Conformational changes in the thiouridine region of Escherichia coli transfer RNA as assessed by photochemically induced crosslinking

Delaney, Pamela; Bierbaum, Joan; Ofengand, James

doi:10.1016/0003-9861(74)90259-8

Cited by 24 publications

(10 citation statements)

References 21 publications

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“…Inspection of the X-ray models suggests that the charge density involved in creating the compact tertiary form is considerable so that electrostatic interactions are crucial. At low ionic strength, in the absence of Mg 2+ or other divalent ions, progressive unfolding of this compact form can be monitored by increase in the intrinsic viscosity, changes in CD spectra, rate and number of exchanging protons (Goldstein, Stefanovic & Kallenbach, 1972), and the rate and extent of photochemical crosslinking between s*U and C 13 (Yaniv, Favre & Barrell, 1969;Ofengand & Bierbaum, 1973;Delaney, Bierbaum & Ofengand, 1974;Favre, Buckingham & Thomas, 1975). On the basis of equilibrium and kinetic absorbance changes in several tRNAs of E. coli, Cole et al (1972) proposed a phase diagram for tRNA involving transitions from the tertiary form to structures approximating clover-leafs at high ionic strength, giving way to distorted extended structures that minimize the increased electrostatic free energy at low ionic strength (Fig.…”

Section: Iq 77)-mentioning

confidence: 99%

RNA structure

Kallenbach

Berman

1977

Quart. Rev. Biophys.

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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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Section: Iq 77)-mentioning

confidence: 99%

RNA structure

Kallenbach

Berman

1977

Quart. Rev. Biophys.

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“…Conditions were those of Methods. Also included (* ) are the data of Delaney et al (7). This is important because it might otherwise be possible that the apparent differences in rate of cross-linking arise from a competing side reaction k 4 k4 8 -13 cross-link -…”

Section: R E S U L T Smentioning

confidence: 99%

tRNA tertiary structure in solution as probed by the photochemically induced 8-13 cross-link

Favre¹,

Buckingham²,

Thomas³

1975

Nucl Acids Res

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The conformation of ten purified tRNAs from Escherichia Coli has been investigated by means of the photo-induced cross-linking of 4Srd8 and Cyd13, which is sensitive to the juxtaposition of the two bases. Three tRNAs photo-react abnormally slowly; tRNAPhe, tRNAMet/m a and tRNAVal/2; a comparison with normally reacting species suggests that base 47 (Urd or modified Urd) is involved in a tertiary interaction in Class I tRNAs with the triplet 8, 14, 28. The UGA suppressor tRNATrp photoreacts significantly slower than the wild type. Thus the single base change Gua 24 to Ade induces a conformational change that alters the rate constant for the cross-linking reaction.

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“…cross-linking reaction (Delaney et al, 1974) were dependent on the Mg2+ concentration, an attempt was made to correlate these differences with the rates of aminoacylation catalyzed by E. coli methionine-tRNA synthetase as a function of Mg2+ concentration. The kinetic experiments were carried out under conditions similar to those used by Lawrence et al, (1973) and the results are plotted in Figure 7 in the form of initial rate vs. MgCL concentration with and without 150 mM NH4CI.…”

Section: Effect Of Mg2+mentioning

confidence: 99%

“…In addition, structural differences in the s4U8 region of the molecule had been inferred from differences in the respective abilities of the two tRNA's to form the photochemically induced cross-linked product between s4U8 and Cl3 (Delaney et al, 1974). It had been noted from the x-ray crystallographic data on yeast tRN Aphe (Kim et al, 1974) that the positively charged m7G is involved in an ionic interaction with nearby phosphate groups; this type of interaction is precluded upon Methods Preparation of tRNAMe,f].…”

mentioning

confidence: 99%

Changes in tertiary structure accompanying a single base change in transfer RNA. Proton magnetic resonance and aminoacylation studies of Escherichia coli tRNA^Metf1 and tRNA^Metf3 and their spin-labeled (S⁴U8) derivatives

