Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Riboswitches01:56

Riboswitches

Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The ultrafine-bridge-associated endonuclease ANKLE1 is stimulated by tension in DNA to process branch-points.

Nucleic acids research·2026
Same author

Site-specific ribozyme-mediated alkylation of DNA substrates.

Nucleic acids research·2026
Same author

Some general principles of riboswitch structure and interactions with small-molecule ligands.

Quarterly reviews of biophysics·2025
Same author

RNA catalysis moving towards metabolic reactions: progress with ribozyme catalyzed alkyl transfer.

Trends in biochemical sciences·2025
Same author

A general strategy for engineering GU base pairs to facilitate RNA crystallization.

Nucleic acids research·2024
Same author

The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.

ACS catalysis·2024

Related Experiment Video

Updated: Jun 3, 2026

Chemical Triphosphorylation of Oligonucleotides
13:19

Chemical Triphosphorylation of Oligonucleotides

Published on: June 2, 2022

Catalysis by the nucleolytic ribozymes.

David M J Lilley1

  • 1Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK. d.m.j.lilley@dundee.ac.uk

Biochemical Society Transactions
|March 25, 2011
PubMed
Summary

Nucleolytic ribozymes utilize general acid-base catalysis for rate enhancement. The Varkud satellite ribozyme employs guanine and adenine in its cleavage reaction, similar to the hairpin ribozyme.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Enzymology

Background:

  • Nucleolytic ribozymes are RNA molecules with catalytic activity, essential for various biological processes.
  • General acid-base catalysis is a key mechanism in enzymatic reactions, facilitating bond cleavage and formation.
  • Understanding ribozyme mechanisms is crucial for deciphering RNA's role in the origin of life and for developing novel biotechnologies.

Purpose of the Study:

  • To elucidate the catalytic mechanisms of nucleolytic ribozymes, focusing on general acid-base catalysis.
  • To investigate the specific roles of guanine and adenine nucleobases in the Varkud satellite ribozyme's cleavage reaction.
  • To compare the catalytic strategies of different nucleolytic ribozymes, including the Varkud satellite and hairpin ribozymes.

Main Methods:

More Related Videos

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
09:04

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

Published on: July 26, 2018

RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes
09:19

RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes

Published on: July 22, 2014

Related Experiment Videos

Last Updated: Jun 3, 2026

Chemical Triphosphorylation of Oligonucleotides
13:19

Chemical Triphosphorylation of Oligonucleotides

Published on: June 2, 2022

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
09:04

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

Published on: July 26, 2018

RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes
09:19

RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes

Published on: July 22, 2014

  • Computational modeling and simulation of ribozyme active sites.
  • Biochemical assays to measure reaction rates and identify catalytic residues.
  • Site-directed mutagenesis to probe the function of specific nucleobases.

Main Results:

  • The Varkud satellite ribozyme utilizes guanine as a general base and adenine as a general acid in its catalytic mechanism.
  • This general acid-base catalysis significantly contributes to the observed rate enhancement in the cleavage reaction.
  • The hairpin ribozyme likely employs a similar catalytic strategy, while other nucleolytic ribozymes present distinct mechanistic features.

Conclusions:

  • Guanine and adenine play critical roles as general acid and base catalysts in the Varkud satellite ribozyme.
  • The findings provide insights into the conserved and divergent mechanisms of nucleolytic ribozymes.
  • This study advances our understanding of RNA-based catalysis and its evolutionary significance.