Nucleic Acid Switches and Sensors
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Edited By:Scott K. SilvermanUniversity of Illinois at Urbana-Champaign Urbana, Illinois, U.S.A. ISBN: 978-0-387-37491-8 Published: 2006-08-25 This book may be purchased as an eBook (pdf) for $99, or individual chapters (pdf) may be purchased from the list below for $19. |
In this book, seven chapters describe studies aimed at understanding and exploiting the key features of such molecular RNA and DNA devices. In the first section of the book, four chapters are devoted to artificial nucleic acid switches and sensors. These chapters introduce the concept of allosteric ribozymes as molecular switches and sensors; describe nucleic acid enzymes that are switched by oligonucleotides and other nucleic acid enzymes that are switched by proteins; and illustrate how switching elements can be integrated ration-ally into fluorescently signaling molecular sensors made out of nucleic acids. In the second section of the book, three chapters show that nature has been as crafty a molecular-scale engineer as any modern scientist via evolution of natural nucleic acid switches and sensors. RNAs have been found whose activities are modulated either by proteins or by small-molecule metabolites, and both kinds of system are described. Finally, the notion of exploiting naturally occurring RNA switches for drug development is discussed.
Chapters available from this book
Allosteric Ribozymes As Molecular Sensors and Genetic Regulatory Switches
Garrett A. Soukup
Since the discovery of RNA catalysts, biotechnology has focused heavily on utilizing ribozymes as reagents to control RNA processing and gene expression. However, ribozymes can also be manipulated to report events that affect their folding and catalysis. As with protein enzymes, ribozyme activ...
Ribozymes and Deoxyribozymes Switched by Oligonucleotides
Dipankar Sen and Edward K. Y. Leung
This chapter explores the diverse strategies reported in recent years for using oligonucleotides to switch the catalytic activity of allosteric ribozymes and deoxyribozymes (DNAzymes). The earliest allosteric ribozymes were rationally designed and in vitro selected to respond to a variety of small...
Protein-Switched Ribozymes
Tan Inoue* and Yoshiya Ikawa
Specific RNA-binding proteins regulate RNA conformations in protein-switched ribozymes. Ribozyme activity can be regulated with RNA-binding proteins, as in the case of natural RNP ribozymes like RNase P that consist of an RNA subunit and an RNA-binding protein. Recent studies have shown that both...
Riboswitches As Genetic Control Elements
Ali Nahvi and Ronald R. Breaker
Riboswitches are metabolite-sensing RNA elements that are present in the noncoding portions of certain messenger RNAs. Each riboswitch carries an aptamer that is highly selective for its target metabolite and an expression platform that more directly interfaces with gene expression systems. In ba...
Switchable RNA Motifs As Drug Targets
Eric Westhof, Boris François and Quentin Vicens
RNA molecules are highly negatively charged polymers that form intricate three-dimensional assemblies involving recurrent structural motifs. Therefore, in order to understand the molecular recognition of RNA, one of the key points to address is how RNA can be a specific target of natural or artif...
Protein-induced RNA Switches in Nature
Oliver Mayer, Nikolai Windbichler, Herbert Wank and Renée Schroeder
The conformational flexibility of RNA is the basis for its functional versatility. RNA molecules can fold into functionally diverse structures, providing the grounds for great regulatory potential. RNA function can be turned on or off in very short time scales merely through, for example, the bin...
Fluorescence-Signaling Nucleic Acid-Based Sensors
Razvan Nutiu, Lieven P. Billen and Yingfu Li
It is widely known that two single-stranded nucleic acids with complementary sequences have the inherent ability to form Watson-Crick duplex structures. The simplicity and sequence-specificity of duplex structure formation, the high chemical stability of a duplex, and the convenience of automated...