Daniel¹,

Cohn²

1976

Biochemistry

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The properties of Escherichia coli tRNAMet f1 and tRNAMet f3 that differ by only one base change, m7G to A at position 47, have been compared structurally by proton magnetic resonance and functionally by the aminoacylation reaction. The NMR spectra of the two tRNA species in the region between 0 and 4 ppm below 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS) (methyl and methylene region) were the same except for the absence of the lowest field peak at 3.8 ppm in tRNAMet f3, thus unequivocally identifying this resonance at the methyl group of m7G47 of tRNAMet f1. The same resonance disappears in tRNAMet f1 spin-labeled at s4U8 and reappears in the diamagnetic reduced spin-labeled tRNAMet f1 from which the average distance between the spin-label and the methyl protons of m7G is estimated to be less than 15 A. The proximity of m7G47 but not T55 to s4U8 in the structure of E. coli tRNAMet f1 in solution is consistant with the crystallographic model for yeast tRNAPhe. A spectral comparison of the hydrogen-bond regions (11-14 ppm below DSS) of tRNAMet f1 and tRNAMet f3 reveals major shifts of four resonances previously assigned to tertiary hydrogen bonds. Of the four, the one at lowest field (14.8 ppm) had been assigned by chemical modification to the tertiary (s4U8-A14) hydrogen bond and the one at 13.3 ppm had been tentatively assigned to the tertiary hydrogen bond G23-m7G47 of the 13-23-47 triple. A more positive assignment of the G23-m7G47 at 13.3 ppm could be made from the additional evidence that this resonance, which was first observed in the difference spectrum between spin-labeled tRNAMet f1 and its reduced form, is the only one missing in the analogous difference spectrum of tRNAMet f3. At low ionic strength and in the absence of magnesium ions, the differences in the hydrogen-bonded region of the NMR spectra of tRNAMet f1 and tRNAMet f3 are much greater than in the presence of magnesium ions. The optimal magnesium concentration required for maximal initial velocities is also higher for tRNAMet f3 than for tRNAMet f1. The perturbation caused by the spin-label in destabilizing hydrogen bonds in the region between 13 and 14 ppm is greater for tRNAMet f3 than tRNAMet f1 but the distance relations for the hydrogen bonds in the region between 12 and 13 ppm (the major paramagnetic perturbations) are conserved in the two species. The disruption of one hydrogen bond relative to native tRNAMet f1 either by spin-labeling (s4U8-A14) or by substitution of m7G by A in tRNAMet f3 has little effect on the aminoacyl acceptor activity or the velocity of the aminoacylation reaction at optimal magnesium concentration, but the absence of both tertiary hydrogen bonds in the augmented D-helix region in the spin-labeled tRNAMet f3 results in approximately 60% reduction both in acceptance activity and in initial velocity of the aminoacylation reaction.

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Conformational changes in the thiouridine region of Escherichia coli transfer RNA as assessed by photochemically induced crosslinking

Cited by 24 publications

References 21 publications

RNA structure

RNA structure

tRNA tertiary structure in solution as probed by the photochemically induced 8-13 cross-link

Changes in tertiary structure accompanying a single base change in transfer RNA. Proton magnetic resonance and aminoacylation studies of Escherichia coli tRNA^Metf1 and tRNA^Metf3 and their spin-labeled (S⁴U8) derivatives

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Conformational changes in the thiouridine region of Escherichia coli transfer RNA as assessed by photochemically induced crosslinking

Cited by 24 publications

References 21 publications

RNA structure

RNA structure

tRNA tertiary structure in solution as probed by the photochemically induced 8-13 cross-link

Changes in tertiary structure accompanying a single base change in transfer RNA. Proton magnetic resonance and aminoacylation studies of Escherichia coli tRNAMetf1 and tRNAMetf3 and their spin-labeled (S4U8) derivatives

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Changes in tertiary structure accompanying a single base change in transfer RNA. Proton magnetic resonance and aminoacylation studies of Escherichia coli tRNA^Metf1 and tRNA^Metf3 and their spin-labeled (S⁴U8) derivatives