Interaction of Thionine with Triple-, Double-, and Single-Stranded RNAs

Abstract

The interaction of thionine with triple, double, and single RNA helices has been fully characterized by thermodynamic and kinetic methods. The nature of the interaction of thionine with the synthetic polynucleotides poly(rU), poly(rA)·poly(rU), and poly(rA)·2poly(rU) has been studied at pH = 7.0 and 25 °C by UV absorbance, fluorescence, circular dichroism spectroscopy, viscometry, differential scanning calorimetry, and T-jump kinetic measurements. The results show that at I = 0.1 M thionine binds to a single poly(rU) strand, destabilizes the poly(rA)·2poly(rU) triplex by external binding, and intercalates into poly(rA)·poly(rU) with similar affinity to the thionine/DNA intercalated complex (Paul, P.; Kumar, G. S. J. Fluoresc. 2012, 22, 71-80). On the other hand, the differential scanning calorimetry measurements performed with thionine display a point in which the heat capacity remains unaltered, revealing the equilibrium of isothermal denaturation: thionine/poly(rA)·2poly(rU) + thionine ⇌ thionine/poly(rA)·poly(rU) + thionine/poly(rU), an outcome supported by the other techniques used. The denaturation equilibrium constant, K(D) (25 °C) = 522 M(-1), was evaluated from the affinity with the single, duplex, and triplex RNA.

RNA triplex-to-duplex and duplex-to-triplex conversion induced by coralyne

“…The peak at C D /C P = 0 corresponds to full denaturation of poly(A)2poly(U) (T m = 58 1C). A similar thermogram was recorded for the denaturation of poly(A)poly(U) (T m = 57 1C), 18 thereby only small differences between the duplex and the triplex were perceptible at C D /C P = 0. Further addition of coralyne up to C D /C P = 0.3 results in two overlapped peaks that correspond to the triplexduplexsingle strand transitions.…”

“…In a similar way, the notable affinity of coralyne with the U strand under conditions C D /C P 4 1 (with K = (4.6 AE 0.5) Â 10 5 M À1 , measured in our laboratory) might afford the driving force for reaction (3). This reaction, which could be regarded as an isothermal denaturation process governed by the excess of coralyne, resembles the reaction between UAU and thionine, 18 even though in the latter there was no evidence for disproportionation. Hence, at 25 1C, coralyne is able to induce either AU disproportionation or UAU denaturation, depending on the concentration and temperature conditions, this feature being a novelty.…”

Binding properties of ruthenium(II) complexes [Ru(bpy)2(ppn)]2+ and [Ru(phen)2(ppn)]2+ with triplex RNA: As molecular “light switches” and stabilizers for poly(U)·poly(A)*poly(U) triplex

“…A recent report on the binding mechanisms of coralyne with poly(U)•poly(A)*poly(U) explains why coralyne tends to stabilize the third strand, due to this small molecule being able to induce the triplex-to-duplex conversion and also the duplex-to-triplex conversion [23]. These results reflect that the stabilization of the RNA triplex is very sensitive to the structural features of the bound small molecule.…”

Interacción de ARN con doxorrubicina: Influencia del ligando y del metal en la actividad biológica de complejos organometálicos

“…[113] at 0.011M (NaCl) ionic strength was corrected for 0.1M (NaCl) [114]. The denaturation process at constant temperature, also has been reported for the RNA/thionine system [102].…”

“…Noncovalent interactions can either stabilize [97,98], destabilize [99,100] the triplex structure or remain the triplex unaltered [101] compared to the duplex. Even isothermal denaturation and disproportionation are also feasible, as observed in the presence of thionine [102] and coralyne [103,104], respectively. These features reveal that small molecules that may affect the stabilization of triplex RNA is an issue more complicated than initially thought.…”