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Probing RNA Structure and Function by Nucleotide Analog Interference Mapping
dc.contributor.authorCochrane, Jesse C.
dc.contributor.authorStrobel, Scott A.
dc.date.accessioned2020-01-13T15:13:36Z
dc.date.available2020-01-13T15:13:36Z
dc.date.issued2004-06
dc.identifier.citationCochrane, Jesse C.; Strobel, Scott A. (2004). "Probing RNA Structure and Function by Nucleotide Analog Interference Mapping." Current Protocols in Nucleic Acid Chemistry 17(1): 6.9.1-6.9.21.
dc.identifier.issn1934-9270
dc.identifier.issn1934-9289
dc.identifier.urihttps://hdl.handle.net/2027.42/152939
dc.description.abstractNucleotide analog interference mapping (NAIM) can be used to simultaneously, yet individually, identify structurally or catalytically important functional groups within an RNA molecule. Phosphorothioate‐tagged nucleotides and nucleotide analogs are randomly incorporated into an RNA of interest by in vitro transcription. The phosphorothioate tag marks the site of substitution and identifies sites at which the modification affects the structure or function of the RNA molecule. This technique has been expanded to include identification of hydrogen bonding pairs (NAIS), ionizable functional groups, metal ion ligands, and the energetics of protein binding (QNAIM). The analogs, techniques, and data analysis used in NAIM are described here.
dc.publisherWiley Periodicals, Inc.
dc.subject.otherphoshphorothioate, nucleotide analog interference mapping
dc.subject.otherRNAM
dc.titleProbing RNA Structure and Function by Nucleotide Analog Interference Mapping
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelChemistry
dc.subject.hlbsecondlevelBiological Chemistry
dc.subject.hlbsecondlevelPublic Health
dc.subject.hlbsecondlevelChemical Engineering
dc.subject.hlbtoplevelHealth Sciences
dc.subject.hlbtoplevelScience
dc.subject.hlbtoplevelEngineering
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/152939/1/cpnc0609.pdf
dc.identifier.doi10.1002/0471142700.nc0609s17
dc.identifier.sourceCurrent Protocols in Nucleic Acid Chemistry
dc.identifier.citedreferenceHeitner, H.I., Sunshine, H.R., and Lippard, S.J. 1972. Metal binding by thionucleosides. J. Am. Chem. Soc. 94: 8936 ‐ 8937.
dc.identifier.citedreferenceJones, F.D. and Strobel, S.A. 2003. Ionization of a critical adenosine residue in the neurospora Varkud Satellite ribozyme active site. Biochemistry 42: 4265 ‐ 4276.
dc.identifier.citedreferenceJones, F.D., Ryder, S.P., and Strobel, S.A. 2001. An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5′‐ and 3′‐termini. Nucl. Acids Res. 29: 5115 ‐ 5120.
dc.identifier.citedreferenceKaye, N.M., Christian, E.L., and Harris, M.E. 2002. NAIM and site‐specific functional group modification analysis of RNase P RNA: Magnesium dependent structure within the conserved P1‐P4 multihelix junction contributes to catalysis. Biochemistry 41: 4533 ‐ 4545.
dc.identifier.citedreferenceKazantsev, A.V. and Pace, N.R. 1998. Identification by modification‐interference of purine N‐7 and ribose 2′‐OH groups critical for catalysis by bacterial ribonuclease P. RNA 4: 937 ‐ 947.
dc.identifier.citedreferenceOyelere, A.K., Kardon, J.R., and Strobel, S.A. 2002. pK(a) perturbation in genomic Hepatitis Delta Virus ribozyme catalysis evidenced by nucleotide analogue interference mapping. Biochemistry 41: 3667 ‐ 3675.
dc.identifier.citedreferencePadilla, R. and Sousa, R. 1999. Efficient synthesis of nucleic acids heavily modified with non‐canonical ribose 2′‐groups using a mutant T7 RNA polymerase (RNAP). Nucl. Acids Res. 27: 1561 ‐ 1563.
dc.identifier.citedreferenceRife, J.P., Cheng, C.S., Moore, P.B., and Strobel, S.A. 1998. N ‐2‐Methylguanosine is iso‐energetic with guanosine in RNA duplexes and GNRA tetraloops. Nucl. Acids Res. 26: 3640 ‐ 3644.
