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Volumn 9, Issue 1, 1998, Pages 59-65

Modern methods for probing RNA structure

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 0031933470     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(98)80085-2     Document Type: Article
Times cited : (7)

References (67)
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    • Frank J. The ribosome at higher resolution - the donut takes shape. Curr Opin Struct Biol. 7:1997;266-272.
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    • Frank, J.1
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    • Arrangement of tRNAs in pre- And post-translocational ribosomes revealed by electron cryomicroscopy
    • of special interest. tRNAs positioned in the P- and E-site of post-translocational ribosomes and at the A- and P-site of pretranslocational ribosomes were visualized at 20 Å resolution. In the paper by Agrawal et al. 1996 [50] all three A-, P-, and E- sites were co-occupied by tRNAs. The significant discrepancies between the proposed models in Agrawal et al. 1996 [50] and this paper may be a consequence of the non-physiological simultaneous binding of three tRNAs in Agrawal et al. [50].
    • Stark H, Orlova EV, Rinke-Appel J, Junke N, Mueller F, Rodnina M, Wintermeyer W, Brimacombe R, van Heel M. Arrangement of tRNAs in pre- and post-translocational ribosomes revealed by electron cryomicroscopy. of special interest Cell. 88:1997;19-28 tRNAs positioned in the P- and E-site of post-translocational ribosomes and at the A- and P-site of pretranslocational ribosomes were visualized at 20 Å resolution. In the paper by Agrawal et al. 1996 [50] all three A-, P-, and E- sites were co-occupied by tRNAs. The significant discrepancies between the proposed models in Agrawal et al. 1996 [50] and this paper may be a consequence of the non-physiological simultaneous binding of three tRNAs in Agrawal et al. [50].
    • (1997) Cell , vol.88 , pp. 19-28
    • Stark, H.1    Orlova, E.V.2    Rinke-Appel, J.3    Junke, N.4    Mueller, F.5    Rodnina, M.6    Wintermeyer, W.7    Brimacombe, R.8    Van Heel, M.9
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    • Direct localization of the tRNAs within the elongating ribosome by means of neutron scattering (proto-spin contrast-variation)
    • of special interest. Neutron scattering has mostly been used for measuring distances between proteins in the ribosome. In this paper a novel technique is employed to measure the movement of the tRNA - mRNA complex within the ribosomal model.
    • Wadzack J, Burkhardt N, Junemann R, Diedrich G, Nierhaus KH, Frank J, Penczek P, Meerwinck W, Schmitt M, Willumeit R, Stuhrmann HB. Direct localization of the tRNAs within the elongating ribosome by means of neutron scattering (proto-spin contrast-variation). of special interest J Mol Biol. 266:1997;343-356 Neutron scattering has mostly been used for measuring distances between proteins in the ribosome. In this paper a novel technique is employed to measure the movement of the tRNA - mRNA complex within the ribosomal model.
    • (1997) J Mol Biol , vol.266 , pp. 343-356
    • Wadzack, J.1    Burkhardt, N.2    Junemann, R.3    Diedrich, G.4    Nierhaus, K.H.5    Frank, J.6    Penczek, P.7    Meerwinck, W.8    Schmitt, M.9    Willumeit, R.10    Stuhrmann, H.B.11
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    • Analysis of the tertiary structure of the ribonuclease P ribozyme - Substrate complex by site-specific photoaffinity crosslinking
    • of special interest. A three-dimensional model for RNase P RNA is proposed based on structural constraints obtained by crosslinks. The photo-reactive groups were introduced using the circular permutation method. Circular permutated RNA was transcribed from a genetically engineered template which is initiated at a selected internal site to produce an RNA with joint native 5′- and 3′-ends. The photo-reactive labels were attached cotranscriptionally or by ligation at the termini. Importantly, it was demonstrated that the crosslinked RNA species retained functionality.
    • Harris ME, Kazantsev AV, Chen J-L, Pace NR. Analysis of the tertiary structure of the ribonuclease P ribozyme - substrate complex by site-specific photoaffinity crosslinking. of special interest RNA. 3:1997;561-576 A three-dimensional model for RNase P RNA is proposed based on structural constraints obtained by crosslinks. The photo-reactive groups were introduced using the circular permutation method. Circular permutated RNA was transcribed from a genetically engineered template which is initiated at a selected internal site to produce an RNA with joint native 5′- and 3′-ends. The photo-reactive labels were attached cotranscriptionally or by ligation at the termini. Importantly, it was demonstrated that the crosslinked RNA species retained functionality.
