RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting

Science

Volumn 279, Issue 5358, 1998, Pages 1940-1943

  Sclavi, Bianca ^a   Sullivan, Michael ^a   Chance, Mark R ^a   Brenowitz, Michael ^a   Woodson, Sarah A ^b  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROXYL RADICAL; RIBOZYME;

ARTICLE; PRIORITY JOURNAL; RNA CONFORMATION; SYNCHROTRON; TETRAHYMENA;

ANIMALS; HYDROXYL RADICAL; KINETICS; MAGNESIUM; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; SOLVENTS; SYNCHROTRONS; TETRAHYMENA; X-RAYS;

TETRAHYMENA;

EID: 0032549780     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.279.5358.1940     Document Type: Article

References (39)

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25. A three-syringe quench-flow device (Kin-Tek, State College, PA) was modified to incorporate an x-ray exposure chamber. Details of the design, installation, and beamline configuration will appear elsewhere (30). The configuration of beamline X-9A allows for footprinting to be conducted with substantially shorter x-ray exposures than previously reported (7).
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27. 2 in CE using two syringes of the stopped-flow apparatus (17) and sampled reactions at times from 20 ms to 8 min. Samples within a single experiment were exposed to the X-9A beam for an identical time. Exposure times (10 to 50 ms) were adjusted so that 10 to 30% of the RNA was cleaved, to ensure that molecules were cleaved no more than once on average. RNA samples (70 μl final volume) were precipitated after the addition of 15 μl of 1.5 M Na-acetate (pH 5), carrier tRNA (0.25 mg/ml), and 300 μl of ethanol and analyzed by denaturing gel electrophoresis (7).
28. -1) was the same as the rate of hydroxyl radical protection of residues in the catalytic center.
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39. Supported by grants from NIH (GM39929, GM51506, and GM52348), the Molecular Biophysics Training Program (GM08572), NSF (MCB-9410748 and MCB-9601148), and the Hirschl Weill-Caulier Trust. S.W. acknowledges the Pew Scholars Program and the Henry and Camille Dreyfus Foundation. The construction and operation of beamline X-9A are supported by the National Center for Research Resources, Biomedical Technology Program (P41-RR01633). The NSLS is supported by the Department of Energy, Division of Materials Sciences. The data in this paper are from a thesis to be submitted by B.S. in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Sue Golding Graduate Division of Medical Sciences, Albert Einstein College of Medicine.