Short Persistence Length Research Articles

Polymer Chains of a Large Persistence Length in a Polymer Brush Require a Lower Force to Be Compressed Than Chains with a Short Persistence Length

The force on a polydisperse polymer brush with chains of increasing persistence length, LP, is obtained by numerical simulations. Unexpectedly, the force needed to compress a stiff brush is smaller...

Measuring the Conformation and Persistence Length of Single-Stranded DNA Using a DNA Origami Structure.

Measuring the mechanical properties of single-stranded DNA (ssDNA) is a challenge that has been addressed by different methods lately. The short persistence length, fragile structure, and the appearance of stem loops complicate the measurement, and this leads to a large variability in the measured values. Here we describe an innovative method based on DNA origami for studying the biophysical properties of ssDNA. By synthesizing a DNA origami structure that consists of two rigid rods with an ssDNA segment between them, we developed a method to characterize the effective persistence length of a random-sequence ssDNA while allowing the formation of stem loops. We imaged the structure with an atomic force microscope (AFM); the rigid rods provide a means for the exact identification of the ssDNA ends. This leads to an accurate determination of the end-to-end distance of each ssDNA segment, and by fitting the measured distribution to the ideal chain polymer model we measured an effective persistence length of 1.98 ± 0.72 nm. This method enables one to measure short or long strands of ssDNA, and it can cope with the formation of stem loops that are often formed along ssDNA. We envision that this method can be used for measuring stem loops for determining the effect of repetitive nucleotide sequences and environmental conditions on the mechanical properties of ssDNA and the effect of interacting proteins with ssDNA. We further noted that the method can be extended to nanoprobes for measuring the interactions of specific DNA sequences, because the DNA origami rods (or similar structures) can hold multiple fluorescent probes that can be easily detected.

The Nanomechanical Properties of Lactococcus lactis Pili Are Conditioned by the Polymerized Backbone Pilin.

Pili produced by Lactococcus lactis subsp. lactis are putative linear structures consisting of repetitive subunits of the major pilin PilB that forms the backbone, pilin PilA situated at the distal end of the pilus, and an anchoring pilin PilC that tethers the pilus to the peptidoglycan. We determined the nanomechanical properties of pili using optical-tweezers force spectroscopy. Single pili were exposed to optical forces that yielded force-versus-extension spectra fitted using the Worm-Like Chain model. Native pili subjected to a force of 0–200 pN exhibit an inextensible, but highly flexible ultrastructure, reflected by their short persistence length. We tested a panel of derived strains to understand the functional role of the different pilins. First, we found that both the major pilin PilB and sortase C organize the backbone into a full-length organelle and dictate the nanomechanical properties of the pili. Second, we found that both PilA tip pilin and PilC anchoring pilin were not essential for the nanomechanical properties of pili. However, PilC maintains the pilus on the bacterial surface and may play a crucial role in the adhesion- and biofilm-forming properties of L. lactis.

Effect of bending flexibility on the phase behavior and dynamics of rods.

We study by means of molecular and Brownian dynamics simulations the influence of bending flexibility on the phase behavior and dynamics of monodisperse hard filamentous particles with an aspect ratio of 8 and persistence lengths equal to 3 and 11 times the particle length. Although our particles are much shorter, the latter corresponds to the values for wild-type and mutant fd virus particles that have been subject of a recent experimental study, where the diffusion of these particles in the nematic and smectic-A phase was investigated by means of video fluorescence microscopy [E. Pouget, E. Grelet, and M. P. Lettinga, Phys. Rev. E 84, 041704 (2011)]. In agreement with theoretical predictions and simulations, we find that for the more flexible particles (shorter persistence length) the nematic (N) to smectic-A (Sm-A) phase transition shifts to larger values of the particle density. Interestingly, we find that for the more rigid particles (larger persistence length), the smectic layer-to-layer distance decreases monotonically with increasing density, whereas for the more flexible ones, it first increases, reaches a maximum and then decreases. For our more flexible particles, we find a smectic-B phase at sufficiently high densities. Moreover, in line with experimental observations and theoretical predictions, we find heterogeneous dynamics in the Sm-A phase, in which particles hop between the smectic layers. We compare the diffusion of our two types of particle at identical values of smectic order parameter, and find that flexibility does not change the diffusive behavior of particles along the director yet significantly slows down the diffusion perpendicular to it. In our simulations, the ratio of diffusion constants along and perpendicular to the director decreases just beyond the N-Sm-A phase transition for both our stiff and more flexible particles.

The Soret effect of mono-, di- and tri-glycols in ethanol

We employed thermal diffusion forced Rayleigh scattering (TDFRS) to investigate the chain length dependence of the thermal diffusion behavior of short glycols in ethanol. We studied three glycols, monoethylenglycol (MEG), diethylenglycol (DEG) and triethylenglycol (TEG), in an ethanol solution. In contrast to the polymer polyethylenglycol, the shorter glycols used within the framework of this study are completely soluble in ethanol, at least for low molar fractions. In order to guarantee a good solubility of the glycols, the measurements were limited to molar fractions of 10% and 20%. As the different glycols only differ by their chain length it will be possible to deduce its influence on the thermal diffusion properties. Due to the fairly short persistence length of the glycols, D(T) reaches already for the dimer a plateau value. This finding agrees with simulation results. Furthermore, the thermal expansion and the kinematic viscosity are measured to investigate if empirical correlations seen for other systems could be confirmed.

