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

11.2K
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...
11.2K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

7.9K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
7.9K
Riboswitches01:56

Riboswitches

8.1K
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...
8.1K
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

5.7K
Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.7K
Allosteric Regulation01:08

Allosteric Regulation

57.9K
Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
57.9K
Improving Translational Accuracy02:07

Improving Translational Accuracy

10.0K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
10.0K

You might also read

Related Articles

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

Sort by
Same author

Computational selection of allosteric RNAs: A review.

International journal of biological macromolecules·2026
Same author

Rational Design of Chimeric Antisense Oligonucleotides that Target FMN Riboswitch mRNAs and Inhibit the Growth of Methicillin-Resistant <i>Staphylococcus aureus</i>.

ACS infectious diseases·2025
Same author

Targeting Bacterial Adenylate Kinase mRNA with a Chimeric Antisense Oligonucleotide for Rational Antibacterial Drug Development.

Molecules (Basel, Switzerland)·2025
Same author

Antisense and Functional Nucleic Acids in Rational Drug Development.

Antibiotics (Basel, Switzerland)·2024
Same author

General and Specific Cytotoxicity of Chimeric Antisense Oligonucleotides in Bacterial Cells and Human Cell Lines.

Antibiotics (Basel, Switzerland)·2024
Same author

Targeting FMN, TPP, SAM-I, and glmS Riboswitches with Chimeric Antisense Oligonucleotides for Completely Rational Antibacterial Drug Development.

Antibiotics (Basel, Switzerland)·2023
Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jun 23, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.0K

Computational Design of Allosteric Ribozymes via Genetic Algorithms.

Dimitrios Kaloudas1, Nikolet Pavlova1, Robert Penchovsky2

  • 1Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria.

Methods in Molecular Biology (Clifton, N.J.)
|June 22, 2024
PubMed
Summary
This summary is machine-generated.

Computational design of allosteric ribozymes offers a faster, more accurate alternative to in vitro selection. This in silico approach, using RNA folding principles, exceeds 90% accuracy, reducing time and cost.

Keywords:
Allosteric ribozymesBiosensorsComputational designHammerhead ribozymesIn silico selectionRibozyme

More Related Videos

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

3.6K
The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy
11:53

The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy

Published on: October 14, 2017

11.6K

Related Experiment Videos

Last Updated: Jun 23, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.0K
An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

3.6K
The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy
11:53

The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy

Published on: October 14, 2017

11.6K

Area of Science:

  • Biochemistry
  • Computational Biology
  • Molecular Biology

Background:

  • In vitro selection of allosteric ribozymes is challenging due to complex procedures, uncertain outcomes, and undesired sequence functionalities.
  • Current methods are time-consuming and costly, hindering rapid development.

Purpose of the Study:

  • To present a precise computational design strategy for allosteric ribozymes.
  • To demonstrate the efficiency and accuracy of in silico design as an alternative to in vitro selection.

Main Methods:

  • Utilized RNA secondary structure folding principles for computational design.
  • Employed experimentally validated (EAs) allosteric elements, random search algorithms, and partition functions for RNA folding.
  • Automated various algorithms with logic gates into computer programs for rapid sequence generation.

Main Results:

  • Achieved over 90% accuracy in the in silico design of allosteric ribozymes.
  • Demonstrated the capability to quickly generate numerous allosteric sequences.
  • Successfully automated design processes through computer programs.

Conclusions:

  • Computational design provides a highly accurate and efficient method for creating allosteric ribozymes.
  • This in silico approach significantly reduces the time and cost associated with allosteric ribozyme development.
  • Eliminates the need for traditional in vitro selection, streamlining the research process.