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A selection system for identifying accessible sites in target RNAs

Published online by Cambridge University Press:  09 April 2001

WEI-HUA PAN ,
HEIDI F. DEVLIN ,
COLLEEN KELLEY ,
HARRIET C. ISOM  and
GARY A. CLAWSON
WEI-HUA PAN
Affiliation:
Department of Pathology, Biochemistry and Molecular Biology, The Gittlen Cancer Research Institute, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA
HEIDI F. DEVLIN
Affiliation:
Department of Pathology, Biochemistry and Molecular Biology, The Gittlen Cancer Research Institute, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA
COLLEEN KELLEY
Affiliation:
Department of Pathology, Biochemistry and Molecular Biology, The Gittlen Cancer Research Institute, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA Department of Microbiology and Immunology, Hershey Medical Center, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA
HARRIET C. ISOM
Affiliation:
Department of Pathology, Biochemistry and Molecular Biology, The Gittlen Cancer Research Institute, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA Department of Microbiology and Immunology, Hershey Medical Center, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA
GARY A. CLAWSON
Affiliation:
Department of Pathology, Biochemistry and Molecular Biology, The Gittlen Cancer Research Institute, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA
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Abstract

Although ribozymes offer tremendous potential for posttranscriptionally controlling expression of targeted genes, their utility is often limited by the accessibility of the targeted regions within the RNA transcripts. Here we describe a method that identifies RNA regions that are accessible to oligonucleotides. Based on this selection protocol, we show that construction of hammerhead ribozymes targeted to the identified regions results in catalytic activities that are consistently and substantially greater than those of ribozymes designed on the basis of computer modeling. Identification of accessible sites should also be widely applicable to design of antisense oligonucleotides and DNAzymes.

Keywords

catalysishammerhead ribozymelibrarymFoldSELEX

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Type
METHOD
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RNA , Volume 7 , Issue 4 , April 2001 , pp. 610 - 621
Copyright
© 2001 RNA Society

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