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Related Concept Videos

RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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...
Allosteric Regulation01:08

Allosteric Regulation

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...
Cooperative Allosteric Transitions01:58

Cooperative 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...

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An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
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ARDesigner: a web-based system for allosteric RNA design.

Wenjie Shu1, Ming Liu, Hebing Chen

  • 1Beijing Institute of Radiation Medicine, Beijing 100850, China. shuwj@bmi.ac.cn

Journal of Biotechnology
|October 26, 2010
PubMed
Summary
This summary is machine-generated.

Researchers developed Allosteric RNA Designer (ARDesigner), a computational tool for engineering novel allosteric RNA molecules. This system aids in designing RNA with specific properties, including mutational robustness, for synthetic biology applications.

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Area of Science:

  • Molecular Biology
  • Synthetic Biology
  • Computational Biology

Background:

  • RNA molecules are crucial for information transfer, structure, and function in molecular biology.
  • Engineering novel allosteric RNA molecules presents significant challenges.
  • Efficient computational design methods are essential for advancing allosteric RNA engineering.

Purpose of the Study:

  • To develop a user-friendly, web-based computational system for designing allosteric RNA molecules.
  • To incorporate mutational robustness into the allosteric RNA design process.
  • To provide researchers with a tool for creating allosteric RNAs with specific, desired properties.

Main Methods:

  • Development of the Allosteric RNA Designer (ARDesigner) system.
  • Integration of mutational robustness considerations into the design algorithm.
  • Validation of the system by engineering a temperature-sensitive allosteric RNA.

Main Results:

  • The Allosteric RNA Designer (ARDesigner) system was successfully developed and made freely available.
  • The system outputs detailed design information in a graphical HTML format.
  • A temperature-sensitive allosteric RNA engineered using ARDesigner met the specified design criteria.

Conclusions:

  • ARDesigner offers a simplified approach for researchers to design allosteric RNAs with tailored properties.
  • The system's versatile framework supports future enhancements for synthetic biology and therapeutic design.
  • ARDesigner serves as a valuable tool for advancing the field of allosteric RNA engineering.