Twist Rigidity Research Articles

Temperature-dependent elasticity of DNA, RNA, and hybrid double helices

Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003–0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.

Increasing Twist Rigidity to Prepare Polyimides with Low Dielectric Constants and Dissipation Factors over a Wide Temperature Range

Increasing Twist Rigidity to Prepare Polyimides with Low Dielectric Constants and Dissipation Factors over a Wide Temperature Range

DNA structural properties of DNA binding sites for 21 transcription factors in the mycobacterial genome.

Mycobacterium tuberculosis, the causative agent of tuberculosis, has evolved over time into a multidrug resistance strain that poses a serious global pandemic health threat. The ability to survive and remain dormant within the host macrophage relies on multiple transcription factors contributing to virulence. To date, very limited structural insights from crystallographic and NMR studies are available for TFs and TF-DNA binding events. Understanding the role of DNA structure in TF binding is critical to deciphering MTB pathogenicity and has yet to be resolved at the genome scale. In this work, we analyzed the compositional and conformational preference of 21 mycobacterial TFs, evident at their DNA binding sites, in local and global scales. Results suggest that most TFs prefer binding to genomic regions characterized by unique DNA structural signatures, namely, high electrostatic potential, narrow minor grooves, high propeller twist, helical twist, intrinsic curvature, and DNA rigidity compared to the flanking sequences. Additionally, preference for specific trinucleotide motifs, with clear periodic signals of tetranucleotide motifs, are observed in the vicinity of the TF-DNA interactions. Altogether, our study reports nuanced DNA shape and structural preferences of 21 TFs.

Progressive twist, displacement and torsional energy around pile groups

ABSTRACT The progressive twist and displacement in the sand are investigated for a set of pile groups (1,2; 1,3; 2,2) corresponding to the application of the torsional loads. A novel numerical model supported by a set of experimental observations has been considered to capture pile-soil interaction for the pile groups subjected to torsional load. The torque mobilization, progressive twist, and displacement have been computed for a range of the initial shear modulus ratio for the entire set of pile groups. As a result of twisting, the torsional energy zones are set into the soil, and there is the formation of a heave and cavity around the pile group. The torsional energy and twist rigidity parameters were evaluated for a range of shear modulus ratios of the soil. It has been observed that the torsional energy of the pile group (1,2) is significantly higher than pile groups (1,3; 2,2). A classification for torsional energy zones associated with twist rigidity and displacement rigidity factor has been suggested to set the limits for twist and displacement of the pile groups relative to a single pile. A relationship of the torsional energy with progressive twist and displacement is obtained. The components of torsional energy associated with progressive twist and displacement were obtained in the range of 0.43–0.50 and 0.50–0.57 respectively

Influences of flexible defect on the interplay of supercoiling and knotting of circular DNA* *The National Natural Science Foundation of China under Grant Nos. 11464004, 11864006 and 11564015, Guizhou Scientific and Technological Program (20185781 and 20185781-15), the Foundation of Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education (Guizhou University), KY2020243.

Knots are discovered in biophysical systems, such as DNA and proteins. Knotted portions in knotted DNA are significantly bent and their corresponding bending angles are comparable with or larger than the sharp bending angle resulting in flexible defects. The role of flexible defects in the interplay of supercoiling and knotting of circular DNA were predicted by a Monte Carlo simulation. In knotted DNA with a particular knot type, a flexible defect noticeably enhances the supercoiling of the knotted DNA and the decreasing excitation energy makes the knotted portion more compact. A reduction in twist rigidity and unwinding of flexible defects are incorporated into the numerical simulations, so that interplay of supercoiling and knotting of circular DNA is studied under torsional conditions. Increasing unwinding not only results in a wider linking number distribution, but also leads to a drift of the distribution to lower values. A flexible defect has obvious effects on knotting probability. The summation of equilibrium distribution probability for nontrivial knotted DNA with different contour length does not change with excitation energy monotonically and has a maximum at an intermediate value of excitation energy around 5k B T. In the phase space of knot length and gyration radius of knotted DNA, knot length does not anticorrelate with its gyration radius, which is attributed to the flexible defect in the knotted portion, which leads to the release of bending energy and inhibited the competition between entropy and bending energy.

