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Nuclease protection of RNAs containing site-specific labels: A rapid method for mapping RNA–protein interactions

Published online by Cambridge University Press:  27 December 2000

PATRICIA A. MARONEY ,
CHARLES M. ROMFO  and
TIMOTHY W. NILSEN
PATRICIA A. MARONEY
Affiliation:
Center for RNA Molecular Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
CHARLES M. ROMFO
Affiliation:
Center for RNA Molecular Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
TIMOTHY W. NILSEN
Affiliation:
Center for RNA Molecular Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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Abstract

This report describes a method that combines nuclease protection and site-specific labeling to determine sites and extents of RNA–protein interactions. The utility of the method is demonstrated by the analysis of the binding of factors to the 3′ splice site region of a pre-mRNA labeled at three specific positions. This “reverse footprinting” technique should be widely applicable to a variety of questions concerning RNA–protein interactions.

Keywords

nuclease protectionRNA–protein interactionsRNase Hsite-specific labeling
Type
METHOD
Information
RNA , Volume 6 , Issue 12 , December 2000 , pp. 1905 - 1909
Copyright
© 2000 RNA Society

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