Literature DB >> 12649489

Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA.

Scott K Silverman1.   

Abstract

Switches and sensors play important roles in our everyday lives. The chemical properties of RNA make it amenable for use as a switch or sensor, both artificially and in nature. This review focuses on recent advances in artificial RNA switches and sensors. Researchers have been applying classical biochemical principles such as allostery in elegant ways that are influencing the development of biosensors and other applications. Particular attention is given here to allosteric ribozymes (aptazymes) that are regulated by small organic molecules, by proteins, or by oligonucleotides. Also discussed are ribozymes whose activities are controlled by various nonallosteric strategies.

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Year:  2003        PMID: 12649489      PMCID: PMC1370404          DOI: 10.1261/rna.2200903

Source DB:  PubMed          Journal:  RNA        ISSN: 1355-8382            Impact factor:   4.942


  55 in total

Review 1.  Aptamers: an emerging class of molecules that rival antibodies in diagnostics.

Authors:  S D Jayasena
Journal:  Clin Chem       Date:  1999-09       Impact factor: 8.327

2.  Engineering precision RNA molecular switches.

Authors:  G A Soukup; R R Breaker
Journal:  Proc Natl Acad Sci U S A       Date:  1999-03-30       Impact factor: 11.205

3.  An allosteric hammerhead ribozyme.

Authors:  H Porta; P M Lizardi
Journal:  Biotechnology (N Y)       Date:  1995-02

4.  Mechanism for allosteric inhibition of an ATP-sensitive ribozyme.

Authors:  J Tang; R R Breaker
Journal:  Nucleic Acids Res       Date:  1998-09-15       Impact factor: 16.971

5.  In vitro selection of an allosteric ribozyme that transduces analytes to amplicons.

Authors:  M P Robertson; A D Ellington
Journal:  Nat Biotechnol       Date:  1999-01       Impact factor: 54.908

6.  Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization.

Authors:  G A Soukup; R R Breaker
Journal:  Structure       Date:  1999-07-15       Impact factor: 5.006

7.  A novel allosterically trans-activated ribozyme, the maxizyme, with exceptional specificity in vitro and in vivo.

Authors:  T Kuwabara; M Warashina; T Tanabe; K Tani; S Asano; K Taira
Journal:  Mol Cell       Date:  1998-11       Impact factor: 17.970

8.  Coupled changes in translation and transcription during cobalamin-dependent regulation of btuB expression in Escherichia coli.

Authors:  X Nou; R J Kadner
Journal:  J Bacteriol       Date:  1998-12       Impact factor: 3.490

9.  Allosteric regulation of a ribozyme activity through ligand-induced conformational change.

Authors:  M Araki; Y Okuno; Y Hara; Y Sugiura
Journal:  Nucleic Acids Res       Date:  1998-07-15       Impact factor: 16.971

10.  Folding intermediates of a self-splicing RNA: mispairing of the catalytic core.

Authors:  J Pan; S A Woodson
Journal:  J Mol Biol       Date:  1998-07-24       Impact factor: 5.469

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  21 in total

1.  Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance.

Authors:  David Rueda; Gregory Bokinsky; Maria M Rhodes; Michael J Rust; Xiaowei Zhuang; Nils G Walter
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-24       Impact factor: 11.205

2.  A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo.

Authors:  Beatrix Suess; Barbara Fink; Christian Berens; Régis Stentz; Wolfgang Hillen
Journal:  Nucleic Acids Res       Date:  2004-03-05       Impact factor: 16.971

Review 3.  Riboswitches and the RNA world.

Authors:  Ronald R Breaker
Journal:  Cold Spring Harb Perspect Biol       Date:  2012-02-01       Impact factor: 10.005

4.  Assembly and activation of a kinase ribozyme.

Authors:  Donald H Burke; Steven S Rhee
Journal:  RNA       Date:  2010-10-08       Impact factor: 4.942

5.  Evolutionary patterns of non-coding RNAs.

Authors:  Athanasius F Bompfünewerer; Christoph Flamm; Claudia Fried; Guido Fritzsch; Ivo L Hofacker; Jörg Lehmann; Kristin Missal; Axel Mosig; Bettina Müller; Sonja J Prohaska; Bärbel M R Stadler; Peter F Stadler; Andrea Tanzer; Stefan Washietl; Christina Witwer
Journal:  Theory Biosci       Date:  2005-04       Impact factor: 1.919

6.  Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme.

Authors:  Chamaree de Silva; Nils G Walter
Journal:  RNA       Date:  2008-11-24       Impact factor: 4.942

Review 7.  Functional nucleic acid sensors.

Authors:  Juewen Liu; Zehui Cao; Yi Lu
Journal:  Chem Rev       Date:  2009-05       Impact factor: 60.622

8.  Light-activation of gene function in mammalian cells via ribozymes.

Authors:  Douglas D Young; R Aaron Garner; Jeffrey A Yoder; Alexander Deiters
Journal:  Chem Commun (Camb)       Date:  2008-12-02       Impact factor: 6.222

9.  Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.

Authors:  Adam Roth; Ali Nahvi; Mark Lee; Inbal Jona; Ronald R Breaker
Journal:  RNA       Date:  2006-02-16       Impact factor: 4.942

10.  Assay for glucosamine 6-phosphate using a ligand-activated ribozyme with fluorescence resonance energy transfer or CE-laser-induced fluorescence detection.

Authors:  Jennifer R W Furchak; Peilin Yang; Colin Jennings; Nils G Walter; Robert T Kennedy
Journal:  Anal Chem       Date:  2008-10-09       Impact factor: 6.986

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