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Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Experimental RNAi02:15

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
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RTRACS: a modularized RNA-dependent RNA transcription system with high programmability.

Shotaro Ayukawa1, Masahiro Takinoue, Daisuke Kiga

  • 1Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan.

Accounts of Chemical Research
|October 21, 2011
PubMed
Summary

Synthetic biology advances with RTRACS, an in vitro system using RNA, DNA, and enzymes. This modular system enables predictable design of complex biological functions, paving the way for smart biomolecular applications.

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Area of Science:

  • Synthetic biology
  • Artificial biological systems
  • Biomolecular engineering

Background:

  • Modular approaches simplify the design of complex artificial biological systems.
  • Accurate mathematical models are crucial for developing predictable, multi-module systems.
  • Existing systems often lack the predictability needed for complex functions.

Purpose of the Study:

  • To review the development of the reverse transcription and transcription-based autonomous computing system (RTRACS).
  • To highlight RTRACS's modularity and model-guided predictability for creating artificial biological systems.
  • To showcase RTRACS's potential for modeling complex cellular functions and enabling new applications.

Main Methods:

  • Development of RTRACS as an in vitro system using RNA, DNA, and enzymes.
  • Assembly of fundamental modules that convert input RNA sequences to programmed output RNA sequences.
  • Construction of modules performing logical operations (e.g., AND) through component substitution.
  • Integration of modules for theoretical design of complex functions like oscillation.
  • Utilizing numerical simulations based on mathematical models with realistic parameters for prediction.

Main Results:

  • Demonstrated a modular artificial biological system (RTRACS) with predictable functionality.
  • Successfully constructed modules capable of performing logical operations.
  • Theoretically designed integrated RTRACS modules for complex functions like oscillation.
  • Model-guided predictability was achieved through numerical simulations.
  • RTRACS modules showed potential for integration with other molecular devices.

Conclusions:

  • RTRACS provides a modular and predictable platform for building artificial biological systems.
  • The system's design facilitates the creation of complex functions through module integration.
  • RTRACS holds promise for modeling cellular processes and developing smart biomolecular applications like drug delivery.