Interhelix Geometry of Stems I and II of a Self-Cleaving Hammerhead RNA

Biochemistry ◽  
1994 ◽  
Vol 33 (7) ◽  
pp. 1788-1796 ◽  
Author(s):  
Frank Ulrich Gast ◽  
Khaled M. A. Amiri ◽  
Paul J. Hagerman
Keyword(s):  
Hammerhead Rna

scholarly journals Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

1999 ◽  
Vol 32 (3) ◽  
pp. 241-284 ◽  
Author(s):  
William G. Scott
Keyword(s):  
Metal Ions ◽  
Conformational Change ◽  
Large Scale ◽  
Enzyme Inhibitor ◽  
Hammerhead Ribozyme ◽  
Three Dimensional ◽  
Chemical Mechanism ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Hammerhead Rna

1. How do ribozymes work? 2412. The hammerhead RNA as a prototype ribozyme 2422.1 RNA enzymes 2422.2 Satellite self-cleaving RNAs 2422.3 Hammerhead RNAs and hammerhead ribozymes 2443. The chemical mechanism of hammerhead RNA self-cleavage 2463.1 Phosphodiester isomerization via an SN2(P) reaction 2473.2 The canonical role of divalent metal ions in the hammerhead ribozyme reaction 2513.3 The hammerhead ribozyme does not actually require metal ions for catalysis 2543.4 Hammerhead RNA enzyme kinetics 2574. Sequence requirements for hammerhead RNA self-cleavage 2604.1 The conserved core, mutagenesis and functional group modifications 2604.2 Ground-state vs. transition-state effects 2615. The three-dimensional structure of the hammerhead ribozyme 2625.1 Enzyme–inhibitor complexes 2625.2 Enzyme–substrate complex in the initial state 2645.3 Hammerhead ribozyme self-cleavage in the crystal 2645.4 The requirement for a conformational change 2655.5 Capture of conformational intermediates using crystallographic freeze-trapping 2665.6 The structure of a hammerhead ribozyme ‘early’ conformational intermediate 2675.7 The structure of a hammerhead ribozyme ‘later’ conformational intermediate 2685.8 Is the conformational change pH dependent? 2695.9 Isolating the structure of the cleavage product 2715.10 Evidence for and against additional large-scale conformation changes 2745.11 NMR spectroscopic studies of the hammerhead ribozyme 2786. Concluding remarks 2807. Acknowledgements 2818. References 2811. How do ribozymes work? 241The discovery that RNA can be an enzyme (Guerrier-Takada et al. 1983; Zaug & Cech, 1986) has created the fundamental question of how RNA enzymes work. Before this discovery, it was generally assumed that proteins were the only biopolymers that had sufficient complexity and chemical heterogeneity to catalyze biochemical reactions. Clearly, RNA can adopt sufficiently complex tertiary structures that make catalysis possible. How does the three- dimensional structure of an RNA endow it with catalytic activity? What structural and functional principles are unique to RNA enzymes (or ribozymes), and what principles are so fundamental that they are shared with protein enzymes?

The hammerhead RNA domain, a model ribozyme

1993 ◽  
Vol 1216 (3) ◽  
pp. 345-359 ◽  
Author(s):  
John Bratty ◽  
Pascal Chartrand ◽  
Gerardo Ferbeyre ◽  
Robert Cedergren
Keyword(s):  
Hammerhead Rna

scholarly journals A computational approach to the mechanism of self-cleavage of hammerhead RNA.

