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Dobek A, Patkowski A, Labuda D. Light scattering by solutions of tRNA molecules oriented in D.C. magnetic field. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/polc.5070610113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Dobek A, Deprez J. Optical Kerr effect induced by picosecond light pulses in tRNA solutions. J Colloid Interface Sci 1986. [DOI: 10.1016/0021-9797(86)90009-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Englander SW, Kallenbach NR. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 1983; 16:521-655. [PMID: 6204354 DOI: 10.1017/s0033583500005217] [Citation(s) in RCA: 965] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Though the structures presented in crystallographic models of macromolecules appear to possess rock-like solidity, real proteins and nucleic acids are not particularly rigid. Most structural work to date has centred upon the native state of macromolecules, the most probable macromolecular form. But the native state of a molecule is merely its most abundant form, certainly not its only form. Thermodynamics requires that all other possible structural forms, however improbable, must also exist, albeit with representation corresponding to the factor exp( —Gi/RT) for each state of free energyGi(see Moelwyn-Hughes, 1961), and one appreciates that each molecule within a population of molecules will in time explore the vast ensemble ofpossiblestructural states.
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Figueroa N, Keith G, Leroy JL, Plateau P, Roy S, Gueron M. NMR study of slowly exchanging imino protons in yeast tRNAasp. Proc Natl Acad Sci U S A 1983; 80:4330-3. [PMID: 6348768 PMCID: PMC384031 DOI: 10.1073/pnas.80.14.4330] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We have monitored the exchange of imino and amino protons by NMR after quick transfer of yeast tRNAAsp in 2H2O solvent. When the concentration of exchange-catalyzing buffer is not too high, one imino proton exchanges considerably more slowly than any other (e.g., 100 hr versus 4 hr for the second-slowest imino proton at 18 degrees C in 15 mM Mg). This provides excellent conditions for identification, by the nuclear Overhauser effect, of the slowest exchanging proton, which we show to be the imino proton of the U-8 . A-14 reverse Hoogsteen tertiary-structure base pair; other slowly exchanging protons are identified as imino protons from A . U-11 and G . psi-13. In preliminary experiments, we find that the exchange of these protons is catalyzed by cacodylate or Tris buffer. The lifetimes of two other imino protons, ca. 10 min at 28 degrees C, are buffer independent. Slowly exchanging amino protons have also been observed. Correlation with the exchange of the uracil-8 imino proton suggests that they may be from adenine-14.
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Ramstein J, Buckingham RH. Tritium exchange on transfer RNA: slowly exchanging protons sensitive to a change in the dihydrouridine stem. Proc Natl Acad Sci U S A 1981; 78:1567-71. [PMID: 7015338 PMCID: PMC319172 DOI: 10.1073/pnas.78.3.1567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Measurements of tritium exchange on tRNA were made for periods from 0.5 min to 8 hr after separation from labeled solvent. The exchange curve was analysed in terms of three kinetic classes of exchanging protons with half-lives of 5 hr (12 protons), 0.54 hr (37 protons) and about 3.5 min (58 protons) at 0 degrees C in 0.14 M K+/10 mM Mg2+. The behaviour under varying ionic conditions of protons in the slowest exchange class and of some protons in the intermediate class suggests that they are dependent on the tertiary structure of the molecule. Moreover, in the same range of exchange times characteristic of these latter protons, about 9 more protons were observed in the case of a mutant form of tRNA Trp, the UGA-suppressor species, than in the wild-type tRNATrp. These two species differ only in base 24 in the dihydrouridine stem. This dynamic difference between the wild-type and suppressor species may be related to a functionally important difference in coupling between the conformation of the molecule and interactions at the anticodon.
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Patkowski A, Chu B. Intensity fluctuation spectroscopy and transfer RNA conformation. III. Influence of NaCl concentration on the size and shape of the initially salt-free tRNA in solution. Biopolymers 1979; 18:2051-72. [PMID: 497354 DOI: 10.1002/bip.1979.360180816] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Kallenbach NR, Brentani MM, Brentani RR. Direct differential absorbance profiles of denaturing transitions in ribosomal and mRNA. Biopolymers 1979; 18:1515-31. [PMID: 465652 DOI: 10.1002/bip.1979.360180614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
Examination of some published values suggests that the concentration of most tRNAs can be evaluated on the basis of epsilon 260 = 7200/base, in magnesium buffer.
