Hydrodynamic properties of a double-helical model for DNA.
TL;DR: The translational and rotational diffusion coefficients of very short DNA fragments have been calculated using a double-helical bead model in which each nucleotide is represented by one bead, indicating that the internal motion of the bases has a remarkable amplitude.
About: This article is published in Biophysical Journal.The article was published on 1994-05-01 and is currently open access. It has received 38 citations till now. The article focuses on the topics: Rotational diffusion & Radius.
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TL;DR: The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in the previous article, using a HYDROPRO public-domain computer program.
1,058 citations
TL;DR: The ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, is extended to models with lower, residue-level resolution, allowing calculations when atomic resolution is not available or coarse-grained models are preferred.
602 citations
Cites background from "Hydrodynamic properties of a double..."
...From early studies of the hydrodynamics of small, quasirigid oligonucleotides (21, 32), we know that nucleotide unit can be represented by a bead with radius 3....
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...This was pioneered by our group for the case of nucleic acids (21)....
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TL;DR: In this article, a review of DLS techniques for studying sizes and shapes of nanoparticles in liquids is presented. But the authors focus on the time fluctuations in the intensity of light scattered by the particle dispersion.
Abstract: Dynamic light scattering (DLS) techniques for studying sizes and shapes of nanoparticles in liquids are reviewed. In photon correlation spectroscopy (PCS), the time fluctuations in the intensity of light scattered by the particle dispersion are monitored. For dilute dispersions of spherical nanoparticles, the decay rate of the time autocorrelation function of these intensity fluctuations is used to directly measure the particle translational diffusion coefficient, which is in turn related to the particle hydrodynamic radius. For a spherical particle, the hydrodynamic radius is essentially the same as the geometric particle radius (including any possible solvation layers). PCS is one of the most commonly used methods for measuring radii of submicron size particles in liquid dispersions. Depolarized Fabry-Perot interferometry (FPI) is a less common dynamic light scattering technique that is applicable to optically anisotropic nanoparticles. In FPI the frequency broadening of laser light scattered by the particles is analyzed. This broadening is proportional to the particle rotational diffusion coefficient, which is in turn related to the particle dimensions. The translational diffusion coefficient measured by PCS and the rotational diffusion coefficient measured by depolarized FPI may be combined to obtain the dimensions of non-spherical particles. DLS studies of liquid dispersions of nanometer-sized oligonucleotides in a water-based buffer are used as examples.
549 citations
TL;DR: A computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure, using bead models for prediction of hydrodynamic properties of arbitrarily shaped particles.
521 citations
TL;DR: The results indicate that nonspecific adsorption of single-stranded DNA on the surface and subsequent two-dimensional diffusion can significantly enhance the overall reaction rate and suggest that there is an optimal surface probe density when 2D diffusion occurs.
236 citations
References
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TL;DR: In this article, a model-free approach to the interpretation of nuclear magnetic resonance relaxation experiments on macromolecules in solution is presented, which uses the above spectral density to least-squares fit relaxation data by treating S/sup 2 and T/sub e/ as adjustable parameters.
Abstract: A new approach to the interpretation of nuclear magnetic resonance relaxation experiments on macromolecules in solution is presented. This paper deals with the theoretical foundations and establishes the range of validity of this approach, and the accompanying paper demonstrates how a wide variety of experimental relaxation data can be successfully analyzed by using this approach. For both isotropic and anisotropic overall motion, it is shown that the unique imformation on fast internal motions contained in relaxation experiments can be completely specified by two model-independent quantities; (1) a generalized order parameter, S, which is a measure of the spatial restriction of the motion, and (2) an effective correlation time, T/sub e/, which is a measure of the rate of motion. A simple expression for the spectral density involving these two parameters is derived and is shown to be exact when the internal (but not overall) motions are in the extreme narrowing limit. The model-free approach (so called because S/sup 2/ and T/sub e/ have model-independent significance) consists of using the above spectral density to least-squares fit relaxation data by treating S/sup 2/ and T/sub e/ as adjustable parameters. The range of validity of this approach is illustrated by analyzing error-free relaxationmore » data generated by using sophisticated dynamical models. Empirical rules are presented that allow one to estimate the of S/sup 2/ and T/sub e/ extracted by using the model-free approach by considering their numerical values, the resonance frequencies, and the parameters for the overall motion. For fast internal motions, it is unnecessary to use approaches based on complicated spectral densities derived within the framework of a model because all models that can give the correct value of S/sup 2/ work equally well.« less
3,562 citations
TL;DR: In this paper, the translational and rotational brownian dynamics of dissolved macromolecules were analyzed using quasielastic light scattering, transient electric birefringence and fluorescence anisotropy decay.
