View Item 

Show simple item record

Probing RNA Structure and Metal‐Binding Sites Using Terbium(III) Footprinting
dc.contributor.authorHarris, Dinari A.
dc.contributor.authorWalter, Nils G.
dc.date.accessioned2020-01-13T15:17:20Z
dc.date.available2020-01-13T15:17:20Z
dc.date.issued2003-06
dc.identifier.citationHarris, Dinari A.; Walter, Nils G. (2003). "Probing RNA Structure and Metal‐Binding Sites Using Terbium(III) Footprinting." Current Protocols in Nucleic Acid Chemistry 13(1): 6.8.1-6.8.8.
dc.identifier.issn1934-9270
dc.identifier.issn1934-9289
dc.identifier.urihttps://hdl.handle.net/2027.42/153092
dc.description.abstractThe function of an RNA molecule is determined by its overall secondary and tertiary structure. The tertiary structure is facilitated and stabilized by the interaction with metal ions. The current chapter offers a detailed protocol on the use of the lanthanide metal ion terbium(III) as a powerful probe of RNA structure and metal‐binding properties. When incubating RNA with low (micromolar) concentrations of terbium(III), specific backbone scission by partially deprotonated aqueous terbium(III) complexes can be used to detect high‐affinity metal‐binding sites, while incubation with high (millimolar) terbium(III) concentrations cleaves the RNA backbone preferentially at structurally accessible regions, providing a footprint of the RNA secondary and tertiary structure.
dc.publisherJohn Wiley & Sons
dc.subject.othermetal probing
dc.subject.othercatalytic RNA
dc.subject.otherlanthanide ion
dc.subject.othersequencing
dc.subject.otherRNA structure probing
dc.titleProbing RNA Structure and Metal‐Binding Sites Using Terbium(III) Footprinting
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelChemistry
dc.subject.hlbsecondlevelChemical Engineering
dc.subject.hlbsecondlevelBiological Chemistry
dc.subject.hlbsecondlevelPublic Health
dc.subject.hlbtoplevelEngineering
dc.subject.hlbtoplevelHealth Sciences
dc.subject.hlbtoplevelScience
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/153092/1/cpnc0608.pdf
dc.identifier.doi10.1002/0471142700.nc0608s13
dc.identifier.sourceCurrent Protocols in Nucleic Acid Chemistry
dc.identifier.citedreferenceCiesiolka, J., Marciniec, T., and Krzyzosiak, W. 1989. Probing the environment of lanthanide binding sites in yeast tRNA(Phe) by specific metal‐ion‐promoted cleavages. Eur. J. Biochem. 182: 445 ‐ 450.
dc.identifier.citedreferenceBaes, C.F. and Mesmer, R.E. 1976. The Hydrolysis of Cations. John Wiley & Sons, New York.
dc.identifier.citedreferenceVaidya, A. and Suga, H. 2001. Diverse roles of metal ions in acyl‐transferase ribozymes. Biochemistry 40: 7200 ‐ 7210.
dc.identifier.citedreferenceSigel, R.K., Vaidya, A., and Pyle, A.M. 2000. Metal ion binding sites in a group II intron core. Nat. Struct. Biol. 7: 1111 ‐ 1116.
dc.identifier.citedreferenceSaito, H. and Suga, H. 2002. Outersphere and innersphere coordinated metal ions in an aminoacyl‐tRNA synthetase ribozyme. Nucl. Acids Res. 30: 5151 ‐ 5159.
dc.identifier.citedreferenceRyder, S.P. and Strobel, S.A. 1999. Nucleotide analog interference mapping. Methods 18: 38 ‐ 50.
dc.identifier.citedreferenceWalter, N.G., Yang, N., and Burke, J.M. 2000. Probing non‐selective cation binding in the hairpin ribozyme with Tb(III). J. Mol. Biol. 298: 539 ‐ 555.
dc.identifier.citedreferencePyle, A.M. 2002. Metal ions in the structure and function of RNA. J. Biol. Inorg. Chem. 7: 679 ‐ 690.
dc.identifier.citedreferenceMatsumura, K. and Komiyama, M. 1997. Enormously fast RNA hydrolysis by lanthanide(III) ions under physiological conditions: Eminent candidates for novel tools of biotechnology. J. Biochem. 122: 387 ‐ 394.
dc.identifier.citedreferenceKaye, N.M., Zahler, N.H., Christian, E.L., and Harris, M.E. 2002. Conservation of helical structure contributes to functional metal ion interactions in the catalytic domain of ribonuclease P RNA. J. Mol. Biol. 324: 429 ‐ 442.
dc.identifier.citedreferenceHargittai, M.R., Mangla, A.T., Gorelick, R.J., and Musier‐Forsyth, K. 2001. HIV‐1 nucleocapsid protein zinc finger structures induce tRNA(Lys,3) structural changes but are not critical for primer/template annealing. J. Mol. Biol. 312: 985 ‐ 997.
dc.identifier.citedreferenceHargittai, M.R. and Musier‐Forsyth, K. 2000. Use of terbium as a probe of tRNA tertiary structure and folding. RNA 6: 1672 ‐ 1680.
dc.identifier.citedreferenceFlynn‐Charlebois, A., Lee, N., and Suga, H. 2001. A single metal ion plays structural and chemical roles in an aminoacyl‐transferase ribozyme. Biochemistry 40: 13623 ‐ 13632.
dc.identifier.citedreferenceFeig, A.L., Panek, M., Horrocks, W.D. Jr., and Uhlenbeck, O.C. 1999. Probing the binding of Tb(III) and Eu(III) to the hammerhead ribozyme using luminescence spectroscopy. Chem. Biol. 6: 801 ‐ 810.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Name:
cpnc0608.pdf
Size:
213.2KB
Format:
PDF
View/Open

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.