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The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme.

Publication ,  Journal Article
Brown, AL; Perrotta, AT; Wadkins, TS; Been, MD
Published in: Nucleic Acids Res
May 2008

The ribozyme self-cleavage site in the antigenomic sequence of hepatitis delta virus (HDV) RNA is 33-nt downstream of the poly(A) site for the delta antigen mRNA. An HDV antigenomic ribozyme precursor RNA that included the upstream poly(A) processing site was used to test the hypothesis that nonribozyme sequence near the poly(A) site could affect ribozyme activity. Relative to ribozyme precursor without the extra upstream sequences, the kinetic profile for self-cleavage of the longer precursor was altered in two ways. First, only half of the precursor RNA self-cleaved. The cleaved fraction could be increased or decreased with mutations in the upstream sequence. These mutations, which were predicted to alter the relative stability of competing secondary structures within the precursor, changed the distribution of alternative RNA structures that are resolved in native-gel electrophoresis. Second, the active fraction cleaved with an observed rate constant that was higher than that of the ribozyme without the upstream sequences. Moreover, the higher rate constants occurred at lower, near-physiological, divalent metal ion concentrations (1-2 mM). Modulation of ribozyme activity, through competing alternative structures, could be part of a mechanism that allows a biologically significant choice between maturation of the mRNA and processing of replication intermediates.

Duke Scholars

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

May 2008

Volume

36

Issue

9

Start / End Page

2990 / 3000

Location

England

Related Subject Headings

  • RNA, Viral
  • RNA, Catalytic
  • RNA Precursors
  • Poly A
  • Nucleic Acid Conformation
  • Molecular Sequence Data
  • Magnesium
  • Kinetics
  • Hepatitis Delta Virus
  • Electrophoresis, Polyacrylamide Gel
 

Citation

APA
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ICMJE
MLA
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Brown, A. L., Perrotta, A. T., Wadkins, T. S., & Been, M. D. (2008). The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme. Nucleic Acids Res, 36(9), 2990–3000. https://doi.org/10.1093/nar/gkn156
Brown, Abigail L., Anne T. Perrotta, Timothy S. Wadkins, and Michael D. Been. “The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme.Nucleic Acids Res 36, no. 9 (May 2008): 2990–3000. https://doi.org/10.1093/nar/gkn156.
Brown AL, Perrotta AT, Wadkins TS, Been MD. The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme. Nucleic Acids Res. 2008 May;36(9):2990–3000.
Brown, Abigail L., et al. “The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme.Nucleic Acids Res, vol. 36, no. 9, May 2008, pp. 2990–3000. Pubmed, doi:10.1093/nar/gkn156.
Brown AL, Perrotta AT, Wadkins TS, Been MD. The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme. Nucleic Acids Res. 2008 May;36(9):2990–3000.
Journal cover image

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

May 2008

Volume

36

Issue

9

Start / End Page

2990 / 3000

Location

England

Related Subject Headings

  • RNA, Viral
  • RNA, Catalytic
  • RNA Precursors
  • Poly A
  • Nucleic Acid Conformation
  • Molecular Sequence Data
  • Magnesium
  • Kinetics
  • Hepatitis Delta Virus
  • Electrophoresis, Polyacrylamide Gel