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Affiliation(s)
- M Guéron
- Groupe de Biophysique, Ecole Polytechnique, Palaiseau, France
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Labuda D, Augustyniak J. Dependence of tRNA structure in solution upon ionic condition of the solvent. Fluorescence studies of monovalent cation binding to tRNAPhe from barley embryos. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 79:303-7. [PMID: 913422 DOI: 10.1111/j.1432-1033.1977.tb11810.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dependence of barley phenylalanine tRNA (tRNAPhe) fluorescence intensity at 430 nm upon LiCl, NaCl, KCl, CsCl or NH4Cl concentration was measured in 0.01 M Tris-HCl, pH 7.5, 0.001 M Na2EDTA solutions. Increase of monovalent cation concentration in the solvent from 0 to 2 M induced about 3-fold fluorescence intensity enhancement. The fractional fluorescence change was used as a measure of bound ligand concentration. Fluorescence Scatchard plots revealed three classes of monovalent cation binding sites on the tRNA molecule: interacting (strong) and independent (weak and very weak) sites. Calculated from Scatchard plots binding constants (K), for strong and weak binding of monovalent cations (in the case of Na+ binding: Ks = 26 M-1 and Kw = 4.3 M-1 respectively) exhibit linear dependence upon ionic radius (r). Two limiting values obtained from the plot of K versus r: K(max) at r = 0 r(max) at K = 0, characterize additionally strong and weak monovalent cation binding sites (Ks(max) = 42 M-1 Kw(max) = 8.5 M-1, rs(max) = 0.23 nm and rw(max) = 0.22 nm). A model of the relationship between weak Mg2+ binding sites and monovalent cation binding sites as well as of monovalent cations binding to tRNA is proposed.
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Labuda D, Haertlé T, Augustyniak J. Dependence of tRNA structure in solution upon ionic condition of the solvent. Fluorescence studies of Mg2+ binding to tRNAPhe from barley embryos. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 79:293-301. [PMID: 913421 DOI: 10.1111/j.1432-1033.1977.tb11809.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Bolton PH, Kearns DR. Effect of magnesium and polyamines on the structure of yeast tRNAPhe. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 477:10-9. [PMID: 884107 DOI: 10.1016/0005-2787(77)90156-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The effect of magnesium and polyamines (spermine, spermidine, putrescine and cadaverine) on the structure of yeast tRNAPhe has been investigated. It is found that magnesium induces structural changes and stabilizes hydrogen bonds in the temperature range 22--44 degrees C in 0.17 M sodium. The number of Mg2+ which affect tRNA structure increases from 1 +/- 1 at 22 degrees C to 4 +/- 1 at 44 degrees C and the number of additional base pairs formed in the presence of magnesium increases from 1 +/- 1 at 22 degrees C to 4 +/- 1 at 44 degrees C. The spectral changes are more-or-less sequential. The polyamine spermine stabilizes some, but not all, of the structural features stabilized by magnesium at 44 degrees C, and the combination of magnesium and spermine, at low levels, is more effective than either cation alone in stabilizing tRNA structure. Comparison of the effects of spermine, spermidine, putrescine and cadaverine indicates that it is the asymmetric triamine unit which is important in the stabilization. Some spectral changes induced by magnesium can be assigned to stabilization of specific tertiary structure interactions and to alteration of stacking adjacent to U8-A14.
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Abstract
This review is concerned primarily with the physical structure and changes in the structure of RNA molecules. It will be evident that we have not attempted comprehensive coverage of what amounts to a vast literature. We have tried to stay away from particular areas that have been recently reviewed elsewhere. Citations to and information from them are included, however, so that access to the literature is available. Much of what we treat in depth deals with the crystal structures and solution behaviour of model RNA compounds, including synthetic polymers and molecular fragments such as dinucleoside phosphates. Sequence data on natural RNA are cited, but not in detail. Similarly, apart from tRNA, natural RNAs the structural determinations of which are presently not so far advanced, are not dwelt upon. We have tried to present in detail the available structural data with scaled drawings that permit facile comparisons of molecular geometries.
