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Chapter 22 : Chemical Cleavage as a Probe of Ribosomal Structure

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Abstract:

This chapter deals with the cleavage of RNA as an approach to the study of ribosome structure. Chemical nucleases, such as EDTA-Fe(II) and phenanthroline-Cu(II), have been widely used to cleave both RNA and DNA, and more recently, they have been used to study ribosomes. The authors have conducted studies, with tethered phenanthroline-Cu(II), that focused primarily on rRNA sites proximal to mRNA, tRNA, and rRNA regions targeted by oligonucleotide probes. The use of different cleavage reagents is warranted due to the quite different mechanisms of cleavage utilized by the two compounds. They have tethered the phenanthroline-Cu(II) to tRNA, mRNA, and, recently, to short DNA oligomers targeted to various sites on the rRNA. Phenanthroline-Cu(II) was then conjugated to these modified transcripts, the conjugated transcripts were bound to the 50S ribosomal subunits on the P-P or P-E sites, and cleavage was induced. More recently, efforts have been made to increase the specificity of the previous study by inserting a single phosphorothioate group between adjacent nucleotides in transcribed tRNA. Because of the fastidious nature of the phenanthroline-Cu(II) cleavage, it can readily be used as a proximity probe to identify movement of the rRNA. By comparing the cleavage patterns before and after an event such as activation or translocation, movement can be discovered. By using tethers of different lengths, the amount of movement may be quantified as well.

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22

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Figures

Image of Figure 1
Figure 1

(A) Diagram showing the structure of phenanthroline coordinated with Cu(II) (left) in a square planar conformation and Cu(I) (right) in a tetrahedral conformation. (B) Space-filling diagram showing tetrahedral phenanthroline-Cu(I) docking in the minor groove of B-form DNA (left) and A-form RNA (right). Note that due to the shallow minor groove in the RNA, phenanthroline cannot dock. (C) Diagram portraying RNA hairpin loop with phenanthroline-Cu(II) partially intercalated. The three larger spheres represent proximal C1? carbon atoms from which a hydrogen may be abstracted. (D) Structure of 5-iodoacetamido-1,10-orthophenanthroline (IoP).

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22
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Image of Figure 2
Figure 2

Domains I, II, and III of 23S rRNA with a portion of domain I enlarged to show phenanthroline-Cu(II) cleavages in the region of the pseudoknot.

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22
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Figure 3

Cleavage of 23S rRNA domain V emanating from phenanthroline-Cu(II) attached to position 8 of tRNAbound to the P or E site on 70S ribosomes.

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22
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Image of Figure 4
Figure 4

Map of cleavages (arowheads) of 16S rRNA emanating from phenanthroline-Cu(II) conjugated to position +5 of mRNA bound to the 30S ribosomal subunit.

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22
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Image of Figure 5
Figure 5

Spaced-filling diagram of phenanthroline-Cu(II) conjugated to a short DNA oligomer which is hybridized to RNA. The view is along the helical axis. Note that the phenanthroline can be positioned at any one of the 11 positions around the helix occupied by a nucleotide.

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22
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Image of Figure 6
Figure 6

Map of cleavages emanating from DNA oligomers complementary to 16S nucleotides 787 to 795 and 1396 to 1403, to which phenanthroline-Cu(II) was conjugated at the 5? ends. Cleavages from 1396 to 1403 occurred only when the 30S ribosomal subunit was in the inactive conformation ( ). Upon activation, all cleavages from the 1396-to-1403 oligomer except those occurring at nucleotides 1404 to 1405 were markedly attenuated or disappeared entirely.

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22
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Image of Figure 7.
Figure 7.

Cleavages of 16S rRNA emanating from a DNA oligomer complementary to 16S nucleotides 1396 to 1403, to which a phenanthroline-Co(II) [or Cu(II)] was conjugated at the 5? end. These cleavages were done for 10 min with inactive 30S subunits. (Left) Lane 1, probe with conjugated phenanthroline-Cu(II) and HO; lane 2, probe with conjugated phenanthroline-Cu(II) without HO; lane 3, mismatch probe with conjugated phenanthroline-Co(II) and HO; lane 4, free phenanthroline-Co(II) and HO. (Right) Lane 1, probe with conjugated phenanthroline-Co(II) without HO; lane 2, probe with conjugated phenanthroline-Co(II) and HO; lane 3, mismatch probe with conjugated phenanthroline-Co(II) and HO; lane 4, free phenanthroline-Co(II) and HO.