Nonlinear vibration mitigation of a flexible rotor shaft carrying a longitudinally dispositioned unbalanced rigid disc

This study is dedicated to investigate the nonlinear dynamics of a system composed of a flexible rotor shaft carrying a longitudinally dispositioned unbalanced rigid disc. The less-attended multi-modal nonlinear vibration analysis of rotor structures, considering the effect of geometric and inertial nonlinearities due to the large deflection of the flexible structure, is investigated in this study. To this end, the flexible shaft is modelled using the Euler–Bernoulli beam theory. In order to model the unbalanced rigid disc, it is considered as combination of a symmetric disc with an additional eccentric lump mass. The equations of motion of the system are derived using the extended Hamilton principle. Assuming the inextensional shaft and considering high twisting rigidity of the shaft, the flexural-flexural vibrations of the system of rotor shaft-disc are studied in this paper. The equations of motion are discretized using the Galerkin method exploiting various reduced order models including single-mode, two-mode, and three-mode approximations. In order to obtain the steady-state response of the system, two methods are used in this study. The first method is to use the semi-analytical modified complex averaging technique along with the numerical arc-length continuation method. The second method is using the direct integration in MATLAB. The nonlinear dynamics of different systems such as a system consisting only a flexible shaft and a system of flexible shaft carrying an unbalanced rigid disc at different positions along the shaft are investigated. The results show that geometric nonlinearity of the flexible shaft is dominating the inertial nonlinearity and hence, the system demonstrates a hardening nonlinear behaviour at the vicinity of the first two resonances. Besides, it is shown that dispositioning the unbalanced disc along the flexible shaft results in change in the nonlinear dynamics of the system at various modes. It is illustrated that if the unbalanced disc is located at the node of one of the modes of the vibration of the system, that mode is not excited, as expected. The results of the paper reveal that the longitudinal disposition plays a key role in the instability analysis of the system of rotor shaft-disc, as well as the radial unbalance. In the second part of the paper, nonlinear vibration of the system of a flexible rotor shaft with a longitudinally dispositioned unbalanced rigid disc is mitigated using nonlinear energy sink (NES). Two different conditions of the unbalanced disc are considered for the system. For each case, the NES is designed to control the undesired nonlinear vibration of the system close to the first two natural frequencies. The results show that the designed NESs are capable of controlling the system with different dynamic responses including periodic, quasi-periodic, chaotic, and also the system with unstable dynamic response that may lead to collapse of the system.

Curaxin-Induced DNA Topology Alterations Trigger the Distinct Binding Response of CTCF and FACT at the Single-Molecule Level

The candidate anticancer drug curaxins can insert into DNA base pairs and efficiently inhibit the growth of various cancers. However, how curaxins alter the genomic DNA structure and affect the DNA binding property of key proteins remains to be clarified. Here, we first showed that curaxin CBL0137 strongly stabilizes the interaction between the double strands of DNA and reduces DNA bending and twist rigidity simultaneously, by single-molecule magnetic tweezers. More importantly, we found that CBL0137 greatly impairs the binding of CTCF but facilitates trapping FACT on DNA. We revealed that CBL0137 clamps the DNA double helix that may induce a huge barrier for DNA unzipping during replication and transcription and causes the distinct binding response of CTCF and FACT on DNA. Our work provides a novel mechanical insight into CBL0137's anticancer mechanisms at the nucleic acid level.

Crucial role of the intrinsic twist rate for the size of an intrinsically curved semiflexible biopolymer

We study the effects of the intrinsic curvature (IC), intrinsic twist rate (ITR), anisotropic bending rigidities, sequence disorder, and temperature (T) on the persistence length (l_{p}) of a two- or three-dimensional semiflexible biopolymer. We develop some general expressions to evaluate exactly these effects. We find that a moderate IC alone reduces l_{p} considerably. Our results indicate that the centerline of the filament keeps as a helix in a rather large range of T when ITR is small. However, a large ITR can counterbalance the effect of IC and the result is insensitive to the twist rigidity. Moreover, a weak randomness in IC and ITR can result in an "overexpanded" state. Meanwhile, when ITR is small, l_{p} is not a monotonic function of T but can have either minimum or maximum at some T, and in the two-dimensional case the maximum is more obvious than that in the three-dimensional case. These results reveal that to obtain a proper size at a finite T for an intrinsically curved semiflexible biopolymer, proper values of bending rigidities and ITR are necessary but a large twist rigidity may be only a by-product. Our findings are instructive in controlling the size of a semiflexible biopolymer in organic synthesis since the mean end-to-end distance and radius of gyration of a long semiflexible biopolymer are proportional to l_{p}.