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Galante E, Caravaggio T, Righetti PG. Binding of ampholine to transfer RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 442:309-15. [PMID: 9139 DOI: 10.1016/0005-2787(76)90305-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The melting temperature of isoaccepting tRNAfMet is affected by Ampholine. The plot of Tm versus the logarithm of Ampholine concentration shows clearly an increasing effect of Ampholine when the pH changes from 7.4 to 4.2. This result is interpreted as binding of Ampholine to the nucleic acid. The effects of Ampholine have been compared with those of soidum, magnesium and tetraethylene pentamine. Ampholine carrier ampholytes at pH 4.2 bind to tRNA with the same affinity as magnesium; at higher pH values they are less active. An hypothesis for the mechanism of action of Ampholine on nucleic acids during isoelectric focusing is proposed.
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Van NT, Holder JW, Woo SL, Means AR, O'Malley BW. Secondary structure of ovalbumin messenger RNA. Biochemistry 1976; 15:2054-62. [PMID: 1276125 DOI: 10.1021/bi00655a005] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The secondary structure of highly purified ovalbumin mRNA was studied by automated thermal denaturation techniques and the data were subjected to computer processing. Comparative studies with 20 natural and synthetic model nucleic acids suggested that the secondary structure of ovalbumin mRNA possesses the following features: the extent of base pairing of ovalbumin mRNA is similar to that found in tRNAs or ribosomal RNAs; the secondary structure of ovalbumin mRNA is more thermolabile than any of the model compounds tested, including the copolymer poly(A-U); ovalbumin mRNA does not have extensive G-C rich stems as found in tRNAs or ribosomal RNAs; the base composition of the double-stranded regions reveals 54% G-C residues which was significantly higher than that noted in the whole molecule (approximately 41.5% G-C). The presence of 46% A-U pairs in short stems of about five base pairs would have a very large destabilizing effect on the secondary structure of ovalbumin mRNA. However, at 0.175 M monovalent cations and 36 degrees C most of the secondary structure of ovalbumin mRNA is preserved. These data suggest that the double-stranded regions in ovalbumin mRNA are of sufficient length to provide the necessary stability for maintaining the open loop regions in an appropriate conformation which may be required for the biological function of ovalbumin mRNA. Furthermore, the lability of the double-stranded regions in ovalbumin mRNA may also be important for the biological function of this mRNA.
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Bonnet J, Ebel JP. Influence of various factors on the recognition specificity of tRNAs by yeast valyl-tRNA synthetase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 58:193-201. [PMID: 241632 DOI: 10.1111/j.1432-1033.1975.tb02364.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Using filtration through nitrocellulose membranes we found that complexes between yeast valyl-tRNA synthetase can easily be detected at low pH and ionic strength with the cognate tRNAVal, but also with several non-cognate tRNAs (tRNAPhe, tRNATyr, tRNAMet and tRNAAsp). We show here that the amino acid linked to the tRNA has no detectable effect on these interactions. The influence of various factors on the discrimination by the enzyme between the cognate and the non-cognate tRNAs has been studied. An increase in pH or ionic strength leads to a decrease in the same ratio of the affinity constants between the enzyme and the cognate as well as the noncognate tRNA. The addition of organic solvents has little effect on these constant either in the cognate or in the non-cognate systems; the addition of substrates of the aminoacylation reaction has not effect on the ratio between the constants. This similar behaviour suggests that at least part of the specific of non-specific interactions must be identical. On the contrary, magnesium between 1 mM and 50 mM increases the specificity of recognition, showing the importance of slight conformational changes in the tRNA molecule to the specificity of interaction.
