DNA electrophoresis in designed channels

Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a device has been designed and fabricated recently by Han et al. for the separation of DNA molecules (Science, 2000). Our simulation reproduces the experimental observation that the mobility increases with the length of the DNA. A detailed d...

Dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE) is studied by a Brownian dynamics (BD) simulation method which we have developed. The method simulates electrophoresis of DNA in a 3 dimensional (3D) space by a chain of electrolyte beads of hard spheres. Under the constraint that the separation of each pair of bonded beads is restricted to be less than a certain fixed value, as well as with the excluded volume effect, the Langevin equation of mot...

The theoretical formulation of driven polymer translocation through nanopores is complicated by the combination of the pore electrohydrodynamics and the nonequilibrium polymer dynamics originating from the conformational polymer fluctuations. In this review, we discuss the modeling of polymer translocation in the distinct regimes of short and long polymers where these two effects decouple. For the case of short polymers where polymer fluctuations are negligible, we present a ...

We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation and pulsed fields. Using Langevin Dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses ca...

We report an alternative method for electrophoretic separation of large DNAs using steric confinement between solid walls, without gel or obstacles. The change of electrophoretic mobility vs confinement thickness is investigated using fluorescence video microscopy. We observe separation at small confinement thicknesses followed by a transition to the bulk behaviour (no separation) at a thickness of about 4 μm (a few radii of gyration for the studied DNA chains). We prese...

Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the electric field inside and outside of a narrow pore is obtained. With an analysis based on "electrohydrodynamic equivalence" we determine the possibility of extension of a charged polymer due to the presence of an electric field gradient in ...

The advent of solid state nanodevices allows for interrogating the physico-chemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been recently characterized by theoretical and computational studies of model polymer chains free from self-entanglement. However, sufficiently long equilibrated chains are necessarily knotted. The impact of such topological "defects" on the tr...

We use computer simulations to study the (driven) dynamics of a charged polymer in a disordered medium, thus mimicking the setting used in gel electrophoresis. In agreement with experiments, we find that inside the gel the mobility of the polymer is only a weak function of its length N. In contrast to this, the mean entrance time into the gel, is a very strong function of N, <tau_e > \propto N^1.3, and does not show any sign of saturation with increasing N. We rationalize thi...

Polymer translocation experiments typically involve anionic polyelectrolytes such as DNA molecules driven through negatively charged nanopores. Quantitative modelling of polymer capture to the nanopore followed by translocation therefore necessitates the consideration of the electrostatic barrier resulting from like-charge polymer-pore interactions. To this end, in this work we couple mean-field level electrohydrodynamic equations with the Smoluchowski formalism to characteri...

We present a numerical study of polyelectrolytes electrophoresing in free solution while squeezed by an axisymmetric confinement force transverse to their net displacement. Hybrid multi-particle collision dynamics and molecular dynamics simulations with mean-field finite Debye layers show that even though the polyelectrolyte chains remain "free-draining", their electrophoretic mobility increases with confinement in nanoconfining potential wells. The primary mechanism leading ...