On the conformation of transfer RNA in solution: Dependence of denaturation temperature and structural parameters of mixed and formylmethionyl Escherichia coli transfer RNA on sodium ion concentration

Goldstein, Richard; Stefanović, S; Kallenbach, Neville R.

doi:10.1016/0022-2836(72)90227-6

Cited by 52 publications

(11 citation statements)

References 59 publications

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“…It has been shown that sodium and magnesium ions act in a very similar way upon the structure of the tRNA (18,19,20,21 and references therein). But, to have an identical effect, concentrations of sodium 100 to 1000 times larger than those of magnesium are required.…”

Section: Resultsmentioning

confidence: 98%

Quantitative study of the ionic interactions between yeast tRNA^Val and tRNA^Phe and their cognate aminoacyl‐tRNA ligases

Bonnet

Renaud

et al. 1975

FEBS Letters

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Section: Resultsmentioning

confidence: 98%

Quantitative study of the ionic interactions between yeast tRNA^Val and tRNA^Phe and their cognate aminoacyl‐tRNA ligases

Bonnet

Renaud

et al. 1975

FEBS Letters

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“…Very short isolated RNA hairpins exhibit a values already comparable to poly(A,G,U,C): for a fragment of tRNA containing 19 nucleotides and a single helical region, for example, a = 7,26 while that of a fragment containing 57 nucleotides and two short helices is 12, identical with intact tRNA. 27 The low values of poly(A,G,U,C) and procollagen mRNA (see Table I) could, in principle, reflect either the presence of only very short mean helical lengths for base-paired sequences or short chain lengths of the RNA preparation. While there are clearly various chain lengths present in the poly(A,G,U,C) preparation, the 22s procollagen mRNA preparation must contain very short helical sequences, since a is not much above that for the shorter tRNA fragment even with the amplifying effect of high molecular weight.…”

Section: Discussionmentioning

confidence: 98%

Direct differential absorbance profiles of denaturing transitions in ribosomal and mRNA

Kallenbach

Brentani²,

Brentani³

1979

Biopolymers

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SynopsisA direct method for measuring the derivative of thermal transition profiles (AAIAT), first described by Pavlov and Lyubchenko [Biopolymers 17, 795-798 (197811, is applied to the secondary structure of several eukaryotic ribosomal and messenger RNAs. The method consists of generating an effective AT between a sample and reference cuvette by altering the T, (midpoint denaturation temperature) of one of the solutions with respect to the other. This can be done by changing salt concentration, solvent, pH, or ligands. Scanning the two cuvettes by varying the wavelength a t different temperatures permits detailed examination of the base composition of differentially melting domains. We report here the AAlAT profiles generated by monovalent ion concentration differences for a number of high-molecular-weight natural RNAs, as well as the synthetic polynucleotides poly(rA) and "random" polylrThe 18s and 28s rRNAs from chick embryos exhibit a reproducible series of peaks in the AAIAT profiles a t low salt with A T = 4K. The high-temperature transitions in 28s rRNA appear to contain G-C base pairs exclusively, in contrast to those in 18s rRNA or any natural mRNA. Each mRNA we have examined (bacteriophage MS2, globin mRNA from rabbit reticulocytes, and procollagen mRNA from chick embryos) exhibits a distinctive AAIAT profile in low salt. The stability of many of the transitions in each of the mRNAs is no greater than that of the secqndary structure in random poly(A,G,U,C) in low salt. More than 50% of the base pairing in procollagen mRNA actually "melts" below the mean for the random copolymer, indicating that despite its high G.C content, this mRNA contains a secondary structure that is exceptionally low in Stability.

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“…(1). In order to check the goodness of this fit, which indicates that the solution is monodisperse, and to obtain r values whenever the correlation function is not a singleexponential one, the cumulants method was used.…”

Section: Translational Diffusionmentioning

confidence: 99%

“…Doppler spectral broadening of the scattered light due to thermal Brownian motions of macromolecules in solution can be described by the translational diffusion coefficient D T, which may be obtained from a photocount autocorrelation function G(2)( 7),12 (1) where the normalized electric field autocorrelation function for a monodisperse sample of noninteracting macromolecules is g(l)( 7 ) = exp( -F7) and the linewidth r = D T K 2 with K = (47rn/Xo) sin (0/2) (2) being the scattering vector; 0, the scattering angle; XO, the wavelength of light in uacuo; and n , the refractive index of the scattering medium.…”

Section: Theory Translational Diffusionmentioning

confidence: 99%

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

Patkowski

Chu

1979

Biopolymers

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SynopsisThe influence of sodium ion concentration in solution on the initially salt-free conformation of bulk tRNA from baker's yeast has been investigated by means of photon correlation spectroscopy. From the measured values of translational (DT) and rotational (DR) diffusion coefficients, the semiaxes of an ellipsoid of revolution, which are hydrodynamically equivalent to the tRNA molecule, were calculated for tRNA solutions in pure HzO as well as in 0.005, 0.1, 0.5M NaCl and 0.01M MgClz solutions a t pH 4.2 and 7.5. These data, combined with our previous studies, suggested a model which describes the formation of an ordered tRNA structure due to increasing NaCl concentrations. Furthermore, we have obtained information concerning intermolecular interactions between tRNA molecules in solution. In low-salt or salt-free tRNA solutions, we detected in the linewidth distribution function an extra-fast component which can be attributed as possibly due to charge fluctuations related to the reaction of ionization of organic bases. In our light-scattering linewidth measurements, we do not see fluctuations of charged and uncharged states directly as concentration fluctuations. Rather, we postulate a modulation of long-range intermolecular electrostatic interactions between the tRNA molecules due to such charge fluctuations. It is this modulation which is related to the fast component of the time correlation function a t finite concentrations. A quantitative theory is needed to provide a more definitive explanation of the dynamical behavior of tRNA in salt-free or low-salt solutions.

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On the conformation of transfer RNA in solution: Dependence of denaturation temperature and structural parameters of mixed and formylmethionyl Escherichia coli transfer RNA on sodium ion concentration

Cited by 52 publications

References 59 publications

Quantitative study of the ionic interactions between yeast tRNA^Val and tRNA^Phe and their cognate aminoacyl‐tRNA ligases

Quantitative study of the ionic interactions between yeast tRNA^Val and tRNA^Phe and their cognate aminoacyl‐tRNA ligases

Direct differential absorbance profiles of denaturing transitions in ribosomal and mRNA

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

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On the conformation of transfer RNA in solution: Dependence of denaturation temperature and structural parameters of mixed and formylmethionyl Escherichia coli transfer RNA on sodium ion concentration

Cited by 52 publications

References 59 publications

Quantitative study of the ionic interactions between yeast tRNAVal and tRNAPhe and their cognate aminoacyl‐tRNA ligases

Quantitative study of the ionic interactions between yeast tRNAVal and tRNAPhe and their cognate aminoacyl‐tRNA ligases

Direct differential absorbance profiles of denaturing transitions in ribosomal and mRNA

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

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Quantitative study of the ionic interactions between yeast tRNA^Val and tRNA^Phe and their cognate aminoacyl‐tRNA ligases

Quantitative study of the ionic interactions between yeast tRNA^Val and tRNA^Phe and their cognate aminoacyl‐tRNA ligases