Electrophoresis of long DNA molecules in linear polyacrylamide solutions

Ueda, Mitsuru; Oana, Hidehiro; Baba, Yoshinobu; Doi, Masao; Yoshikawa, Kenichi

doi:10.1016/s0301-4622(98)00093-3

Cited by 49 publications

(56 citation statements)

References 41 publications

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“…3,57 U-shape or V-shape conformation has also been found in other simulation studies. 14,15 Figure 4 shows the time development variation of the x component of the DNA end-to-end distance X end and the maximum bead-bead distance within the DNA chain in the x direction X max , respectively.…”

Section: Ion Distribution Patternsupporting

confidence: 81%

“…[1][2][3][4] Significant progress has been made in developing simulation models of DNA and protein electrophoresis in nanofluidic devices and other systems primarily using implicit solvent methods. For example, the bond-fluctuation Monte-Carlo method has been used for simulating the motion of long polyelectrolytes inside an array of microscopic traps.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Ion Distribution Patternsupporting

confidence: 81%

Section: Introductionmentioning

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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“…We immediately see that on average, the DNA adopt extended so-called ''I-shape'' configurations and traverse the pores in the same manner as observed in concentrated agarose or polyacrylamide solutions. 15,48,49 This is best seen by observing the third, fourth, and fifth images of Fig. 5a.…”

mentioning

confidence: 84%

Methods to electrophoretically stretch DNA: microcontractions, gels, and hybrid gel-microcontraction devices

2006

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“…A series of videomicroscopy studies [17,[40][41][42][43][44][45] of large linear DNA in polymer solutions has revealed that the DNA molecule undergoes significant conformational changes during electrophoretic migration. Carlsson et al [43] and Morris and co-workers [44,45] in their visualization studies found that, although the dynamics of DNA migrating through polymer solutions have some characteristics similar to that of DNA migrating in gels, the apex of the U-shape conformation for linear DNA migrates in polymer solution whereas in gels the apex remains stationary.…”

Section: Videomicroscopymentioning

confidence: 99%

Electrophoretic mobility of linear and star‐branched DNA in semidilute polymer solutions

2006

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Electrophoresis of large linear T2 (162 kbp) and 3-arm star-branched (N(Arm) = 48.5 kbp) DNA in linear polyacrylamide (LPA) solutions above the overlap concentration c* has been investigated using a fluorescence visualization technique that allows both the conformation and mobility mu of the DNA to be determined. LPA solutions of moderate polydispersity index (PI approximately 1.7-2.1) and variable polymer molecular weight Mw (0.59-2.05 MDa) are used as the sieving media. In unentangled semidilute solutions (c* < c < c(e)), we find that the conformational dynamics of linear and star-branched DNA in electric fields are strikingly different; the former migrating in predominantly U- or I-shaped conformations, depending on electric field strength E, and the latter migrating in a squid-like profile with the star-arms outstretched in the direction opposite to E and dragging the branch point through the sieving medium. Despite these visual differences, mu for linear and star-branched DNA of comparable size are found to be nearly identical in semidilute, unentangled LPA solutions. For LPA concentrations above the entanglement threshold (c > c(e)), the conformation of migrating linear and star-shaped DNA manifest only subtle changes from their unentangled solution features, but mu for the stars decreases strongly with increasing LPA concentration and molecular weight, while mu for linear DNA becomes nearly independent of c and Mw. These findings are discussed in the context of current theories for electrophoresis of large polyelectrolytes.

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Electrophoresis of long DNA molecules in linear polyacrylamide solutions

Cited by 49 publications

References 41 publications

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

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

Methods to electrophoretically stretch DNA: microcontractions, gels, and hybrid gel-microcontraction devices

Electrophoretic mobility of linear and star‐branched DNA in semidilute polymer solutions

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