Identification of effects of YOYO-1 intercalation on the topological states of circular DNA

YOYO-1 intercalation leads to the reduction of twist rigidity, unwinding of DNA, elongation of DNA contour length and YOYO-1 concentration-dependent persistence length, until now few works identified their roles in determining the topological states of circular DNA. Based on the convolution of the writhe distribution of circular DNA obtained by using Monte Carlo simulation and the twist distribution, effects of YOYO-1 intercalation on the linking number distribution of circular DNA are predicted and identified. YOYO-1 intercalation leads to larger fluctuation, but not to the obvious enlargement of the writhe distribution, so that the variance of the linking number distribution mainly depends on the variance of the twist distribution. The unwinding angle contributes to the drifting of the linking number distribution away from the original equilibrium value of zero and has no effects on the variance of the linking number distribution, converse to the roles of the reduced twist rigidity in the linking number distribution. Furthermore, the method used in the work can be generalized to detect the effects of other intercalators on the topological states of circular DNA.

Effects of dielectric inhomogeneity on electrostatic twist rigidity of a helical biomolecule in Debye-Hückel regime.

The electrostatic interactions play a crucial role in biological systems. Here we consider an impermeable dielectric molecule in the solvent with a different dielectric constant. The electrostatic free energy in the problem is studied in the Debye-Hückel regime using the analytical Green function that is calculated in the paper. Using this electrostatic free energy, we study the electrostatic contribution to the twist rigidity of a double stranded helical molecule such as a DNA and an actin filament. The dependence of the electrostatic twist rigidity of the molecule to the dielectric inhomogeneity, structural parameters, and the salt concentration is studied. It is shown that, depending on the parameters, the electrostatic twist rigidity could be positive or negative.

Effect of Temperature on Topological States of Circular DNA**Supported by the National Natural Science Foundation of China under Grant Nos. 11047022, 11204045, and 11464004, Guizhou Provincial Tracking Key Program of Social Development (SY20123089, SZ20113069), the General Financial Grant from the China Postdoctoral Science Foundation (2014M562341), the Research Foundation for Young University Teachers from Guizhou University (201311), and College Innovation Talent

The different topological states of circular double-stranded DNA can be defined by their linking number. The equilibrium distribution of linking number can be obtained by circularizing a linear DNA into a circle by ligase. Based on the recent experimental results that the DNA bending rigidity and twist rigidity strongly depend on temperature, the reduced bending rigidity can be approximated by over the temperature interval (5 ∼ 53) °C, and the temperature dependence of twist rigidity can be fitted by nm. The temperature dependence of the linking number distribution of circular DNAs can be predicted by using Monte Carlo simulation. The variance of linking number distribution on temperature is in accordance with the previous experimental results. Compared with the temperature dependence of bending rigidity, the temperature dependence of twist rigidity causes a noticeable fluctuation in linking number distribution and mainly contribute towards the variance change of linking number distribution of circular DNA. The variance of the writhe number and twist number in the equation depends on the length of circular DNA. When the length of circular DNA is less than 230 nm, the variance of twist number is dominant over the variance of writhe number , whereas for the condition that the length of the circular DNA is larger than 370 nm.

Application of DKMQ24 shell element for twist of thin-walled beams: Comparison with Vlassov theory

ABSTRACTThis article presents the application of DKMQ24 shell element for twist of thin-walled beams. This element passed the patch tests for membrane, bending and shear problems and gave fine results for plate and shell problems analysis without shear locking. Thin-walled cantilever beams are analyzed using this element. DKMQ24 gives good results for cantilever beams with open cross-section for a very few number of element. Moreover, the comparison of the results obtained with Vlassov analytical solution enables to evaluate the accuracy of the twist rigidity, Jd, which depends on an empirical coefficient in Vlassov theory.

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond.

Chiral structure of F-actin bundle formed by multivalent counterions

The mechanism of multivalent counterion-induced bundle formation by filamentous actin (F-actin) is studied using a coarse-grained model and molecular dynamics simulation. Real diameter size, helically ordered charge distribution and twist rigidity of F-actin are taken into account in our model. The attraction between parallel F-actins induced by multivalent counterions is studied in detail and it is found that the maximum attraction occurs between their closest charged domains. The model F-actins aggregate due to the like-charge attraction and form closely packed bundles. Counterions are mostly distributed in the narrowest gaps between neighboring F-actins inside the bundles and the channels between three adjacent F-actins correspond to low density of the counterions. Density of the counterions varies periodically with a wave length comparable to the separation between consecutive G-actin monomers along the actin polymers. Long-lived defects in the hexagonal order of F-actins in the bundles are observed that their number increases with increasing the bundles size. Combination of electrostatic interactions and twist rigidity has been found not to change the symmetry of F-actin helical conformation from the native 13/6 symmetry. Calculation of zero-temperature energy of hexagonally ordered model F-actins with the charge of the counterions distributed as columns of charge domains representing counterion charge density waves has shown that helical symmetries commensurate with the hexagonal lattice correspond to local minima of the energy of the system. The global minimum of energy corresponds to 24/11 symmetry with the columns of charge domains arranged in the narrowest gaps between the neighboring F-actins.

