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PMID: 1542571 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Deletion of internal sequence on the HDV-ribozyme: elucidation of functionally important single-stranded loop regions.

Nucleic acids research ·Vol. 20 ·No. 4 ·1992-02-25 ·Pages 747-53

Suh YA, Kumar PK, Nishikawa F, Kayano E, Nakai S, Odai O, Uesugi S, Taira K, Nishikawa S

Abstract

In elucidating functionally important single-stranded loop regions derived mainly from three models in genomic hepatitis delta virus (HDV) ribozyme possessing self-cleavage activity, we have constructed several internal deletion variants of the HDV133 molecule (654-786 nt on genomic RNA) by oligonucleotide-directed mutagenesis. When self-cleavage activities were compared among variants, the HDV133DI-1 (deletion of 701-718 nt) and HDV133DI-3 (deletion of 740-752 nt) ribozyme could maintain their self-cleavage activity, despite at reduced level. However, the activity could be regained in both mutants by some extent under partially denaturing conditions. These results suggest that the above two single-stranded RNA loop regions in HDV ribozyme are not part of the catalytic core but might be involved in the stability of the molecule. In contrast, deletion mutants such as HDV133DI-2 (deletion of 696-722 nt), HDV88DI-1 (deletion of 701-718 nt), HDV88DI-2 (deletion of 696-722 nt), and HDV88DI-4 (deletion of 733-760 nt) abolished catalytic activity. These results suggest that the remaining single-stranded regions of bases between 726-731 and 762-766 in the HDV88 ribozyme may be the potential regions to interact with Mg2+ ions.

MeSH Terms
Base Composition Base Sequence Hepatitis Delta Virus/genetics Molecular Sequence Data Mutagenesis, Site-Directed Nucleic Acid Conformation RNA, Catalytic/genetics,metabolism RNA, Viral/genetics,metabolism
Chemicals
RNA, Catalytic RNA, Viral
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Suh Y A
Fermentation Research Institute, Agency of Industrial Science & Technology, MITI, Tsukuba Science City, Japan.
Kumar P K
Nishikawa F
Kayano E
Nakai S
Odai O
Uesugi S
Taira K
Nishikawa S
References (29)
29 references, click to expand
  1. The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA.
    Nucleic Acids Res. 1985 Dec 20;13(24):8749-64 PMID: 3001649
  2. Fulminant B viral hepatitis: role of delta agent.
    Gastroenterology. 1984 Jun;86(6):1417-20 PMID: 6714570
  3. Vectors for selective expression of cloned DNAs by T7 RNA polymerase.
    Gene. 1987;56(1):125-35 PMID: 3315856
  4. Molecular cloning and sequencing of a human hepatitis delta (delta) virus RNA.
    Nature. 1987 Sep 24-30;329(6137):343-6 PMID: 3627276
  5. Energetics of RNA cleavage: implications for the mechanism of action of ribozymes.
    Protein Eng. 1990 Aug;3(8):691-701 PMID: 1699223
  6. Antigenomic Hepatitis delta virus ribozymes self-cleave in 18 M formamide.
    Nucleic Acids Res. 1991 Mar 25;19(6):1285-9 PMID: 1709487
  7. Preferential chelation of cationic ligands to axial-equatorial oxygens over equatorial-equatorial dianionic oxygens: implication to the mechanism of action of ribozymes.
    Nucleic Acids Symp Ser. 1991;(25):107-8 PMID: 1842042
  8. Efficient trans cleavage and a common structural motif for the ribozymes of the human hepatitis delta agent.
    Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10163-7 PMID: 1946436
  9. Mixed deoxyribo- and ribo-oligonucleotides with catalytic activity.
    Nature. 1990 Apr 5;344(6266):565-7 PMID: 2181322
  10. Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions.
    Biochemistry. 1990 Sep 4;29(35):8011-6 PMID: 2261458
  11. RNA-protein interaction. An analysis with RNA oligonucleotides of the recognition by alpha-sarcin of a ribosomal domain critical for function.
    J Biol Chem. 1990 Feb 5;265(4):2216-22 PMID: 2298746
  12. Human hepatitis delta virus RNA subfragments contain an autocleavage activity.
    Proc Natl Acad Sci U S A. 1989 Mar;86(6):1831-5 PMID: 2648383
  13. Mixed DNA/RNA polymers are cleaved by the hammerhead ribozyme.
    Biochemistry. 1990 Dec 25;29(51):11156-60 PMID: 1703011
  14. Relationship between 2'-hydroxyls and magnesium binding in the hammerhead RNA domain: a model for ribozyme catalysis.
    Biochemistry. 1991 Apr 23;30(16):4020-5 PMID: 1708285
  15. Rate limiting P-O(5') bond cleavage of RNA fragment: ab initio molecular orbital calculations on the base-catalyzed hydrolysis of phosphate.
    Nucleic Acids Res. 1991 May 25;19(10):2747-53 PMID: 1710344
  16. Self-cleavage of a 71 nucleotide-long ribozyme derived from hepatitis delta virus genomic RNA.
    Nucleic Acids Res. 1991 Dec 11;19(23):6519-25 PMID: 1754389
  17. Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures.
    Nucleic Acids Res. 1991 Oct 11;19(19):5409-16 PMID: 1923826
  18. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA.
    Nature. 1991 Apr 4;350(6317):434-6 PMID: 2011192
  19. Non-ribozyme sequences enhance self-cleavage of ribozymes derived from Hepatitis delta virus.
    Nucleic Acids Res. 1991 Feb 11;19(3):559-64 PMID: 2011528
  20. 'Hairpin' catalytic RNA model: evidence for helices and sequence requirement for substrate RNA.
    Nucleic Acids Res. 1990 Jan 25;18(2):299-304 PMID: 2183177
  21. The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant.
    Nucleic Acids Res. 1990 Dec 11;18(23):6821-7 PMID: 2263447
  22. RNA conformational requirements of self-cleavage of hepatitis delta virus RNA.
    Mol Cell Biol. 1990 Oct;10(10):5575-9 PMID: 2398903
  23. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage.
    J Virol. 1988 Aug;62(8):2674-9 PMID: 2455816
  24. Self-cleavage of RNA in the replication of small pathogens of plants and animals.
    Trends Biochem Sci. 1989 Nov;14(11):445-50 PMID: 2696172
  25. The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA.
    Nucleic Acids Res. 1985 Dec 20;13(24):8765-85 PMID: 3001650
  26. Inhibition of restriction endonuclease Nci I cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis.
    Nucleic Acids Res. 1986 Dec 22;14(24):9679-98 PMID: 3027659
  27. Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus.
    J Virol. 1988 Dec;62(12):4439-44 PMID: 3184270
  28. Production of single-stranded plasmid DNA.
    Methods Enzymol. 1987;153:3-11 PMID: 3323803
  29. RNA N-glycosidase activity of ricin A-chain. Mechanism of action of the toxic lectin ricin on eukaryotic ribosomes.
    J Biol Chem. 1987 Jun 15;262(17):8128-30 PMID: 3036799
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/20.4.747
Published
1992-02-25
Pages
747-53
Language
English
Region
England
NLM ID
0411011
PMCID
PMC312013
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/20.4.747 PMC Full Text View journal details
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