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22
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Image of Figure 8.
Figure 8.

Map of cleavages (arrowheads) emanating from a DNA oligomer complementary to 23S nucleotides 2580 to 2588, to which phenanthroline-Cu(II) was conjugated at the 3'end.

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22
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References

/content/book/10.1128/9781555818142.chap22
1. Alexander, R. W.,, P. Muralikrishna,, and B. S. Cooperman. 1994. Ribosomal components surrounding the conserved 518-533 loop of 16S rRNA in 30S subunits. Biochemistry 33:1210912118.
2. Atmadja, J.,, W. Stiege,, M. Zobawa,, B. Greuer,, M. Osswald,, and R. Brimacombe. 1986. The tertiary folding of Escherichia coli 16S RNA, as studied by in situ intra-RNA cross-linking of 30S ribosomal subunits with bis-(2-chloroethyl)-methylamine. Nucleic Acids Res. 14:659674.
3. Baliga, R.,, J. W. Singleton,, and P. B. Dervan. 1995. RecA oligonucleotide filaments bind in the minor groove of doublestranded DNA. Proc. Natl. Acad. Sci. USA 92:1039310397.
4. Bhangu, R.,, and P. Wollenzien. 1992. The mRNA binding track in the Escherichia coli ribosome for mRNAs of different sequences. Biochemistry 31:59375944.
5. Bucklin, D. J.,, M. A. van Waes,, J. M. Bullard,, and W. E. Hill. 1997. Cleavage of 16S rRNA within the ribosome by mRNA modified in the A-site codon with phenanthroline-Cu(II). Biochemistry 36:79517957.
6. Bullard, J. M.,, M. A. van Waes,, D. J. Bucklin,, and W. E. Hill. 1995. Regions of 23S ribosomal RNA proximal to transfer RNA bound at the P and E sites. J. Mol. Biol. 252:572582.
7. Bullard, J. M.,, M. A. van Waes,, D. J. Bucklin,, M. J. Rice,, and W. E. Hill. 1998. Regions of 16S ribosomal RNA proximal to transfer RNA bound at the P-site of Escherichia coli ribosomes. Biochemistry 37:13501356.
8. Bullard, J. M.,, S. A. Martinus,, and W. E. Hill. Regions of 23S ribosomal RNA proximal to a transfer RNA acceptor stem microhelix bound at the E site of Escherichia coli ribosomes. Nucleic Acids Res., in press.
9. Burkitt, M. J. 1994. Copper-DNA adducts. Methods Enzymol. 234:6679.
10. Burrows, C. J.,, and J. G. Muller. 1998. Oxidative nucleobase modifications leading to strand scission. Chem. Rev. 98:11091151.
11. Burrows, C. J.,, and S. E. Rokita. 1996. Nickel complexes as probes of guanine sites in nucleic acid folding. Met. Ions Biol. Syst. 33: 537560.
12. Burrows, C. J.,, J. G. Muller,, G. T. Poulter,, and S. E. Rokita. 1996. Nickel-catalyzed oxidations: from hydrocarbons to DNA. Acta Chem. Scand. 50:337344.
13. Chen, C. B.,, M. B. Gorin,, and D. S. Sigman. 1993a. Sequencespecific scission of DNA by the chemical nuclease activity of 1,10-phenanthroline-copper(I) targeted by RNA. Proc. Natl. Acad. Sci. USA 90:42064210.
14. Chen, C. H.,, A. Mazumder,, J. F. Constant,, and D. S. Sigman. 1993b. Nuclease activity of 1,10-phenanthroline-copper. Newconjugates with low molecular weight targeting ligands. Bioconjug. Chem. 4:6977.
15. Chen, C.-H. B.,, and D. S. Sigman. 1988. Sequence specific scission of RNA by 1,10 phenanthroline-copper linked to deoxyoligonucleotides. J. Am. Chem. Soc. 110:65706572.
16. Chen, T.,, and M. M. Greenberg. 1998. Model studies indicate that copper phenanthroline induces direct strand breaks via betaelimination of the 2′-deoxyribonolactone intermediate observed in enediyne mediated DNA damage. J. Am. Chem. Soc. 120: 38153816.
17. Culver, G. M.,, G. M. Heilek,, and H. F. Noller. 1999. Probing the rRNA environment of ribosomal protein S5 across the subunit interface and inside the 30 S subunit using tethered Fe(II). J. Mol. Biol. 286:355364.
