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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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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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