Hydrodynamic properties of a double-helical model for DNA

Torre, José Garcı́a de la; Navarro, Sonia; Martı́nez, M.C.

doi:10.1016/s0006-3495(94)80949-x

Cited by 39 publications

(29 citation statements)

References 22 publications

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“…At the core of HYDRONMR there is a simplified version of HYDRO (16,30) in which some features or options of the general version are removed or preset. Thus, we have suppressed the calculation of the sedimentation coefficient and the intrinsic viscosity, which requires data for molecular weight and the partial specific volume of the macromolecule.…”

Section: Hydrodynamic Calculationsmentioning

confidence: 99%

HYDRONMR: Prediction of NMR Relaxation of Globular Proteins from Atomic-Level Structures and Hydrodynamic Calculations

Torre

Huertas

Carrasco

2000

Journal of Magnetic Resonance

511

415

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Section: Hydrodynamic Calculationsmentioning

confidence: 99%

HYDRONMR: Prediction of NMR Relaxation of Globular Proteins from Atomic-Level Structures and Hydrodynamic Calculations

Torre

Huertas

Carrasco

2000

Journal of Magnetic Resonance

511

415

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“…20 The choice of a particular one depends on the size of the molecule and the kind of information desired. A convenient model is bead per residue (BPR) model, which has been successfully applied for tRNA 21 and DNA, 22 and in which each nucleotide is replaced by a bead of the radius . In this article, we have assumed a more complex version of this model, namely a double bead per residue (DBPR) model, which has been tested for tRNA and short sections of DNA.…”

Section: Bead Modelmentioning

confidence: 99%

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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“…23,24 DNA surface areas were estimated from the length of each oligomer, calculated as described above, assuming a radius of 10Å for dsDNA 39 and 5Å for ssDNA. 40 As expected from Figure 6, the mobilities calculated from the Manning equation (open circles) in Figure 8A are very close to the observed mobilities (solid circles).…”

Section: Resultsmentioning

confidence: 99%

Electrophoretic Mobilities of the Charge Variants of DNA and Other Polyelectrolytes: Similarities, Differences, and Comparison with Theory

Stellwagen

2017

J. Phys. Chem. B

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The free solution electrophoretic mobilities of polyelectrolytes with different charge densities have been analyzed using data taken from the literature. The polyions include single- and double-stranded DNA oligomers, small aromatic molecules, peptides, proteins and synthetic copolymers. Mobility variations due to differences in the background electrolytes were minimized by calculating mobility ratios, dividing the mobility of each charge variant in each data set by the mobility of the most highly charged polyion in that data set. In all cases, the mobility ratios increase linearly with the logarithm of the fractional charge, not the first power of the charge as usually assumed. In addition, the mobility ratios observed for all polyelectrolytes except the synthetic copolymers exhibit a common dependence on the logarithm of fractional charge. The unique results observed for the synthetic copolymers may be due to the flexibility of their hydrocarbon backbones, in contrast to the relatively rigid hydrophilic backbones of the other polyelectrolytes. The mobilities observed for the DNA charge variants are well predicted by the Manning electrophoresis equation, while the mobilities predicted by zeta potential theories are too high. However, mobility ratios calculated from both theories agree with the observed results.

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Hydrodynamic properties of a double-helical model for DNA

Cited by 39 publications

References 22 publications

HYDRONMR: Prediction of NMR Relaxation of Globular Proteins from Atomic-Level Structures and Hydrodynamic Calculations

HYDRONMR: Prediction of NMR Relaxation of Globular Proteins from Atomic-Level Structures and Hydrodynamic Calculations

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

Electrophoretic Mobilities of the Charge Variants of DNA and Other Polyelectrolytes: Similarities, Differences, and Comparison with Theory

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