501
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Abstract
Chromatography on Concanavalin A sepharose is a simple procedure for partial purification of spleen phosphodiesterase. This procedure removes much, but not all, of the ribonuclease activity found as contaminant in most spleen phosphdisterase preparations.
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502
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Wetzel R, Söll D. Analogs of methionyl-tRNA synthetase substrates containing photolabile groups. Nucleic Acids Res 1977; 4:1681-94. [PMID: 331263 PMCID: PMC343781 DOI: 10.1093/nar/4.5.1681] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Three photolabile analogs of substrates of methionyl-tRNA synthetase were synthesized. In one, the 4-thiouridine at the 8 position of E. coli tRNAfMet was alkylated with [14C]p-azidobromoacetanilide. In the second, [14C]p-azidobenzoic acid hydrazide was condensed with the 3'-terminal dialdehyde of periodate-oxidized Escherichia coli tRNAfMet. The modified tRNAs could be purified by chromatography on benzoylated DEAE-cellulose. The third photolabile compound was [3H]methioninyl-8-azido-adenosine 5'-phosphate, an analog of the methionyl adenylate intermediate in the aminoacylation reaction. Irradiation of each of these compounds in the presence of equimolar amounts of E. coli methionyl-tRNA synthetase of micrometer concentrations gave 5-15% crosslinking.
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503
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Vögeli G, Stewart TS, McCutchan T, Söll D. Isolation of Escherichia coli precursor tRNAs containing modified nucleoside Q. J Biol Chem 1977; 252:2311-8. [PMID: 321455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Affinity chromatography based on the complex formation of the modified nucleoside Q with boronic acid has been applied to the isolation of specific tRNA precursors containing this modified nucleoside. When [32P]RNA isolated from an Escherichia coli strain containing a thermolabile ribonuclease P was chromatographed on dihydroxyboryl-substituted cellulose, the precursors for asparagine, aspartate, histidine, and tyrosine tRNA were specifically retained. All precursors were monomeric. The nucleotide sequences of four asparagine tRNA precursors were determined.
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504
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Vögeli G, Stewart TS, McCutchan T, Söll D. Isolation of Escherichia coli precursor tRNAs containing modified nucleoside Q. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40556-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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505
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Grosjean H, Söll D, Crothers D. Proceedings: Studies of the complex between transfer RNA'S with complementary anticodons: origins of enhanced affinity between complementary triplets. ARCHIVES INTERNATIONALES DE PHYSIOLOGIE ET DE BIOCHIMIE 1976; 84:163-4. [PMID: 60940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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506
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Grosjean H, Söll D, Crothers D. Studies of the complex between transfer RNA molecules and complementary anticodons: kinetic and thermodynamic aspects. ARCHIVES INTERNATIONALES DE PHYSIOLOGIE ET DE BIOCHIMIE 1975; 83:970-1. [PMID: 58627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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507
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Vögeli G, Grosjean H, Söll D. A method for the isolation of specific tRNA precursors. Proc Natl Acad Sci U S A 1975; 72:4790-4. [PMID: 1108001 PMCID: PMC388817 DOI: 10.1073/pnas.72.12.4790] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
tRNA affinity chromatography, based on complex formation between tRNAs with complementary anticodons, has been applied to the isolation of specific tRNA precursors. When [32P]RNA, isolated from an Escherichia coli strain containing a thermolabile ribonuclease P, was chromatographed on resin-bound yeast phenylalanine tRNA, precursor tRNAGlu (possessing the complementary anticodon) was specifically retained. Likewise, precursor tRNAPhe was isolated from a column of resin-bound E. coli glutamate tRNA. Both precursor tRNAs isolated were monomeric and may be processed products of an originally larger RNA precursor. Both tRNA precursors contain additional nucleotides beyond the 5'-end of the mature tRNA and have all modified bases found in mature tRNA. The method can be extended to isolate other tRNA precursors by affinity chromatography with different tRNAs. Since the principle of complementary anticodon interaction is not restricted to any particular organism, specific precursor tRNAs from other sources may also be isolated in this way.
