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.