A Quantitative Analysis of Proflavine Binding to Polyadenylic Acid, Polyuridylic Acid, and Transfer RNA

Abstract

Absorbance measurements show that the binding of proflavine to poly (A) and poly(U) can be quantitatively resolved (within ± 10% relative error) by the consideration of two bound species whose spectral properties and mechanisms of interaction are similar to those found in the DNA. proflavin systems: cooperative binding along the phosphate backbone (process I) and interaction between the aromatic rings of base and dye resulting presumably from some kind of interacalation of the ligand between consecutive bases (process II). The comparison with a simple theoretical model shows that process I and process II are not independent but coupled. The spectrophotometric method is able to resolve the binding of proflavine to a tRNA species with the same accuracy as that obtained for poly(A) and poly(U). Accordingly, it is proposed that the mode of interaction between proflavine and all classes of polynucleotides (DNA, RNA, synthetic polymers) is similar in nature. From the differences observed in the distribution of the bound dye between the two complexes, the existence of a close correlation between the secondary structure of the polymer and its ability for binding the dye in complex II is proposed.