Nucleic Acids Research, 2003, Vol. 31, No. 14 3901-3908
© 2003 Oxford University Press
Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction
Department of Biotechnology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China, 1 Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ 08854-5635 and 2 Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
*To whom correspondence should be addressed. Tel: +86 27 87216207; Fax: +86 27 87871945; Email: yizhang{at}whu.edu.cn
Folding of the major population of Tetrahymena intron RNA into the catalytically active structure is trapped in a slow pathway. In this report, folding of Candida albicans intron was investigated using the trans-acting Ca.L-11 ribozyme as a model. We demonstrated that both the catalytic activity (kobs) and compact folding equilibrium of Ca.L-11 are strongly dependent on Mg2+ at physiological concentrations, with both showing an Mg2+ Hill coefficient of 3. Formation of the compact structure of Ca.L-11 is shown to occur very rapidly, on a subsecond time scale similar to that of RNase T1 cleavage. Most of the ribozyme RNA population folds into the catalytically active structure with a rate constant of 2 min–1 at 10 mM Mg2+; neither slower kinetics nor obvious Mg2+ inhibition is observed. These results suggest that folding of the Ca.L-11 ribozyme is initiated by a rapid magnesium-dependent RNA compaction, which is followed by a slower searching for the native contacts to form the catalytically active structure without interference from the long-lived trapped states. This model thus provides an ideal system to address a range of interesting aspects of RNA folding, such as conformational searching, ion binding and the role of productive intermediates.
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