NMR structure study of DNA G-quadruplexes and ligand complexes

G-quadruplexes (G4s) have emerged as one of the most exciting nucleic acid secondary structures. G-quadruplexes are non-canonical, four-stranded nucleic acid structures formed in sequences with consecutive runs of guanine bases. Unlike duplex DNA, G-quadruplexes are globularly folded structures and can readily form under physiologically relevant solution conditions. G-quadruplex structures have been found in biologically significant nucleic acid regions, including human telomeres, oncogene-promoter regions, replication initiation sites, and untranslated regions (UTRs) of mRNA. They have been shown to be important regulatory motifs in a number of critical cellular processes including gene transcription, translation, DNA replication, and genomic stability. G-quadruplexes have become a new class of molecular targets for drug development. Nuclear magnetic resonance (NMR) spectroscopy is the major method for studying the structures of G-quadruplexes under physiologically relevant solution conditions. NMR spectroscopy is a powerful tool for studying G-quadruplex interactions with small molecule ligands in solution. To date, most G-quadruplex structures have been determined using NMR techniques. This review provides a comprehensive overview of the NMR methods used to determine DNA G-quadruplex structures and their ligand interactions in solution. It covers essential steps such as resonance assignment, which is foundational for all NMR studies, as well as the determination of G-quadruplex folding topology and structure using NMR spectroscopy. Additionally, it discusses NMR structural studies of small molecule interactions with DNA G-quadruplexes. Through examples of NMR-based structure characterization of G-quadruplexes and G-quadruplex-ligand complexes, this review illustrates the rich information that NMR spectroscopy can provide, demonstrating its applicability to a broad range of biologically relevant DNA G-quadruplexes and their ligand interactions.