Simulations of the overshoot in the build‐up of orientation of long DNA during gel electropohoresis based on a distribution of oscillation times

Carlsson, Christina; Larsson, Anette

doi:10.1002/elps.1150170906

Cited by 3 publications

(1 citation statement)

References 34 publications

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“…The reason is that the gel interactions which cause the cycling by leading to hooking of the DNA are stochastic because of gel heterogeneity. The distribution of period times therefore is wide, with a width similar to its mean, resulting in that the initially coherent cycles performed by different molecules become out of phase already after about one period …”

Section: Discussionmentioning

confidence: 99%

DNA Electrophoresis in Gellan Gels. The Effect of Electroosmosis and Polymer Additives

2002

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The polysacharide gellan forms hydrogels if a divalent ion such as calcium is added at millimolar concentrations. The gel can be reversed to solution by adding EDTA, which makes it a promising candidate for preparative electrophoretic separation of biomolecules. We have studied the electrophoretic migration of double-stranded T4 DNA (164 kilobase pairs) in gellan gels by velocity measurements and by linear dichroism spectroscopy studies of the DNA coil conformation during the migration. The gels either contained 0.3% of high molecular weight (5 × 10 6 ) poly(ethylene oxide) (PEO), to suppress the electroosmosis induced by the negative charges of the gellan polymer, or were free of such added polymer and therefore exhibited an electroosmotic flow which is opposite to the DNA migration. In both cases, the viral DNA migrate in an oscillatory manner between stretched and coiled states, because it becomes entangled with the gellan gel fibers. In the stretched state of the cycle, the molecules are substantially aligned with the field. As the field is turned off, the alignment relaxes first by a rapid (seconds) stretch relaxation along the aligned path in the gel, followed by a slower (minutes) end-on type of motion to the equilibrium isotropic coil state. The added PEO has two effects on the DNA migration. An indirect effect is that the quenched electroosmosis leads to a stronger stretching of the DNA and to shorter cycle period times because the ends of the molecules move faster in the absence of the counter flow. A direct effect is that the PEO itself retards the DNA motion, most likely because of a combination of hydrodynamic interactions and entanglement effects. The net result of these two opposing PEO effects is that the center-of-mass velocity of the DNA increases by a factor of about 2 upon addition of PEO.

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Section: Discussionmentioning

confidence: 99%

DNA Electrophoresis in Gellan Gels. The Effect of Electroosmosis and Polymer Additives

2002

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Pulsed Field Gel Electrophoresis: Past, present, and future

López‐Canovas¹,

Benitez²,

Isidrón

et al. 2019

Analytical Biochemistry

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Designs for the self-assembly of open and closed macromolecular structures and a molecular switch using DNA methyltransferases to order proteins on nucleic acid scaffolds

Smith¹

2002

Nanotechnology

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The methyltransferase-directed addressing of fusion proteins to DNA scaffolds offers an approach to the construction of protein/nucleic acid biostructures with potential in a variety of applications. The technology is currently only limited by the yield of high occupancy structures. However, current evidence shows that DNA scaffolds that contain three or four targeted proteins can be reliably constructed. This permits a variety of macromolecular designs, several of which are given in this paper. Designs for open and closed two-dimensional and three-dimensional assemblies and a design for a molecular switch are discussed. The closed two-dimensional assembly takes the form of a square, and could find application as a component of other systems including a macromolecular rotaxane. The closed three-dimensional system takes the form of a trigonal bipyramid and could find application as a macromolecular carcerand. The molecular switch could find application as a peptide biosensor. Guidelines for the construction and structural verification of these designs are reported.

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Simulations of the overshoot in the build‐up of orientation of long DNA during gel electropohoresis based on a distribution of oscillation times

Cited by 3 publications

References 34 publications

DNA Electrophoresis in Gellan Gels. The Effect of Electroosmosis and Polymer Additives

DNA Electrophoresis in Gellan Gels. The Effect of Electroosmosis and Polymer Additives

Pulsed Field Gel Electrophoresis: Past, present, and future

Designs for the self-assembly of open and closed macromolecular structures and a molecular switch using DNA methyltransferases to order proteins on nucleic acid scaffolds

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