Literature DB >> 19720518

RNA-based computation in live cells.

Yaakov Benenson1.   

Abstract

Man-made molecular 'computers' that operate inside live cells will enable unprecedented level of control over cellular physiology. A promising approach to building these computers uses RNA molecules and RNA-based regulation. RNA naturally lends itself to create 'digital' molecular networks that embody standardized (normal) forms of logic functions. The network's inputs, that may or may not be inverted by single-input NOT logic gates, feed into multi-input AND gates whose outputs are in turn integrated in a multi-input OR gate. Below I review recent steps that have been taken toward implementing these networks with allosteric riboswitches and ribozymes in bacteria and yeast, and RNAi in mammalian cells. I also propose how to co-opt recently discovered additional RNA regulation mechanisms into future construction efforts.

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Year:  2009        PMID: 19720518      PMCID: PMC2764246          DOI: 10.1016/j.copbio.2009.08.002

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  29 in total

1.  Molecular computation: RNA solutions to chess problems.

Authors:  D Faulhammer; A R Cukras; R J Lipton; L F Landweber
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-15       Impact factor: 11.205

2.  Engineered riboregulators enable post-transcriptional control of gene expression.

Authors:  Farren J Isaacs; Daniel J Dwyer; Chunming Ding; Dmitri D Pervouchine; Charles R Cantor; James J Collins
Journal:  Nat Biotechnol       Date:  2004-06-20       Impact factor: 54.908

3.  Exogenous control of mammalian gene expression through modulation of RNA self-cleavage.

Authors:  Laising Yen; Jennifer Svendsen; Jeng-Shin Lee; John T Gray; Maxime Magnier; Takashi Baba; Robert J D'Amato; Richard C Mulligan
Journal:  Nature       Date:  2004-09-23       Impact factor: 49.962

4.  Programmable ligand-controlled riboregulators of eukaryotic gene expression.

Authors:  Travis S Bayer; Christina D Smolke
Journal:  Nat Biotechnol       Date:  2005-02-20       Impact factor: 54.908

Review 5.  Riboswitches as versatile gene control elements.

Authors:  Brian J Tucker; Ronald R Breaker
Journal:  Curr Opin Struct Biol       Date:  2005-06       Impact factor: 6.809

6.  In vitro selection of RNA molecules that bind specific ligands.

Authors:  A D Ellington; J W Szostak
Journal:  Nature       Date:  1990-08-30       Impact factor: 49.962

Review 7.  Control of transcription termination in prokaryotes.

Authors:  T M Henkin
Journal:  Annu Rev Genet       Date:  1996       Impact factor: 16.830

Review 8.  Regulatory RNAs in bacteria.

Authors:  Lauren S Waters; Gisela Storz
Journal:  Cell       Date:  2009-02-20       Impact factor: 41.582

9.  The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.

Authors:  Derrick H Lenz; Kenny C Mok; Brendan N Lilley; Rahul V Kulkarni; Ned S Wingreen; Bonnie L Bassler
Journal:  Cell       Date:  2004-07-09       Impact factor: 41.582

10.  An autonomous molecular computer for logical control of gene expression.

Authors:  Yaakov Benenson; Binyamin Gil; Uri Ben-Dor; Rivka Adar; Ehud Shapiro
Journal:  Nature       Date:  2004-04-28       Impact factor: 49.962

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  23 in total

1.  Rationally designed families of orthogonal RNA regulators of translation.

Authors:  Vivek K Mutalik; Lei Qi; Joao C Guimaraes; Julius B Lucks; Adam P Arkin
Journal:  Nat Chem Biol       Date:  2012-03-25       Impact factor: 15.040

2.  RNA nanotechnology for computer design and in vivo computation.

Authors:  Meikang Qiu; Emil Khisamutdinov; Zhengyi Zhao; Cheryl Pan; Jeong-Woo Choi; Neocles B Leontis; Peixuan Guo
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2013-09-02       Impact factor: 4.226

3.  Evolution of a split RNA polymerase as a versatile biosensor platform.

Authors:  Jinyue Pu; Julia Zinkus-Boltz; Bryan C Dickinson
Journal:  Nat Chem Biol       Date:  2017-02-13       Impact factor: 15.040

Review 4.  Regulatory RNAs: charming gene management styles for synthetic biology applications.

Authors:  Jorge Vazquez-Anderson; Lydia M Contreras
Journal:  RNA Biol       Date:  2013-11-18       Impact factor: 4.652

Review 5.  Engineering biological systems with synthetic RNA molecules.

Authors:  Joe C Liang; Ryan J Bloom; Christina D Smolke
Journal:  Mol Cell       Date:  2011-09-16       Impact factor: 17.970

Review 6.  Biomolecular computing systems: principles, progress and potential.

Authors:  Yaakov Benenson
Journal:  Nat Rev Genet       Date:  2012-06-12       Impact factor: 53.242

Review 7.  Programming cells: towards an automated 'Genetic Compiler'.

Authors:  Kevin Clancy; Christopher A Voigt
Journal:  Curr Opin Biotechnol       Date:  2010-08-09       Impact factor: 9.740

8.  A survey of advancements in nucleic acid-based logic gates and computing for applications in biotechnology and biomedicine.

Authors:  Cuichen Wu; Shuo Wan; Weijia Hou; Liqin Zhang; Jiehua Xu; Cheng Cui; Yanyue Wang; Jun Hu; Weihong Tan
Journal:  Chem Commun (Camb)       Date:  2015-03-04       Impact factor: 6.222

Review 9.  The emerging field of RNA nanotechnology.

Authors:  Peixuan Guo
Journal:  Nat Nanotechnol       Date:  2010-11-21       Impact factor: 39.213

10.  A Panel of Protease-Responsive RNA Polymerases Respond to Biochemical Signals by Production of Defined RNA Outputs in Live Cells.

Authors:  Jinyue Pu; Ian Chronis; Daniel Ahn; Bryan C Dickinson
Journal:  J Am Chem Soc       Date:  2015-12-17       Impact factor: 15.419

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