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Ajitkumar P, Cherayil JD. Thionucleosides in transfer ribonucleic acid: diversity, structure, biosynthesis, and function. Microbiol Rev 1988; 52:103-13. [PMID: 3280963 PMCID: PMC372707 DOI: 10.1128/mr.52.1.103-113.1988] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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2
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Abstract
The nucleotide sequence of Xenopus laevis phenylalanine tRNA extracted from oocytes was determined to be: pGCCGAAAUAm2GCUCm1AG DDGGGAGAGCm22 G psi psi AGACmUGmAAYA psi C UAAAGm7GDCm5CCUGGT psi CGm1AUCCCGG GUUUCGGCACCAoH. This result was achieved by analysing, with classical procedures [6], the oligonucleotides obtained after digestion by T1 or pancreatic ribonuclease. This sequence is identical to the mammalian sequence. It has been entirely conserved during 10(8) years, the time lapse between the divergence of amphibians and mammals in evolution. In contrast to 5S RNA, no important heterogeneity has been found in the oocyte sequence, suggesting that there is only a single sequence for tRNAphe in X. laevis. Small differences are seen in the elution pattern from RPC-5 columns for immature oocyte and somatic tRNAphe. They are probably due to a submodification of methyl-5-cytidine residues, which appear to be about half methylated in tRNAphe as well as in total tRNA from immature oocytes.
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3
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Inokuchi H, Kodaira M, Yamao F, Ozeki H. Identification of transfer RNA suppressors in Escherichia coli. II. Duplicate genes for tRNA2Gln. J Mol Biol 1979; 132:663-77. [PMID: 160950 DOI: 10.1016/0022-2836(79)90381-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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5
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Berman HM, Marcu D, Narayanan P. Modified bases in tRNA: the structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine. Nucleic Acids Res 1978; 5:893-903. [PMID: 643621 PMCID: PMC342031 DOI: 10.1093/nar/5.3.893] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The crystal structures of two nucleosides, 5-carbamoylmethyluridine (1) and 5-carboxymethyluridine (2), were determined from three-dimensional x-ray diffraction data, and refined to R = 0.036 and R = 0.047, respectively. Compound 1 is in the C3'-endo conformation with chi +5.2 degrees (anti), psiinfinity = +63.4 degrees and psialpha = +180.0 degrees (tt); 2 is in the C2'endo conformation with chi +49.4 degrees (anti), psiinfinity -60.5 degrees and psialpha +60.0 degrees (gg). For each derivative, the plane of the side chain substituent is skewed with respect to the plane of the nucleobase; for 1, the carboxamide group is on the same side of the uracil plane vis a vis the ribose ring; for 2, the carboxyl group is on the opposite side of this plane. No base pairing is observed for either structure. Incorporation of structure 1 into a 3'-stacked tRNA anticodon appears to place 08 within hydrogen bonding distance of the 02' hydroxyl of ribose 33, which may limit the ability of such a molecule of tRNA to "wobble".
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6
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Feinstein SI, Altman S. Coding properties of an ochre-suppressing derivative of Escherichia coli tRNAITyr. J Mol Biol 1977; 112:453-70. [PMID: 327078 DOI: 10.1016/s0022-2836(77)80192-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Abstract
Base pairing in codon-anticodon interaction has been investigated in order to understand the basis on which particular base pairs have been selected for or against participation at the wobble position and the basis for codon-anticodon infidelity.
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8
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Yaniv M, Folk WR. The nucleotide sequences of the two glutamine transfer ribonucleic acids from Escherichia coli. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41506-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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9
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Kuntzel B, Weissenbach J, Wolff RE, Tumaitis-Kennedy TD, Lane BG, Dirheimer G. Presence of the methylester of 5-carboxymethyl uridine in the wobble position of the anticodon of tRNAIII Arg from brewer's yeast. Biochimie 1975; 57:61-70. [PMID: 167871 DOI: 10.1016/s0300-9084(75)80110-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The methylester of 5-carboxymethyluridine (mcm5U), its degradation product 5-carboxymethyluridine (cm5U) and the corresponding nucleotide (cm5Up) were isolated from brewer's yeast tRNAIII Arg or from the dodecanucleotide containing the anticodon. Their chromatographic and electrophoretic properties and their UV absorbing spectra were identical to that of the corresponding synthetic compounds. The gas chromatographic behavior and the mass spectrum of mcm5U obtained from tRNAIII Arg and of a synthetic sample were also identical ; the rare occurence of a thermal reciprocal bimolecular methyl-hydrogen transfer in the mass spectrometer ion source was observed. A mild alkaline treatment of tRNAIII Arg leads to the saponification of mcm5U into cm5U (within the tRNA), which can be again esterified in the presence of a yeast homogenate and (methyl-14C) S adenosylmethionine. The radioactivity was found in the mcm5U located in the wobble position of the anticodon of tRNAIII Arg. The presence of this odd nucleotide in that position could possibly restrict the codon-anticodon interaction of tRNAIII Arg.
