Relaxation Dynamics of Semiflexible Polymers

Bohbot-Raviv, Yardena; Zhao, W. Z.; Feingold, Mario; Wiggins, Chris H.; Granek, Rony

doi:10.1103/physrevlett.92.098101

Cited by 44 publications

(54 citation statements)

References 24 publications

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“…A significant advantage of this combined experimental configuration is the possibility to control the rate of DNA stretching, as the external force used to stretch DNA can be modified by more than an order of magnitude. Our results are compared with previous studies that addressed the relaxation dynamics of tethered DNA molecules (16)(17)(18)(19). In addition, we present analytical results that, with only minimal approximations, accurately describe the quasistatic DNA dynamics observed.…”

mentioning

confidence: 48%

Fast dynamics of supercoiled DNA revealed by single-molecule experiments

Crut

Köster²,

Seidel³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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The dynamics of supercoiled DNA play an important role in various cellular processes such as transcription and replication that involve DNA supercoiling. We present experiments that enhance our understanding of these dynamics by measuring the intrinsic response of single DNA molecules to sudden changes in tension or torsion. The observed dynamics can be accurately described by quasistatic models, independent of the degree of supercoiling initially present in the molecules. In particular, the dynamics are not affected by the continuous removal of the plectonemes. These results set an upper bound on the hydrodynamic drag opposing plectoneme removal, and thus provide a quantitative baseline for the dynamics of bare DNA.magnetic tweezers ͉ optical tweezers ͉ polymer dynamics T he degree of DNA supercoiling affects a number of important cellular processes, such as gene expression (1), initiation of DNA replication (2), binding kinetics of sequence-specific proteins to their targets (3), and site-specific recombination (4, 5). A strict regulation of DNA supercoiling is therefore essential for cell survival. This regulation results from a complex interplay between the occurrence of processes that generate local supercoiling of DNA, such as replication and transcription, and the action of topoisomerases, which are able to modify the global linking number (Lk) of DNA molecules via a mechanism of transient DNA strand breakage and religation (for reviews, see refs. 6 and 7).DNA supercoiling dynamics, i.e., the rate at which supercoils are created, propagated and removed on a DNA molecule, represent an important aspect of the regulation process. This can be clearly illustrated by the example of transcription-induced supercoiling. As initially proposed by Liu and Wang (8) and confirmed by later experiments in vitro (9) and in vivo (10, 11), the inability of a transcription complex of increasing molecular weight to rotate around helical DNA results in the supercoiling of DNA in its immediate vicinity: positively supercoiled domains are generated ahead of the transcription complex, whereas negatively supercoiled domains are generated behind it. In the simple case of a single transcription complex bound to a circular DNA molecule, these supercoiled domains of opposite sign can be relaxed in one of two ways, either by the action of topoisomerases or by their mutual annihilation following their propagation along the connecting DNA segment. These two processes can have very different consequences for DNA topology: the action of topoisomerases induces a modification of Lk unless these enzymes relax positive and negative supercoils in a perfectly balanced way, whereas the merging of oppositely supercoiled domains does not influence the global Lk. Thus, the relative kinetics of these two processes appears as a major determinant of the degree of supercoiling of DNA in steady state. Within this context, DNA internal dynamics play an important role because they determine the rate at which oppositely supercoiled domains propagate and mer...

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mentioning

confidence: 48%

Fast dynamics of supercoiled DNA revealed by single-molecule experiments

Crut

Köster²,

Seidel³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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“…Few aspects of DNA dynamics have been treated before, such as the DNA dynamics in a strong stretching regime where r ∼ L [17], the DNA dynamics in response to stretching forces [18], or the dynamics of a tethered particle in the case of DNA looping [19,20] [22,23], and the statistics of Markovian processes for measuring the rate of loop formation due to protein action [19,20]. The full dynamics as we described above, however, have not been considered.…”

Section: Experiments and Simulationsmentioning

confidence: 99%

Dynamic analysis of a diffusing particle in a trapping potential

Lindner

Nir²,

Vivante³

et al. 2013

Phys. Rev. E

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The dynamics of a diffusing particle in a potential field is ubiquitous in physics, and it plays a pivotal role in single-molecule studies. We present a formalism for analyzing the dynamics of diffusing particles in harmonic potentials at low Reynolds numbers using the time evolution of the particle probability distribution function. We demonstrate the power of the formalism by simulation and by measuring and analyzing a nanobead tethered to a single DNA molecule. It allows one to simultaneously extract all the parameters that describe the system, namely, the diffusion coefficient and the restoring-force constant.

