the RNA duplex is higher than with ctDNA, a striking outcome as long as the binding of DOX to DNA seems to be the origin of its biological action. The higher affinity of DOX with AU to give the intercalated complex AU/DOX is responsible for the disproportionation of the groove binding complex, UAU/DOX, to give rise to the AU/DOX and the U/DOX complexes at 25 °C