DNA Electrophoresis on a Flat Surface

Pernodet, Nadine; Samuilov, Vladimir; Shin, Keun Wook; Sokolov, Jonathan; Rafailovich, Miriam; Gersappe, Dilip; Chu, Benjamin

doi:10.1103/physrevlett.85.5651

Cited by 50 publications

(90 citation statements)

References 25 publications

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“…Pernodet and co-workers [29] recently proposed and tested a novel method for the separation of DNA fragments based on the strikingly simple process of inducing electrophoretic migration near a smooth surface. Using this approach, DNA strands migrate across a planar sub- Figure 1.…”

Section: Surface Electrophoresismentioning

confidence: 99%

“…In order to better understand the separation mechanisms at work in surface electrophoresis, Luo and Gersappe [29,31] performed Brownian Dynamics simulations of adsorbed chains subjected to a low intensity electric field. They used a standard coarse-grained approach in which all monomers interact via a Lennard-Jones (LJ) potential while adjacent ones interact via a finitely-extensible nonlinear elastic (FENE) potential [32].…”

Section: Surface Electrophoresismentioning

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: Surface Electrophoresismentioning

confidence: 99%

Section: Surface Electrophoresismentioning

confidence: 99%

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

et al. 2002

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“…The development of accurate and versatile DNA separation technique is currently a significant issue in nanobiotechnology. 1 Recently, Pernodet et al 2 reported separation of DNA chains on a surface without any topological restrictions or any solution sieving media. This can be a significant benefit over conventional separation methods.…”

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confidence: 99%

Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface

Park

Aluru

2010

Applied Physics Letters

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In this paper, we investigate, using molecular dynamics simulations, the conformation and diffusion of longer and shorter single-strand DNA ͑ssDNA͒ as a function of water film thickness. While the conformation of the shorter ssDNA is significantly affected and the diffusion is suppressed with reduction in water film thickness, the conformation and diffusion of the longer DNA is not influenced. We explain our observations by considering the competition between stacking interaction of bases and solvation tendency of ssDNA. This paper suggests an approach to control the surface motion of ssDNA in nanoscale water films using film thickness. © 2010 American Institute of Physics. ͓doi:10.1063/1.3366725͔ DNA separation is an essential technique for gene sequencing and DNA fingerprinting. The development of accurate and versatile DNA separation technique is currently a significant issue in nanobiotechnology. 1 Recently, Pernodet et al. 2 reported separation of DNA chains on a surface without any topological restrictions or any solution sieving media. This can be a significant benefit over conventional separation methods. However, a detailed physical understanding of surface transport of DNA is currently not available. 3 For example, it is commonly known that the diffusion coefficient of DNA decreases with increase in DNA size in free solution 4 and under two-dimensional confinement. 5 However, a recent experimental study on electrophoresis of DNA on an atomic force microscopy surface showed the faster movement of longer DNA in a thin pure water film. 6 According to the Nernst-Einstein relation between mobility and diffusion, this implies that the longer DNA has higher diffusion than the shorter DNA.To understand the reasons behind the ambiguities in the physics of surface transport of DNA, in this paper, we investigate, using extensive molecular dynamics ͑MD͒ simulations, the diffusion of DNA in nanometer-thick water films by considering DNA of various sizes. As shown in the schematic in Fig. 1͑a͒, a single-strand DNA ͑ssDNA͒ was solvated in a pure water film on a solid surface. Following the experiment, 6 the surface was made by grafting the poly͑eth-ylene glycol͒-silanes ͑PEG-silanes͒ on a solid substrate. The size of the surface is 20ϫ 20 nm 2 and it consists of 1600 PEG-silane molecules. The PEG-silane has 32 atoms and it is attached to the substrate atom ͓see Fig. 1͑b͔͒. The initial configuration and the atomic partial charges of PEG-silane molecule were obtained from PRODRG ͑Ref. 7͒ using GRO-MOS forcefield and charge. The substrate atoms were assumed frozen and their atomic charges were adjusted to make the entire system neutral. We considered two small ssDNAs fragments with 6 and 12 bases. Although recent DNA sequencing technologies utilize tens of millions of small DNA fragments, 8 efficient separation of such small fragments is still challenging. 9 The longer 12-base ssDNA of 5Ј − CGCGAATTCGCG− 3Ј was prepared by unzipping the well-known Dickerson's B-DNA dodecamer ͑double stranded͒, 10 while the shorter 6-bas...

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“…By the process of changing the surface energy of a flat surface, it is possible to change the size range of DNA that can be separated by this method. Molecular dynamics (MD) simulation [12] confirms the separation of DNA molecules by modifying the interaction between the DNA and substrate surface.…”

Section: Introductionmentioning

confidence: 93%

“…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: Introductionmentioning

confidence: 99%

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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DNA Electrophoresis on a Flat Surface

Cited by 50 publications

References 25 publications

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface

Dna Electrophoresis at Surfaces

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