dc.identifier.citedreferenceRyder, S.P. and Strobel, S.A. 1999a. Nucleotide analog interference mapping. Methods 18: 38 ‐ 50.
dc.identifier.citedreferenceRyder, S.P. and Strobel, S.A. 1999b. Nucleotide analog interference mapping of the hairpin ribozyme: Implications for secondary and tertiary structure formation. J. Mol. Biol. 291: 295 ‐ 311.
dc.identifier.citedreferenceRyder, S.P., Ortoleva‐Donnelly, L., Kosek, A.B., and Strobel, S.A. 2000. Chemical probing of RNA by nucleotide analog interference mapping. Methods Enzymol. 317: 92 ‐ 109.
dc.identifier.citedreferenceRyder, S.P., Oyelere, A.K., Padilla, J.L., Klostermeier, D., Millar, D.P., and Strobel, S.A. 2001. Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping. RNA 7: 1454 ‐ 1463.
dc.identifier.citedreferenceSchwans, J.P., Cortez, C.N., Olvera, J.M., and Piccirilli, J.A. 2003. 2′‐Mercaptonucleotide interference reveals regions of close packing within folded RNA molecules. J. Am. Chem. Soc. 125: 10012 ‐ 10018.
dc.identifier.citedreferenceSood, V.D., Beattie, T.L., and Collins, R.A. 1998. Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme. J. Mol. Biol. 282: 741 ‐ 750.
dc.identifier.citedreferenceSoukup, J.K., Minakawa, N., Matsuda, A., and Strobel, S.A. 2002. Identification of A‐minor tertiary interactions within a bacterial group I intron active site by 3‐deazaadenosine interference mapping. Biochemistry 41: 10426 ‐ 10438.
dc.identifier.citedreferenceSousa, R. and Padilla, R. 1995. A mutant T7 RNA polymerase as a DNA polymerase. EMBO J. 14: 4609 ‐ 4621.
dc.identifier.citedreferenceStrobel, S.A. and Ortoleva‐Donnelly, L. 1999. A hydrogen‐bonding triad stabilizes the chemical transition state of a group I ribozyme. Chem. Biol. 6: 153 ‐ 165.
dc.identifier.citedreferenceStrobel, S.A. and Shetty, K. 1997. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. Proc. Natl. Acad. Sci. U.S.A. 94: 2903 ‐ 2908.
dc.identifier.citedreferenceStrobel, S.A., Ortoleva‐Donnelly, L., Ryder, S.P., Cate, J.H., and Moncoeur, E. 1998. Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nat. Struct. Biol. 5: 60 ‐ 66.
dc.identifier.citedreferenceSzewczak, A.A., Ortoleva‐Donnelly, L., Ryder, S.P., Moncoeur, E., and Strobel, S.A. 1998. A minor groove RNA triple helix within the catalytic core of a group I intron. Nat. Struct. Biol. 5: 1037 ‐ 1042.
dc.identifier.citedreferenceSzewczak, A.A., Ortoleva‐Donnelly, L., Zivarts, M.V., Oyelere, A.K., Kazantsev, A.V., and Strobel, S.A. 1999. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site. Proc. Natl. Acad. Sci. U.S.A. 96: 11183 ‐ 11188.
dc.identifier.citedreferenceSzewczak, L.B., DeGregorio, S.J., Strobel, S.A., and Steitz, J.A. 2002. Exclusive interaction of the 15.5 kD protein with the terminal box C/D motif of a methylation guide snoRNP. Chem. Biol. 9: 1095 ‐ 1107.
dc.identifier.citedreferenceWong, I. and Lohman, T.M. 1993. A double‐filter method for nitrocellulose‐filter binding: Application to protein‐nucleic acid interactions. Proc. Natl. Acad. Sci. U.S.A. 90: 5428 ‐ 5432.
dc.identifier.citedreferenceOrtoleva‐Donnelly, L., Szewczak, A.A., Gutell, R.R., and Strobel, S.A. 1998. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA 4: 498 ‐ 519.
dc.identifier.citedreferenceOyelere, A.K. and Strobel, S.A. 2000. Biochemical detection of cytidine protonation within RNA. J. Am. Chem. Soc. 122: 10259 ‐ 10267.