    • (1997) RNA , vol.3 , pp. 561-576
    • Harris, M.E.1    Kazantsev, A.V.2    Chen J-L3    Pace, N.R.4
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    • A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. Fitting the RNA to a 3D electron microscopic map at 20 Å
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    • Mueller, F.1    Brimacombe, R.2
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    • A new technique for the characterization of long-range tertiary contacts in large RNA molecules: Insertion of a photolabel at a selected position in 16S rRNA within the Escherichia coli ribosome
    • of special interest. Description of the internal gap method where RNase H in the presence of a complementary chimeric oligonucleotide is used to cleave the RNA at a specified site. A photo-reactive label was attached at the termini using T4 RNA ligase.
    • Baranov PV, Dokudovskaya SS, Oretskaya TS, Dontsova OA, Bogdanov AA, Brimacombe R. A new technique for the characterization of long-range tertiary contacts in large RNA molecules: insertion of a photolabel at a selected position in 16S rRNA within the Escherichia coli ribosome. of special interest Nucleic Acids Res. 25:1997;2266-2273 Description of the internal gap method where RNase H in the presence of a complementary chimeric oligonucleotide is used to cleave the RNA at a specified site. A photo-reactive label was attached at the termini using T4 RNA ligase.
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    • Baranov, P.V.1    Dokudovskaya, S.S.2    Oretskaya, T.S.3    Dontsova, O.A.4    Bogdanov, A.A.5    Brimacombe, R.6
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    • Site-specific crosslinking of mammalian U11 and u6atac to the 5′ splice site of an AT-AC intron
    • of special interest. 365 nm UV irradiation of RNA with site specifically incorporated 4-thiouridine was used to identify RNAs associated with the 5′-splice site of AT-AC introns. 4-thiouridine has been used widely as a 'zero length' photo-reactive label.
    • Yu YT, Steitz JA. Site-specific crosslinking of mammalian U11 and u6atac to the 5′ splice site of an AT-AC intron. of special interest Proc Natl Acad Sci USA. 94:1997;6030-6035 365 nm UV irradiation of RNA with site specifically incorporated 4-thiouridine was used to identify RNAs associated with the 5′-splice site of AT-AC introns. 4-thiouridine has been used widely as a 'zero length' photo-reactive label.
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    • Yu, Y.T.1    Steitz, J.A.2
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    • Mapping the rRNA neighborhood of the acceptor end of tRNA in the ribosome
    • of outstanding interest. This study demonstrates a novel approach to identify regions of an RNA molecule located in the vicinity of functional sites. Hydroxyl radicals generated in the vicinity of an Fe(II) metal ion tethered to the 5′- end of a tRNA, cleave the 23 S rRNA in the neighborhood of the tRNA bound to the ribosome. This method was used to map regions close to the A, P or E sites of the 23 S rRNA.
    • Joseph S, Noller HF. Mapping the rRNA neighborhood of the acceptor end of tRNA in the ribosome. of outstanding interest EMBO J. 15:1996;910-916 This study demonstrates a novel approach to identify regions of an RNA molecule located in the vicinity of functional sites. Hydroxyl radicals generated in the vicinity of an Fe(II) metal ion tethered to the 5′- end of a tRNA, cleave the 23 S rRNA in the neighborhood of the tRNA bound to the ribosome. This method was used to map regions close to the A, P or E sites of the 23 S rRNA.
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    • Joseph, S.1    Noller, H.F.2
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    • Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5
    • of special interest. Fe(II) tethered to different position the ribosomal protein S5 was used to generate cleavage patterns on 16 S rRNA. Different locations were selected on the surface of S5 based on the X-ray structure and mutagenized to unique cysteine residues. These residues were used as targets to derivative with 1-(p-bromoacetamidobenzyl)-EDTA (BABE). The cleavage pattern was used to constrain the folding of 16 S rRNA and model S5 on the 16 S rRNA structure.
    • Heilek GM, Noller HF. Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5. of special interest Science. 272:1996;1659-1662 Fe(II) tethered to different position the ribosomal protein S5 was used to generate cleavage patterns on 16 S rRNA. Different locations were selected on the surface of S5 based on the X-ray structure and mutagenized to unique cysteine residues. These residues were used as targets to derivative with 1-(p-bromoacetamidobenzyl)-EDTA (BABE). The cleavage pattern was used to constrain the folding of 16 S rRNA and model S5 on the 16 S rRNA structure.
