Hydrodynamic Properties of Wormlike Macromolecules: Monte Carlo Simulation and Global Analysis of Experimental Data

Abstract

A Monte Carlo simulation, coupled with beadmodel hydrodynamic calculation, has been employed to predict hydrodynamic coefficients and other solution properties, of wormlike macromolecules, covering the full range of the wormlike model, from short cylinders to very long, fully flexible chains, eventually including excluded-volume effects. The results have been implemented in a computational tool, Multi-HYDFIT, which performs the determination of the structural parameters from a set of experimental data of various properties for multiple samples with varying molecular weight. An analysis of experimental data of double-stranded DNA demonstrates that the Multi-HYDFIT treatment, with our simulation results, predicts the various solution properties of DNA in an extremely wide range of sizes, from 8 to 200 000 base pairs, yielding values of the parameters that agree with those of the double helix. The scheme is also applied to other synthetic and biological macromolecules, like the very stiff, triple-helical schizophyllan polysaccharide or the very flexible poly(isobutylene) polymer, the latter covering again an extremely wide range that includes quite short oligomers.

Hydrodynamic Models of G-Quadruplex Structures

“…HYDROPRO has been proven to be able to accurately predict the hydrodynamic properties of short DNA duplex strucutures (Fernandes, et al, 2002), longer worm-like DNA duplexes (Amorós, et al, 2011) and monomeric folded quadruplex structures (Le, et al, 2014). These validations lend confidence to efforts to use HYDROPRO to predict more complex higher-order quadruplex structures and to use the predictions to select plausible models for structures that would otherwise be intractable by current crystallographic and NMR methods.…”

“…There are many possible approaches for constructing models, but Garcia de la Torre has provided the particularly useful HYDROPRO (Garcia de la Torre & Harding, 2013; Garcia De La Torre, Huertas, & Carrasco, 2000; Ortega, Amoros, & Garcia de la Torre, 2011) suite of programs to facilitate hydrodynamic bead modeling. HYDROPRO has been validated by studies of both short DNA oligonucleotides (Fernandes, Ortega, Lopez Martinez, & Garcia de la Torre, 2002) and of longer DNA polymers (Amorós, Ortega, & García de la Torre, 2011). Our laboratory has used HYDROPRO to study a variety of G-quadruplex structures.…”

Viscosity Radius of Polymers in Dilute Solutions: Universal Behavior from DNA Rheology and Brownian Dynamics Simulations

“…3m/2 (25) where, the suffixes on the parameters a, b and c indicate the relevant crossover function. The red curve in Fig.…”

“…(25) implies that the excluded volume limit value of the ratio, from fitting Brownian dynamics simulations is, (U ∞ ηR /U θ ηR ) = c η /c g 3m/2 = 0.749. Experimental measurements appear to indicate a value of the ratio, Φ/Φ 0 ≈ 0.773 [19], while the Monte Carlo rigid body simulations of Garcia Bernal et al [31] lead to Φ/Φ 0 ≈ 0.76.…”

Mobility of a Semiflexible Chain Confined in a Nanochannel

“…(5), we computed the Kirkwood mobility through a Monte Carlo integration of eq. (1) [27]. For a given chain configuration, we computed the 3×3 chain hydrodynamic tensor $$\Omega =\frac{1}{{N_b}^2}\sum _{i,j}^{N_b}true[\frac{{\delta }_{ij}}{6\pi \eta a}\mathbf{I}+(1-{\delta }_{ij}){bold\Omega }^{\mathrm{OB}}\left({\mathbf{r}}_{ij}\right)+{bold\Omega }^{\mathrm{normalW}}({\mathbf{r}}_i,{\mathbf{r}}_j)true]$$ In the latter, δ ij is the Kronecker delta, r i and r j are the positions of bead i and j respectively and r ij = r j – r i .…”