Comparison of the structure of ribosomal 5S RNA from E. coli and from rat liver using X-ray scattering and dynamic light scattering

Jj, Müller; Tn, Zalkova; Zirwer, Dietrich; Misselwitz, Rolf; Gast, Klaus; In, Serdyuk; Welfle, Heinz; Damaschun, G.

doi:10.1007/bf00254212

Cited by 22 publications

(7 citation statements)

References 20 publications

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“…35 In these conditions as a result of electrostatic interactions the diffusion coefficient value extrapolated to the zero concentration is charged with a relatively great error (due to the strong dependence of D T on polymer concentration usually observed at low ionic strength), nevertheless the value obtained by Müller in the limit of error is comparable with that obtained by us (Table I).…”

Section: Discussionsupporting

confidence: 81%

Structural similarity of E. coli 5S rRNA in solution and within the ribosome

et al. 2004

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The article presents translational and rotational diffusion coefficients of 5S rRNA determined experimentally by the method of dynamic light scattering (DLS) and its comparison with the values predicted for different models of this molecule. The tertiary structure of free 5S rRNA was proposed on the basis of the atomic structures of the 5S rRNA from E. coli and H. marismortui extracted from the ribosome. A comparison of the values of DT, tauR, and Rg predicted for different models with experimental results for the free molecule in solution suggests that free 5S rRNA is less compact than that in the complex with ribosomal proteins. In general, the molecules of 5S rRNA consist of three domains: a short one and two longer ones. As follows from a comparison of the results of our simulations with experimental values, in the molecule in solution the two closest helical fragments of the longer domains remain collinear, whereas the short domain takes a position significantly deviated from them.

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Section: Discussionsupporting

confidence: 81%

Structural similarity of E. coli 5S rRNA in solution and within the ribosome

et al. 2004

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“…The diffusion coefficients, D, and hydrodynamic radii, r h , were calculated from the determined diffusion times at saturation (Table 1). These values correspond to the theoretically calculated data and are comparable to experimental data using other RNA molecules, e.g., 5S rRNA (120 nt) with D ¼ 5.9 Â 10 À11 m 2 /s and r h ¼ 3.6 Â 10 À9 m (24).…”

Section: Resultssupporting

confidence: 88%

Fluorophore Binding Aptamers as a Tool for RNA Visualization

Eydeler

Magbanua

Werner

et al. 2009

Biophysical Journal

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Fluorescence correlation spectroscopy (FCS) is suitable for the detection of fluorescent molecules in living cells. For the visualization of mRNA, we genetically fused a fluorophore-specific RNA aptamer to the coding mRNA of the green fluorescent protein, as well as to noncoding sequences. Using these constructs, we showed that the aptamer portion of the mRNA still binds the fluorophore in the nanomolar range as determined via FCS. Furthermore, the binding took place in the context of total RNA extract. A tandem construct of the RNA aptamer even exhibited a lower K(d) than the monomer. This FCS-based method establishes a tool for minimal invasive detection of RNA at the single molecule level in individual living cells.

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“…As observed, the results coming from our BD simulations agree relatively well with both experimental data and rigid body hydrodynamic predictions. In particular, our predictions for D t and R g are coincident with some of the experimental measurements collected in Table 2 [ 48 , 49 ]. If we use our predicted D t value (6.2×10 −7 cm 2 /s) and the Svedberg equation ( ), we obtain a value for the sedimentation coefficient s ≃5 S what further supports the validity of the scheme employed in this work.…”

Section: Resultssupporting

confidence: 85%

Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA

et al. 2015

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BackgroundThe possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational scheme for predicting global properties and mimicking the internal dynamics of RNA molecules in solution. A simple coarse-grained model with one bead per nucleotide and two types of intra-molecular interactions (elastic interactions and excluded volume interactions) is used to represent the RNA chain. The elastic interactions are modeled by a set of Hooke springs that form a minimalist elastic network. The Brownian dynamics technique is employed to simulate the time evolution of the RNA conformations.ResultsThat scheme is applied to the 5S ribosomal RNA of E. Coli and the yeast phenylalanine transfer RNA. From the Brownian trajectory, several solution properties (radius of gyration, translational diffusion coefficient, and a rotational relaxation time) are calculated. For the case of yeast phenylalanine transfer RNA, the time evolution and the probability distribution of the inter-arm angle is also computed.ConclusionsThe general good agreement between our results and some experimental data indicates that the model is able to capture the tertiary structure of RNA in solution. Our simulation results also compare quite well with other numerical data. An advantage of the scheme described here is the possibility of visualizing the real time macromolecular dynamics.Electronic supplementary materialThe online version of this article (doi:10.1186/s13628-015-0025-7) contains supplementary material, which is available to authorized users.

show abstract

Comparison of the structure of ribosomal 5S RNA from E. coli and from rat liver using X-ray scattering and dynamic light scattering

Cited by 22 publications

References 20 publications

Structural similarity of E. coli 5S rRNA in solution and within the ribosome

Structural similarity of E. coli 5S rRNA in solution and within the ribosome

Fluorophore Binding Aptamers as a Tool for RNA Visualization

Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA

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