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Literature DB >> 17556712

Efficiency of a self-aminoacylating ribozyme: effect of the length and base-composition of its 3' extension.

Jean Lehmann¹, Amy Reichel, Axel Buguin, Albert Libchaber.

Abstract

Variants of a previously described small self-aminoacylating ribozyme are tested in order to uncover the potentialities of a 3' extension responsible for the esterification. The base-composition and the length of this specific part of the ribozyme are investigated. Very short extensions can still reach the active site, reflecting the small persistence length of RNA. The yield of aminoacylation is particularly high for ribozymes with extensions made up of a poly-U, for which a maximum of efficiency is observed for a total length of about 10 nucleotides. A simple model describing the behavior of this region of the ribozyme can account for the data.

Mesh：

Substances：
RNA, Catalytic
Poly U

Year: 2007 PMID： 17556712 PMCID： PMC1924886 DOI： 10.1261/rna.500907

Source DB: PubMed Journal: RNA ISSN： 1355-8382 Impact factor: 4.942

21 in total

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Authors: D S Wilson; J W Szostak
Journal: Annu Rev Biochem Date: 1999 Impact factor: 23.643

2. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. III. Isolation of amino acid-acceptor ribonucleic acids from Escherichia coli.

Authors: E J OFENGAND; M DIECKMANN; P BERG
Journal: J Biol Chem Date: 1961-06 Impact factor: 5.157

3. Elastic properties of a single-stranded charged homopolymeric ribonucleotide.

Authors: Yeonee Seol; Gary M Skinner; Koen Visscher
Journal: Phys Rev Lett Date: 2004-09-10 Impact factor: 9.161

4. Solution structure of an RNA internal loop with three consecutive sheared GA pairs.

Authors: Gang Chen; Brent M Znosko; Scott D Kennedy; Thomas R Krugh; Douglas H Turner
Journal: Biochemistry Date: 2005-03-01 Impact factor: 3.162

5. Elasticity and structure of eukaryote chromosomes studied by micromanipulation and micropipette aspiration.

Authors: B Houchmandzadeh; J F Marko; D Chatenay; A Libchaber
Journal: J Cell Biol Date: 1997-10-06 Impact factor: 10.539

6. Persistence length changes dramatically as RNA folds.

Authors: G Caliskan; C Hyeon; U Perez-Salas; R M Briber; S A Woodson; D Thirumalai
Journal: Phys Rev Lett Date: 2005-12-29 Impact factor: 9.161

7. Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution.

Authors: Martin Egli; George Minasov; Li Su; Alexander Rich
Journal: Proc Natl Acad Sci U S A Date: 2002-03-19 Impact factor: 11.205

8. Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy.

Authors: Meredith Newby Lambert; Eva Vöcker; Seth Blumberg; Stefanie Redemann; Arivalagan Gajraj; Jens-Christian Meiners; Nils G Walter
Journal: Biophys J Date: 2006-02-24 Impact factor: 4.033

9. Essential structures of a self-aminoacylating RNA.

Authors: M Illangasekare; O Kovalchuke; M Yarus
Journal: J Mol Biol Date: 1997-12-12 Impact factor: 5.469

10. Aminoacyl-tRNA synthesis by a resin-immobilized ribozyme.

Authors: Hiroshi Murakami; Neil J Bonzagni; Hiroaki Suga
Journal: J Am Chem Soc Date: 2002-06-19 Impact factor: 15.419

8 in total

1. Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles.

Authors: Tara L Benz-Moy; Daniel Herschlag
Journal: Biochemistry Date: 2011-09-19 Impact factor: 3.162

Efficiency of a self-aminoacylating ribozyme: effect of the length and base-composition of its 3' extension.

Review 1. In vitro selection of functional nucleic acids.

2. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. III. Isolation of amino acid-acceptor ribonucleic acids from Escherichia coli.

3. Elastic properties of a single-stranded charged homopolymeric ribonucleotide.

4. Solution structure of an RNA internal loop with three consecutive sheared GA pairs.

5. Elasticity and structure of eukaryote chromosomes studied by micromanipulation and micropipette aspiration.

6. Persistence length changes dramatically as RNA folds.

7. Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution.

8. Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy.

9. Essential structures of a self-aminoacylating RNA.

10. Aminoacyl-tRNA synthesis by a resin-immobilized ribozyme.

1. Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles.

Review 2. Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.

3. Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

4. Effects of long DNA folding and small RNA stem-loop in thermophoresis.

5. A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome.

6. Reciprocal Nucleopeptides as the Ancestral Darwinian Self-Replicator.

7. Emergence of a code in the polymerization of amino acids along RNA templates.

8. Kinetics of bulge bases in small RNAs and the effect of pressure on it.