Computational Methods to Study G-Quadruplex–Ligand Complexes

Abstract

Quadruplexes are four-stranded DNA or RNA structures formed from tandem repeats of guanine-rich sequences. They are present throughout the genome, namely at telomeres, in promoter and untranslated regions of important genes. Quadruplexes are thermodynamically stable structures and once formed can be a hindrance to cellular processes like transcription, translation, replication among others. Based on these findings, it has been proposed that small molecules can be used to selectively bind and stabilise quadruplexes. In this review, we explore computational methods that can be used to study quadruplex–ligand interactions. These methods not only provide interpretation of experimental data but also generate information that cannot be accessed by experimental methods.