Out-of-Plane Elastic Deformation of Honeycomb Core (Second Report: Analysis of Torsion Deformation of Hexagon Honeycomb)

In this research, the influence of the boundary condition on the torsion deformation of hexagon honeycomb is studied. It is found that, for the twisting moment distributed over each unit of a honeycomb, if the honeycomb deformation is periodic for each unit, the ratio of moment Mxy|unit to Myx|unit should be a special value given by a formula shown in this study. Therefore, the influence of the boundary condition on the torsion deformation is dependent on this ratio of Mxy|unit to Myx|unit. When on the boundary, the ratio of moment Mxy|unit to Myx|unit is not equal to the value given by the theoretical formula, as the unit separates from the boundary. Therefore, an error arises in the theoretical solution calculated using equivalent twisting rigidity Dxy. This error is related to the size of a model; the error becomes small, so that the analyzed model is large.

Coupling of twist and writhe in short DNA loops

While bending and twist can be treated as independent degrees of freedom for linear DNA molecules, the loop closure constraint introduces a coupling between these variables in circular DNA. We performed Monte Carlo simulations of wormlike rods with both bending and twist rigidity in order to study the coupling between the writhe and twist distributions for various DNA lengths. We find that for sufficiently short DNA, the writhe distribution differs from that of a model with bending energy only. We show that the factorization approximation introduced by previous researchers coincides, within numerical accuracy, with our simulation results, and conclude that the closure constraint is fully accounted for by the White-Fuller relation. Experimental tests of our results for short DNA plasmids are proposed.

Mechanical Constraints on Confined DNA

A confined DNA molecule adopts various conformations, driven by entropy and constrained, in particular, by excluded volume interaction. But DNA also has some specific mechanical characteristics, such as twisting and bending elasticity. These properties influence the way DNA compacts itself inside the confined space, by favoring some conformations and impeding others. This situation is notably observed in E. Coli cells. Our model allows to simulate long polymer chains with given twist and bend elasticity constants, using the Monte Carlo method. Generating conformations with various twisting and bending rigidity gives detailed information on how DNA could be organized in such cells. By tuning the model with data from experiments on DNA mechanical properties, it becomes possible to make predictions on the DNA structure inside the cell nucleus.

1113 タイヤ自由度を考慮した二輪車の動特性に関する研究(OS2-3 路面とタイヤ,OS2 交通・物流システムのダイナミクス,オーガナイズド・セッション(OS))

In the theoretical research maneuverability and stability of the two-wheeled vehicle, the most famous one is called four degree of freedom model that sharp announced. The dynamic characteristic of the tire is considered in this model, cornering stiffness and camber stiffness are generated by the delay for the sideslip and camber angle by the first. However, when such tire characteristics are used, the vibration phenomenons wobble and weave is not theoretically expressible. So this paper, it focuses attention on the side rigidity and twist rigidity of the tire and analyzed the tire model consider the rigidity value into the four degree of freedom model.

The features of ribbon‐like polymers in thin films

AbstractThe features of ribbon‐like polymers in thin film, which are anisotro‐pic in cross section, are considered using a lattice model of oriented self‐correlated walks (OSCW). The local properties of the ribbon‐like chain are assumed to be strongly anisotropic: bending is possible only in the plane of the ribbon (the orientation of this plane can change due to molecule twist). On the basis of this model, the phase transition of the ribbon‐like polymers possessing certain bending and twist rigidity into the rotator phase is described in the mean‐field approximation. The dimension reducing of the polymer system results in an increase of phase transition temperature. Moreover, spontaneous polarization arises in a non‐orientated system and that is the most interesting phenomenon caused by confinement of polymer macromolecules.

Worm-like polymer loops and Fourier knots

Every smooth closed curve can be represented by a suitable Fourier sum. We show that the ensemble of curves generated by randomly chosen Fourier coefficients with amplitudes inversely proportional to spatial frequency (with a smooth exponential cutoff), can be accurately mapped on the physical ensemble of worm-like polymer loops. We find that measures of correlation on the scale of the entire loop yield a larger persistence length than that calculated from the tangent-tangent correlation function at small length scales. The conjecture that physical loops exhibit additional rigidity on scales comparable to the entire loop due to the contribution of twist rigidity, can be tested experimentally by determining the persistence length from the local curvature and comparing it with that obtained by measuring the radius of gyration of dsDNA plasmids. The topological properties of the ensemble randomly generated worm-like loops are shown to be similar to that of other polymer models.