scholarly journals Diffusely Bound Mg2+Ions Slightly Reorient Stems I and II of the Hammerhead Ribozyme To Increase the Probability of Formation of the Catalytic Core†

Biochemistry ◽  
2003 ◽  
Vol 42 (33) ◽  
pp. 9924-9936 ◽  
Author(s):  
David Rueda ◽  
Katrin Wick ◽  
S. Elizabeth McDowell ◽  
Nils G. Walter
Keyword(s):  
Hammerhead Ribozyme ◽  
Catalytic Core

Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

2003 ◽  
Vol 10 (9) ◽  
pp. 708-712 ◽  
Author(s):  
Anastasia Khvorova ◽  
Aurélie Lescoute ◽  
Eric Westhof ◽  
Sumedha D Jayasena
Keyword(s):  
Hammerhead Ribozyme ◽  
Catalytic Core ◽  
Intracellular Activity ◽  
Sequence Elements

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.

A Conformational Change in the Catalytic Core of the Hammerhead Ribozyme upon Cleavage of an RNA Substrate†

Biochemistry ◽  
1997 ◽  
Vol 36 (3) ◽  
pp. 518-525 ◽  
Author(s):  
Jean-Pierre Simorre ◽  
Pascale Legault ◽  
Arlene B. Hangar ◽  
Paul Michiels ◽  
Arthur Pardi
Keyword(s):  
Conformational Change ◽  
Hammerhead Ribozyme ◽  
Catalytic Core

scholarly journals Erratum: Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

2003 ◽  
Vol 10 (10) ◽  
pp. 872-872 ◽  
Author(s):  
Anastasia Khvorova ◽  
Aurélie Lescoute ◽  
Eric Westhof ◽  
Sumedha D Jayasena
Keyword(s):  
Hammerhead Ribozyme ◽  
Catalytic Core ◽  
Intracellular Activity ◽  
Sequence Elements

scholarly journals Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium

2020 ◽  
Vol 6 (1) ◽  
pp. 14
Author(s):  
Mohammad Reza Naghdi ◽  
Emilie Boutet ◽  
Clarisse Mucha ◽  
Jonathan Ouellet ◽  
Jonathan Perreault
Keyword(s):  
Divalent Cations ◽  
Hammerhead Ribozyme ◽  
Single Mutation ◽  
Hammerhead Ribozymes ◽  
Catalytic Core ◽  
Cleavage Activity ◽  
Naturally Occurring

Hammerhead ribozymes are one of the most studied classes of ribozymes so far, from both the structural and biochemical point of views. The activity of most hammerhead ribozymes is cation-dependent. Mg2+ is one of the most abundant divalent cations in the cell and therefore plays a major role in cleavage activity for most hammerhead ribozymes. Besides Mg2+, cleavage can also occur in the presence of other cations such as Mn2+. The catalytic core of hammerhead ribozymes is highly conserved, which could contribute to a preference of hammerhead ribozymes toward certain cations. Here, we show a naturally occurring variation in the catalytic core of hammerhead ribozymes, A6C, that can favor one metallic ion, Mn2+, over several other cations.

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