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Related Concept Videos

Riboswitches01:56

Riboswitches

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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...
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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
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RNA Interference01:23

RNA Interference

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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...
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Experimental RNAi02:15

Experimental RNAi

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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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Ribozymes02:47

Ribozymes

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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...
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Synthetic Biology02:55

Synthetic Biology

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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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Updated: Jun 12, 2025

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
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A Computational Approach for Designing Synthetic Riboswitches for Next-Generation RNA Therapeutics.

Sumit Mukherjee1,2, Sunanda Biswas Mukherjee3, Danny Barash4

  • 1Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA. sumit.mukherjee@nih.gov.

Methods in Molecular Biology (Clifton, N.J.)
|September 23, 2024
PubMed
Summary
This summary is machine-generated.

Riboswitches are RNA molecules that control gene expression by binding to specific ligands. Computational strategies are advancing the design of synthetic riboswitches for novel RNA-based therapeutics and biosensors.

Keywords:
Inverse RNA FoldingRNA-based therapeuticsRiboswitchRibozymeSynthetic biology

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Area of Science:

  • Molecular Biology
  • Synthetic Biology
  • Bioinformatics

Background:

  • Riboswitches are natural RNA regulators controlling gene expression via ligand binding.
  • They function as molecular switches, altering RNA structure and protein synthesis.
  • Their protein-independent interaction with metabolites makes them valuable for biotechnology.

Purpose of the Study:

  • To explore the application of riboswitches in synthetic biology for biosensors and genetic circuits.
  • To highlight the potential of riboswitches in developing targeted RNA-based therapeutics.
  • To discuss computational techniques crucial for designing synthetic riboswitches.

Main Methods:

  • Review of existing literature on riboswitch mechanisms and applications.
  • Discussion of computational strategies for synthetic riboswitch design.
  • Analysis of riboswitch potential in genetic engineering and therapeutic development.

Main Results:

  • Riboswitches offer precise control mechanisms for genetic engineering.
  • Synthetic riboswitches can be designed to target disease-specific metabolites.
  • Computational approaches are key to advancing synthetic riboswitch development.

Conclusions:

  • Riboswitches are versatile tools for synthetic biology, enabling advanced biosensors and genetic circuits.
  • The design of synthetic riboswitches holds significant promise for RNA-based therapeutics and targeted gene therapy.
  • Sophisticated computational strategies are revolutionizing the field, paving the way for innovative RNA-based solutions.