Studies of the binding properties of the food preservative thiabendazole to DNA by computer simulations and NMR relaxation

Abstract

The groove binding of thiabendazole and hsDNA was studied by computer simulation and experimental methods.

Characterization of the Binding Properties of Sorafenib to c-MYC G-Quadruplexes: Evidence for Screening Potential Ligands

“…Usually, when small molecules take an embedded binding mode to bind to DNA, an increase in the viscosity coefficient eventually leads to an increase in the viscosity of the solution to be measured thanks to the increase in the axial length of DNA. , On the contrary, binding by covalent bonds results in a reduction in viscosity. However, the nonembedding mode represented by the groove binding mode does not cause any significant change in solution viscosity when acting on DNA . The results are shown in Figure B.…”

“…In the absence of G4, Sor exhibited a decay curve, while the binding of G4 to Sor did not cause a significant change in this curve (Figure F). During the static quenching, the decay time of the free fluorophore is unchanged, while in the dynamic quenching, the average decay time of the whole excited state should decrease . The fluorescence lifetime data of Sor before and after the addition of G4 are summarized in Table .…”

“…However, the nonembedding mode represented by the groove binding mode does not cause any significant change in solution viscosity when acting on DNA. 25 The results are shown in Figure 3B. It is observed that a relatively small increase in solution viscosity occurred, suggesting that Sor may bind to the groove position of G4.…”

“…During the static quenching, the decay time of the free fluorophore is unchanged, while in the dynamic quenching, the average decay time of the whole excited state should decrease. 25 The fluorescence lifetime data of Sor before and after the addition of G4 are summarized in Table 1. Therefore, there was a static quenching mechanism, which agreed well with the results of the fluorescence quenching analysis.…”

Systematic bio-fabrication of aptamers and their applications in engineering biology

“…Therefore, similar predictive calculations can never be completely reliable, but this model can be used as a starting point for further experiments to guide future research [ 79 ]. In addition to the prediction models, relevant experimental methods such as NMR have also been used to reveal the spatial structure of DNA/RNA, which provide reasonable and reliable data for clarifying the binding properties of aptamers [ 80 ].…”