Nucleic Acid Switches and Sensors / Edition 1

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This book reviews studies showing that interesting and useful molecular-scale switches and sensors can be made out of nucleic acids, by both artificial and natural means. The first section of the book is devoted to artificial nucleic acid switches and sensors. In second section, three chapters show that nature has been as crafty a molecular-scale engineer as any modern scientist, in the evolution of natural nucleic acid switches and sensors.

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Product Details

  • ISBN-13: 9780387374918
  • Publisher: Springer US
  • Publication date: 8/30/2006
  • Series: Molecular Biology Intelligence Unit Series
  • Edition description: 2006
  • Edition number: 1
  • Pages: 125
  • Product dimensions: 9.25 (w) x 6.27 (h) x 0.56 (d)

Table of Contents

Preface     ix
Artificial Nucleic Acid Switches and Sensors
Allosteric Ribozymes as Molecular Switches and Sensors   Garrett A. Soukup     3
Introduction     3
Genesis of Allosteric Ribozymes     5
Allosteric Ribozymes as Molecular Sensors     14
Allosteric Ribozymes as Genetic Regulatory Switches     18
Perspective     20
Ribozymes and Deoxyribozymes Switched by Oligonucleotides   Dipankar Sen   Edward K.Y. Leung     25
Introduction     25
Disruptive Inhibition of Natural Ribozymes Using Antisense Oligonucleotides     26
Destabilized Ribozymes and Maxizymes     26
Of TRAPs and Related Strategies     27
Interference with Substrate Binding: Expansive Regulation and Deoxyribozyme Logic Gates     29
Defective Ribozymes and "Half"-Ribozymes     30
Unique Systems     33
Perspective     33
Ribozymes Switched by Proteins   Tan Inoue   Yoshiya Ikawa     37
Introduction     37
From a Self-Splicing Group I Intron RNA to a Self-Splicing RNP     40
Design of Protein-Dependent Allosteric Hammerhead Ribozymes     42
Selection of Protein-Activated Artificial Ribozymes     42
Applications of Protein-Switched Ribozymes     44
Perspective     45
Fluorescence-Signaling Nucleic Acid-Based Sensors   Razvan Nutiu   Lieven P. Billen   Yingfu Li     49
Introduction     49
Molecular Beacons for Nucleic Acid Detection     51
Signaling Aptamers     55
Signaling Ribozymes and Deoxyribozymes     60
Perspective     68
Natural Nucleic Acid Switches and Sensors
Protein-Induced RNA Switches in Nature   Oliver Mayer   Nikolai Windbichler   Herbert Wank   Renee Schroeder     75
Introduction     75
Proteins That Bind RNA with High Affinity and Stabilize Specific Structures     76
RNA Helicases     77
NPH-II     79
CYT-19     79
Hfq, A Protein That Assists RNA Molecules to Anneal     79
Proteins with RNA Chaperone Activity     82
E. coli Protein StpA     82
Nucleocapsid Protein of HIV-1     83
Proteins That Assist with the Formation of RNA-Protein Complexes     84
Perspective     85
Riboswitches as Genetic Control Elements   Ali Nahvi   Ronald R. Breaker      89
Introduction     89
Why RNA Can Serve as a Metabolite-Sensing Genetic Switch     90
Identifying the First Riboswitches     91
Dissecting Riboswitches into Functional Components     92
Simple Riboswitches     93
A Ribozyme Riboswitch     97
A Cooperative Riboswitch     99
Finding New Riboswitches     101
Are Riboswitches Ancient?     103
Perspective     103
Switchable RNA Motifs as Drug Targets   Eric Westhof   Boris Francois   Quentin Vicens     107
Introduction     107
Constraints of RNA Folding on the Choice of RNA Target     108
Which RNA Dynamics Should Be Targeted?     109
Mechanisms of Action of Aminoglycosides     110
Mode of Binding of Aminoglycosides to the A Site: Stabilization of One Conformational State     112
The Decoding Process by the Two Bulging Adenines of the A Site     114
The Importance of Targeting a Molecular Switch     116
Perspective     117
Index     123
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