Literature DB >> 30602542

RNA Switches for Synthetic Biology.

Calvin M Schmidt1, Christina D Smolke1,2.   

Abstract

In addition to coding for protein sequences, RNA molecules encode a diverse set of gene-regulatory elements. RNA switches are one class of gene-regulatory elements that control protein expression in a manner that is dependent on the concentration of specific ligand molecules. These allosteric gene-regulatory elements have been shown as useful tools in engineering diverse cell types to display novel function. In particular, RNA switches have been used as genetically encoded biosensors and conditional controllers to direct cellular decisions based on the system's changing environment. A significant focus in the field has been the generation of novel RNA switches that are tailored for different biological systems. We review approaches that have been used to generate RNA switches, which leverage the unique physical properties of RNA and the myriad ways in which RNA can modulate gene expression.
Copyright © 2019 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2019        PMID: 30602542      PMCID: PMC6314069          DOI: 10.1101/cshperspect.a032532

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  33 in total

1.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.

Authors:  C Tuerk; L Gold
Journal:  Science       Date:  1990-08-03       Impact factor: 47.728

2.  Synthetic riboswitches that induce gene expression in diverse bacterial species.

Authors:  Shana Topp; Colleen M K Reynoso; Jessica C Seeliger; Ian S Goldlust; Shawn K Desai; Dorothée Murat; Aimee Shen; Aaron W Puri; Arash Komeili; Carolyn R Bertozzi; June R Scott; Justin P Gallivan
Journal:  Appl Environ Microbiol       Date:  2010-10-08       Impact factor: 4.792

3.  Post-transcriptional Boolean computation by combining aptazymes controlling mRNA translation initiation and tRNA activation.

Authors:  Benedikt Klauser; Athanasios Saragliadis; Simon Ausländer; Markus Wieland; Michael R Berthold; Jörg S Hartig
Journal:  Mol Biosyst       Date:  2012-07-09

4.  Regulation of gene expression in diverse cyanobacterial species by using theophylline-responsive riboswitches.

Authors:  Amy T Ma; Calvin M Schmidt; James W Golden
Journal:  Appl Environ Microbiol       Date:  2014-08-22       Impact factor: 4.792

Review 5.  An in vitro selection for small molecule induced switching RNA molecules.

Authors:  Laura Martini; Andrew D Ellington; Sheref S Mansy
Journal:  Methods       Date:  2016-02-17       Impact factor: 3.608

Review 6.  Synthetic biology: advancing the design of diverse genetic systems.

Authors:  Yen-Hsiang Wang; Kathy Y Wei; Christina D Smolke
Journal:  Annu Rev Chem Biomol Eng       Date:  2013-02-13       Impact factor: 11.059

7.  Naringenin-responsive riboswitch-based fluorescent biosensor module for Escherichia coli co-cultures.

Authors:  Yu Xiu; Sungho Jang; J Andrew Jones; Nicholas A Zill; Robert J Linhardt; Qipeng Yuan; Gyoo Yeol Jung; Mattheos A G Koffas
Journal:  Biotechnol Bioeng       Date:  2017-06-05       Impact factor: 4.530

8.  Ribozyme-based aminoglycoside switches of gene expression engineered by genetic selection in S. cerevisiae.

Authors:  Benedikt Klauser; Janina Atanasov; Lena K Siewert; Jörg S Hartig
Journal:  ACS Synth Biol       Date:  2014-05-28       Impact factor: 5.110

9.  Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots.

Authors:  A Xayaphoummine; T Bucher; H Isambert
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

10.  High-throughput cellular RNA device engineering.

Authors:  Brent Townshend; Andrew B Kennedy; Joy S Xiang; Christina D Smolke
Journal:  Nat Methods       Date:  2015-08-10       Impact factor: 28.547

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  9 in total

Review 1.  Engineering synthetic RNA devices for cell control.

Authors:  Peter B Dykstra; Matias Kaplan; Christina D Smolke
Journal:  Nat Rev Genet       Date:  2022-01-04       Impact factor: 59.581

2.  In Vivo Validation of a Reversible Small Molecule-Based Switch for Synthetic Self-Amplifying mRNA Regulation.

Authors:  Sean Mc Cafferty; Joyca De Temmerman; Tasuku Kitada; Jacob R Becraft; Ron Weiss; Darrell J Irvine; Mathias Devreese; Siegrid De Baere; Francis Combes; Niek N Sanders
Journal:  Mol Ther       Date:  2020-11-11       Impact factor: 11.454

3.  A convolutional neural network for the prediction and forward design of ribozyme-based gene-control elements.

Authors:  Calvin M Schmidt; Christina D Smolke
Journal:  Elife       Date:  2021-04-16       Impact factor: 8.140

Review 4.  The case of the missing allosteric ribozymes.

Authors:  Shanker S S Panchapakesan; Ronald R Breaker
Journal:  Nat Chem Biol       Date:  2021-01-25       Impact factor: 15.040

5.  Translational control of enzyme scavenger expression with toxin-induced micro RNA switches.

Authors:  Nina M Pollak; Justin J Cooper-White; Joanne Macdonald
Journal:  Sci Rep       Date:  2021-01-28       Impact factor: 4.379

6.  MoiRNAiFold: a novel tool for complex in silico RNA design.

Authors:  Gerard Minuesa; Cristina Alsina; Juan Antonio Garcia-Martin; Juan Carlos Oliveros; Ivan Dotu
Journal:  Nucleic Acids Res       Date:  2021-05-21       Impact factor: 16.971

7.  Rational design of hairpin RNA excited states reveals multi-step transitions.

Authors:  Ge Han; Yi Xue
Journal:  Nat Commun       Date:  2022-03-21       Impact factor: 14.919

8.  Modulating myoblast differentiation with RNA-based controllers.

Authors:  Peter B Dykstra; Thomas A Rando; Christina D Smolke
Journal:  PLoS One       Date:  2022-09-27       Impact factor: 3.752

9.  A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs.

Authors:  Akito Taneda; Kengo Sato
Journal:  Int J Mol Sci       Date:  2021-03-08       Impact factor: 5.923

  9 in total

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