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508
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Kwong TC, Steege D, Lawler D, Söll D. Bacteriophage lambda induction causes increased production of E. coli lysine transfer RNA. Arch Biochem Biophys 1975; 170:651-8. [PMID: 1103738 DOI: 10.1016/0003-9861(75)90161-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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509
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McCutchan TF, Gilham PT, Söll D. An improved method for the purification of tRNA by chromatography on dihydroxyboryl substituted cellulose. Nucleic Acids Res 1975; 2:853-64. [PMID: 1096084 PMCID: PMC343472 DOI: 10.1093/nar/2.6.853] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
An improved method for the rapid separation of aminoacyl-tRNA from tRNA by chromatography on dihydroxyboryl-substituted cellulose has been developed. The method relies on the selective binding of unacylated tRNA to the cell cellulose support containing dihydroxyboryl groups. This binding is the result of complex formation between the cis-diol group of the 3'-terminal ribose in tRNA and the dihydroxyboryl groups immobilized on the resin. Aminoacyl-tRNA cannot undergo borate complex formation and is not retained on the resin. The separation is carried out at near neutral pH values ensuring stability of the aminoacyl ester linkage. The aminoacyl-tRNAs are obtained in very high purity. Aminoacyl-tRNA species containing the modified nucleoside Q are also retained on dihydroxyboryl cellulose. Conditions for isolating all Q base containing tRNA species from unfractionated tRNA are described.
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510
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Agris PF, Armstrong DJ, Schäfer KP, Söll D. Maturation of a hypermodified nucleoside in transfer RNA. Nucleic Acids Res 1975; 2:691-8. [PMID: 49880 PMCID: PMC343621 DOI: 10.1093/nar/2.5.691] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
E. coli C6 rel- met- cys- was cultured in a fully supplemented medium and in media lacking cysteine or methionine. tRNA isolated from the three cultures containted, respectively, a normal complement of modified nucleosides; a deficiency in thiolated nucleosides and a deficiency in methylated nucleosides. Both sulfur-deficient tRNA and methyl-deficient tRNA contained large amounts of N-6- (delta-2-isopentenyl) adenosine and small amounts of the 2-methylthio derivative. Methyl-deficient tRNA contained, in addition a large amount of a cytokinin active, differently modified nucleoside that is believed to be a sulfur derivative of N6-(delta-2-isopentenyl) adenosine. The structure of this compound is unknown. When methly-deficient tRNA and the precusor the tRNA-Tyr su3-+ A25 were enzymatically methylated in vitro, methyl groups were incorporated into derivatives of isopentenyladenosine. These results indicate that the biosynthesis of the 2-methylthio derivative of isopentenyladenosine may occur in a sequential manner, i.e., thiolation of isopentenyladenosine followed by methylation.
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511
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Marinus MG, Morris NR, Söll D, Kwong TC. Isolation and partial characterization of three Escherichia coli mutants with altered transfer ribonucleic acid methylases. J Bacteriol 1975; 122:257-65. [PMID: 1091626 PMCID: PMC235665 DOI: 10.1128/jb.122.1.257-265.1975] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Seven transfer ribonucleic acid (tRNA) methylase mutants were isolated from Escherichia coli K-12 by examining the ability of RNA prepared from clones of unselected mutagenized cells to accept methyl groups from S-adenosylmethionine catalyzed by crude enzymes from wild-type cells. Five of the mutants had an altered uracil-tRNA methylase; consequently their tRNA's lacked ribothymidine. One mutant had tRNA deficient in 7-methylguanosine, and one mutant contained tRNA lacking 2-thio-5-methylaminomethyluridine. The genetic loci of the three tRNA methylase mutants were distributed over the E. coli genome. The mutant strain deficient in 7-methylguanosine biosynthesis showed a reduced efficiency in the suppression of amber mutations carried by T4 or lambda phages.
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512
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Schulman RG, Hilbers CW, Söll D, Yang SK. Letter: Nuclear magnetic resonance of protein-nucleic acid interactions. II. The E. coli tRNA-Glu complex with glutamyl-tRNA synthetase. J Mol Biol 1974; 90:609-11. [PMID: 4615173 DOI: 10.1016/0022-2836(74)90238-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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513
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Körner A, Magee BB, Liska B, Low KB, Adelberg EA, Söll D. Isolation and partial characterization of a temperature-sensitive Escherichia coli mutant with altered glutaminyl-transfer ribonucleic acid synthetase. J Bacteriol 1974; 120:154-8. [PMID: 4153616 PMCID: PMC245744 DOI: 10.1128/jb.120.1.154-158.1974] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A temperature-sensitive mutant of Escherichia coli has been found in which the conditional growth is a result of a thermosensitive glutaminyl-transfer ribonucleic acid synthetase. The corresponding genetic locus glnS is cotransduced with lip. In a strain containing the mutationally altered glutaminyl-transfer ribonucleic acid synthetase, no derepression of the enzyme itself nor of glutamine synthetase was observed.
