Modeling the dynamics of DNA electrophoresis on a flat surface

Luo, Hui; Gersappe, Dilip

doi:10.1002/1522-2683(200208)23:16<2690::aid-elps2690>3.0.co;2-r

Cited by 17 publications

(18 citation statements)

References 15 publications

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“…A possible new approach to performing electrophoresis is to utilize the effect of surface interactions. In our recent work [12][13][14] it has been shown that the local friction between a fully absorbed DNA molecule and a flat homogeneous surface can result in the separation of long DNA fragment. In this approach the friction between the adsorbed segments and the surface is controlled by coating the surface with well controlled silane monolayer films.…”

Section: Introductionsupporting

confidence: 54%

Dna Electrophoresis at Surfaces

Rafailovich¹,

Sokolov²,

Gersappe³

2003

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Summary:During this year we performed two major projects:I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. (See manuscript below which is being submitted to the journal Electrophoresis for publication. )II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient These results are being submitted for publication to JACS (see attached). Personnel:Two graduate students were supported by this grant; Binquan Li and Xiaohua Fang.Both have obtained their PhD this year and are employed as postdoctoral associated at Columbia University.One undergraduate student was supported; Eric Petersen who is now a sophomore at Harvard University.One Research Associate Young Soo Seo, was also supported. He is now employed by LG Electronics.One faculty member; Dilip Gersappe received summer (2 months) salary. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation.6

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Section: Introductionsupporting

confidence: 54%

Dna Electrophoresis at Surfaces

Rafailovich¹,

Sokolov²,

Gersappe³

2003

Self Cite

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“…In some sense, this new idea lies somewhere between conventional electrophoresis and chromatography: an electric field drives molecules across the device, but the length dependence of the mobility arises due to surface interactions, rather than topological constraints. This research group has studied surface electrophoresis experimentally as well as with computer simulations, and they have updated their findings in two articles published this year [30,31].…”

Section: Surface Electrophoresismentioning

confidence: 99%

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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“…(4) and (5), the temperature T can be automatically controlled, the solvent friction is also included, and they can be considered as the extension of Langevin dynamics equation for the beads such that the energy, momentum as well as mass are conserved. 5,14,15,36 The particles (polymer beads and the solvent particles) in our method are coarse-grained. The mass of the polymer bead m b is set as unit mass.…”

Section: Methodsmentioning

confidence: 99%

“…As a computationally efficient explicitsolvent method, CGH-MD is potentially useful for simulating systems of large number of water particles to complement more rigorous methods. It may also be applied to the study of polar and hydrophobic effects, 13 nonuniformly distributed electrostatic interactions, and the effects associated with bound and sequestered water molecules 12,13 in various bio-macromolecular and nanofluidic systems such as the electrophoresis of DNA, 36 proteins, 60 viral particles, and complexes 61 in nanofluidic, 34,58,59,62 microfluidic, 63,64 and microstructure array 16,65 systems. …”

Section: Ion Distribution Patternmentioning

confidence: 99%

Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse‐grained hybrid molecular dynamics approach

Wang

Liu

et al. 2008

J Comput Chem

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Simulation of DNA electrophoresis facilitates the design of DNA separation devices. Various methods have been explored for simulating DNA electrophoresis and other processes using implicit and explicit solvent models. Explicit solvent models are highly desired but their applications may be limited by high computing cost in simulating large number of solvent particles. In this work, a coarse-grained hybrid molecular dynamics (CGH-MD) approach was introduced for simulating DNA electrophoresis in explicit solvent of large number of solvent particles. CGH-MD was tested in the simulation of a polymer solution and computation of nonuniform charge distribution in a cylindrical nanotube, which shows good agreement with observations and those of more rigorous computational methods at a significantly lower computing cost than other explicit-solvent methods. CGH-MD was further applied to the simulation of DNA electrophoresis in a polymer solution and in a well-studied nanofluidic device. Simulation results are consistent with observations and reported simulation results, suggesting that CGH-MD is potentially useful for studying electrophoresis of macromolecules and assemblies in nanofluidic, microfluidic, and microstructure array systems that involve extremely large number of solvent particles, nonuniformly distributed electrostatic interactions, bound and sequestered water molecules.

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Modeling the dynamics of DNA electrophoresis on a flat surface

Cited by 17 publications

References 15 publications

Dna Electrophoresis at Surfaces

Dna Electrophoresis at Surfaces

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse‐grained hybrid molecular dynamics approach

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