dc.identifier.citedreferenceBasu, S. and Strobel, S.A. 1999. Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4–P6 domain. RNA 5: 1399 ‐ 1407.
dc.identifier.citedreferenceBasu, S. and Strobel, S.A. 2001. Biochemical detection of monovalent metal ion binding sites within RNA. Methods 23: 264 ‐ 275.
dc.identifier.citedreferenceBasu, S., Rambo, R.P., Strauss‐Soukup, J., Cate, J.H., Ferre‐D’Amare, A.R., Strobel, S.A., and Doudna, J.A. 1998. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat. Struct. Biol. 5: 986 ‐ 992.
dc.identifier.citedreferenceBatey, R.T., Rambo, R.P., Lucast, L., Rha, B., and Doudna, J.A. 2000. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287: 1232 ‐ 1239.
dc.identifier.citedreferenceBatey, R.T., Sagar, M.B., and Doudna, J.A. 2001. Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. J. Mol. Biol. 307: 229 ‐ 246.
dc.identifier.citedreferenceBoudvillain, M. and Pyle, A.M. 1998. Defining functional groups, core structural features and inter‐domain tertiary contacts essential for group II intron self‐splicing: A NAIM analysis. EMBO J. 17: 7091 ‐ 7104.
dc.identifier.citedreferenceCech, T.R. 1990. Self‐splicing of group I introns. Annu. Rev. Biochem. 59: 543 ‐ 568.
dc.identifier.citedreferenceChamberlin, M., Kingston, R., Gilman, M., Wiggs, J., and de Vera, A. 1983. Isolation of bacterial and bacteriophage RNA polymerases and their use in synthesis of RNA in vitro. Methods Enzymol. 101: 540 ‐ 568.
dc.identifier.citedreferenceCochrane, J.C., Batey, R.T., and Strobel, S.A. 2003. Quantitation of free energy profiles in RNA‐ligand interactions by nucleotide analog interference mapping. RNA 9: 1282 ‐ 1289.
dc.identifier.citedreferenceConrad, F., Hanne, A., Gaur, R.K., and Krupp, G. 1995. Enzymatic synthesis of 2′‐modified nucleic acids: Identification of important phosphate and ribose moieties in RNase P substrates. Nucl. Acids Res. 23: 1845 ‐ 1853.
dc.identifier.citedreferenceDouglas, K.T., Bunni, M.A., and Baindur, S.R. 1990. Thallium in biochemistry. Int. J. Biochem. Cell Biol. 22: 429 ‐ 438.
dc.identifier.citedreferenceEckstein, F. 1985. Nucleoside phosphorothioates. Annu. Rev. Biochem. 54: 367 ‐ 402.
dc.identifier.citedreferenceFischer, B., Chulkin, A., Boyer, J.L., Harden, K.T., Gendron, F.P., Beaudoin, A.R., Chapal, J., Hillaire‐Buys, D., and Petit, P. 1999. 2‐Thioether 5′‐ O ‐(1‐thiotriphosphate)adenosine derivatives as new insulin secretagogues acting through P2Y‐Receptors. J. Med. Chem. 42: 3636 ‐ 3646.
dc.identifier.citedreferenceGaur, R.K. and Krupp, G. 1993. Enzymatic RNA synthesis with deoxynucleoside 5′‐ O ‐(1‐thiotriphosphates). FEBS Lett. 315: 56 ‐ 60.
dc.identifier.citedreferenceGish, G. and Eckstein, F. 1988. DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240: 1520 ‐ 1522.
dc.identifier.citedreferenceGriffiths, A.D., Potter, B.V., and Eperon, I.C. 1987. Stereospecificity of nucleases towards phosphorothioate‐substituted RNA: Stereo‐chemistry of transcription by T7 RNA poly‐merase. Nucl. Acids Res. 15: 4145 ‐ 4162.
dc.identifier.citedreferenceHardt, W.D., Erdmann, V.A., and Hartmann, R.K. 1996. R p ‐deoxy‐phosphorothioate modification interference experiments identify 2′‐OH groups in RNase P RNA that are crucial to tRNA binding. RNA 2: 1189 ‐ 1198.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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