1989 ◽  
Vol 86 (24) ◽  
pp. 9727-9731 ◽  
Author(s):  
H. Y. Mei ◽  
T. W. Kaaret ◽  
T. C. Bruice
Keyword(s):  
Computational Approach ◽  
Hammerhead Rna

Relationship between 2'-hydroxyls and magnesium binding in the hammerhead RNA domain: a model for ribozyme catalysis

Biochemistry ◽  
1991 ◽  
Vol 30 (16) ◽  
pp. 4020-4025 ◽  
Author(s):  
Jean Pierre Perreault ◽  
Damian Labuda ◽  
Nassim Usman ◽  
Jing Hua Yang ◽  
Robert Cedergren
Keyword(s):  
Magnesium Binding ◽  
Hammerhead Rna

Role of divalent metal ions in the hammerhead RNA cleavage reaction

Biochemistry ◽  
1991 ◽  
Vol 30 (39) ◽  
pp. 9464-9469 ◽  
Author(s):  
SueAnn C. Dahm ◽  
Olke C. Uhlenbeck
Keyword(s):  
Metal Ions ◽  
Divalent Metal ◽  
Rna Cleavage ◽  
Divalent Metal Ions ◽  
Cleavage Reaction ◽  
Hammerhead Rna

scholarly journals Substrate sequence effects on "hammerhead" RNA catalytic efficiency.

1990 ◽  
Vol 87 (5) ◽  
pp. 1668-1672 ◽  
Author(s):  
M. J. Fedor ◽  
O. C. Uhlenbeck
Keyword(s):  
Catalytic Efficiency ◽  
Sequence Effects ◽  
Hammerhead Rna

scholarly journals Non-enzymatic assembly of active chimeric ribozymes from aminoacylated RNA oligonucleotides

2021 ◽  
Author(s):  
Aleksandar Radakovic ◽  
Saurja Dasgupta ◽  
Tom H Wright ◽  
Harry R.M. Aitken ◽  
Jack W Szostak
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Amino Acid ◽  
Ribosomal Protein ◽  
Rna World ◽  
Directed Assembly ◽  
Enzymatic Function ◽  
Hammerhead Rna ◽  
Rna Backbone ◽  
Ribosomal Protein Synthesis

Aminoacylated tRNAs, which harbor a covalent linkage between amino acids and RNA, are a universally conserved feature of life. Because they are essential substrates for ribosomal translation, aminoacylated oligonucleotides must have been present in the RNA World prior to the evolution of the ribosome. One possibility we are exploring is that the aminoacyl ester linkage served another function before being recruited for ribosomal protein synthesis. The nonenzymatic assembly of ribozymes from short RNA oligomers under realistic conditions remains a key challenge in demonstrating a plausible pathway from prebiotic chemistry to the RNA World. Here, we show that aminoacylated RNAs can undergo template-directed assembly into chimeric amino acid-RNA polymers that are active ribozymes. We demonstrate that such chimeric polymers can retain the enzymatic function of their all-RNA counterparts by generating chimeric hammerhead, RNA ligase, and aminoacyl transferase ribozymes. Amino acids with diverse side chains form linkages that are well tolerated within the RNA backbone, potentially bringing novel functionalities to ribozyme catalysis. Our work suggests that aminoacylation chemistry may have played a role in primordial ribozyme assembly. Increasing the efficiency of this process provides an evolutionary rationale for the emergence of sequence and amino acid specific aminoacyl-RNA synthetase ribozymes, which could then have generated the substrates for ribosomal protein synthesis.

Synthesis and Properties of Non-Hammerhead RNA Using 1-(2-Chloroethoxy)-ethyl Group for the Protection of 2′-Hydroxyl Function

1991 ◽  
Vol 10 (1-3) ◽  
pp. 141-153 ◽  
Author(s):  
Osamu Sakatsume ◽  
Takashi Ogawa ◽  
Hideo Hosaka ◽  
Masahiko Kawashima ◽  
Makoto Takaki ◽  
...  
Keyword(s):  
Ethyl Group ◽  
Hammerhead Rna

ChemInform Abstract: Synthesis and Properties of Non-Hammerhead RNA Using a 1-(2- Chloroethoxy)ethyl Group for the Protection of the 2′-Hydroxyl Function

ChemInform ◽  
2010 ◽  
Vol 22 (43) ◽  
pp. no-no
Author(s):  
O. SAKATSUME ◽  
T. OGAWA ◽  
H. HOSAKA ◽  
M. KAWASHIMA ◽  
M. TAKAKI ◽  
...  
Keyword(s):  
Ethyl Group ◽  
Hammerhead Rna
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