The effect of on the conformational

The effect of on the conformational of G-quadruplexes was investigated with circular dichroism (CD) spectroscopy. In the absence of , the CD spectra of parallel G-quadruplex exhibited a characteristic positive peak at about 265 nm, and a negative peak at about 240 nm; antiparallel G-quadruplex showed a characteristic positive peak at about 290 nm, and a negative peak at about 250 nm. As shown in a, had a negligible impact on the characteristic peaks of . Similar results were observed when treated with antiparallel G-quadruplex (b). And no induced CD signal peaks in the wavelength longer than 350 nm could be detected. These indicated that can sense G-quadruplexes without affecting their topologies. The FID assay has been used to evaluate the binding affinity of a Lapatinib for quadruplex DNA. This assay utilizes a light-up probe like , which is virtually nonfluorescent in the free state and becomes strongly fluorescent upon binding to quadruplex DNA. Thus, the binding affinity of a compound can be determined through its ability to displace from the DNA target and can be readily monitored via the decrease of its fluorescence . As shown in , in agreement with fluorescence results, compound showed high selectivity for parallel G-quadruplex and with DC values of 0.44 and 0.49 μM, and equilibrium dissociation constants () of 1.9 × 10 M and 2.0 × 10 M, respectively. Higher concentrations of L-1 were required to displace 50% from hybrid and G-quadruplexes with DC values >1.0 μM. It exhibited a value of 0.74 × 10 M and 0.92 × 10 M for and quadruplexes, respectively. In the case of anti-parallel G-quadruplex , DC value was not obtained, indicating excellent binding affinity of for parallel over other G-quadruple structures. The binding mode plays a very important role in the discussion of the interaction between the compounds and DNAs. Studies show the main binding modes of compounds with G-quadruplex DNAs are grooves and end-stacking binding. In order to elucidate the binding mode of with G-quadruplexes, potassium iodide (KI) quenching was presented. Iodide ions effectively quench the fluorescence of small compounds in solution. When the compound intercalates within DNA, the fluorescence intensity is well protected from being quenched. However, groove binding affords little shield for the bounded compounds, so the compound is exposed to the external environment and iodide anions can quench their fluorescence without difficulty even in the presence of DNA . Thus, the relative quenching of the fluorescence of by iodide ions were studied in the absence and presence of different types of G-quadruplex DNAs. As shown in , the obtained fluorescence quenching data were analyzed using the Stern-Volmer equation as follows: where and denote the steady-state fluorescence intensities in the absence and in the presence of KI, respectively, is a linear Stern-Volmer quenching constant, [Q] is the concentration of KI . According to the quench curve, the values for in the absence of , , , and were estimated as 2.9 M, 10.1 M, 3.2 M, 2.19 M and 2.6 M, respectively, larger than that in the absence of G-quadruplex DNA, which was 0.28 M. These findings are good proof of groove binding mode. To explore the potential binding mode between the and the G-quadruplex DNA, the molecular docking and molecular dynamics simulations were performed using the AutoDock vina 1.1.2 and Amber14 software package. The binding mode of G-quadruplex DNA with was determined by 20-ns molecular dynamics simulations based on the docking results. To explore the dynamic stability of the complex and to ensure the rationality of the sampling strategy, the root-mean-square deviation (RMSD) value of the DNA backbone based on the starting structure along the simulation time was calculated and the G-quadruplex DNA- complex was stabilized during the 20-ns simulation (a). The interaction between the and the G-quadruplex DNA was shown in b. Compound adopted compact conformation to bind in the major groove of the G-quadruplex DNA (c). The was positioned at the surface of the major groove, surrounded by the nucleotides DG-3, DG-4, DG-10, DG-16, DT-17 and DG-21, forming strong contacts. Detailed analysis showed that the phenyl group of the formed π-π stacking interaction with the nucleotide DG-4. All these interactions helped to anchor in the binding site of the G-quadruplex DNA.