Distribution of single DNA molecule electrophoretic mobilities in semidilute and dilute hydroxyethylcellulose solutions

Yamaguchi, Yoshihiro; Todorov, Todor I.; Morris, Michael D.; Larson, Ronald G.

doi:10.1002/elps.200305783

Cited by 13 publications

(10 citation statements)

References 30 publications

(22 reference statements)

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“…While these limitations tend to have a small effect on the mean of the distribution, they substantially reduce its standard deviation. A previous single molecule videomicroscopy study [27] experienced similar difficulties.…”

Section: Average Trapping Timementioning

confidence: 76%

Motion of single long DNA molecules through arrays of magnetic columns

et al. 2005

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We present a videomicroscopy study of T4 DNA (169 kbp) in microfluidic arrays of posts formed by the self-assembly of magnetic beads. We observe DNA moving through an area of 10 000 microm(2), typically containing 100-600 posts. We determine the distribution of the contact times with the posts and the distribution of passage times across the field of view for hundreds of DNA per experiment. The contact time is well approximated by a Poisson process, scaling like the inverse of the field strength, independent of the density of the array. The distribution of passage times allows us to estimate the mean velocity and dispersivity of the DNA during its motion over distances long compared to our field of view. We compare these values with those computed from a lattice Monte Carlo model and geometration theory. We find reasonable quantitative agreement between the lattice Monte Carlo model and experiment, with the error increasing with increasing post density. The deviation between theory and experiment is attributed to the high mobility of DNA after disengaging from the posts, which leads to a difference between the contact time and the total time lost by colliding. Classical geometration theory furnishes surprisingly good agreement for the dispersivity, while geometration theory with a mean free path significantly overestimates the dispersivity.

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Section: Average Trapping Timementioning

confidence: 76%

Motion of single long DNA molecules through arrays of magnetic columns

et al. 2005

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“…However, the velocity of the apex of the “U” varies randomly from one DNA molecule to another [203,217], suggesting either that the entangling polymer matrix is not homogeneous [203] or that different DNA molecules drag different numbers of polymer chains with them. Fluorescence recovery after photobleaching (FRAP) studies have shown that DNA molecules drag dextran chains with them during electrophoresis [210]; presumably other hydrophilic polymers can be dragged by the DNA as well.…”

Section: Capillary Electrophoresismentioning

confidence: 99%

Effect of the matrix on DNA electrophoretic mobility

Stellwagen

2009

Journal of Chromatography A

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DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.

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“…The interactions between DNA and polymer molecules have been confirmed by another study that shows dynamic formation and deformation of U-shape in DNA conformation [30]. Although ultradilute polymer solutions have been used for the separation of long DNA under a constant electric field [31][32][33][34][35][36], they do not provide highresolving power for small DNA fragments.…”

Section: Introductionmentioning

confidence: 85%

Nanomaterials and chip‐based nanostructures for capillary electrophoretic separations of DNA

Lin

Huang

2005

Electrophoresis

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Capillary electrophoresis (CE) and microchip capillary electrophoresis (MCE) using polymer solutions are two of the most powerful techniques for the analysis of DNA. Problems, such as the difficulty of filling polymer solution to small separation channels, recovering DNA, and narrow separation size ranges, have put a pressure on developing new techniques for DNA analysis. In this review, we deal with DNA separation using chip-based nanostructures and nanomaterials in CE and MCE. On the basis of the dependence of the mobility of DNA molecules on the size and shape of nanostructures, several unique chip-based devices have been developed for the separation of DNA, particularly for long DNA molecules. Unlike conventional CE and MCE methods, sieving matrices are not required when using nanostructures. Filling extremely low-viscosity nanomaterials in the presence and absence of polymer solutions to small separation channels is an alternative for the separations of DNA from several base pairs (bp) to tens kbp. The advantages and shortages of the use of nanostructured devices and nanomaterials for DNA separation are carefully addressed with respect to speed, resolution, reproducibility, costs, and operation.

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Distribution of single DNA molecule electrophoretic mobilities in semidilute and dilute hydroxyethylcellulose solutions

Cited by 13 publications

References 30 publications

Motion of single long DNA molecules through arrays of magnetic columns

Motion of single long DNA molecules through arrays of magnetic columns

Effect of the matrix on DNA electrophoretic mobility

Nanomaterials and chip‐based nanostructures for capillary electrophoretic separations of DNA

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