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Literature DB >> 21734469

HDV-like self-cleaving ribozymes.

Abstract

HDV ribozymes catalyze their own scission from the transcript during rolling circle replication of the hepatitis delta virus. In vitro selection of self-cleaving ribozymes from a human genomic library revealed an HDV-like ribozyme in the second intron of the human CPEB3 gene and recent results suggest that this RNA affects episodic memory performance. Bioinformatic searches based on the secondary structure of the HDV/CPEB3 fold yielded numerous functional ribozymes in a wide variety of organisms. Genomic mapping of these RNAs suggested several biological roles, one of which is the 5' processing of non-LTR retrotransposons. The family of HDV-like ribozymes thus continues to grow in numbers and biological importance.

Entities: Disease Gene Species

Mesh：

Substances：

Year: 2011 PMID： 21734469 PMCID： PMC3256349 DOI： 10.4161/rna.8.5.16226

Source DB: PubMed Journal: RNA Biol ISSN： 1547-6286 Impact factor: 4.652

47 in total

1. Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme.

Authors: H Fauzi; J Kawakami; F Nishikawa; S Nishikawa
Journal: Nucleic Acids Res Date: 1997-08-01 Impact factor: 16.971

2. Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength.

Authors: Trevor S Brown; Durga M Chadalavada; Philip C Bevilacqua
Journal: J Mol Biol Date: 2004-08-13 Impact factor: 5.469

3. Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions.

Authors: S P Rosenstein; M D Been
Journal: Biochemistry Date: 1990-09-04 Impact factor: 3.162

4. From alpaca to zebrafish: hammerhead ribozymes wherever you look.

Authors: Carsten Seehafer; Anne Kalweit; Gerhard Steger; Stefan Gräf; Christian Hammann
Journal: RNA Date: 2010-11-16 Impact factor: 4.942

5. Crystal structure of a hepatitis delta virus ribozyme.

Authors: A R Ferré-D'Amaré; K Zhou; J A Doudna
Journal: Nature Date: 1998-10-08 Impact factor: 49.962

6. A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduceskinetic trapping of inactive conformations.

Authors: A T Perrotta; O Nikiforova; M D Been
Journal: Nucleic Acids Res Date: 1999-02-01 Impact factor: 16.971

7. Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme.

Authors: A Lupták; A R Ferré-D'Amaré; K Zhou; K W Zilm; J A Doudna
Journal: J Am Chem Soc Date: 2001-09-05 Impact factor: 15.419

8. Structure-based search reveals hammerhead ribozymes in the human microbiome.

Authors: Randi M Jimenez; Eric Delwart; Andrej Lupták
Journal: J Biol Chem Date: 2011-01-21 Impact factor: 5.157

9. Widespread occurrence of self-cleaving ribozymes.

Authors: Chiu-Ho T Webb; Nathan J Riccitelli; Dana J Ruminski; Andrej Lupták
Journal: Science Date: 2009-11-13 Impact factor: 47.728

10. Constructing an efficient trans-acting genomic HDV ribozyme.

Authors: J Kawakami; K Yuda; Y A Suh; P K Kumar; F Nishikawa; H Maeda; K Taira; E Ohtsuka; S Nishikawa
Journal: FEBS Lett Date: 1996-09-30 Impact factor: 4.124

43 in total

1. Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism.

Authors: Abir Ganguly; Philip C Bevilacqua; Sharon Hammes-Schiffer
Journal: J Phys Chem Lett Date: 2011-11-17 Impact factor: 6.475

Review 2. The ubiquitous hammerhead ribozyme.

Authors: Christian Hammann; Andrej Luptak; Jonathan Perreault; Marcos de la Peña
Journal: RNA Date: 2012-03-27 Impact factor: 4.942

3. Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes.

Authors: Dana J Ruminski; Chiu-Ho T Webb; Nathan J Riccitelli; Andrej Lupták
Journal: J Biol Chem Date: 2011-10-12 Impact factor: 5.157

HDV-like self-cleaving ribozymes.

1. Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme.

2. Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength.

3. Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions.

4. From alpaca to zebrafish: hammerhead ribozymes wherever you look.

5. Crystal structure of a hepatitis delta virus ribozyme.

6. A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduceskinetic trapping of inactive conformations.

7. Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme.

8. Structure-based search reveals hammerhead ribozymes in the human microbiome.

9. Widespread occurrence of self-cleaving ribozymes.

10. Constructing an efficient trans-acting genomic HDV ribozyme.

1. Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism.

Review 2. The ubiquitous hammerhead ribozyme.

3. Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes.

4. Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain.

5. A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.

6. Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.

7. Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.

Review 8. Single molecule fluorescence approaches shed light on intracellular RNAs.

Review 9. The evolution and clinical impact of hepatitis B virus genome diversity.

10. Identification of the catalytic Mg²⁺ ion in the hepatitis delta virus ribozyme.