| The focus of this dissertation is to develop a sequence-independent spin probe for measuring distances in nucleic acids. This nitroxide probe, which is designated as R5 throughout the dissertation, can be introduced at any sequence position of a nucleic acid in an efficient and cost-effective manner. Calibration studies have been carried out in two nucleic acid model systems: one is a dodecameric DNA B-form duplex with a known NMR structure; the other is a dodecameric RNA A-form duplex with a known X-ray crystal structure. These studies demonstrated successful nanometer distance measurements using the R5 probe, and established the procedures for correlating the measured inter-R5 distances to the parent nucleic acid structures. This lays a foundation for the application of Site-directed spin labeling for the unrestricted global structure mapping in nucleic acids and protein-nucleic acid complexes. |
