A Base Change in the Catalytic Core of the Hairpin Ribozyme Perturbs Function but Not Domain Docking†

Biochemistry ◽  
2001 ◽  
Vol 40 (8) ◽  
pp. 2580-2587 ◽  
Author(s):  
Nils G. Walter ◽  
Philip A. Chan ◽  
Ken J. Hampel ◽  
David P. Millar ◽  
John M. Burke
Keyword(s):  
Base Change ◽  
Hairpin Ribozyme ◽  
Catalytic Core ◽  
Domain Docking

Sequence elements outside the catalytic core of natural hairpin ribozymes modulate the reactions differentially

2011 ◽  
Vol 392 (7) ◽  
Author(s):  
Preeti Bajaj ◽  
Gerhard Steger ◽  
Christian Hammann
Keyword(s):  
Mutational Analysis ◽  
Hammerhead Ribozyme ◽  
The Other ◽  
Hairpin Ribozyme ◽  
Catalytic Core ◽  
Arabis Mosaic Virus ◽  
Sequence Elements ◽  
Satellite Rnas ◽  
Hairpin Ribozymes

AbstractHairpin ribozymes occur naturally only in the satellite RNAs of tobacco ringspot virus (TRsV), chicory yellow mottle virus (CYMoV) and arabis mosaic virus (ArMV). The catalytic centre of the predominantly studied sTRsV hairpin ribozyme, and of sArMV is organised around a four-way helical junction. We show here that sCYMoV features a five-way helical junction instead. Mutational analysis indicates that the fifth stem does not influence kinetic parameters of the sCYMoV hairpin ribozymein vitroreactions, and therefore seems an appendix to that junction in the other ribozymes. We report further that all three ribozymes feature a three-way helical junction outside the catalytic core in stem A, with Watson-Crick complementarity to loop nucleotides in stem B. Kinetic analyses of cleavage and ligation reactions of several variants of the sTRsV and sCYMoV hairpin ribozymesin vitroshow that the presence of this junction interferes with their reactions, particularly the ligation. We provide evidence that this is not due to a presumed interaction of the afore-mentioned elements in stems A and B. The evolutionary survival of thiscis-inhibiting element seems rather to be caused by the coincidence of its position with that of the hammerhead ribozyme in the other RNA polarity.

scholarly journals Single-Atom Imino Substitutions at A9 and A10 Reveal Distinct Effects on the Fold and Function of the Hairpin Ribozyme Catalytic Core

Biochemistry ◽  
2009 ◽  
Vol 48 (33) ◽  
pp. 7777-7779 ◽  
Author(s):  
Robert C. Spitale ◽  
Rosaria Volpini ◽  
Michael V. Mungillo ◽  
Jolanta Krucinska ◽  
Gloria Cristalli ◽  
...  
Keyword(s):  
Single Atom ◽  
Hairpin Ribozyme ◽  
Catalytic Core ◽  
And Function

scholarly journals Intermolecular domain docking in the hairpin ribozyme

RNA Biology ◽  
2013 ◽  
Vol 10 (3) ◽  
pp. 425-435 ◽  
Author(s):  
Minako Sumita ◽  
Neil A. White ◽  
Kristine R. Julien ◽  
Charles G. Hoogstraten
Keyword(s):  
Hairpin Ribozyme ◽  
Domain Docking
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