Nonlinear viscoelasticity of entangled DNA molecules

Jary, Dorothée; Sikorav, Jean‐Louis; Lairez, D.

doi:10.1209/epl/i1999-00252-0

Cited by 29 publications

(42 citation statements)

References 13 publications

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“…This concentration is very close to the critical concentration (∼9c Ã ) for the onset of entangled regime in semidilute DNA solutions (34) and thus can possibly lead to selfentangling of the molecule. However, an internal DNA concentration of 7c Ã alone does not give rise to enough entanglements to fully account for the observed slow expansion as it only corresponds to an equilibrium number of entanglements on order of 1 (35). It is useful to compare our results to DNA packaged in a capsid because the knotting observed in this biological con-text is believed to arise primarily due to confinement effects (36,37).…”

Section: Resultsmentioning

confidence: 93%

Compression and self-entanglement of single DNA molecules under uniform electric field

Tang

Doyle

2011

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

137

169

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We experimentally study the effects of a uniform electric field on the conformation of single DNA molecules. We demonstrate that a moderate electric field (∼200 V∕cm) strongly compresses isolated DNA polymer coils into isotropic globules. Insight into the nature of these compressed states is gained by following the expansion of the molecules back to equilibrium after halting the electric field. We observe two distinct types of expansion modes: a continuous molecular expansion analogous to a compressed spring expanding, and a much slower expansion characterized by two long-lived metastable states. Fluorescence microscopy and stretching experiments reveal that the metastable states are the result of intramolecular self-entanglements induced by the electric field. These results have broad importance in DNA separations and single molecule genomics, polymer rheology, and DNA-based nanofabrication.DNA conformation | electrophoresis | polymer physics | knots | microfluidic T he use of electric fields to transport DNA has become an essential technique for a variety of research areas including molecular biology, gene therapy, and fundamental studies of polyelectrolytes (1). In most applications, nonlinear electrokinetics (2) due to the interplay of negatively charged DNA and the electric field are neglected. However, Viovy and coworkers (3, 4) demonstrated the ability of an electric field on order of 100 V∕cm to induce strong intermolecular DNA aggregation in a standard electrophoresis buffer in the absence of a sieving matrix. Follow-up studies (5, 6) have attributed the aggregation to an electrohydrodynamic instability triggered by a coupling of macroion (DNA) concentration fluctuations and electric field induced flows beyond the Debye length scale in a moderately concentrated DNA solution (around the DNA overlap concentration c Ã ). These results shed light onto why it is so difficult to separate large DNA molecules using capillary electrophoresis.Over the last decade there has been a shift from techniques measuring ensemble-averaged molecular properties (e.g., the aforementioned capillary electrophoresis experiments), to techniques that manipulate single, dilute DNA molecules in micro/ nanofluidic devices or nanopores (7-9). Electric fields are a convenient mode to transport DNA as they scale favorably with device dimensions. The long standing belief in such dilute, single molecule experiments is that uniform DC (direct current) electric fields (up to a few hundred V∕cm in standard electrophoresis buffers) do not greatly perturb the conformation of large DNA unless some sort of sieving matrix is used (e.g., gel or microfabricated post array) (1). Numerous fluorescence microscopy experiments confirm this belief to be true [see (10) for a recent review], but are typically limited to field strengths of a few tens of V∕cm to avoid image blur. Much larger electric fields give rise to some chain orientation and possibly some slight chain stretching (11), though the stretching is inconclusive because it is not directly meas...

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Section: Resultsmentioning

confidence: 93%

Compression and self-entanglement of single DNA molecules under uniform electric field

Tang

Doyle

2011

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

137

169

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“…They have noted that the measured viscoelastic spectra do not fit the standard reptation model for flexible polymers [6]. Measurements of the nonlinear rheology of entangled T4 Bacteriophage DNA molecules [7] show a plateau region in the stress σ after an initial Newtonian regime at very low shear ratesγ, similar to the flow curves seen in surfactant gels [8,9].…”

Section: Introductionmentioning

confidence: 99%

Rheology of semi-dilute solutions of calf-thymus DNA

Bandyopadhyay

Sood

2002

Pramana - J Phys

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We study the rheology of semi-dilute solutions of the sodium salt of calf-thymus DNA in the linear and nonlinear regimes. The frequency response data can be fitted very well to the hybrid model with two dominant relaxation times τ 0 and τ 1 . The ratio´τ 0 τ 1 µ 5 is seen to be fairly constant on changing the temperature from 20 to 30 AE C. The shear rate dependence of viscosity can be fitted to the Carreau model.

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“…The systems considered are aqueous solutions of surfactants, but some results are clearly generalized to other self-assembled phases of anisotropic structures [85,86,89,90,92,93,[237][238][239][240]. Our approach has been to show the existence of a common rheological behavior shared by most semi-dilute and concentrated wormlike micellar solutions.…”

Section: Conclusion and Perspectives For The Futurementioning

confidence: 99%

Rheology of Wormlike Micelles: Equilibrium Properties and Shear Banding Transitions

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We review the experimental and theoretical results obtained during the past decade on the structure and rheology of wormlike micellar solutions. We focus on the linear and nonlinear viscoelasticity and emphasize the analogies with polymers. Based on a comprehensive survey of surfactant systems, the present study shows the existence of standard rheological behaviors for semidilute and concentrated solutions. One feature of this behavior is a shear banding transition associated with a stress plateau in the nonlinear mechanical response. For concentrated solutions, we show that in the plateau region the shear bands are isotropic and nematic.

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Nonlinear viscoelasticity of entangled DNA molecules

Cited by 29 publications

References 13 publications

Compression and self-entanglement of single DNA molecules under uniform electric field

Compression and self-entanglement of single DNA molecules under uniform electric field

Rheology of semi-dilute solutions of calf-thymus DNA

Rheology of Wormlike Micelles: Equilibrium Properties and Shear Banding Transitions

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