Application of the SwitchSense Technique for the Study of Small Molecules’ (Ethidium Bromide and Selected Sulfonamide Derivatives) Affinity to DNA in Real Time

Abstract

The discovery and introduction of the switchSense technique in the chemical laboratory have drawn well-deserved interest owing to its wide range of applications. Namely, it can be used to determine the diameter of proteins, alterations in their tertiary structures (folding), and many other conformational changes that are important from a biological point of view. The essence of this technique is based on its ability to study of the interactions between an analyte and a ligand in real time (in a buffer flow). Its simplicity, on the other hand, is based on the use of a signaling system that provides information about the ongoing interactions based on the changes in the fluorescence intensity. This technique can be extremely advantageous in the study of new pharmaceuticals. The design of compounds with biological activity, as well as the determination of their molecular targets and modes of interactions, is crucial in the search for new drugs and the fight against drug resistance. This article presents another possible application of the switchSense technique for the study of the binding kinetics of small model molecules such as ethidium bromide (EB) and selected sulfonamide derivatives with DNA in the static and dynamic modes at three different temperatures (15, 25, and 37 °C) each. The experimental results remain in very good agreement with the molecular dynamics docking ones. These physicochemical insights and applications obtained from the switchSense technique allow for the design of an effective strategy for molecular interaction assessments of small but pharmaceutically important molecules with DNA.

Exploring novel Cd(ii) complexes with 5-methyl-4-imidazolecarboxaldehyde: synthesis, structure, computational insights, and affinity to DNA through switchSense methodology

“…All response curves as fluorescence changed during the ongoing processes (as one data set for the results of five different concentrations) were fitted using an interaction model and then the association/dissociation constants were calculated as previously described in detail. 36 Thermodynamic parameters. To estimate the entropic (ΔS) and energetic (ΔH) contributions to the ΔG, first, we calculated ΔG i of association process (K Ai ) obtained utilizing switchSense at a given temperature (T i ) as expressed by eqn (4).…”

“…Compounds were studied toward their stability in solution with the use of UV-Vis, and interaction with DNA using the switchSense technique. 35,36…”

Application of the switchSENSE® technology for real-time study of pesticides interaction with biological molecules

“…This technology can provide information about structures of biomolecules such as size, shape and conformation. Moreover, SST enables to give an understanding of interactions at the molecular level and to provide kinetic research data [8]. This method employs chips featuring a gold surface, overlaid with DNA nanolevers, which are electrically switchable.…”

“…To obtain information regarding molecular interaction, the device combines automatic fluid distribution, control over measurements modes (static or dynamic), temperature regulation, chip management, and the implementations of various modifications to the nanolever system. Additionally, the utilization of microfluidics system, minimal sample usage and biochip regeneration make the SST cost-effective and environmentally friendly [8]. SST has demonstrated utility and efficiency in obtaining the association and dissociation kinetic parameters for interactions between small molecules and human serum albumin [9].…”

Self-Assembled Monolayer Transporters Enable Reagentless Analysis of Small Molecule Analytes

“…Similar dynamic DNA modulation has also been demonstrated in optical systems employing DNA nanolevers. [9][10][11] While MPs function well for proteins and larger analytes, their dependence on hydrodynamic radius changes makes them difficult to implement for smaller, less bulky targets. Here, we present a new approach that allows for reagentless analysis of electroactive small molecules.…”