Mechanical and structural properties of YOYO-1 complexed DNA

YOYO-1 is a fluorescent dye widely used for probing the statistical–mechanical properties of DNA. However, currently contradicting data exist how YOYO-1 binding alters the DNA structure and rigidity. Here, we systematically address this problem using magnetic tweezers. Remarkably, we find that the persistence length of DNA remains constant independent of the amount of bound YOYO-1, which contrasts previous assumptions. While the ionic conditions can considerably alter the stability of YOYO-1 binding, the DNA bending rigidity seems not to be affected. We furthermore determine important structural parameters such as the binding site size, the elongation, as well as the untwisting angle per bound YOYO-1 molecule. We expect that our assay, in which all the parameters are determined within a single experiment, will be beneficial for a large range of other DNA binding drugs.     

Mechanical properties of films and three-dimensional scaffolds made of fibroin and gelatin

Silk fibroin is a biocompatible and biodegradable material, which can be used in surgery and tissue engineering. To improve the cell adhesion on fibroin surface, gelatin can be added to the items made of fibroin. This work compares the mechanical properties of films and three-dimensional scaffolds made of fibroin and fibroin with gelatin. The addition of 30% gelatin to the fibroin scaffold does not change its microstructure or swelling. The addition of gelatin decreases the mechanical properties of films (decreases the Young’s modulus, the maximum strain and elongation) but increases the shear modulus of the scaffolds.     

Mechanical and barrier properties of nanocrystalline cellulose reinforced chitosan based nanocomposite films

Nanocrystalline cellulose (NCC) reinforced chitosan-based biodegradable films were prepared by solution casting. The NCC content in the films was varied from 1 to 10% (dry wt. basis). It was found that the tensile strength (TS) of the nanocomposite films with 5% (w/w) NCC content was optimum with an improvement of 26% compared to the control chitosan films. Incorporation of NCC also significantly improved barrier properties. Water vapor permeability (WVP) of the chitosan/NCC films was decreased by 27% for the optimum 5% (w/w) NCC content. Swelling studies revealed a decrease in water uptake of the NCC-reinforced chitosan films. Analyses of thermal properties showed no significant effect of NCC whereas X-ray diffraction studies confirmed the appearance of crystalline peaks in the nanocomposite films. Surface morphology of the films was investigated by scanning electron microscopy and it was found that NCC was dispersed homogenously into chitosan matrix.     

Mechanical deformation behaviors and structural properties of ligated DNA crystals

DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here, we investigate the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We perform coarse-grained molecular dynamics simulations and confirm the results with nanoindentation experiments using atomic force microscopy. We observe various deformation modes, including untension, linear elasticity, duplex dissociation, and single-stranded component stretch. We find that the mechanical properties of a DNA architecture are correlated with those of its components. However, the structure shows complex behaviors which may not be predicted by components alone and the architectural design must be considered.     

Mechanical properties of high-G.C content DNA with a-type base-stacking

The sequence of a DNA molecule is known to influence its secondary structure and flexibility. Using a combination of bulk and single-molecule techniques, we measure the structural and mechanical properties of two DNAs which differ in both sequence and base-stacking arrangement in aqueous buffer, as revealed by circular dichroism: one with 50% G·C content and B-form and the other with 70% G·C content and A-form. Atomic force microscopy measurements reveal that the local A-form structure of the high-G·C DNA does not lead to a global contour-length decrease with respect to that of the molecule in B-form although it affects its persistence length. In the presence of force, however, the stiffness of high-G·C content DNA is similar to that of balanced-G·C DNA as magnetic and optical tweezers measured typical values for the persistence length of both DNA substrates. This indicates that sequence-induced local distortions from the B-form are compromised under tension. Finally, high-G·C DNA is significantly harder to stretch than 50%-G·C DNA as manifested by a larger stretch modulus. Our results show that a local, basepair configuration of DNA induced by high-G·C content influences the stretching elasticity of the polymer but that it does not affect the global, double-helix arrangement.     

Mechanical properties and water vapor transmission in some blends of cassava starch edible films

The continuous increase of consumer interest in quality, convenience and food quality has encouraged further research into edible films and coatings from natural polymers, such as polysaccharides. Ecoefficient products are the new generation of biobased products prepared with sustainable materials, that agree with ecological and economic requirements including environmentally acceptable disposal of post-user waste. The numerous potential applications of natural polymers such as polysaccharides stimulated the study with edible films based on cassava starch. Blends of glycerol (GLY) and polyethylene glycol (PEG) as plasticizers, and glutaraldehyde (GLU) as crosslinking agent were prepared in order to determine the mechanical properties and water vapor transmission of those films. A response surface methodology was applied on the results to identify the blend with the best mechanical properties and lowest water vapor transmission. The crosslinking effect of glutaraldehyde in the films can be observed. The plasticizing action of polyethylene glycol was restrained by more than 0.5 g of glutataraldehyde. The use of glycerol was less evident for this property even after 284 h of contact time with water vapor.     

