Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling
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Andersen, 1984, 5 S rRNA structure and interaction with transcription factor TFIIIA. A: ribonucleases probe of the structure of 5 S rRNA from Xenopus laevis oocytes, Biochemistry, 23, 5752, 10.1021/bi00319a013
Baudin, 1991, Involvement of “hinge” nucleotides of Xenopus laevis 5 S rRNA in the RNA structural organization and in the binding of transcription factor TFIIIA, J. Mol. Biol., 218, 69, 10.1016/0022-2836(91)90874-6
Böhm, 1981, Structural analysis of the A and B conformers of Escherichia coli 5 S rRNA by infrared spectroscopy, FEBS Letters, 132, 357, 10.1016/0014-5793(81)81197-0
Brosius, 1981, Construction and fine mapping of recombinant plasmids containing the rrnB ribosomal RNA operon of E. coli, Plasmid, 6, 112, 10.1016/0147-619X(81)90058-5
Brunel, 1990, Effect of mutations in domain 2 on the structural organization of oocyte 5 S rRNA from Xenopus laevis, J. Mol. Biol., 215, 103, 10.1016/S0022-2836(05)80099-3
Cheong, 1990, Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC, Nature (London), 346, 680, 10.1038/346680a0
Christensen, 1985, Alternative conformers of 5 S rRNA and their biological relevance, Biochemistry, 24, 2284, 10.1021/bi00330a024
Christiansen, 1985, Xenopus transcription factor TFIIIA binds primarily at junctions between double helical stems and internal loops in oocyte 5 S rRNA, EMBO J., 4, 1019, 10.1002/j.1460-2075.1985.tb03733.x
Christiansen, 1987, Does unpaired adenosine 66 from helix II of E. coli bind to protein L18?, EMBO J., 2, 1309
De Wachter, 1984, Equilibria in 5 S rRNA secondary structure: bulges and interior loops in 5 S rRNA secondary structure may serve as articulations for a flexible molecule, Eur. J. Biochem., 143, 175, 10.1111/j.1432-1033.1984.tb08356.x
Dock-Brégeon, 1989, Solution structure of a tRNA with a large variable region: yeast tRNASer, J. Mol. Biol., 207, 707, 10.1016/0022-2836(89)90578-0
Douthwaite, 1982, Binding sites of ribosomal proteins on prokaryotic 5 S ribonucleic acids: a study with ribonucleases, Biochemistry, 21, 2313, 10.1021/bi00539a007
Egebjerg, 1989, Protein L18 binds primarily at the junctions of helix II and internal loops A and B in Escherichia coli 5 S rRNA, J. Mol. Biol., 206, 651, 10.1016/0022-2836(89)90573-1
England, 1978, 3′ terminal labeling of RNA with T4 RNA ligase, Nature (London), 275, 560, 10.1038/275560a0
Farber, 1981, A slow tritium exchange study of the solution structure of Escherichia coli 5 S rRNA, J. Mol. Biol., 146, 241, 10.1016/0022-2836(81)90434-4
Fox, 1982, Acquisition of native conformation of 5 S rRNA from E. coli. Hydrodynamic and spectroscopic studies on the unfolding and refolding of ribonucleic acid, J. Biol. Chem., 254, 10139, 10.1016/S0021-9258(19)86684-X
Garrett, 1984, Mechanisms of protein-RNA recognition and assembly in ribosomes, vol. 19, 331
Gewirth, 1987, Secondary structure of 5 S RNA: NMR experiments on RNA molecules partially labeled with nitrogen 15, Biochemistry, 26, 5213, 10.1021/bi00390a047
Göringer, 1986, Does 5 S rRNA from E. coli have a pseudoknotted structure?, Nucl. Acids Res., 14, 7473, 10.1093/nar/14.18.7473
Gornicki, 1989, Use of lead(II) to probe the structure of large RNAs. Conformation of the 3′ terminal domain of E. coli 16 S rRNA and its involvement in building the tRNA binding sites, J. Biomol. Struct. Dynam., 5, 971, 10.1080/07391102.1989.10506525
Hancock, 1982, A structural model of 5 S rRNA from E. coli based on intramolecular cross-linking evidence, Nucl. Acids Res., 10, 1257, 10.1093/nar/10.4.1257
Herr, 1979, Protection of specific sites in 23 S and 5 S rRNA from chemical modification by association of 30 S and 50 S ribosomes, J. Mol. Biol., 130, 421, 10.1016/0022-2836(79)90432-7
Kao, 1980, A proton-coupled conformation switch of Escherichia coli 5 S rRNA, Nucl. Acids Res., 77, 3360
Kim, 1990, Dynamic structure of bacterial 5 S rRNA: helices II and III of B. megaterium 5 S rRNA, Biochem. Biophys. Res. Commun., 169, 1068, 10.1016/0006-291X(90)92003-I
Kime, 1982, NMR evidence for the existence of two native conformations of 5 S rRNA, Nucl. Acids Res., 10, 4973, 10.1093/nar/10.16.4973
Kime, 1983, Nuclear Overhauser experiments at 500 MHz on the downfield proton spectra of 5 S rRNA and its complex with ribosomal protein L25, Biochemistry, 22, 2622, 10.1021/bi00280a005
