Abstract
RNA molecules can fold into extensive structures containing regions of double-stranded duplex, hairpins, internal loops, bulged bases, and pseudo-knotted structures (1). Owing to the complexity of RNA structure, the rules governing sequence-specific RNA-protein recognition are not well understood. RNA-protein interactions are vital for many regulatory processes, especially in gene regulation where proteins specifically interact with binding sites found within RNA transcripts. In the absence of high-resolution crystallographic and nuclear magnetic resonance data, new methods are needed to determine the topology of RNA-protein complexes under physiological conditions. We have devised a new method based on psoralen photochemistry to identify specific contacts in RNA-protein complexes (2,3).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Reference
Tinoco, I., Jr., Puglisi, J. D., and Wyatt, J. R. (1990) RNA folding. Nucleic Acids Mol. Biol. 4, 205–226.
Wang, Z. and Rana, T. M. (1995) Chemical conversion of a TAR RNA-binding fragment of HIV-1 Tat protein into a site-specific crosslinking agent. J. Am. Chem. Soc. 117, 5438–5444.
Wang, Z., Wang, X., and Rana, T. M. (1996) Protein orientation in the Tat-TAR complex determined by psoralen photocross-linking. J. Biol. Chem. 271, 16,995–16,998.
Cimino, G. D., Gamper, H. B., Isaacs, S. T., and Hearst, J. E. (1985) Psoralens as photoactive probes of nucleic acid structure and function: organic chemistry, photochemistry, and biochemistry. Ann. Rev. Biochem. 54, 1151–1193.
Spielmann, H. P., Dwyer, T. J., Sastry, S. S., Hearst, J. E., and Wemmer, D. E. (1995) DNA structural reorganization upon conversion of a psoralen furan-side monoadduct to an interstrand cross-link: implications for DNA repair. Proc. Natl. Acad. Sci. USA 92, 2345–2349.
Hearst, J. E. (1988) A photochemical investigation of the dynamics of oligonucleotide hybridization. Annu. Rev. Phys. Chem. 39, 291–315.
Gamper, H. B., Cimino, G. D., Isaacs, S. T., Ferguson, M., and Hearst, J. E. (1986) Reverse southern hybridization. Nucleic Acids Res. 14, 9943–9954.
Van Houten, B., Gamper, H. B., Hearst, J. E., and Sancar, A. (1986) Construction of DNA substrates modified with psoralen at a unique site and study of the action of ABC excinuclease on these uniformly modified substrates. J. Biol. Chem. 261, 14,135–14,141.
Takasugi, M., Guendouz, A., Chassingnol, M., Decout, J. L., Lhomme, J., Thuong, N. T., and Helene, C. (1991) Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide. Proc. Natl. Acad. Sci. USA 88, 5602–5606.
Lee, B. L., Murakami, A., Blake, K. R., Lin, S.-B., and Miller, P. S. (1988) Interaction of psoralen-derived oligodeoxyribonucleoside methylphosphonates with single-stranded DNA. Biochemistry 27, 3197–3203.
Kean, J. M. and Miller, P. S. (1994) Effect of target structure on cross-linking by psoralen-derivatized oligonucleoside methylphosphonates. Biochemistry 33, 9178–9186.
Youvan, D. C, and Hearst, J. E. (1981) A sequence from Drosophila melanogaster 18S rRNA bearing the conserved hypermodified nucleoside amψ: analysis by reverse transcription and high-performance liquid chromatography. Nucleic Acids Res. 9, 1723–1741.
Youvan, D. C. and Hearst, J. E. (1982) Sequencing psoralen photochemically reactive sites in Escherichia coli 16 S rRNA. Anal. Biochem. 119, 86–89.
Ericson, G. and Wollenzien, P. (1988) Use of reverse transcription to determine the exact locations of psoralen crosslinks in RNA. Anal. Biochem. 174, 215–223.
Burgin, A. B. and Pace, N. R. (1990) Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent. EMBO J. 9, 4111–4118.
Harris, M. E., Nolan, J. M., Malhotra, A., Brown, J. W., Harvey, S. C, and Pace, N. R. (1994) Use of photoaffinity crosslinking and molecular modeling to analyze the global architecture of ribonuclease P RNA. EMBO J. 13, 3953–3963.
Nolan, J. M., Burke, D. H., and Pace, N. R. (1993) Circularly permutated tRNAs as specific photoaffinity probes of ribonuclease P RNA structure. Science 261, 762–765.
Ericson, G. and Wollenzien, P. (1989) An RNA secondary structure switch between the active and inactive conformations of the Escherichia coli 30S ribosomal unit. J. Biol. Chem. 264, 540–545.
Watkins, K. P., Dungan, J. M., and Agabian, N. (1994) Identification of a small RNA that interacts with the 5′ splice site of the trypanasoma brucei spliced leader RNA in vivo. Cell 76, 171–182.
Fried, M. and Crothers, D. M. (1981) Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 9, 6505–6525.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1999 Humana Press Inc.
About this protocol
Cite this protocol
Wang, Z., Rana, T.M. (1999). Probing RNA-Protein Interactions by Psoralen Photocrosslinking. In: Haynes, S.R. (eds) RNA-Protein Interaction Protocols. Methods in Molecular Biology™, vol 118. Humana Press. https://doi.org/10.1385/1-59259-676-2:49
Download citation
DOI: https://doi.org/10.1385/1-59259-676-2:49
Publisher Name: Humana Press
Print ISBN: 978-0-89603-568-3
Online ISBN: 978-1-59259-676-8
eBook Packages: Springer Protocols