Polyelectrolyte/post collisions during electrophoresis: Influence of hydrodynamic interactions

André, Paulo C.; Long, Didier; Ajdari, Armand

doi:10.1007/s100510050384

Cited by 44 publications

(43 citation statements)

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“…The resolution ranged from 5.5 kbp for the 15-33.5 kbp samples to 11.6 kbp for the 33.5-48.5 kbp samples. Size separation in these systems is achieved due to polymer post entrapment [88]. The polymer forms a pulley like structure, where the two downfield arms of the polymer compete to release the molecule.…”

Section: Magnetic Self-assembling Sievesmentioning

confidence: 99%

“…The polymer forms a pulley like structure, where the two downfield arms of the polymer compete to release the molecule. The time it takes to disentangle from the post is a function of the molecular contour length and hence separation is possible [87][88][89][90]. This is unlike gel electrophoresis where a long DNA molecule is actually colliding with many gel fibers simultaneously.…”

Section: Magnetic Self-assembling Sievesmentioning

confidence: 99%

“…Nixon et al [89] were the first to carry out simulations of polymers colliding with fixed immovable objects using 2-D Brownian dynamics; these simulations confirmed that the DNA becomes trapped in a pulley-like configuration. One key aspect missing in most simulations is the inclusion of the effects of hydrodynamics, which can play a crucial role in the dynamics of DNA post collisions and the subsequent escape mechanism as illustrated in the theory of André et al [88]. Our group is currently carrying out molecular dynamics simulations, which examine the effects of hydrodynamics (via the explicit inclusion of solvent) on the escape times of DNA colliding with such obstacles.…”

Section: Magnetic Self-assembling Sievesmentioning

confidence: 99%

“…Other groups have also carried computer simulations which examine the dynamics of colliding chains, most notably Starkweather et al [115,119,120] have used extensive Monte Carlo simulations of the collision of charged polymers with both fixed and flexible polymer chains. André et al [88] have very succinctly illustrated the importance of including hydrodynamics when examining the entanglement dynamics of polymers, a crucial element which most current computer simulations are lacking.…”

Section: Dilute Solutions Of Sieving Polymersmentioning

confidence: 99%

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Theory of DNA electrophoresis (∼ 1999 –2002 ½)

et al. 2002

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Over the last two decades, the introduction of new methods such as pulsed-field gel electrophoresis and capillary array electrophoresis has made it possible to map and sequence entire genomes, including our own. The development of these experimental methods has been helped by the progress of theoretical and computational sciences, and the interactions between these three modi operandi of modern science are still pushing the limits of our technologies. We now see a clear trend towards proteomics and microfluidic (even nanofluidic!) devices. In this review, we take a look at the progress of the field over the last 3 years using the glasses of the theoretical scientist and focusing mostly on new ideas and concepts. About a dozen different subfields are discussed and reviewed. We conclude by giving a commented list of some of the best review articles published over the last 2-3 years.

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Section: Magnetic Self-assembling Sievesmentioning

confidence: 99%

Section: Magnetic Self-assembling Sievesmentioning

confidence: 99%

Section: Magnetic Self-assembling Sievesmentioning

confidence: 99%

Section: Dilute Solutions Of Sieving Polymersmentioning

confidence: 99%

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Theory of DNA electrophoresis (∼ 1999 –2002 ½)

et al. 2002

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“…[15][16][17][18][19][20] These studies began by looking at the single obstacle collision event of a Rouse-like bead-spring chain at high fields. Geometric arguments were then used to scale these single collision results to an obstacle course separation device.…”

Section: Introductionmentioning

confidence: 99%

Collision of a DNA Polymer with a Small Obstacle

2006

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Using single molecule fluorescence microscopy, we study the dynamics of an electric-field-driven DNA molecule colliding with a single stationary post. The radius of the obstacle is small compared to the contour length of the molecules. Molecules that achieve hooked configurations which span the obstacle were chosen for study. Four different types of hooked configurations were found: symmetric hairpins with constant extension during unhooking, asymmetric hairpins with constant extension during unhooking, asymmetric hairpins with increasing extension during unhooking, and rare multiply looped entangled configurations. The important physics describing the unhooking dynamics for each classification differ and models are proposed to predict unhooking times. Surprisingly, we find that most collisions do not follow classic rope-on-pulley motion but instead form hairpins with increasing total extension during the unhooking process (called X collisions). Last, we show that unraveling to form a hairpin and center-of-mass motion during unhooking affect the overall center of mass holdup time during a collision process.

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