Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

doi:10.1073/pnas.141039198

Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8

Edited by Marlene Belfort, New York State Department of Health, Albany, NY, and approved May 14, 2001 (received for review January 24, 2001)

Abstract

Kissing interactions in RNA are formed when bases between two hairpin loops pair. Intra- and intermolecular kissing interactions are important in forming the tertiary or quaternary structure of many RNAs. Self-cleavage of the wild-type Varkud satellite (VS) ribozyme requires a kissing interaction between the hairpin loops of stem-loops I and V. In addition, self-cleavage requires a rearrangement of several base pairs at the base of stem I. We show that the kissing interaction is necessary for the secondary structure rearrangement of wild-type stem-loop I. Surprisingly, isolated stem-loop V in the absence of the rest of the ribozyme is sufficient to rearrange the secondary structure of isolated stem-loop I. In contrast to kissing interactions in other RNAs that are either confined to the loops or culminate in an extended intermolecular duplex, the VS kissing interaction causes changes in intramolecular base pairs within the target stem-loop.

Footnotes

↵ † To whom reprint requests should be addressed at: Department of Molecular and Medical Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, Canada M5S 1A8. E-mail: rick.collins{at}utoronto.ca.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations:

D,

downstream cleavage product;

Pre,

precursor(s);

DMS,

dimethyl sulfate;

Δk,

disrupting kissing interaction;

VS,

Varkud satellite