Kime, 1984, Assignment of resonances in the downfield proton spectrum of Escherichia coli 5 S rRNA and its nucleo-protein complexes using components of a ribonuclease resistant fragment, Biochemistry, 23, 3559, 10.1021/bi00310a027
Labuda, 1985, Co-operativity in low affinity Mg2+ binding to tRNA, J. Biol. Chem., 260, 1103, 10.1016/S0021-9258(20)71213-5
Leal de Stevenson, 1991, Structural studies on site-directed mutants of domain 3 of X. laevis 5 S rRNA, J. Mol. Biol., 219, 243, 10.1016/0022-2836(91)90565-N
Leontis, 1986, NMR evidence for dynamic secondary structure in helices II and III of the 5 S rRNA of E. coli, Biochemistry, 25, 3916, 10.1021/bi00361a027
Leontis, 1986, Effect of magnesium ion on the structure of the 5 S rRNA from E. coli. An imino proton magnetic resonance study of the helix I, IV and V regions of the molecule, Biochemistry, 25, 7386, 10.1021/bi00371a021
Müller, 1986, Comparison of the structure of 5 S rRNA from E. coli and from rat liver using X-ray scattering and dynamic light scattering, Eur. Biophys. J., 13, 301, 10.1007/BF00254212
Österberg, 1976, Molecular model for 5 S rRNA: a small angle X-ray scattering study of native, denatured and aggrevated 5 S rRNA from E. coli ribosome, Eur. J. Biochem., 68, 481, 10.1111/j.1432-1033.1976.tb10835.x
Peattie, 1980, Chemical probes for higher-order structure in RNA, 77, 4679
Pieler, 1982, Three-dimensional structural model of eubacterial 5 S rRNA that has functional implications, 79, 4599
Puglisi, 1990, Solution conformation of an RNA hairpin loop, Biochemistry, 29, 4215, 10.1021/bi00469a026
Romaniuk, 1988, A comparison of the solution structures and conformational properties of the somatic and oocyte 5 S rRNA of Xenopus laevis, Nucl. Acids Res., 16, 2295, 10.1093/nar/16.5.2295
Romby, 1988, Higher-order structure of chloroplastic 5 S rRNA from spinach, Biochemistry, 27, 4712, 10.1021/bi00413a021
Romby, 1990, Ribosomal 5 S rRNA from X. laevis oocytes: conformation and interaction with transcription factor IIIA, Biochimie, 72, 437, 10.1016/0300-9084(90)90068-R
SantaLucia, 1990, Effects of GA mismatches on the structure and thermodynamics of RNA internal loops, Biochemistry, 29, 8813, 10.1021/bi00489a044
Shinagawa, 1979, Inhibition of a nuclease contaminant in the commercial preparation of E. coli alkaline phosphatase, Anal. Biochem., 95, 458, 10.1016/0003-2697(79)90756-5
Silberklang, 1977, The use of P1 nuclease in sequence analysis of end-group labeled RNA, Nucl. Acids Res., 4, 4091, 10.1093/nar/4.12.4091
Silberklang, 1983, Chemical reactivity of E. coli 5 S rRNA in situ in the 50 S ribosomal subunit, Nucl. Acids Res., 11, 605, 10.1093/nar/11.3.605
Stahl, 1984, An unusual 5 S rRNA from Sulfolobus acido caldarius and its implications for a general 5 S rRNA structure, J. Biol. Chem., 259, 11448, 10.1016/S0021-9258(18)90881-1
Toukifimpa, 1989, Characterization and footprint of two 5 S rRNA binding proteins from spinach chloroplast ribosomes, Biochemistry, 28, 5840, 10.1021/bi00440a021
Trakhanov, 1987, Crystallization of 70 S ribosomes and 30 S ribosomal subunits from Thermus thermophilus, FEBS Letters, 220, 319, 10.1016/0014-5793(87)80838-4
Tuerk, 1988, CUUCGG hairpins: extraordinary stable RNA secondary structures associated with various biochemical processes, 85, 1364
Varani, 1989, Conformation and dynamics of an RNA internal loop, Biochemistry, 28, 7760, 10.1021/bi00445a036
Webster, 1990, Crystal structure and sequence-dependent conformation of the A-G mispaired oligonucleotide d(CGCAAGCTGGCG), 87, 6693
Westhof, 1985, Crystallographic refinement of yeast aspartic acid transfer RNA, J. Mol. Biol., 184, 119, 10.1016/0022-2836(85)90048-8
Westhof, 1989, Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs, J. Mol. Biol., 207, 417, 10.1016/0022-2836(89)90264-7
Westhof, 1990, Computer-aided structural biochemistry of ribonucleic acids, 399
Wolters, 1988, Collection of published 5 S, 5·8 S and 4·5 S ribosomal RNA sequences, Nucl. Acids Res., 16, r1, 10.1093/nar/16.suppl.r1
Wu, 1990, 500-Mhz proton NMR evidence for two solution structures of the common arm base-paired segment of wheat germ 5 S rRNA, Biochemistry, 29, 1722, 10.1021/bi00459a009
Yonath, 1989, Crystallography and image reconstructions of ribosomes, 134
Zhang, 1989, An NMR study in the helix V-loop E region of the 5 S RNA from E. coli, Biochemistry, 28, 4607, 10.1021/bi00437a015