Summary
RNA helicases are essential for the adenosine 5′-triphosphate (ATP)-driven rearrangement of many RNAs and RNA-protein complexes (ribonucleoproteins, RNPs) throughout RNA metabolism. We describe assays to measure RNA and RNP remodeling by RNA helicases in vitro. We show how to prepare substrates for these reactions and how to monitor unwinding of RNA duplexes and displacement of proteins from RNA using standard molecular biology techniques.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Tanner, N. K., and Linder, P. (2001) DExD/H box RNA helicases. From generic motors to specific dissociation functions. Mol, Cell 8, 251–261.
Jankowsky, E., and Fairman, M. (2007) RNA helicases—one fold for many functions. Curr. Opin. Struct. Biol. 17, 316–324.
Jankowsky, E., and Bowers, H. (2006) Remodeling of ribonucleoprotein complexes with DExH/D RNA helicases. Nucleic Acids Res. 34, 4181–4188.
Linder, P. (2004) The life of RNA with proteins. Science 304, 694–695.
Yang, Q., and Jankowsky, E. (2006) The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases. Nat. Struct. Mol. Biol. 13, 981–986.
Shuman, S. (1993) Vaccinia virus RNA helicase. Directionality and substrate specificity. J. Biol. Chem. 268, 11798–11802.
Halls, C., Mohr, S., Del Campo, M., Yang, Q., Jankowsky, E., and Lambowitz, A. M. (2007) Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity. J. Mol. Biol. 365, 835–855.
Rogers, G. W., Richter, N. J., and Merrick, W. C. (1999) Biochemical and kinetic characterization of the RNA helicase activity of eukaryotic initiation factor 4A. J. Biol. Chem. 274, 12236–12244.
Rogers, G. W. J., Lima, W. F., and Merrick, W. C. (2001) Further characterization of the helicase activity of eIF4A. Substrate specificity. J. Biol. Chem. 276, 12598–12608.
Yang, Q., and Jankowsky, E. (2005) ATP- and ADP-dependent modulation of RNA unwinding and strand annealing activities by the DEAD-box protein DED1. Biochemistry 44, 13591–13601.
Pyle, A. M., Chu, V. T., Jankowsky, E., and Boudvillain, M. (2000) Using DNAzymes to cut, process, and map RNA molecules for structural studies or modification. Meth. Enzymol. 317, 140–146.
Jankowsky, E., Gross, C. H., Shuman, S., and Pyle, A. M. (2000) The DExH protein NPH-II is a processive and directional motor for unwinding RNA. Nature 403, 447–451.
Jankowsky, E., Gross, C. H., Shuman, S., and Pyle, A. M. (2001) Active disruption of an RNA-protein interaction by a DExH/D RNA helicase. Science 291, 121–125.
Fairman, M., Maroney, P. A., Wang, W., et al. (2004) Protein displacement by DExH/D RNA helicases without duplex unwinding. Science 304, 730–734.
Bowers, H. A., Maroney, P. A., Fairman, M. E., et al. (2006) Discriminatory RNP remodeling by the DEAD-box protein DED1. RNA 12, 903–912.
Lorsch, J. R., and Herschlag, D. (1998) The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. Biochemistry 37, 2180–2193.
Linder, P. (2006) Dead-box proteins: a family affair—active and passive players in RNP-remodeling. Nucleic Acids Res. 34, 4168–4180.
Pang, P. S., Jankowsky, E., Planet, P., and Pyle, A. M. (2002) The hepatitis C viral NS3 protein is a processive DNA helicase with co-factor enhanced RNA unwinding. EMBO J. 21, 1168–1176.
Shuman, S. (1992) Vaccinia virus RNA helicase: an essential enzyme related to the DE-H family of RNA-dependent NTPases. Proc. Natl. Acad. Sci. U. S. A. 89, 10935–10939.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Humana Press, a part of Springer Science + Business Media, LLC
About this protocol
Cite this protocol
Jankowsky, E., Fairman, M.E. (2008). Duplex Unwinding and RNP Remodeling With RNA Helicases. In: Lin, RJ. (eds) RNA-Protein Interaction Protocols. Methods in Molecular Biology, vol 488. Humana Press. https://doi.org/10.1007/978-1-60327-475-3_22
Download citation
DOI: https://doi.org/10.1007/978-1-60327-475-3_22
Publisher Name: Humana Press
Print ISBN: 978-1-58829-419-7
Online ISBN: 978-1-60327-475-3
eBook Packages: Springer Protocols