Gel electrophoretic mobility of single-stranded DNA: The two reptation field-dependent factors

Rousseau, Jean; Drouin, Guy; Slater, Gary W.

doi:10.1002/(sici)1522-2683(20000501)21:8<1464::aid-elps1464>3.0.co;2-e

Cited by 25 publications

(24 citation statements)

References 48 publications

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“…This empirical result gives a free-solution mobility m 0 = 3.56610 -4 cm 2 /Vs, quite similar to the values reported elsewhere [1,7,10,12,14]. However, the linear correction factor 1-g(C) = [C/6.14%] is surprisingly large, and this may mean Eq.…”

Section: The Zero-size Mobilitymentioning

confidence: 96%

“…have been validated by numerous experimental studies [1,7]. In the case of the vWBR experiments with agarose gels, the DNA persistence length p D is probably smaller than the gel pore size a(C) and the reptation model then predicts that [1] m ?…”

Section: The Asymptotic Mobilitymentioning

confidence: 99%

“…The biased reptation model does indeed predict this very form in the limit where the molecules are small enough that the electric forces do not lead to molecular orientation [1,3,7]. Therefore, vWBR's model recovers both the plateau behaviour (Eq.…”

Section: The Reptation Regimementioning

confidence: 99%

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A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

Slater

2002

Electrophoresis

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The separation of DNA fragments by gel electrophoresis has been studied extensively over the last two decades. More recently, similar studies have been carried out to characterize the separation achieved by the current capillary array electrophoresis systems and their sieving polymer solutions. In all cases, at least three different mobility regimes have been shown to exist: the Ogston regime when the radius of gyration of the DNA fragment is smaller than the pore size, the reptation regime when the DNA is larger than the pore size but remains in a random coil conformation, and finally the reptation-with-orientation regime where the DNA orients in the field direction and essentially all resolution is lost. Unfortunately, although theory helps us understand the different regimes and how to properly exploit them, we still have no theory-based general equations that would apply to all regimes. Such equations would be especially useful to analyze data, optimize separation systems and interpolate mobilities to estimate unknown molecular sizes. Recently, van Winkle, Beheshti and Rill (Electrophoresis 2002, 23, 15-19) proposed an intriguing empirical formula that seems to adequately fit the mobility of dsDNA fragments across all three regimes. In this paper, I investigate the relation between this empirical formula and the known theories of gel electrophoresis, and I study the dependence of its fitting parameters upon the experimental conditions. Finally, I examine how this equation may need to be modified to capture the more subtle details predicted by fundamental theories of DNA gel electrophoresis.

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Section: The Zero-size Mobilitymentioning

confidence: 96%

Section: The Asymptotic Mobilitymentioning

confidence: 99%

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A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

Slater

2002

Electrophoresis

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“…where E is the field intensity, M is the molecular size (e.g., in bases), and the parameters a and b are functions of the gel concentration C. These two limiting cases have been clearly observed both in agarose and polyacrylamide gels, and Rousseau et al [129] reported that b = 2 a. Similar relations exist for the diffusion coefficient D [125][126].…”

Section: A Universal Mobility Relation For Gel Electrophoresis?mentioning

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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“…The contour length of a nucleic acid molecule is typically many persistence lengths, leading to a large amount of conformational entropy, which when coupled with the field sensitivity induced by the molecule's large linear charge density leads to a strong dependence of its mobility on field strength (6). A more accurate expression for the mobility of a nucleic acid is therefore (E) ϭ 0 ϩ kE, where E is the magnitude of the field and k is the linear field dependence of the mobility, which captures the quadratic dependence of reptating DNA velocity on field.…”

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confidence: 99%

Nonlinear electrophoretic response yields a unique parameter for separation of biomolecules

Pel

Broemeling

Mai

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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We demonstrate a unique parameter for biomolecule separation that results from the nonlinear response of long, charged polymers to electrophoretic fields and apply it to extraction and concentration of nucleic acids from samples that perform poorly under conventional methods. Our method is based on superposition of synchronous, time-varying electrophoretic fields, which can generate net drift of charged molecules even when the time-averaged molecule displacement generated by each field individually is zero. Such drift can only occur for molecules, such as DNA, whose motive response to electrophoretic fields is nonlinear. Consequently, we are able to concentrate DNA while rejecting high concentrations of contaminants. We demonstrate one application of this method by extracting DNA from challenging samples originating in the Athabasca oil sands.concentration ͉ DNA ͉ electrophoresis ͉ purification ͉ SCODA M ethods for separating different molecular species are the cornerstone of analytic techniques in molecular biology. Of these, nucleic acid extraction from complex sources is a molecular separation problem of great importance to current challenges in genomics, metagenomics, forensics, biodefense, food and water safety, and clinical molecular diagnostics.The ubiquitous column-and bead-based nucleic acid extraction methods that dominate the field of nucleic acid extraction use selective chemical affinity between nucleic acids and ion exchange or similar resins and beads to capture target molecules. Although these methods often involve mechanical steps including filtration and centrifugation, they are relatively inexpensive and work well in a variety of samples. Their inadequacy lies in the fact that the separations are based on chemical affinity and therefore perform poorly in the presence of contaminant molecules that either have similar chemical properties to nucleic acids or foul the capture matrix (1). Precipitation methods are often used after column or bead extractions to remove contaminants that carry through; however, this further reduces yield of the methods, particularly in cases with low target concentrations.This weakness of existing methods is a critical problem for DNA extraction from environmental samples. For example, humic acids, a family of contaminants abundant in soil, coextract with DNA in phenol-based separations owing to their solubility in the aqueous phase (1) and partly carry through column-and bead-based methods. The situation worsens with a low starting concentration of nucleic acids because the dual challenge must then be faced of concentrating few nucleic acids while rejecting large amounts of contaminants. A universal, simple, and highly selective method to concentrate DNA from contaminated and low-abundance sources would be very desirable.We have found a unique solution to this problem in the physics of electrophoresis. It has long been known that nucleic acid molecules, because of their exceptionally long contour lengths and high linear charge density, exhibit complex electrophoretic...

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Gel electrophoretic mobility of single-stranded DNA: The two reptation field-dependent factors

Cited by 25 publications

References 48 publications

A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

Nonlinear electrophoretic response yields a unique parameter for separation of biomolecules

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