18. Dervan, P. B. 1986. Design of sequence-specific DNA-binding molecules. Science 232:464471.
19. Dontsova, O.,, A. Kopylov,, and R. Brimacombe. 1991. The location of mRNA in the ribosomal 30S initiation complex: sitedirected cross-linking of mRNA analogues carrying several photo-reactive labels simultaneously on either side of the AUG start codon. EMBO J. 10:26132620.
20. Dontsova, O.,, S. Dokudovskaya,, A. Kopylov,, A. Bogdanov,, J. Rinke-Appel,, N. Jünke,, and R. Brimacombe. 1992. Three widely separated positions in the 16S RNA lie in or close to the ribosomal decoding region: a site-directed cross-linking study with mRNA analogues. EMBO J. 11:31053116.
21. Dreyer, G. B.,, and P. B. Dervan. 1985. Sequence-specific cleavage of single-stranded DNA: oligodeoxynucleotide-EDTA X Fe(II). Proc. Natl. Acad. Sci. USA 82:968972.
22. Gallagher, J.,, C. H. Chen,, C. Q. Pan,, D. M. Perrin,, Y. M. Cho,, and D. S. Sigman. 1996. Optimizing the targeted chemical nuclease activity of 1,10-phenanthroline-copper by ligand modification. Bioconjug. Chem. 7:413420.
23. Han, H.,, and P. B. Dervan. 1994. Visualization of RNA tertiary structure by RNA-EDTA•Fe(II) autocleavage: analysis of tRNA(Phe) with uridine-EDTA•Fe(II) at position 47. Proc. Natl. Acad. Sci. USA 91:49554959.
24. Heilek, G. M.,, and H. F. Noller. 1996a. Directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S223 using tethered Fe(II). RNA 2:597602.
25. Heilek, G. M.,, and H. F. Noller. 1996b. Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5. Science 272:16591662.
26. Hertzberg, R. P.,, and P. B. Dervan. 1982. Cleavage of doublehelical DNA by (methidiumpropyl-EDTA)-iron(II). J. Am. Chem. Soc. 104:313315.
27. Hertzberg, R. P.,, and P. B. Dervan. 1984. Cleavage of DNA with methidiumpropyl-EDTA-iron(II): reaction conditions and product analyses. Biochemistry 23:39343945.
28. Hill, W.,, W. Tapprich,, and A. Tassanakajohn. 1986. Probing ribosomal structure and function, p. 233252. In B. Hardesty, (ed.), The Structure, Function and Genetics of Ribosomes. Springer-Verlag, New York, N.Y.
29. Hill, W. E.,, and A. Tassanakajohn. 1987. Probing ribosome structure using short oligodeoxyribonucleotides: the question of resolution. Biochimie 69:10711080.
30. Hill, W. E.,, J. W. Weller,, T. Gluick,, C. Merryman,, R. Marconi,, and W. E. Tapprich,. 1990. Probing the function and structure of the ribosome using short, complementary DNA oligomers, p. 253261. In W. E. Hill, , A. E. Dahlberg, , R. A. Garrett, , P. B. Moore, , D. Schlessinger, , and J. R. Warner (ed.), The Ribosome: Structure, Function, and Evolution. American Society for Microbiology, Washington, D.C.
31. Hill, W. E.,, D. J. Bucklin,, J. M. Bullard,, A. L. Galbraith,, N. V. Jammi,, C. C. Rettberg,, B. S. Sawyer,, and M. A. van Waes. 1995. Identification of ribosome-ligand interactions using cleavage reagents. Biochem. Cell Biol. 73:10331039.
32. Huttenhofer, A.,, and H. F. Noller. 1992. Hydroxyl radical cleavage of tRNA in the ribosomal P site. Proc. Natl. Acad. Sci. USA 89:78517855.
33. Huttenhofer, A.,, and H. F. Noller, 1994. Footprinting mRNAribosome complexes with chemical probes. EMBO J. 13:38923901.
34. Johnson, G. R. A.,, and N. B. Nazhat. 1987. Kinetics and mechanism of the reaction of the bis(1,10-phenanthroline)copper(I) ion with hydrogen peroxide in aqueous solution. J. Am. Chem. Soc. 109:19901994.
35. Juzumiene, D.,, and P. Wollenzien. 1997. Determination of the 16S ribosomal RNA folded structure with site-directed photoreactive reagents in the 5′ and central pseudoknot region. Nucleic Acids Symp. Ser. 36:168170.
