Semiflexible Chains at Surfaces: Worm-Like Chains and beyond

Baschnagel, J.; Meyer, H.; Wittmer, J. P.; Kulić, Igor M.; Mohrbach, Hervé; Ziebert, Falko; Nam, Ga Eun; Lee, Nam-Kyung; Johner, A.

doi:10.3390/polym8080286

Cited by 41 publications

(31 citation statements)

References 160 publications

(263 reference statements)

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“…[ 17 ]. In the so far undertaken molecular dynamics and analytical studies of the adsorption of semiflexible polymer chains based on the WLC model, the different adsorption potentials were probed, but the perturbative impact of lateral forces has not been taken into consideration as the surface was assumed to be two-dimensionally uniform [ 50 , 51 ].…”

Section: Resultsmentioning

confidence: 99%

Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

et al. 2021

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Highlights DNA kinking is inevitable for the highly anisotropic 1D–1D electrostatic interaction with the one-dimensionally periodically charged surface. The double helical structure of the DNA kinetically trapped on positively charged monomolecular films comprising the lamellar templates is strongly laterally stressed and extremely perturbed at the nanometer scale. The DNA kinetic trapping is not a smooth 3D—> 2D conformational flattening but is a complex nonlinear in-plane mechanical response (bending, tensile and unzipping) driven by the physics beyond the scope of the applicability of the linear worm-like chain approximation. Abstract Up to now, the DNA molecule adsorbed on a surface was believed to always preserve its native structure. This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated. High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled. We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress (> 30 pNnm) inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges. In addition, the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity. The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending. The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics. The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear. The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.

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Section: Resultsmentioning

confidence: 99%

Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

et al. 2021

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“…Care is needed, however, when one deals with the adsorption of semiflexible polymers on planar surfaces [14][15][16][17][18][19][20]. When a polymer gets adsorbed, its conformation changes from three-dimensional to (quasi) two-dimensional [21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Semiflexible Polymers Interacting with Planar Surfaces: Weak versus Strong Adsorption

Milchev

Binder

2020

Polymers

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Semiflexible polymers bound to planar substrates by a short-range surface potential are studied by Molecular Dynamics simulations to clarify the extent to which these chain molecules can be considered as strictly two-dimensional. Applying a coarse-grained bead-spring model, the chain length N and stiffness κ as well as the strength of the adsorption potential ϵ w a l l are varied over a wide range. The excluded-volume (EV) interactions inherent in this model can also be “switched off” to provide a discretized version of the Kratky–Porod wormlike chain model. We study both local order parameters (fraction f of monomers within the range of the potential, bond-orientational order parameter η ) and the mean square gyration radius parallel, ⟨ R g 2 ⟩ | | , and perpendicular, ⟨ R g 2 ⟩ ⊥ , to the wall. While for strongly adsorbed chains EV has negligible effect on f and η , we find that ⟨ R g 2 ⟩ | | is strongly affected when the chain contour length exceeds the persistence length. Monomer coordinates in perpendicular (⊥) direction are correlated over the scale of the deflection length which is estimated. It is found that f , η , and ⟨ R g 2 ⟩ ⊥ converge to their asymptotic values with 1 / N corrections. For both weakly and strongly adsorbed chains, the distribution functions of “loops”, “trains”, and “tails” are analyzed. Some consequences pertaining to the analysis of experiments on adsorbed semiflexible polymers are pointed out.

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“…We confine our discussion to linear coarse-grained polymers at low density. This excludes topics, such as polymer melts [ 12 ], polymer networks [ 13 ] and polymer nanocomposites [ 14 ]. We assume implicit solvents and incorporate excluded volume, self- and mutual-attraction, as well as semiflexibility.…”

Section: Introductionmentioning

confidence: 99%

Dilute Semiflexible Polymers with Attraction: Collapse, Folding and Aggregation

2016

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Abstract:We review the current state on the thermodynamic behavior and structural phases of self-and mutually-attractive dilute semiflexible polymers that undergo temperature-driven transitions. In extreme dilution, polymers may be considered isolated, and this single polymer undergoes a collapse or folding transition depending on the internal structure. This may go as far as to stable knot phases. Adding polymers results in aggregation, where structural motifs again depend on the internal structure. We discuss in detail the effect of semiflexibility on the collapse and aggregation transition and provide perspectives for interesting future investigations.

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Semiflexible Chains at Surfaces: Worm-Like Chains and beyond

Cited by 41 publications

References 160 publications

Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

Semiflexible Polymers Interacting with Planar Surfaces: Weak versus Strong Adsorption

Dilute Semiflexible Polymers with Attraction: Collapse, Folding and Aggregation

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