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Quadruplex nucleic acids are discrete higher-order four-stranded structures formed from short repetitive guanine-rich DNA or RNA sequences. They are over-represented in eukaryotic telomeric DNA sequences, in promoter sequences and in untranslated regions, especially of genes involved in cancer initiation and progression. Quadruplexes, once formed, can be impediments to transcription, translation or replication, depending on their genomic context and on whether there are cellular mechanisms to unravel them. Cancer cells can have defects in DNA repair, so that otherwise transient quadruplexes may be stabilised with the aid of quadruplex-selective small molecules. This chapter discusses the application of molecular modelling and simulation methods to the in silico study of quadruplex–small-molecule interactions. These approaches can facilitate the determination and systematic exploration of plausible low-energy binding geometries, optimise the evaluation of a library of compounds, and can enable the determination of binding energies with accuracy that can be similar to that of experiment. The various methods in common use in the quadruplex field are illustrated with examples.

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