Crystal violet as a fluorescent switch-on probe for i-motif: label-free DNA-based logic gate.

The first application of crystal violet as a selective fluorescent switch-on probe for i-motif DNA has been reported. This interaction has been exploited to develop a label-free DNA-based "OR" logic gate for potassium and hydrogen ions.

Molecular modeling of drug-DNA interactions: virtual screening to structure-based design.

Virtual ligand screening (VLS) and structure-based design are strategies that have been routinely used for the development of pharmaceuticals, particularly those targeting enzymes and other protein targets. In recent years, an increased understanding of the role played by nucleic acids in biological systems made DNA an alternative candidate for the development of new drugs. This review highlights some successful applications of molecular modeling in virtual ligand screening and structure-based design of organic and inorganic molecules that target non-canonical nucleic acid structures such as G-quadruplex and triplex DNA.

Structure-based optimization of FDA-approved drug methylene blue as a c-myc G-quadruplex DNA stabilizer.

G-quadruplexes are non-canonical DNA secondary structures putatively present in the promoter regions of oncogenes in the human genome. The targeting of promoter G-quadruplex structures to repress oncogene transcription represents a potential anticancer strategy. Here, we have used high-throughput virtual screening to identify FDA-approved drug methylene blue (MB) as a promising scaffold for binding the c-myc oncogene G-quadruplex DNA. Based on molecular docking analysis of MB to the c-myc G-quadruplex, we designed and screened 50 MB derivatives containing side chains that could interact with the G-quadruplex grooves. As a proof-of-concept, the highest-scoring compounds were synthesized and the interactions with the c-myc G-quadruplex were investigated using the FID assay. The results showed that the methylene blue derivatives 6a-c were able to bind to the c-myc G-quadruplex with greater binding affinity compared to the known G-quadruplex binding ligand, crystal violet. The activity of the most potent compound identified from the FID assay, 6b, as an inhibitor for polymerase-drive DNA extension was examined using a PCR-stop assay and compared against that of the parent compound methylene blue. The results of the PCR-stop assay showed that the addition of the side chain improved the activity of the derivatives as an inhibitor compared to the parent compound. The MB derivative 6b was shown to be highly selective towards c-myc G-quadruplex over double-stranded DNA and other biologically relevant G-quadruplexes using UV-visible spectroscopy and mass spectrometry, respectively. The MB derivative 6b could induce or stabilize c-myc G-quadruplex formation in both cell-free and cellular biological models, and displayed higher cytoxicity against human hepatocarcinoma cells compared to the parent compound, MB.