A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion

Journal of Molecular Biology

Volumn 305, Issue 5, 2001, Pages 1045-1055

  Wadkins, Timothy S ^a   Shih, I Hung ^a   Perrotta, Anne T ^a   Been, Michael D ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Acid base catalysis; Catalytic RNA; Hepatitis delta virus; Protonated cytosine; Ribozyme

Indexed keywords

MAGNESIUM ION; RIBOZYME; SODIUM CHLORIDE;

ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVITY; GENE DELETION; HEPATITIS DELTA VIRUS; MOLECULAR INTERACTION; MUTATION; NONHUMAN; PH; PRIORITY JOURNAL; PROTEIN FOLDING; PROTON TRANSPORT;

DELTA VIRUS; HEPATITIS DELTA VIRUS;

EID: 0035793217     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.4368     Document Type: Article

References (26)

1. Role of divalent metal ions in the hammerhead RNA cleavage reaction
2. Cloning and expression of the gene for bacteriophage T7 RNA polymerase
3. The role of metal ions in RNA biochemistry
4. Crystallization and structure determination of a hepatitis delta virus ribozyme: Use of the RNA-binding protein U1A as a crystallization module
5. Crystal structure of a hepatitis delta virus ribozyme
6. In vitro selection of self-cleaving RNAs with a low pH optimum
7. Rapid and efficient site-specific mutagenesis without phenotypic selection
8. Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus
9. A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate
10. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
11. Mechanistic aspects of enzymatic catalysis: Lessons from comparison of RNA and protein enzymes
12. Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot
13. Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage
14. A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation
15. A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduces kinetic trapping of inactive conformations
16. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
17. Kinemages-simple macromolecular graphics for interactive teaching and publication
18. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage
19. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot
20. A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses
21. Production of single-stranded plasmid DNA
22. Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus
23. A nested double-pseudoknot is required for self-cleavage activity of both the genomic and antigenomic HDV ribozymes
24. Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis
25. Human hepatitis 8 virus RNA sub fragments contain an autocleavage activity