Decoding DNA Structure using NMR Spectroscopy

During the past few decades, Nuclear Magnetic Resonance (NMR) spectroscopy has been extensively used for decoding the nucleic acid structure. The presence of nuclei possessing net spin (1H, 13C, 15N and 31P) in the basic unit of DNA makes it a befitting subject to be studied, utilizing the tenets of NMR spectroscopy. Apart from elucidating the structure, magnetic resonance spectroscopy also uncovers the strand multiplicity and thereby successfully differentiates among various secondary structures of DNA, for instance, duplex, hairpin, triplex, i-motif and quadruplex.

NMR spectroscopy also unravels interactions of nucleic acids with ligands like drugs, mutagens, and proteins. The highlighting feature in elucidating the structure and dynamics of DNA interaction with ligands is that these studies can be conducted in their natural solution environment. The interpretation of structural and chemical basis of ligands is very crucial for the development of new therapeutic agents. NMR parameters like coupling constant and peak integration successfully shed light on integral features of DNA structure such as glycosidic bond angles, sugar pucker conformations and dihedral angles. Other geometrical properties including bent helices, coaxial stacking and non-Watson-Crick base pairing can also be explored using NMR spectroscopy.

This chapter aims to provide a paradigm to understand the features of 1H, 31P, 13C NMR spectroscopy involved in the determination of nucleic acid structure. It also outlines the characteristic features of NMR spectra, which are associated with various DNA topologies.

Keywords: Applications of NMR, NMR of DNA, NMR of DNA triplex, NMR of Duplex, NMR of Quadruplex, NMR Spectroscopy.