Microtubule elasticity: Connecting all-atom simulations with continuum mechanics

The mechanical properties of microtubules have been extensively studied using a wide range of biophysical techniques, seeking to understand the mechanics of these cylindrical polymers. Here we develop a method for connecting all-atom molecular dynamics simulations with continuum mechanics and show how this can be applied to understand microtubule mechanics. Our coarse-graining technique applied to the microscopic simulation system yields consistent predictions for the Young’s modulus and persistence length of microtubules, while clearly demonstrating how binding of the drug Taxol decreases the stiffness of microtubules. The techniques we develop should be widely applicable to other macromolecular systems. Microtubules are essential players in a wide range of cellular functions. The protein tubulin polymerizes to form these filaments resulting in a hollow cylinder with a diameter of about 25 nm and lengths that range from tens of nanometers to tens of microns. Microtubules are the most rigid structures within the cell and their mechanical stability is particularly important for the role that microtubules play in cell division, cellular transport, and their basic ability to help provide cell shape. The mechanical properties of purified microtubules have been studied extensively using many biophysical techniques, including atomic force microscopy, thermal bending, and single molecule techniques [1–11]. Since microtubules are dynamic polymers and have intrinsic instability, many of these experimental studies have been performed on Taxol-stabilized microtubules, although the mechanical consequences of the drug Taxol for microtubule mechanics remains unclear. The majority of studies have found that the addition of Taxol results in ‘‘softer’’ microtubules with a shorter persistence length and lower Young’s modulus [1–5], while one published study had found the opposite result [6]. Recently, even the standard elastic model of microtubules characterized by a single elastic bending constant has been called into question by reports of length-dependent stiffness [12]. Thus, in spite of decades of experimental study, many basic questions and puzzles remain concerning the mechanics of even individual microtubules in vitro, let alone in vivo. Here, we combine all-atom simulations and continuum elastic modeling in order to determine both the elastic parameters of persistence length and Young’s modulus, as well as to test the applicability of simple, continuum shell elasticity for microtubules. Based on a molecular dynamics simulation of a small section of six tubulin monomers [13], we show that the observed fluctuations of this section are consistent with linear elastic constants for both bending and stretching along the microtubule axis. From these measurements, we determine the effective elastic properties for the microtubule wall, treated as an elastic sheet. With the addition of Taxol, we find increased flexibility and reduced bending and stretching moduli. We then examine the shear strain fluctuations of the tubulin sheet and find evidence for enhanced shear compliance, relative to the predictions of homogenous and isotropic elasticity. While anomalously large shear compliance has been suggested recently in connection with lengthdependent bending stiffness of microtubules [12], we find a much smaller degree of anisotropy than previously suggested. The shear elasticity we find is closer to recent experiments [9].

Formation and interaction of membrane tubes.

We show that the formation of membrane tubes (or membrane tethers), which is a crucial step in many biological processes, is highly nontrivial and involves first-order shape transitions. The force exerted by an emerging tube is a nonmonotonic function of its length. We point out that tubes attract each other, which eventually leads to their coalescence. We also show that detached tubes behave like semiflexible filaments with a rather short persistence length. We suggest that these properties play an important role in the formation and structure of tubular organelles.

Stretching Single-Stranded DNA on a Surface

A sufficiently long strand of DNA bends and balls up, like any other polymer longer than its persistence length. The ability to stretch a DNA molecule lengthwise on a substrate has garnered a great deal of attention in the past several years. There has been notable success in stretching double-stranded DNA (dsDNA), but it is more difficult to stretch single-stranded DNA (ssDNA), both because of the very short persistence length and because it is very “sticky,” and attaches nonspecifically to surfaces. In this issue of Nano Letters, Woolley and Kelly present a new method for stretching single-stranded DNA strands on surfaces.

Dynamics of poly(p-phenylene) ladder polymers in solution

Photon correlation spectroscopy in both polarized and depolarized geometry was employed to investigate the dynamics of ribbon-type polymer exhibiting good solubility. In dilute solution, the translational diffusion for all examined molecular weights has confirmed the picture of wormlike chains with rather short (∼ 7 nm) persistence length (Macromolecules 1997, 30, 273). In the semidilute regime, the total concentration fluctuations display, besides the fast dominant cooperative diffusion, a second slower diffusive process that exhibits weak concentration dependence and is not related to the self-diffusion measured by pulse-field-gradient NMR. The concentration dependence of the cooperative and the self-diffusion coefficient as well as of the zero-shear viscosity cannot be consistently described by neither flexible nor stiff chain models. Presence of aggregates was revealed at high concentrations. Owing to the short persistence length, the rotational diffusion is too fast to be adequately investigated.