36. Kuwabara, M. D.,, and D. S. Sigman. 1987. Footprinting DNAprotein complexes in situ following gel retardation assays using 1,10-phenanthroline-copper ion: Escherichia coli RNA polymerase-lac promoter complexes. Biochemistry 26:72347238.
37. Lata, K. R.,, R. K. Agrawal,, P. Penczek,, R. Grassucci,, J. Zhu,, and J. Frank. 1996. Three-dimensional reconstruction of the Escherichia coli 30S ribosomal subunit on ice. J. Mol. Biol. 262:4352.
38. Lieberman, K. R.,, and H. F. Noller. 1998. Ribosomal protein L15 as a probe of 50 S ribosomal subunit structure. J. Mol. Biol. 284: 13671378.
39. Malhotra, A.,, and S. C. Harvey. 1994. A quantitative model of the Escherichia coli 16S RNA in the 30S ribosomal subunit. J. Mol. Biol. 240:308340.
40. Meijler, M. M.,, O. Zelenko,, and D. S. Sigman. 1997. Chemical mechanism of DNA scission by (1,10-phenanthroline)copper. Carbonyl oxygen of 5-methylenefuranone is derived from water. J. Am. Chem. Soc. 119:11351136.
41. Merryman, C.,, D. Moazed,, J. McWhirter,, and H. F. Noller. 1999. Nucleotides in 16S rRNA protected by the association of 30S and 50S ribosomal subunits. J. Mol. Biol. 285:97105.
42. Moazed, D.,, and H. F. Noller. 1989. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342:142148.
43. Moazed, D.,, B. Van Stolk,, S. Douthwaite,, and H. F. Noller. 1986. Interconversion of active and inactive 30S ribosomal subunits is accompanied by a conformational change in the decoding region of 16S RNA. J. Mol. Biol. 191:483493.
44. Mueller, F.,, and R. Brimacombe. 1997. A new model for the threedimensional folding of Escherichia coli 16S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 A. J. Mol. Biol. 271:524544.
45. Mundus, D.,, and P. Wollenzien. 1998. Neighborhood of 16S rRNA nucleotides U788/U789 in the 30S ribosomal subunit determined by site-directed crosslinking. RNA 4:13731385.
46. Muralikrishna, P.,, and B. S. Cooperman. 1994. A photolabile oligodeoxyribonucleotide probe of the decoding site in the small subunit of the Escherichia coli ribosome: identification of neighboring ribosomal components. Biochemistry 33:13921398.
47. Muth, G. W.,, C. M. Thompson,, and W. E. Hill. 1999a. Cleavage of a 23S rRNA pseudoknot by phenanthroline-Cu(II). Nucleic Acids Res. 27:19061911.
48. Muth, G. W.,, S. Hennelley,, and W. E. Hill. 1999b. Positions in the 30S ribosomal subunit proximal to the 790 loop as determined by phenanthroline cleavage. RNA 5:856864.
49. Muth, G. W.,, S. P. Hennelley,, and W. E. Hill. Conformational changes of the rRNA within 30S ribosomal subunits as elucidated by phenanthroline cleavage. Biochemistry, in press.
50. Newcomb, L. F.,, and H. F. Noller. 1999. Directed hydroxyl radical probing of 16S ribosomal RNA in 70S ribosomes from internal positions of the RNA. Biochemistry 38:945951.
51. Noller, H. F.,, R. Green,, G. Heilek,, V. Hoffarth,, A. Huttenhofer,, S. Joseph,, I. Lee,, K. Lieberman,, A. Mankin,, and C. Merryman. 1995. Structure and function of ribosomal RNA. Biochem. Cell Biol. 73:9971009. (Erratum, 74:417, 1996.)
52. Oakley, M. G.,, and P. B. Dervan. 1990. Structural motif of the GCN4 DNA binding domain characterized by affinity cleaving. Science 248:847850.
53. Pearson, L.,, C. B. Chen,, R. P. Gaynor,, and D. S. Sigman. 1994. Footprinting RNA-protein complexes following gel retardation assays: application to the R-17-procoat-RNA and tat-TAR interactions. Nucleic Acids Res. 22:22552263.
54. Perrin, D. M.,, A. Mazumder,, and D. S. Sigman. 1996. Oxidative chemical nucleases. Prog. Nucleic Acid Res. Mol. Biol. 52:123151.
55. Pogozelski, W. K.,, and T. D. Tullius. 1998. Oxidative strand scission of nucleic acids: routes inititated by hydrogen abstraction from the sugar moiety. Chem. Rev. 98:10891107.
