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Crystal Structures of Two Plasmid Copy Control Related RNA Duplexes:  An 18 Base Pair Duplex at 1.20 Å Resolution and a 19 Base Pair Duplex at 1.55 Å Resolution

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Department of Molecular Biophysics and Biochemistry, Department of Chemistry, and Howard Hughes Medical Institute, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520-8114
Cite this: Biochemistry 1999, 38, 45, 14784–14792
Publication Date (Web):October 21, 1999
https://doi.org/10.1021/bi9912793
Copyright © 1999 American Chemical Society

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    Abstract

    The structures of two RNA duplexes, whose sequences correspond to portions of the ColE1 plasmid copy control RNA I and RNA II, have been determined. Crystals containing the 18mers 5‘-CA CCGUUGGUAGCGGUGC-3‘ and 5‘-CACCGCUACCAACGGUGC-3‘ diffract to 1.20 Å resolution while those containing the 19mers 5‘-GCACCGUUGGUAGCGGUGC-3‘ and 5‘-GCACCGCUACCAACGGUGC-3‘ diffract to 1.55 Å resolution. Both duplexes are standard A form, with Watson−Crick base pairing throughout. Use of anisotropic atomic displacement factors in refinement of the 1.20 Å structure dramatically improved refinement statistics, resulting in a final Rfree of 15.0% and a crystallographic R-factor of 11.6%. Perhaps surprisingly, these crystals of the 18 base pair RNA exhibit a 36-fold static disorder, resulting in a structure with a single sugar−phosphate backbone conformation and an averaged base composition at each residue. Since the sugar−phosphate backbone structure is identical in the 36 different nucleotides that are superimposed, there can be no sequence-dependent variation in the structure. The average ribose pucker amplitude is 45.8° for the 18 base pair structure and 46.4° for the 19 base pair structure; these values are respectively 19% and 20% larger than the average pucker amplitude reported from nucleoside crystal structures. A standard RNA water structure, based on analysis of the hydration of these crystal structures and that of the TAR RNA stem [Ippolito, J. A., and Steitz, T. A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9819−9824], has been derived, which has allowed us to predict water positions in lower resolution RNA crystal structures. We report a new RNA packing motif, in which three pro-Sp phosphate oxygens interact with an ammonium ion.

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     Research funded by NIH Grant PO1-GM22778.

     Department of Molecular Biophysics and Biochemistry.

    §

     Present address:  McKinsey and Co., 600 Campus Drive, Floram Park, NJ 07932.

    *

     To whom correspondence should be addressed. Phone:  (203) 432-5619. Fax:  (203) 432-3282.

     Department of Chemistry.

     Howard Hughes Medical Institute.

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