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10
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Kobayashi T, Irie T, Yoshida M, Takeishi K, Ukita T. The primary structure of yeast glutamic acid tRNA specific to the GAA codon. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 366:168-81. [PMID: 4376021 DOI: 10.1016/0005-2787(74)90331-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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11
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Hoffman JL, McConnell KP. The presence of 4-selenouridine in Escherichia coli tRNA. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 366:109-13. [PMID: 4371478 DOI: 10.1016/0005-2787(74)90323-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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12
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13
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Wong TW, Harris MA, Jankowicz CA. Transfer ribonucleic acid sulfurtransferase isolated from rat cerebral hemispheres. Biochemistry 1974; 13:2805-12. [PMID: 4601536 DOI: 10.1021/bi00711a004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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14
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Watanabe K, Oshima T, Saneyoshi M, Nishimura S. Replacement of ribothymidine by 5-methyl-2-thiouridine in sequence GT psi C in tRNA of an extreme thermophile. FEBS Lett 1974; 43:59-63. [PMID: 4369142 DOI: 10.1016/0014-5793(74)81105-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Yaniv M, Folk WR, Berg P, Soll L. A single mutational modification of a tryptophan-specific transfer RNA permits aminoacylation by glutamine and translation of the codon UAG. J Mol Biol 1974; 86:245-60. [PMID: 4606150 DOI: 10.1016/0022-2836(74)90016-3] [Citation(s) in RCA: 124] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Madison JT, Boguslawski SJ. Partial digestion of a yeast lysine transfer ribonucleic acid and reconstruction of the nucleotide sequence. Biochemistry 1974; 13:524-7. [PMID: 4589316 DOI: 10.1021/bi00700a019] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Harada F, Nishimura S. Purification and characterization of AUA specific isoleucine transfer ribonucleic acid from Escherichia coli B. Biochemistry 1974; 13:300-7. [PMID: 4589307 DOI: 10.1021/bi00699a011] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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18
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Kerr SJ, Heady JE. Modulation of tRNA methyltransferase activity by competing enzyme systems. ADVANCES IN ENZYME REGULATION 1974; 12:103-17. [PMID: 4376890 DOI: 10.1016/0065-2571(74)90009-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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19
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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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20
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Vorbrüggen H, Strehlke P. Nucleosidsynthesen, VII. Eine einfache Synthese von 2-Thiopyrimidin-nucleosiden. ACTA ACUST UNITED AC 1973. [DOI: 10.1002/cber.19731060936] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Yang S, Reinitz ER, Gefter ML. Role of modifications in tyrosine transfer RNA. II. Ribothymidylate-deficient tRNA. Arch Biochem Biophys 1973; 157:55-62. [PMID: 4352057 DOI: 10.1016/0003-9861(73)90389-5] [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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22
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Weiss GB. Translational control of protein synthesis by tRNA unrelated to changes in tRNA concentration. J Mol Evol 1973; 2:199-204. [PMID: 4620076 DOI: 10.1007/bf01654000] [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: 01/11/2023]
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23
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The Nucleotide Sequences and Coding Properties of the Major and Minor Lysine Transfer Ribonucleic Acids from the Haploid Yeast Saccharomyces cerevisiae αS288C. J Biol Chem 1973. [DOI: 10.1016/s0021-9258(19)43792-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Kerr SJ, Borek E. Regulation of the tRNA methyltransferases in normal and neoplastic tissues. ADVANCES IN ENZYME REGULATION 1973; 11:63-77. [PMID: 4799201 DOI: 10.1016/0065-2571(73)90009-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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25
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Bruenn J, Jacobson KB. New species of tyrosine tRNA in nonsense suppressor strain of yeast. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 287:68-76. [PMID: 4569159 DOI: 10.1016/0005-2787(72)90330-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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26
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27
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Abstract
Two isoacceptor transfer RNA's for lysine were found in rabbit reticulocytes. The codon recognition properties of these isoacceptors were studied in hemoglobin synthesis in a cell-free systemn. The two isoacceptors transferred lysine into different sites in hemoglobin, but showed no preference for one chain over the other. Codon cross recognition was less than 4 percent.
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28
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Saelinger DA, Hoffman JL, McConnell KP. Biosynthesis of selenobases in transfer RNA by Escherichia coli. J Mol Biol 1972; 69:9-17. [PMID: 4560763 DOI: 10.1016/0022-2836(72)90020-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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29
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Folk WR, Yaniv M. Coding properties and nucleotide sequences of E. coli glutamine tRNAs. NATURE: NEW BIOLOGY 1972; 237:165-6. [PMID: 4556376 DOI: 10.1038/newbio237165a0] [Citation(s) in RCA: 47] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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30
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Madison JT, Boguslawski SJ, Teetor GH. Nucleotide sequence of a lysine transfer ribonucleic Acid from bakers' yeast. Science 1972; 176:687-9. [PMID: 17778175 DOI: 10.1126/science.176.4035.687] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The nucleotide sequence of one of the two major lysine transfer RNA's from bakers' yeast has been determined. Its structure is compared to that of a lysine tRNA from a haploid yeast. A total of 21 nucleotides differ in the two molecules. Only the T-psi-C-G (thymidine-pseudouridine-cytidine-guanosine) loop and its supporting stem are identical.
