title: Nanometer distance measurements in RNA using site-directed spin labeling.
abstract: The method of site-directed spin labeling (SDSL) utilizes a stable nitroxide radical to obtain structural and dynamic information on biomolecules. Measuring dipolar interactions between pairs of nitroxides yields internitroxide distances, from which quantitative structural information can be derived. This study evaluates SDSL distance measurements in RNA using a nitroxide probe, designated as R5, which is attached in an efficient and cost-effective manner to backbone phosphorothioate sites that are chemically substituted in arbitrary sequences. It is shown that R5 does not perturb the global structure of the A-form RNA helix. Six sets of internitroxide distances, ranging from 20 to 50 A, were measured on an RNA duplex with a known X-ray crystal structure. The measured distances strongly correlate (R(2) = 0.97) with those predicted using an efficient algorithm for determining the expected internitroxide distances from the parent RNA structure. The results enable future studies of global RNA structures for which high-resolution structural data are absent.
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA.
authors.forename: Qi
authors.initials: Q
authors.lastname: Cai
authors.forename: Ana Karin
authors.initials: AK
authors.lastname: Kusnetzow
authors.forename: Kálmán
authors.initials: K
authors.lastname: Hideg
authors.forename: Eric A
authors.initials: EA
authors.lastname: Price
authors.forename: Ian S
authors.initials: IS
authors.lastname: Haworth
authors.forename: Peter Z
authors.initials: PZ
authors.lastname: Qin
mesh_terms: D001483:Base Sequence; D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D004578:Electron Spin Resonance Spectroscopy; D008958:Models, Molecular; D015394:Molecular Structure; D036103:Nanotechnology; D009589:Nitrogen Oxides; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D013113:Spin Labels; D013816:Thermodynamics
chemical_list: D009589:Nitrogen Oxides; D009843:Oligoribonucleotides; D013113:Spin Labels; D012313:RNA; C039900:nitroxyl