Microcalorimetrics Studies of the Thermodynamics and Binding Mechanism between l-Tyrosinamide and Aptamer

Abstract

In recent years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complex interactions. In some cases, however, the aptamer complex binding behavior and mechanism are not clearly understood, especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC) and circular dichroism (CD) were useful tools for studying the fundamental binding mechanism between a DNA aptamer and L-tyrosinamide (L-TyrNH2). To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value, analogue of L-TyrNH2, and metal ion were carried out. The thermodynamic signature along with the coupled CD spectral change suggest that this binding behavior is an enthalpy-driven process, and the aptamer has a conformational change from B-form to A-form. The results showed that the interaction is an induced fit binding, and the driving forces in this binding behavior may include electrostatic interactions, hydrophobic effects, hydrogen bonding, and the binding-linked protonation process. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg(2+) not only improves binding affinity but also helps change the structure of the DNA aptamer.

Copolymer micelles function as pH-responsive nanocarriers to enhance the cytotoxicity of a HER2 aptamer in HER2-positive breast cancer cells

“…Since the same concentrations of HApt were analyzed for free HApt and HApt-MNPs, the larger peak values for HApt-MNPs may be caused by condensation of HApt within the MNPs. [46][47][48] The CD spectra of the free and MNP-encapsulated NCApt were similar ( Figure S1). …”

Nucleic acid aptamer molecular recognition principles and application in liquid chromatography and capillary electrophoresis

“…ÁH values as high as -150 kJ/mol can be retrieved, even for a small target binding to aptamer [31,32]. Such very favourable enthalpic contribution can be attributed not only to the formation of strong intermolecular bonds between the target and the aptamer (see above), but also to the target-induced intramolecular interactions within the aptamer.…”

“…Such argininamide encapsulation would be accompanied by a strong reduction of the solvent accessible surface area upon complex formation, in the order of 1000 2 [31]. Another circular dichroism analysis has shown that the anti-tyrosinamide DNA aptamer undergoes a DNA B-form to A-form transition upon the target binding [32]. For a larger target such as proteins, both the aptamer and the target are assumed to display conformational adaptability allowing the association between the two partners [21].…”

G-quadruplex DNA aptamers generated for systemin

“…30,31 In order to have a better insight into the interaction between S-5-1 and systemin, the influences of pH and ionic strength on aptamer binding were evaluated. Usually, hydrogen bonds, electrostatic interactions, stacking interactions, molecular shape complementarity and hydrophobic effect are considered to be involved in the binding between an aptamer and its target molecule.…”