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31
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Rudloff E, Hilse K. Properties of isoaccepting species of lysine tRNA from rabbit reticulocytes in codon recognition and in haemoglobin biosynthesis in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 24:313-20. [PMID: 4945501 DOI: 10.1111/j.1432-1033.1971.tb19688.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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32
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Abstract
The molecular events leading to the synthesis of mature tRNA are only now becoming amenable to experimental study. In bacterial and mammalian cells tRNA genes are transcribed into precursor tRNA. These molecules, when isolated, contain additional nucleotides at both ends (20) of the mature tRNA and lack most modified nucleosides. Presumably, specific nucleases ("trimming" enzymes) cut the precursor to proper tRNA size. The C-C-A nucleotide sequence of the amino acid acceptor end common to all tRNA's does not seem to be coded by tRNA genes (30), and may be added to the trimmed molecules by the tRNA-CMP-AMP-pyrophosphorylase (71). Modifications at the polynucleotide level of the heterocyclic bases or the sugar residues give rise to the modified nucleosides in tRNA. Although newly available substrates have allowed the detection of more of the enzymes involved in these reactions, there is still no knowledge about the sequence of modification or trimming events leading to the synthesis of active tRNA. Progress in these studies may not be easy because enzyme preparations free of nucleases or other tRNA modifying enzymes are required. The role of the modified nucleosides in the biological functions of tRNA is still unknown. Possibly pseudouridine is required for ribosome mediated protein synthesis; some other modified nucleosides in tRNA are not required for this reaction, but may enhance its rate. What might be the role of the large variety of modified nucleosides in tRNA? One is tempted to speculate that such nucleosides are important in other cellular processes in which tRNA is thought to participate such as virus infection, cell differentiation, and hormone action (2, 3). Mutants in a number of tRNA-modifying enzymes are needed in order to extend our knowledge of their purpose and of tRNA involvement in other biological processes. But unless tRNA-modifying enzymes specific for a particular tRNA species exist, no simple selection procedure can be devised. Possibly some of the regulatory mutants of amino acid biosynthesis may prove to affect tRNA-modifying enzymes (72). Transfer RNA's are macromolecules well suited for the study of nucleic acid-protein interactions. The tRNA molecules are structurally very similar, and they interact with a large number of enzymes or protein factors (2, 3). Each aminoacyl-tRNA synthetase, for instance, very precisely recognizes a set of cognate isoacceptor tRNA's (2, 73). The availability of the tRNA- modifying enzymes adds another dimension to the problem of the nature of specific recognition of tRNA by proteins. There are some tRNA-modifying enzymes, such as the uracil-tRNA methylase, which may recognize all tRNA species, while others, such as the isopentenyl-tRNA transferase, probably recognize only a selected set of tRNA molecules, even with different amino acid accepting capacities. With well-characterized RNA precursor and tRNA molecules we can hope to delineate those features of primary, secondary, and tertiary structure involved in the specific interactions of tRNA with these enzymes.
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33
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Eisinger J. Complex formation between transfer RNA'S with complementary anticodons. Biochem Biophys Res Commun 1971; 43:854-61. [PMID: 4935289 DOI: 10.1016/0006-291x(71)90695-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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34
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Bhaduri S, Bose KK, Chatterjee NK, Gupta NK. Purification of Two Valine Transfer Ribonucleic Acid Species from Escherichia coli and Their Coding Properties. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(18)62286-0] [Citation(s) in RCA: 4] [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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35
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Kimura-Harada F, Saneyoshi M, Nishimura S. 5-methyl-2-thiouridine: A new sulfur-containing minor constituent from rat liver glutamic acid and lysine tRNAs. FEBS Lett 1971; 13:335-338. [PMID: 11945700 DOI: 10.1016/0014-5793(71)80254-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- F Kimura-Harada
- National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
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37
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Jukes TH, Gatlin L. Recent studies concerning the coding mechanism. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1971; 11:303-50. [PMID: 4934249 DOI: 10.1016/s0079-6603(08)60331-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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38
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Kwong TC, Lane BG. Differential labelling of the thio, carboxymethyl and methyl substituents of 2-thio-5-carboxymethyluridine methyl ester, a trace nucleoside constituent of yeast transfer RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 224:405-12. [PMID: 5498073 DOI: 10.1016/0005-2787(70)90573-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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39
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Oashi Z, Saneyoshi M, Harada F, Hara H, Nishimura S. Presumed anticodon structure of glutamic acid tRNA from E. coli: a possible location of a 2-thiouridine derivative in the first position of the anticodon. Biochem Biophys Res Commun 1970; 40:866-72. [PMID: 4924671 DOI: 10.1016/0006-291x(70)90983-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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