Contribution in an anthology

Appeared in: RNA-Protein Interaction Protocols

Editor list: Haynes, SR

Publication year: 1999

Pages: 93-103

ISBN: 978-0-89603-568-3

eISBN: 978-1-59259-676-8

DOI Link: https://doi.org/10.1385/1-59259-676-2:93

Title of series: Methods in Molecular Biology

Number in series: 118

Abstract: 

This chapter focuses on the analysis of RNA-protein complexes (RNPs,
ribonucleoprotein particles) by oligonucleotide-targeted RNase H
digestion, a powerful approach to probe the domain structure of an RNP,
both in crude extracts and in purified preparations. RNase H requires
DNA-RNA hybrids of at least four basepairs for cleaving the RNA strand.
Therefore, RNase H-mediated cleavage can be directed to a short,
specific RNA sequence by hybridization of a complementary DNA
oligonucleotide. Oligonucleotide-targeted RNase H cleavage was first
used to analyze RNA structures.
The approach has been adopted to RNA-protein complexes, and an
important early example is the study of the basepairing potential of the
5′ end of U1 snRNA in the U1 snRNP.
Subsequently, oligonucleotide-targeted RNase H cleavage has been used
in various systems to disrupt RNPs for functional studies and in
protection assays to map RNP protein-binding domains. Examples include
in vitro studies that established snRNA sequences essential for
spliceosome assembly and pre-mRNA splicing in the mammalian system and
in yeast, studies on the assembly of the yeast
and mammalian spliceosome, investigations on the U7 snRNA function in
histone 3′ end processing, and the analysis of snRNA requirements for trans splicing in trypanosome cell

Harvard Citation style: Günzl, A. and Bindereif, A. (1999) Oligonucleotide-targeted RNase H protection analysis of RNA-protein complexes., in Haynes, S. (ed.) RNA-Protein Interaction Protocols. New York: Humana Press, pp. 93-103. https://doi.org/10.1385/1-59259-676-2:93

APA Citation style: Günzl, A., & Bindereif, A. (1999). Oligonucleotide-targeted RNase H protection analysis of RNA-protein complexes.. In Haynes, S. (Ed.), RNA-Protein Interaction Protocols (pp. 93-103). Humana Press. https://doi.org/10.1385/1-59259-676-2:93