Binding of malachite green promotes stability and shows preference for a human telomere DNA G-quadruplex

Photoinduced binding of malachite green copolymer to parallel G-quadruplex DNA

Designing ligands that selectively target G-quadruplex DNAs has gained attention due to their possible roles in regulation of gene expression and as anti-cancer agents. In this article, we report irradiation-induced ligand binding to G-quadruplex DNAs which offers a novel approach to targeting specific G-quadruplexes. Photoinduced binding to G-quadruplex DNAs was observed for copolymers of poly(vinyl alcohol) carrying a malachite green moiety (PVAMG). This molecule has an aromatic ring with cationic charge, which after irradiation becomes a binding site for G-quadruplex DNA. PVAMGs acted as neutral polymers with no binding affinity under dark conditions. The photoinduced binding was revealed by fluorescence spectroscopy, NMR spectroscopy, UV melting curve, and DNA polymerase stop assay. PVAMGs showed preference to parallel G-quadruplex structures over mixed parallel/antiparallel structures. PVAMGs were found to be noncytotoxic under both dark and irradiated conditions up to a concentration of 20 μM.

Detection of radon with biosensors based on the lead(II)-induced conformational change of aptamer HTG and malachite green fluorescence probe

The aim of this paper is to assemble a new biosensor for detecting the accumulated radon dose in the environment to achieve rapid monitor of radon. Based on the correlation between radon and its stable decay daughter ²¹⁰Pb, a biosensor using the lead-induced specific aptamer HTG conformational changes, and the organic dye malachite green (MG) as a fluorescent probe was assembled. In these studies, we explored a novel, sensitive, label-free, fluorescence biosensing method for the detection of both radon and lead. The fluorescence intensity difference has a linear relationship with Pb²⁺ and the accumulated radon concentration from 6.87 × 10³ Bq·h/m³ to 3.49 × 10⁵ Bq·h/m³. The lead and radon detection limits of this method are 6.7 nmol/L and 2.06 × 10³ Bq·h/m³, respectively. The student's t-test results indicated that the new method was reliable and stable. The detection method is sensitive, accurate, easy to operate, has a wide linear range and is highly selective. In the sampling and determination processes of radon, the radiation harm to human health can be effectively avoided.

Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands have been developed, their low potency and selectivity to G-quadruplexes over duplex remains unsolved. Recently, a crystal structure of a telomeric 3' quadruplex-duplex hybrid was reported and the quadruplex-duplex interface was suggested to a good target to address the issues. However, there are no high-resolution complex structures reported for G-quadruplex ligands except for a docked BSU6037. In this study, molecular dynamic (MD) binding simulations with a free ligand were used to study binding poses and dynamics of four representative ligands: telomestatin, TMPyP4, BSU6037, and BRACO19. The MD data showed that BSU6037 was able to fully intercalate into the interface whereas TMPyP4 and BRACO19 could only maintain partial intercalation into the interface and telomestatin only binds at the quadruplex and duplex ends. Both linear ligands, BSU6037 and BRACO19, were able to interact with the interface, yet they were not selective over duplex DNA. The DNA geometry, binding modes, and binding pathways were systematically characterized, and the binding energy was calculated and compared for each system. The interaction of the ligands to the interface was by the means of an induced-fit binding mechanism rather than a lock-key mechanism, consisting of the DNA unfolding at the interface to allow entrance of the drug and then the refolding and repacking of the DNA and the ligand to further stabilize the G-quadruplex. On the basis of the findings in this study, modifications were suggested to optimize the interface binding for TMPyp4 and telomestatin.