Mechanical properties of double-stranded DNA biolayers immobilized on microcantilever under axial compression

In label-free biodetections based on microcantilever technology, double-stranded DNA (dsDNA) structures form through the linkage between probe single-stranded DNA (ssDNA) molecules immobilized on solid substrates and target ssDNA molecules in solutions. Mechanical/electrical properties of these biolayers are important factors for nanomechanical deflections of microcantilevers. In this paper, the biolayer immobilized on microcantilever is treated as a bar with a macroscopic elastic modulus on the basis of continuum mechanics viewpoints. In consideration of hydration force, screened electrostatic repulsion and conformational fluctuation in biolayers, load-deformation curves of dsDNA biolayers under axial compression are depicted with the help of the energy conservation law and a mesoscopic free energy presented by Strey et al. (1997, 1999) [Strey, H.H., Parsegian, V.A., Podgornik, R., 1997. Equation of state for DNA liquid crystals: fluctuation enhanced electrostatic double layer repulsion. Physical Review Letters 78, 895–898; Strey, H.H., Parsegian, V.A., Podgornik, R., 1999. Equation of state for polymer liquid crystals: theory and experiment. Physical Review E 59, 999–1008] from a liquid crystal theory. And the analytical relation between macroscopic Young's modulus of biolayers and nanoscopic geometrical properties of dsDNA, packing density, buffer salt solution concentration, etc. is also formulated.     

Mechanical,barrier and morphological properties of pea starch and peanut protein isolate blend films

Mechanical, barrier and morphological properties of edible films based on blends of Pea starch (PS) and Peanut protein isolate (PPI) plasticized with glycerol (30%, w/w) were investigated. As PPI ratio in PS/PPI blends increased, the thickness of films decreased, the opacity slightly elevated and color intensified. The addition of PPI to the PS film significantly reduced tensile strength from 5.44 MPa to 3.06 MPa, but increased elongation from 28.56% to 98.12% with the incorporation of PPI into PS at 50% level. Film solubility value fell from 22.31% to 9.78% upon the incorporation of PPI ranged from 0 to 50% level. When PPI was added into PS film at 40% level, the WVP and WVTR of the films markedly dropped from 11.18% to 4.19% and 6.16 to 1.95%, respectively. Scanning electron microscopy (SEM) of the surface of films showed that many swollen starch granules were presented in the 100% PS film, while 100% PPI film was observed to have rougher surfaces with presence of pores or cavities. The PS/PPI blend films upon the incorporation of PPI at 20% and 50% level were not homogeneous. However, the smoother film surface was observed in PS/PPI blend films with the addition of PPI at 40% level. SEM image of the cross-sections of the films revealed that the 100% PS film showed a uniform and compact matrix without disruption, and pore formation and 100% PPI film displayed a smooth structure. Rougher and flexible network was shown in blend film with the addition of PPI reaching 40% level.     

Mechanical properties of chitosan/bamboo charcoal composite films made with normal and surface oxidized charcoal

Chitosan/bamboo charcoal composite films were prepared by blending chitosan with either virgin bamboo charcoal or bamboo charcoal modified by nitric acid oxidation to provide more hydrophilic regions on the bamboo charcoal surface. Investigation of the physical properties of these composite films revealed that the tensile strength and Young’s modulus of the chitosan films were enhanced in a dose-dependent manner by the inclusion of modified bamboo charcoal at up to 1% (w/w), whilst the elongation at break was increased by inclusion of modified bamboo charcoal at up to 0.5% (w/w). In contrast, chitosan composites with virgin bamboo charcoal at up to 0.5% or 1.0% (w/w) showed no enhancement of the tensile strength or Young’s modulus, respectively, and both parameters were reduced with higher levels of virgin bamboo charcoal. Oil, and especially water, absorption of the composite films displayed a marked and dose-dependent increase compared to those of the pure chitosan film.     

