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Related Concept Videos

Experimental RNAi02:15

Experimental RNAi

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...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
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Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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Ribosome Profiling02:24

Ribosome Profiling

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What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
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What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
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DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
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Published on: December 29, 2021

Model-driven engineering of RNA devices to quantitatively program gene expression.

James M Carothers1, Jonathan A Goler, Darmawi Juminaga

  • 1California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley CA 94720, USA.

Science (New York, N.Y.)
|December 24, 2011
PubMed
Summary
This summary is machine-generated.

Scientists developed a new design approach for synthetic biology using mechanistic modeling and RNA folding simulations to engineer gene expression controls. This method enables predictable and precise engineering of RNA-based genetic devices for various applications.

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Area of Science:

  • Synthetic biology
  • Molecular biology
  • Biochemical engineering

Background:

  • Limited availability of models and simulation tools for designing complex synthetic biological devices.
  • Need for robust methods to engineer predictable gene expression controls.

Purpose of the Study:

  • To formulate a design-driven approach for engineering RNA-regulated genetic devices.
  • To enable quantitatively predictable control of gene expression using RNA-based components.

Main Methods:

  • Utilized mechanistic modeling and kinetic RNA folding simulations.
  • Assembled and characterized ribozyme, metabolite-controlled, and aptazyme-regulated expression devices.
  • Validated the design strategy through in vitro, in vivo, and in silico analyses.

Main Results:

  • Successfully engineered 28 Escherichia coli expression devices.
  • Achieved excellent quantitative agreement between predicted and measured gene expression levels (r = 0.94).
  • Demonstrated application of the technology to engineer RNA-regulated controls in metabolic pathways.

Conclusions:

  • The developed design approach provides a framework for studying RNA functions.
  • Highlights the potential of biochemical and biophysical modeling for advancing biological design methods.
  • Enables the creation of functionally complex and predictably regulated synthetic biological systems.