56. Pope, L. E.,, and D. S. Sigman. 1984. Secondary structure specificity of the nuclease activity of the 1,10-phenanthroline-copper complex. Proc. Natl. Acad. Sci. USA 81:37.
57. Powers, T.,, and H. F. Noller. 1995. Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA. RNA 1:194209.
58. Que, B. G.,, K. M. Downey,, and A. G. So. 1980. Degradation of deoxyribonucleic acid by a 1,10-phenanthroline-copper complex: the role of hydroxyl radicals. Biochemistry 19:59875991.
59. Rinke-Appel, J.,, N. Junke,, K. Stade,, and R. Brimacombe. 1991. The path of mRNA through the Escherichia coli ribosome; sitedirected cross-linking of mRNA analogues carrying a photoreactive label at various points 3′ to the decoding site. EMBO J. 10:21952202.
60. Rinke-Appel, J.,, N. Jünke,, R. Brimacombe,, S. Dokudovskaya,, O. Dontsova,, and A. Bogdanov. 1993. Site-directed cross-linking of mRNA analogues to 16S ribosomal RNA: a complete scan of cross-links from all positions between ′+1′ and ′+16′ on the mRNA, downstream from the decoding site. Nucleic Acids Res. 21:28532859.
61. Ross, S. A.,, and C. J. Burrows. 1996. Cytosine-specific chemical probing of DNA using bromide and monoperoxysulfate. Nucleic Acids Res. 24:50625063.
62. Sigman, D. S. 1990. Chemical nucleases. Biochemistry 29:90979105.
63. Sigman, D. S.,, D. R. Graham,, V. D'Aurora,, and A. M. Stern. 1979. Oxygen-dependent cleavage of DNA by 1,10-phenanthrolinecuprous complex. J. Biol. Chem. 254:1226912272.
64. Sigman, D. S.,, C. H. Chen,, and M. B. Gorin. 1993a. Sequencespecific scission of DNA by RNAs linked to a chemical nuclease. Nature 363:474475.
65. Sigman, D. S.,, A. Mazumder,, and D. M. Perrin. 1993b. Chemical nucleases. Chem. Rev. 93:22952316.
66. Sigmund, C. D.,, M. Ettayebi,, and E. A. Morgan. 1984. Antibiotic resistance mutations in 16 S and 23 S ribosomal RNA genes of Escherichia coli. Nucleic Acids Res. 12:46534663.
67. Sluka, J. P.,, S. J. Horvath,, A. C. Glasgow,, M. I. Simon,, and P. B. Dervan. 1990. Importance of minor-groove contacts for recognition of DNA by the binding domain of Hin recombinase. Biochemistry 29:65516561.
68. Strobel, S. A.,, and P. B. Dervan. 1990. Site-specific cleavage of a yeast chromosome by oligonucleotide-directed triple-helix formation. Science 249:7375.
69. Sugden, K. D.,, R. D. Geer,, and S. J. Rogers. 1992. Oxygen radicalmediated DNA damage by redox-active Cr(III) complexes. Biochemistry 31:1162611631.
70. Sugden, K. D.,, and K. E. Wetterhahn. 1997. Direct and hydrogen peroxide-induced chromium(V) oxidation of deoxyribose in single-stranded and double-stranded calf thymus DNA. Chem. Res. Toxicol. 10:13971406.
71. Van Dyke, M. W.,, and P. B. Dervan. 1983. Footprinting with MPE•Fe(II). Complementary-strand analyses of distamycin- and actinomycin-binding sites on heterogeneous DNA. Cold Spring Harb. Symp. Quant. Biol. 47:347353.
72. Wilson, K. S.,, and H. F. Noller. 1998. Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing. Cell 92:131139.
73. Zamir, A.,, R. Miskin,, and D. Elson. 1971. Inactivation and reactivation of ribosomal subunit amino acyl-transfer RNA binding activity of the 30S subunit of E. coli. J. Mol. Biol. 60:347364.
74. Zheng, P.,, C. J. Burrows,, and S. E. Rokita, 1998. Nickel- and cobalt-dependent reagents identify structural features of RNA that are not detected by dimethyl sulfate or RNase T1. Biochemistry 37:22072214.

Tables

Generic image for table
Table 1.

Results of cleavage by targeted DNA oligomers

Citation: Hill W, Bullard J, Hennelly S, Yuan J, Grace W, Bucklin D, Van Waes M, Muth G, Thompson C. 2000. Chemical Cleavage as a Probe of Ribosomal Structure, p 257-270. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch22

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