Conformational characterization of duplex DNA with solution-state NMR spectroscopy

Abstract

DNA is the hereditary material for living organisms. Understanding the structural features of DNA is essential to comprehend various biological processes. This review outlines the application of solution-state NMR methods to study the structure and dynamics of duplex DNA. A brief overview of the context of NMR in the earlier days of nucleic acids research is discussed. Sample preparation methods and pertinent NMR measurables are introduced, followed by sequential resonance assignment protocol of DNA duplexes. A summary of results obtained from the application of NMR methodology to compare, contrast, and validate initial crystal crystallographic studies of DNA structure, especially the Drew-Dickerson dodecamer and A-tract sequences, is presented. This is followed by a survey of structural insights obtained in studies involving sequence-specific characteristics and mispairs. Results from relaxations experiments that reveal base pairs opening dynamics and short lived transient states of DNA is summarized. Overall, this review aims to introduce the atomistic characterization of DNA using NMR spectroscopy to a beginner level researcher.