Related Experiment Video
Updated: Jun 21, 2026
11:27
Studying DNA Looping by Single-Molecule FRET
Published on: June 28, 2014
Coordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction
Shigeyoshi Matsumura1, Rei Ohmori, Hirohide Saito
1Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan.
FEBS Letters
|July 28, 2009
Summary
Researchers enhanced a synthetic RNA ligase ribozyme (DSL) into a trans-acting form (tDSL-1/GUAA). This modified ribozyme showed significantly higher activity and turnover capabilities, highlighting the importance of loop-receptor interactions for its function.
Area of Science:
- Biochemistry
- Molecular Biology
- Synthetic Biology
Background:
- A synthetic cis-acting RNA ligase ribozyme, termed "designed and selected ligase" (DSL), was previously developed for 3"-5" joining.
- The modular architecture of DSL facilitated its transformation into a trans-acting ribozyme.
Purpose of the Study:
- To investigate the modular properties and turnover capabilities of a trans-acting DSL, specifically the tDSL-1/GUAA variant.
- To understand the role of specific interactions in the efficiency of trans-acting ribozymes.
Main Methods:
- Modification of the cis-acting DSL into a trans-acting form (tDSL-1/GUAA).
- Assay of the catalytic activity and turnover number of the trans-acting ribozyme.
Main Results:
- The trans-acting tDSL-1/GUAA exhibited significantly higher catalytic activity compared to the parental cis-acting DSL.
- tDSL-1/GUAA demonstrated a high turnover number, indicating efficient catalytic cycles.
- Loop-receptor interactions were identified as critical for the enhanced activity and multiple turnover capabilities.
Conclusions:
- The trans-acting DSL, tDSL-1/GUAA, is a highly active RNA ligase with efficient turnover capabilities.
- Loop-receptor interactions are a key determinant of trans-acting ribozyme activity and performance.
- The modular design of DSL enables the development of efficient trans-acting ribozymes for various applications.
Related Concept Videos
01:56Riboswitches
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...
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
01:27Transducer Mechanism: Enzyme-Linked Receptors
Enzyme-linked receptors are cell-surface receptors acting as an enzyme or associating with an enzyme intracellularly. They make excellent drug targets. Drugs can bind to the extracellular ligand-binding domain or directly affect their enzymatic domain and alter their activity.
Major types that are helpful drug targets include:
Major types that are helpful drug targets include:
01:58Cooperative Allosteric Transitions
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...
01:58Cooperative Allosteric Transitions
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...
01:58Cooperative Allosteric Transitions
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...
02:13Cooperative Binding of Transcription Regulators
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...