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Rordorf BF, Kearns DR. NMR investigation of proton exchange in transfer RNA by high resolution NMR. Biochem Biophys Res Commun 1975; 65:857-62. [PMID: 239713 DOI: 10.1016/s0006-291x(75)80464-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Bonnet J, Renaud M, Raffin JP, Remy P. Quantitative study of the ionic interactions between yeast tRNA-Val and tRNA-Phe and their cognate aminoacyl-tRNA ligases. FEBS Lett 1975; 53:154-8. [PMID: 1095410 DOI: 10.1016/0014-5793(75)80008-1] [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: 12/25/2022]
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21
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Wong KL, Wong YP, Kearns DR. Investigation of the thermal unfolding of secondary and tertiary structure in E. coli tRNAfMet by high-resolution Nmr. Biopolymers 1975; 14:749-62. [PMID: 1098699 DOI: 10.1002/bip.1975.360140407] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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22
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Fleming EW, Tewari S, Noble EP. Effects of chronic ethanol ingestion on brain aminoacyl-tRNA synthestases and tRNA. J Neurochem 1975; 24:553-60. [PMID: 234522 DOI: 10.1111/j.1471-4159.1975.tb07674.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Price CC, Yip MTL. Rates of Aziridinium Alkylation of Polynucleotides and Ribonucleic Acid. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42136-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Fasiolo F, Ebel JP. Yeast phenylalanyl-tRNA synthetase. Stoichiometry of the phenylalanyl adenylate-enzyme complex and transfer of phenylalanine from this complex to tRNA-PHE. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 49:257-63. [PMID: 4617679 DOI: 10.1111/j.1432-1033.1974.tb03830.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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25
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Krauskopf M, Araya A, Litvak S. Studies on fish liver protein synthesis. I. Isolation and characterization of shark liver transfer ribonucleic acid. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1974; 48:619-28. [PMID: 4367139 DOI: 10.1016/0305-0491(74)90142-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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26
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Brandts JF, Jackson WM, Ting TY. A calorimetric study of the thermal transitions of three specific transfer ribonucleic acids. Biochemistry 1974; 13:3595-600. [PMID: 4602947 DOI: 10.1021/bi00714a030] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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27
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Crothers DM, Cole PE, Hilbers CW, Shulman RG. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol 1974; 87:63-88. [PMID: 4610153 DOI: 10.1016/0022-2836(74)90560-9] [Citation(s) in RCA: 193] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Trifunac NP, Krasna AI. Alterations in structure and function of transfer ribonucleic acid on chemical methylation. Biochemistry 1974; 13:2403-9. [PMID: 4598625 DOI: 10.1021/bi00708a026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [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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Schuber F, Pinck M. On the chemical reactivity of aminacyl-tRNA ester bond. 3. Influence of ionic strength, spermidine and methanol on the rate of hydrolysis. Biochimie 1974; 56:397-403. [PMID: 4853441 DOI: 10.1016/s0300-9084(74)80148-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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30
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Lynch DC, Schimmel PR. Cooperative binding of magnesium to transfer ribonucleic acid studied by a fluorescent probe. Biochemistry 1974; 13:1841-52. [PMID: 4601164 DOI: 10.1021/bi00706a012] [Citation(s) in RCA: 86] [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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31
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Conformational changes in the thiouridine region of Escherichia coli transfer RNA as assessed by photochemically induced crosslinking. Arch Biochem Biophys 1974. [DOI: 10.1016/0003-9861(74)90259-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Nauheimer U, Hedgcoth C. Activation of several tRNAs of Escherichia coli by the phenoxyacetyl derivative of N-hydroxysuccinimide. Arch Biochem Biophys 1974; 160:631-42. [PMID: 4598621 DOI: 10.1016/0003-9861(74)90440-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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33
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McIntosh AR, Caron M, Dugas H. A specific spin labeling of the anticodon of E. coli tRNA-Glu. Biochem Biophys Res Commun 1973; 55:1356-63. [PMID: 4358937 DOI: 10.1016/s0006-291x(73)80043-9] [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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34
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Buckingham RH, Danchin A, Grunberg-Manago M. The effect of an intramolecular cross-link on reversible denaturation in tryptophan transfer ribonucleic acid from Escherichia coli. Biochemistry 1973; 12:5393-9. [PMID: 4586519 DOI: 10.1021/bi00750a023] [Citation(s) in RCA: 10] [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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35
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Revzin A, Neumann E, Katchalsky A. Metastable secondary structures in ribosomal RNA: a new method for analyzing the titration behavior of rRNA. Biopolymers 1973; 12:2353-83. [PMID: 4592991 DOI: 10.1002/bip.1973.360121216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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Kallenbach NR, Ma RI, Ofengand J, Siddiqui MA. Thermal transitions in E. coli +RNA fMet and two of its molecular fragments. Biopolymers 1973; 12:1247-57. [PMID: 4581148 DOI: 10.1002/bip.1973.360120605] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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