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 * proflavine 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 intercalation of the ligand between consecutive bases (process 11). The comparison with a simple theoretical model shows that process I and process I1 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 I1 is proposed.Numerous and extensive studies have been reported on the interactions between acridine dyes and nucleic acids (mainly DNA). It is generally agreed that two kinds of complexes are formed between DNA and the dye in its cationic form [l]. At low ionic strength and small polymer to dye ratios (P/D < 1, where P is the total concentration of polymer expressed in nucleotide equivalents per liter, and D the total concentration of dye), the marked hypochromism and blue shift observed in the visible absorption spectrum of the dye suggest that most bound molecules are stacked along the phosphate backbone outside the double helix [a]. This All the quantitative studies report that the amount of bound ligand in complex I1 never exceeds one molecule per two base pairs. The model usually hypothesized for the interpretation of the results assumes a priori the independence of the binding sites. Accordingly, the number of type11 binding sites is found to be limited (a typical value of 0.2 binding sites per phosphate is generally reported). A recent study of Armstrong et al. shows that the experimental results can also be accounted for by assuming that every slot between two successive base pair plates is a potential binding site and that the binding of a dye molecule prevents further binding to the two adjacent sites [el. This second model is fundamentally opposite to the first one because it rests upon the existence of drastic interactions between nearest neighbors. I n several respects [el, the understanding of the phenomena is clarified by the model of Armstrong et al. However, it is quite possible that the exact behavior does not imply so strong interactions between adjacent sites, and therefore it might be better rationalized by an anticooperative binding process model with one binding site per base pair [7,8]. (In this report, "cooperativ...

Cytotoxic Activities and DNA Binding Properties of 1-Methyl-7H-indeno[1,2-b]Quinolinium-7-(4-dimethylamino) Benzylidene Triflate

“…A considerable decrease in the absorption of the compound and a weak red shift of the spectra was observed when DNA was added. As reported, a hypochromic effect and blue shift of the absorption spectra are signs of external binding, while a red shift and of the spectra is a sign of intercalation (Dourlent and Hélène, 1971;Long and Barton, 1990;Timtcheva et al, 2000). It can be seen from Figure 2 that MIDBT had strong absorption peaks at 285 nm and 355 nm.…”

Sequence specificity of mutagen-nucleic acid complexes in solution: Intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes

“…At low nucleotide/dye ratios, there is a blue shift in the visible spectrum of the dye which is attributed to stacking of dye aggregates along the sugar-phosphate backbone (1). The published optical studies include a quantitative analysis of the binding of proflavine to polynucleotides and transfer RNA (3,4), to DNA (5,6), and to bacteriophage (7,8).…”

Investigation on the toxic interaction of toluidine blue with calf thymus DNA

“…As reported in other dye-DNA systems [10][11][12], a hypochromic effect and blue shift of the absorption spectra are signs of external binding, while a red shift of the spectra is a sign of intercalation. It can be seen from Fig.…”