Mechanical properties of actin

We used a cone and plate rheometer to evaluate the mechanical properties of actin over a wide range of oscillation frequencies and shear rates. Remarkably, both filamentous and nonfilamentous actin behaved as viscoelastic solids in both oscillatory and shear type experiments, providing that they were given ample time to equilibrate. Actin was purified by gel filtration from rabbit skeletal muscle and Acanthamoeba. Nonfilamentous actin in 2 different buffers had similar properties. In a low ionic strength buffer the absence of filaments was confirmed by electron microscopy, ultracentrifugation, and the fluorescence of pyrene-labeled actin. In 0.6 M KI, actin was monomeric by gel filtration. Filamentous actin had similar properties in 2 mM MgCl2 with either 50 mM KC1 or 500 mM KC1. Under all 4 of these conditions, actin required about 1000 min at 25 degrees C for the rheological properties to equilibrate. Under conditions where the oscillation of the rheometer did not affect the mechanical properties, all of the actin preparations had dynamic viscosities that were inverse functions of the frequency and dynamic elasticites that leveled off at low frequencies as expected for viscoelastic solids. For filamentous actin, the values of these parameters were about 2 times higher than for nonfilamentous actin. In shear experiments, both filamentous and nonfilamentous actin exhibited shear rate-dependent yield stresses. When filamentous and nonfilamentous actin structures were disrupted by transient shearing, the dynamic elasticity recovered to 90% in 30 min. Ovalbumin in the low ionic strength buffer also behaved as a viscoelastic material with elasticity and viscosity about 10 times lower than nonfilamentous actin, while cytochrome c behaved as a Newtonian fluid with a viscosity of 0.02 poise.     

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric A_nT_n and asymmetric A_2n tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and twisting relevant for looping. The symmetric tracts, in contrast, are more rigid than asymmetric tracts and the control, both locally and globally. Our results can reconcile the contradictory stiffness data on A-tracts and suggest symmetric A-tracts to be more efficient in nucleosome exclusion than the asymmetric ones. This would open a new possibility of gene expression manipulation using A-tracts.     

Mechanical properties of cytoskeletal polymers

The mechanical properties of cytoplasm are dominated by microfilaments, microtubules, and intermediate filaments, collectively termed the cytoskeleton. This review discusses how the physical properties of these biopolymer systems are related to their molecular structures and interactions, and how remodelling of these biopolymers in vivo affects cell shape and motility.     

Mechanical properties of wheatflake components

The mechanical behaviour of breakfast wheat flake materials of different composition reconstituted as bar-shaped test pieces, to reduce the geometry and structure effects and allow better comparison of the matrix properties, is reported. The ground flakes comprised a control formulation and others in which one or more components had been subtracted. The aim was to compare the mechanical properties of pressed specimens of multiple-component systems with those published for simpler one- and two-component materials. The results on the bending modulus, E, at 20 °C fell into two groups, depending on whether sucrose (wheat:sucrose = 5.9-6.1:1) was present. Sucrose lowered the modulus but by progressively less with decreasing water content below 22% (wet weight basis, w.w.b), the difference becoming negligible at water contents of 7–10% (w.w.b). However, the energy to break samples at 7% water content (w.w.b) was greater when sucrose was subtracted from the control formulation sample.     

Mechanical properties of pleural membrane

The pleural membrane is modeled as a planar collection of interconnected randomly oriented line elements. By assuming that the line elements follow the strain field of a continuum, a strain-energy function is formulated. From the strain-energy function, an explicit stress-strain equation for large deformations is derived. In the linear approximation of the stress-strain equation the shear modulus and the area modulus of the membrane are respectively found to be 2.4 and 2.8 times the tension at the reference state. The stress-strain equation for large deformations is used to predict the displacement field around a circular hole in pleura. Good agreement is found between these predictions and measurements made on ablated pleura from dog lungs. From these theoretical and experimental results the conclusion is drawn that the pleura has a significant role in carrying shear forces and maintaining the lung's shape.     

Mechanical properties of collagen fibrils

The formation of collagen fibers from staggered subfibrils still lacks a universally accepted model. Determining the mechanical properties of single collagen fibrils (diameter 50-200 nm) provides new insights into collagen structure. In this work, the reduced modulus of collagen was measured by nanoindentation using atomic force microscopy. For individual type 1 collagen fibrils from rat tail, the modulus was found to be in the range from 5 GPa to 11.5 GPa (in air and at room temperature). The hypothesis that collagen anisotropy is due to the subfibrils being aligned along the fibril axis is supported by nonuniform surface imprints performed by high load nanoindentation.     

Mechanical properties of DNA-like polymers

The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of the relative roles of attractive base stacking forces and repulsive electrostatic forces creating this stiffness. To gain insight, we have created a family of double-helical DNA-like polymers where one of the four normal bases is replaced with various cationic, anionic or neutral analogs. We apply DNA ligase-catalyzed cyclization kinetics experiments to measure the bending and twisting flexibilities of these polymers under low salt conditions. Interestingly, we show that these modifications alter DNA bending stiffness by only 20%, but have much stronger (5-fold) effects on twist flexibility. We suggest that rather than modifying DNA stiffness through a mechanism easily interpretable as electrostatic, the more dominant effect of neutral and charged base modifications is their ability to drive transitions to helical conformations different from canonical B-form DNA.