Kinetic and binding analysis of the catalytic involvement of ribose moieties of a trans-acting delta ribozyme

J Biol Chem. 2002 Jul 19;277(29):26508-16. doi: 10.1074/jbc.M203468200. Epub 2002 May 15.

Abstract

We have identified ribose 2'-hydroxyl groups (2'-OHs) that are critical for the activity of a trans-cleaving delta ribozyme derived from the antigenomic strand of the hepatitis delta virus. Initially, an RNA-DNA mixed ribozyme composed of 26 deoxyribo- (specifically the nucleotides forming the P2 stem and the P4 stem-loop) and 31 ribonucleotides (those forming the catalytic center) was engineered. This mixed ribozyme catalyzed the cleavage of a small substrate with kinetic parameters virtually identical to those of the all-RNA ribozyme. The further substitution of deoxyribose for ribose residues permitted us to investigate the contribution of all 2'-OHs to catalysis. Determination of the kinetic parameters for the cleavage reaction of the resulting ribozymes revealed (i) 10 2'-OH groups appear to be important in supporting the formation of several hydrogen bonds within the catalytic core, (ii) none of the important 2'-OHs seem to coordinate a magnesium cation, and (iii) 1 of the tested RNA-DNA mixed polymers appeared to stabilize the ribozyme-substrate transition-state complex, resulting in an improvement over the all-RNA counterpart. The contribution of the 2'-OHs to the catalytic mechanism is discussed, and differences with the crystal structure of a genomic delta self-cleaved product are explained. Clearly, the 2'-OHs are essential components of the network of interactions involved in the formation of the catalytic center of the delta ribozyme.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Catalysis
  • Hepatitis Delta Virus / genetics*
  • Hydroxides
  • Kinetics
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Binding
  • RNA, Catalytic / chemistry*
  • RNA, Viral / chemistry*

Substances

  • Hydroxides
  • RNA, Catalytic
  • RNA, Viral
  • hydroxide ion