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514
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515
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Yang C, Söll D. Covalent attachment of fluorescent groups to transfer ribonucleic acid. Reactions with 4-bromomethyl-7-methoxy-2-oxo-2H-benzopyran. Biochemistry 1974; 13:3615-21. [PMID: 4367729 DOI: 10.1021/bi00714a033] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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516
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Yang CH, Söll D. Studies of transfer RNA tertiary structure of singlet-singlet energy transfer. Proc Natl Acad Sci U S A 1974; 71:2838-42. [PMID: 4527991 PMCID: PMC388567 DOI: 10.1073/pnas.71.7.2838] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Five species of tRNAs bearing two different fluorescent groups were synthesized. These were suitable for intramolecular distance measurements by singlet-singlet energy transfer. The efficiency of energy transfer was determined from the sensitized emission of the energy acceptor. With the assumption that the relative orientation of donor and acceptor is random, the apparent distances between the 5'-end and the 3'-end, the 4-thiouridine and the 3'-end, the pseudouridine and 3'-end, the pseudouridine and the dihydrouridine in Escherichia coli formyl methionine tRNA, and between the 2-thiouridine (in the anticodon) and the 3'-end in E. coli glutamate tRNA were calculated to be 24 A, 38 A, 55 A, 36 A, and >65 A, respectively.
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517
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Seno T, Agris PF, Söll D. Involvement of the anticodon region of Escherichia coli tRNAGln and tRNAGlu in the specific interaction with cognate aminoacyl-tRNA synthetase. Alteration of the 2-thiouridine derivatives located in the anticodon of the tRNAs by BrCN or sulfur deprivation. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 349:328-38. [PMID: 4366808 DOI: 10.1016/0005-2787(74)90120-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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518
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Körner A, Söll D. N-(purin-6-ylcarbamoyl)threonine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli. FEBS Lett 1974; 39:301-6. [PMID: 4604806 DOI: 10.1016/0014-5793(74)80135-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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519
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Szeto KS, Söll D. Fingerprinting nonradioactive ribonucleic acid with the aid of polynucleotide phosphorylase. Nucleic Acids Res 1974; 1:171-81. [PMID: 10793669 PMCID: PMC343333 DOI: 10.1093/nar/1.1.171] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We describe a method for obtaining radioactive fingerprints from nonradioactive ribonucleic acid. Fragments derived by T1 ribonuclease digestion of RNA are dephosphorylated with bacterial alkaline phosphatase. When these fragments are used as primers for the reaction of primer dependent polynucleotide phosphorylase with [alpha-(32)P]GDP in the presence of T1 ribonuclease the 3'-hydroxyl group of each fragment becomes phosphorylated. The degree of phosphorylation is reasonably uniform. The method has been applied to T1 ribonuclease digests of Escherichia coli tRNA(Met) (f); the oligonucleotides were further analyzed by spleen phosphodiesterase digestion. In a similar manner fingerprints of pancreatic ribonuclease digests of RNA can be obtained, when [alpha-(32)P]UDP, polynucleotide phosphorylase and pancreatic ribonuclease are used.
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520
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Schaefer KP, Altman S, Söll D. Nucleotide modification in vitro of the precursor of transfer RNA of Escherichia coli. Proc Natl Acad Sci U S A 1973; 70:3626-30. [PMID: 4587257 PMCID: PMC427294 DOI: 10.1073/pnas.70.12.3626] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Certain nucleotides in precursor RNA of tRNA(Tyr) of Escherichia coli were modified in vitro with a preparation of partially purified E. coli enzyme containing ribothymidine- and pseudouridine-forming activity. The only nucleotides modified in vitro are the same as those found modified in mature tRNA. The best substrate for these modifying enzymes is the RNase P cleavage product of the precursor RNA, which contains the mature tRNA sequence. Of the two pseudouridines found in mature tRNA, one (in the TPsiC sequence) can be formed in intact precursor RNA. The other (in the anticodon stem) can only be formed in the cleaved precursor RNA. The presence of modified nucleotides in the precursor RNA does not enhance its rate of cleavage by RNase P.
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521
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Agris PF, Söll D, Seno T. Biological function of 2-thiouridine in Escherichia coli glutamic acid transfer ribonucleic acid. Biochemistry 1973; 12:4331-7. [PMID: 4584321 DOI: 10.1021/bi00746a005] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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522
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523
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Singer M, Söll D, Leder P, Gefter ML. NUCLEIC ACIDS. Photochem Photobiol 1973. [DOI: 10.1111/j.1751-1097.1973.tb06366.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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524
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Yang CH, Söll D. Covalent attachment of fluorescent groups to the 5'-end of transfer RNA. Arch Biochem Biophys 1973; 155:70-81. [PMID: 4351348 DOI: 10.1016/s0003-9861(73)80010-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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525
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Agris PF, Koh H, Söll D. The effect of growth temperatures on the in vivo ribose methylation of Bacillus stearothermophilus transfer RNA. Arch Biochem Biophys 1973; 154:277-82. [PMID: 4689778 DOI: 10.1016/0003-9861(73)90058-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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