Site-directed Spin Labeling Studies on Nucleic Acid Structure and Dynamics

Abstract

Publisher Summary This chapter summarizes the current site-directed spin labeling (SDSL) studies on nucleic acids, with discussions focusing on literature from the last decade. SDSL is useful in studying high molecular weight systems under physiological conditions. It has been particularly successful in studying systems (e.g., membrane proteins) that are difficult to investigate using other methods, such as X-ray crystallography and NMR spectroscopy. SDSL has been used to study nucleic acids, and data suggest that one can obtain unique structural and dynamic information about DNA and RNA at the level of individual nucleotides. The majority of nucleic acid SDSL studies have used one of two types of EPR measurements. Distance measurements between pairs of nitroxides provide direct structural constraints in nucleic acid systems. In addition, the mobility of a single-labeled nitroxide can be measured to yield structural and dynamic information at the labeling site. Because nucleic acids are different from proteins in the nature of the basic chemical constituents (4 nucleotides vs. 20 amino acids) and their secondary structural units (B-form/A-form doubled-stranded helix vs. α -helix/ β -sheet), SDSL of nucleic acids requires unique methodologies, particularly in the areas of nitroxide attachment and the correlation of the nitroxide behavior to that of the parent molecule.