Abstract: Among the Various methods for characterizing macromolecules in solution, hydrodynamic techniques play a major role. Since the advent of the ultracentrifuge and the development of viscometric apparatus, sedimentation coefficients and intrinsic viscosities have been extensively used to learn about the size and shape of synthetic and biological polymers. More recently, refined techniques such as quasielastic light scattering, transient electric birefringence and fluorescence anisotropy decay have made it possible to obtain in a simple and rapid way quantitative information of high precision on the translational and rotational brownian dynamics of dissolved macromolecules.
588 citations
TL;DR: Tirado et al. as mentioned in this paper extended the formalism for the calculation of translational friction coefficients of symmetric top macromolecules and derived analytical solutions that reduce to those obtained by other authors when the unmodified interaction tensor is used.
Abstract: The formalism for the calculation of translational friction coefficients of symmetric top macromolecules presented in a previous paper [M. M. Tirado and J. Garcia de la Torre, J. Chem. Phys. 71, 2585 (1979)] is here extended to the evaluation of rotational friction and diffusion coefficients. We show how the introduction of symmetry considerations leads to a great reduction of the computational requirements needed to solve the hydrodynamic interaction equations. We also obtain the translation–rotation coupling tensor from which the center of hydrodynamic stress can be obtained. For a rigid ring we have derived analytical solutions that reduce to those obtained by other authors when the unmodified interaction tensor is used. The general formalism is finally applied to the calculation of the rotational diffusion coefficients of circular cylinders modeled as stacks of rings and extrapolated to zero bead size. The resulting values are critically compared with those from earlier studies.
382 citations
TL;DR: In this article, the hydrodynamic interaction equations and the interaction tensor that appear in the theoretical formalism for calculating translational friction coefficients of rigid particles modeled as assemblies of beads, are formulated in cylindrical coordinates.
Abstract: The hydrodynamic interaction equations and the interaction tensor that appear in the theoretical formalism for calculating translational friction coefficients of rigid particles modeled as assemblies of beads, are formulated in cylindrical coordinates For symmetric top particles, the cylindrical shielding tensors of symmetry‐equivalent beads are the same, and have only five nonzero components This effects a great simplification with respect to the Cartesian formalism Application is made to the end‐effect correction, for translational motion of right circular cylinders modeled as stacks of rings, extrapolated to zero bead size No appreciable changes in the translational friction coefficients are found when the hollow cylindrical models are capped at the ends with disc‐shaped plates For finite cylinders with axial ratio p≳2, our results, as well as those from other theoretical and experimental studies, are in remarkable disagreement with the previous calculations by Broersma
378 citations
TL;DR: It is shown that, in the limit of a continuous surface distribution, a shell model reproduces Stoke's law for a sphere.
Abstract: The theory of Kirkwood for the translational frictional coefficients of structures composed of subunits has been generalized in two ways in order to consider aggregates of nonidentical subunits. One of these generalizations fails when the sizes of subunits are too disparate; the other, derived from a surface shell distribution of frictional elements, is effective over the whole range of relative sizes. It is shown that, in the limit of a continuous surface distribution, a shell model reproduces Stoke's law for a sphere. Comparison is made between the frictional coefficients of spheres, ellipsoids, and rods modeled by finite numbers of subunits and by continuous shells of frictional elements, and those calculated from other theories. Agreement is generally good, though the shell model for prolate ellipsoids of revolution deviates by a few per cent from the Perrin value.
349 citations