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Science 7 November 1997:
Vol. 278. no. 5340, pp. 1093 - 1098
DOI: 10.1126/science.278.5340.1093
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Research Articles

Mapping the Inside of the Ribosome with an RNA Helical Ruler

Simpson Joseph, Bryn Weiser, Harry F. Noller *

The structure of ribosomal RNA (rRNA) in the ribosome was probed with hydroxyl radicals generated locally from iron(II) tethered to the 5' ends of anticodon stem-loop analogs (ASLs) of transfer RNA. The ASLs, ranging in length from 4 to 33 base pairs, bound to the ribosome in a messenger RNA-dependent manner and directed cleavage to specific regions of the 16S, 23S, and 5S rRNA chains. The positions and intensities of cleavage depended on whether the ASLs were bound to the ribosomal A or P site, and on the lengths of their stems. These data predict the three-dimensional locations of the rRNA targets relative to the positions of A- and P- site transfer RNAs inside the ribosome.

The authors are at the Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA.
*   To whom correspondence should be addressed.

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