Show simple item record

Time‐Resolved Hydroxyl Radical Footprinting of RNA with X‐Rays

dc.contributor.authorWoodson, Sarah A.
dc.contributor.authorDeras, Michael L.
dc.contributor.authorBrenowitz, Michael
dc.date.accessioned2020-01-13T15:10:18Z
dc.date.available2020-01-13T15:10:18Z
dc.date.issued2001-09
dc.identifier.citationWoodson, Sarah A.; Deras, Michael L.; Brenowitz, Michael (2001). "Time‐Resolved Hydroxyl Radical Footprinting of RNA with X‐Rays." Current Protocols in Nucleic Acid Chemistry 6(1): 11.6.1-11.6.24.
dc.identifier.issn1934-9270
dc.identifier.issn1934-9289
dc.identifier.urihttps://hdl.handle.net/2027.42/152803
dc.description.abstractRNA tertiary structure and protein interactions can be detected by protection from hydroxyl radical cleavage. Generation of hydroxyl radicals with a synchrotron X‐ray beam provides analysis on a short timescale (50 msec to 100 sec), which enables the structures of folding intermediates or other transient conformational states to be determined. This unit provides detailed instructions on the use of the synchrotron beamline for hydroxyl radical footprinting.
dc.publisherWiley Periodicals, Inc.
dc.publisherPractical Applications.
dc.titleTime‐Resolved Hydroxyl Radical Footprinting of RNA with X‐Rays
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelBiological Chemistry
dc.subject.hlbsecondlevelChemical Engineering
dc.subject.hlbsecondlevelChemistry
dc.subject.hlbsecondlevelPublic Health
dc.subject.hlbtoplevelHealth Sciences
dc.subject.hlbtoplevelScience
dc.subject.hlbtoplevelEngineering
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/152803/1/cpnc1106.pdf
dc.identifier.doi10.1002/0471142700.nc1106s06
dc.identifier.sourceCurrent Protocols in Nucleic Acid Chemistry
dc.identifier.citedreferenceMilligan, J.F. and Uhlenbeck, O.C. 1989. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180: 51 ‐ 62.
dc.identifier.citedreferenceBrenowitz, M., Senear, D.F., Shea, M.A., and Ackers, G.K. 1986. Quantitative DNase footprint titration: A method for studying protein‐DNA interactions. Methods Enzymol. 130: 132 ‐ 181.
dc.identifier.citedreferenceCate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R., and Doudna, J.A. 1996. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273: 1678 ‐ 1685.
dc.identifier.citedreferenceCelander, D.W. and Cech, T.R. 1990. Iron(II)‐ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single‐ and double‐stranded forms. Biochemistry 29: 1355 ‐ 1361.
dc.identifier.citedreferenceCelander, D.W. and Cech, T.R. 1991. Visualizing the higher order folding of a catalytic RNA molecule. Science 251: 401 ‐ 407.
dc.identifier.citedreferenceChaulk, S.G. and MacMillan, A.M. 2000. Kinetic footprinting of an RNA‐folding pathway using peroxynitrous acid. Angew. Chem. Int. Ed. Engl. 39: 521 ‐ 523.
dc.identifier.citedreferenceDeras, M.L., Brenowitz, M., Ralston, C.Y., Chance, M.R., and Woodson, S.A. 2000. Folding mechanism of the Tetrahymena ribozyme P4‐P6 domain. Biochemistry 39: 10975 ‐ 10985.
dc.identifier.citedreferenceDhavan, G.M., Chance, M.R., and Brenowitz, M. 2001. Kinetics analysis of DNA‐protein interactions by time resolved synchrotron X‐ray footprinting. Practical Applications. In press. In
dc.identifier.citedreferenceDixon, W.J., Hayes, J.J., Levin, J.R., Weidner, M.F., Dombroski, B.A., and Tullius, T.D. 1991. Hydroxyl radical footprinting. Methods Enzymol. 208: 380 ‐ 413.
dc.identifier.citedreferenceDizdaroglu, M. and Bergtold, D.S. 1986. Characterization of free radical‐induced base damage in DNA at biologically relevant levels. Anal. Biochem. 156: 182 ‐ 188.
dc.identifier.citedreferenceHampel, K.J. and Burke, J.M. 2001. Time‐resolved hydroxyl‐radical footprinting of RNA using Fe(II)‐EDTA. Methods 23: 233 ‐ 239.
dc.identifier.citedreferenceKing, P.A., Jamison, E., Strahs, D., Anderson, V.E., and Brenowitz, M. 1993. ’Footprinting’ proteins on DNA with peroxynitrous acid. Nucl. Acids Res. 21: 2473 ‐ 2478.
dc.identifier.citedreferenceKlassen, N.V. 1987. Primary products in radiation chemistry. Radiation Chemistry: Principles & Applications ( I. Farhatazis and M.A. Rodgers eds.)pp. 29 ‐ 61. VCH Publishers, New York. In
dc.identifier.citedreferenceLatham, J.A. and Cech, T.R. 1989. Defining the inside and outside of a catalytic RNA molecule. Science 245: 276 ‐ 282.
dc.identifier.citedreferenceMilligan, J.F., Groebe, D.R., Witherell, G.W., and Uhlenbeck, O.C. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 15: 8783 ‐ 8798.
dc.identifier.citedreferenceRalston, C.Y., He, Q., Brenowitz, M., and Chance, M.R. 2000a. Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation. Nat. Struct. Biol. 7: 371 ‐ 374.
dc.identifier.citedreferenceRalston, C.Y., Sclavi, B., Sullivan, M., Deras, M.L., Woodson, S.A., Chance, M.R., and Brenowitz, M. 2000b. Time‐resolved synchrotron X‐ray footprinting and its application to RNA folding. Methods Enzymol. 317: 353 ‐ 368.
dc.identifier.citedreferenceSclavi, B., Woodson, S., Sullivan, M., Chance, M.R., and Brenowitz, M. 1997. Time‐resolved synchrotron X‐ray “footprinting” a new approach to the study of nucleic acid structure and function: Application to protein‐DNA interactions and RNA folding. J. Mol. Biol. 266: 144 ‐ 159.
dc.identifier.citedreferenceSclavi, B., Sullivan, M., Chance, M.R., Brenowitz, M., and Woodson, S.A. 1998a. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279: 1940 ‐ 1943.
dc.identifier.citedreferenceSclavi, B., Woodson, S., Sullivan, M., Chance, M., and Brenowitz, M. 1998b. Following the folding of RNA with time‐resolved synchrotron X‐ray footprinting. Methods Enzymol. 295: 379 ‐ 402.
dc.identifier.citedreferenceStrahs, D. and Brenowitz, M. 1994. DNA conformational changes associated with the cooperative binding of cI‐repressor of bacteriophage lambda to OR. J. Mol. Biol. 244: 494 ‐ 510.
dc.identifier.citedreferenceTullius, T.D. and Dombroski, B.A. 1985. Iron(II) EDTA used to measure the helical twist along any DNA molecule. Science 230: 679 ‐ 681.
dc.identifier.citedreferenceWallace, S.S. 1998. Enzymatic processing of radiation‐induced free radical damage in DNA. Radiat. Res. 150: S60 ‐ 79.
dc.identifier.citedreferenceBalasubramanian, B., Pogozelski, W.K., and Tullius, T.D. 1998. DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. U.S.A. 95: 9738 ‐ 9743.
dc.identifier.citedreferenceBreen, A.P. and Murphy, J.A. 1995. Reactions of oxyl radicals with DNA. Free Radic. Biol. Med. 18: 1033 ‐ 1077.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

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.