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Nucleic Acids Research, 1989, Vol. 17, No. 14 5665-5677
© 1989

MOLECULAR BIOLOGY

RNA stem stability in the formation of a self-cleaving hammerhead structure

Candice C. Sheldon and Robert H. Symons*

Department of Biochemistry, University of Adelaide Adelaide, SA 5000, Australia

*To whom correspondence should be addressed

Received May 17, 1989. Revised June 7, 1989. Accepted June 7, 1989.

The proposed single-hammerhead structure of the self-cleaving newt RNA is unstable due to a weak stem in and therefore is unable to mediate self-cleavage. A double-hammerhead structure with greater theoretical stability has been shown to mediate the self-cleavage of this RNA (Forster et al., 1988, Nature 334, 265). We have found that the double-hammerhead mediated self-cleavage reaction of a 40 base RNA containing the newt sequence (termed nCG) can be converted to a single-hammerhead reaction by increasing the size of stem III and≤or of its loop, thereby enabling a single-hammerhead structure to form. In addition, the 5’-self-cleavage fragment of the nCG RNA can act in trans to mediate the self-cleavage of a full-length RNA by the formation of a partial double-hammerhead structure.


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