    • (1996) Science , vol.272 , pp. 1659-1662
    • Heilek, G.M.1    Noller, H.F.2
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    • Probing RNA tertiary structure: Interhelical crosslinking of the hammerhead ribozyme
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    • Sigurdsson, S.T.1    Tuschl, T.2    Eckstein, F.3
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    • Dynamics of thermal motion within a large catalytic RNA investigated by cross-linking with thioldisulfide interchange
    • of outstanding interest. The first direct demonstration of large thermal movements in RNA. Alkylphenyl disulfide and alkyl thiol were attached to a chemically incorporated amino group at the 2′-positions of specified nucleotides. The advantage of these disulfide crosslinking is that the crosslink can be generated under physiological conditions.
    • Cohen SB, Cech TR. Dynamics of thermal motion within a large catalytic RNA investigated by cross-linking with thioldisulfide interchange. of outstanding interest J Am Chem Soc. 119:1997;6259-6268 The first direct demonstration of large thermal movements in RNA. Alkylphenyl disulfide and alkyl thiol were attached to a chemically incorporated amino group at the 2′-positions of specified nucleotides. The advantage of these disulfide crosslinking is that the crosslink can be generated under physiological conditions.
    • (1997) J Am Chem Soc , vol.119 , pp. 6259-6268
    • Cohen, S.B.1    Cech, T.R.2
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    • Metal ion catalysis during splicing of premessenger RNA
    • 2+ rescue assay to demonstrate that the two steps in pre-mRNA splicing proceed by different catalytic mechanisms. Pre-mRNA with a 3′-sulfur substitution at the 5′-splice was used to demonstrate that the spliceosome acts as an metalloenzyme in the first reaction step. A 3′-sulfur substitution at the 3′-splice site, however, provides no evidence for metal ion interaction at the second reaction step.
    • 2+ rescue assay to demonstrate that the two steps in pre-mRNA splicing proceed by different catalytic mechanisms. Pre-mRNA with a 3′-sulfur substitution at the 5′-splice was used to demonstrate that the spliceosome acts as an metalloenzyme in the first reaction step. A 3′-sulfur substitution at the 3′-splice site, however, provides no evidence for metal ion interaction at the second reaction step.
    • (1997) Nature , vol.388 , pp. 801-805
    • Sontheimer, E.J.1    Sun, S.2    Piccirilli, J.A.3
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    • A second catalytic metal ion in group I ribozyme
    • of special interest. The same procedure described by Sontheimier et al. 1997 [62] was used to study the self-splicing of group I intron from Tetrahymena. Contrary to pre-mRNA splicing there is evidence that both steps in self-splicing of group I introns require metal ion interaction.
    • Weinstein LB, Jones BC, Cosstick R, Cech TR. A second catalytic metal ion in group I ribozyme. of special interest Nature. 388:1997;805-808 The same procedure described by Sontheimier et al. 1997 [62] was used to study the self-splicing of group I intron from Tetrahymena. Contrary to pre-mRNA splicing there is evidence that both steps in self-splicing of group I introns require metal ion interaction.
    • (1997) Nature , vol.388 , pp. 805-808
    • Weinstein, L.B.1    Jones, B.C.2    Cosstick, R.3    Cech, T.R.4
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    • 0030965811 scopus 로고    scopus 로고
    • Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping
    • of special interest. This paper reports the use of a nucleotide analogue interference mapping assay where random incorporation of 5′-O-(1-thio)inosine monophosphate (IMPaS) in RNA provides an efficient method for evaluating the contribution of N2 exocyclic amines of G. The concomitant incorporation of the phosphothioate with the base modification provides a general applicable method to test the role of modified nucleotides in RNA folding or function. The selective sensitivity of phosphothioates to iodine cleavage provides an easy identification of the modified nucleotide.
    • Strobel SA, Shetty K. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. of special interest Proc Natl Acad Sci USA. 94:1997;2903-2908 This paper reports the use of a nucleotide analogue interference mapping assay where random incorporation of 5′-O-(1-thio)inosine monophosphate (IMPaS) in RNA provides an efficient method for evaluating the contribution of N2 exocyclic amines of G. The concomitant incorporation of the phosphothioate with the base modification provides a general applicable method to test the role of modified nucleotides in RNA folding or function. The selective sensitivity of phosphothioates to iodine cleavage provides an easy identification of the modified nucleotide.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 2903-2908
    • Strobel, S.A.1    Shetty, K.2
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    • Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme
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    • Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks
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    • Zarrinkar, P.P.1    Williamson, J.R.2


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