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“…In order to describe this feedback mechanism, we start with a scaling analysis and treat the simpler athermal case first. To connect to the biologically important situations of prestressed actin networks [11] and prestretched DNA [12], we then extend a recent theory of tension dynamics [13] to calculate the nonlinear response for unstretched and prestretched initial conditions.…”

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confidence: 99%

Coupling of Transverse and Longitudinal Response in Stiff Polymers

Obermayer

Hallatschek

2007

Phys. Rev. Lett.

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The time-dependent transverse response of stiff inextensible polymers is well understood on the linear level, where transverse and longitudinal displacements evolve independently. We show that for times beyond a characteristic time t f , longitudinal friction considerably weakens the response compared to the widely used linear response predictions. The corresponding feedback mechanism is explained by scaling arguments and quantified by a systematic theory. Our scaling laws and exact solutions for the transverse response apply to cytoskeletal filaments as well as DNA under tension. PACS numbers: 61.41.+e, 87.15.La, 87.15.He, 98.75.Da In tracing back the viscoelasticity of the cell to properties of its constituents, a detailed understanding of the mechanical response of single cytoskeletal filaments is indispensable. Due to their large bending stiffness, these filaments exhibit highly anisotropic static [1] and dynamic [2,3,4] features, such as the anomalous t 3 /4 -growth of fluctuation amplitudes in the transverse direction [5,6], i.e., perpendicular to the local tangent. The related response to a localized transverse driving force has so far been examined only by neglecting longitudinal degrees of freedom [6,7], although these polymers are virtually inextensible, and transverse and longitudinal contour deformations therefore coupled. In this Letter we show that longitudinal motion strongly affects the transverse response even for weakly-bending filaments and leads to relevant nonlinearities beyond a characteristic time t f .The physical key factors controlling the transverse response may be understood from Fig. 1, which shows a weakly-bending polymer (bending undulations are exaggerated for visualization) shortly after a transverse driving force f ⊥ has been applied in the bulk. In response to this force, the contour develops a bulge. Due to the backbone inextensibility, this bulge can continue growing only by pulling in contour length from the filament's tails. This effectively reduces the thermal roughness of the contour [8,9,10], at a rate substantially limited by longitudinal solvent friction. The resulting coupling to the longitudinal response tends to slow down the bulge growth. In order to describe this feedback mechanism, we start with a scaling analysis and treat the simpler athermal case first. To connect to the biologically important situations of prestressed actin networks [11] and prestretched DNA [12], we then extend a recent theory of tension dynamics [13] to calculate the nonlinear response for unstretched and prestretched initial conditions. Consider the overdamped dynamics of an initially straight stiff rod of total length L. Suddenly applying a transverse pulling force f ⊥ , for simplicity in the center of the rod, leads to the growth of a bulge deformation. The generated friction in the transverse and longitudinal direction needs to be balanced by corresponding driving forces. Viscous solvent friction is modeled via anisotropic friction coefficients (per length) ζ ⊥ and ζ = ζζ ⊥ with ζ ≈ ...

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Relaxation Dynamics of Semiflexible Polymers

Cited by 44 publications

References 24 publications

Fast dynamics of supercoiled DNA revealed by single-molecule experiments

Fast dynamics of supercoiled DNA revealed by single-molecule experiments

Dynamic analysis of a diffusing particle in a trapping potential

Coupling of Transverse and Longitudinal Response in Stiff Polymers

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