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Nucleic Acids Research, 1994, Vol. 22, No. 4 604-612
© 1994

RNA

Structural characterization of a ribonuclease III processing signal

David C. Schweisguth, Bhadrani S. Chelladurai1, Allen W. Nicholson1,* and Peter B. Moore

Departments of Chemistry and Molecular Biophysics and Biochemistry Yale University, PO Box 6666, New Haven, CT 06511-8118 1Department of Biological Sciences Wayne State University, Detroit, Ml 48202, USA

*To whom correspondence should be addressed

Received November 10, 1993. Accepted January 13, 1994.

The structure of a ribonuclease III processing signal from bacteriophage T7 was examined by NMR spectroscopy, optical melting, and chemical and enzymatic modification. A 41 nucleotlde variant of the T7 R1.1 processing signal has two Watson - Crick base-paired helices separated by an internal loop, consistent with Its predicted secondary structure. The Internal loop is neither rigidly structured nor completely exposed to solvent, and seems to be helical. The secondary structure of R1.1 RNA Is largely insensitive to the monovalent cation concentration, which suggests that the monovalent cation sensitivity of secondary site cleavage by RNase III Is not due to a low salt-Induced RNA conformatlonal change. However, spectroscopic data show that Mg2+ affects the conformation of the Internal loop, suggesting a divalent cation binding slte(s) within this region. The Mg2+-dependence of RNase III processing of some substrates may reflect not only a requirement for a divalent cation as a catalytic cofactor, but also a requirement for a local RNA conformation which is divalent cation-stabilized.


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