Concave ferguson plots of DNA fragments and convex ferguson plots of bacteriophages: Evaluation of molecular and fiber properties, using desktop computers

Tietz, Dietmar; Chrambach, Andreas

doi:10.1002/elps.1150130160

Cited by 46 publications

(13 citation statements)

References 35 publications

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“…In gels, a linear dependence of log@) vs. gel concentration is generally observed in a given range of particle sizes and gel concentrations, and the associated "Ferguson plots" [29] have proven useful to rationalize data and to determine molecular dimensions. This approach has been generalized by Tietz et al [30] to nonlinear Ferguson plots, by introducing an "effective particle radius" varying with concentration, but a theory for the variation of this effective radius with physical parameters such as particle flexibility and conformation or electric-field strength is still to be formulated. Overall, it seems fair to say that the different ver-sions of the model are able to provide a reasonably comprehensive molecular understanding of the evolution of the retardation coefficient only in a limited range of DNA sizes, corresponding to a radius of gyration comparable with the average pore size of the gel [31,32].…”

Section: The Ogston Modelmentioning

confidence: 97%

DNA electrophoresis in polymer solutions: Ogston sieving, reptation and constraint release

1993

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The electrophoresis of long polyelectrolytes is considered theoretically, with special attention to duplex DNA. We first discuss quantitative approaches to determine unambiguously the entanglement properties of polymer solutions. Following an idea proposed by Grossman and Soane, we then assume that the "mesh" size of the solution plays the role of a dynamic "pore size" in order to apply theories for gel electrophoresis. In the framework of the Ogston model, we predict that duplex DNA up to 1 kb or more should be separable in dilute (i.e. nonentangled) solutions of high molecular weight polymers. In an entangled solution, and for DNA larger than the pore size, we use a recently developed fluctuation-reptation model to predict the range of sizes in which separation should be possible as a function of electric field E and pore size zeta b. For zeta b larger than the Kuhn length of DNA, we predict a separation up to a size N*scaling as E-1 zeta b-1. For zeta b smaller than the Kuhn length, two different regimes are expected. For small electric fields (typically of the order of 10 V/cm), N*should be proportional to E-1 zeta b-3/2, whereas for high electric fields such as encountered in capillary electrophoresis, we expect that N*is proportional to E-2/5 zeta b-12/5. These predictions are qualitatively different from earlier ones. Finally, we demonstrate that the finite lifetime of the "pores" in an entangled solution (as opposed to a gel) may lead to a new migration mechanism by constraint release, which is not size-dependent.(ABSTRACT TRUNCATED AT 250 WORDS)

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Section: The Ogston Modelmentioning

confidence: 97%

DNA electrophoresis in polymer solutions: Ogston sieving, reptation and constraint release

1993

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“…Electrophoresis of rod-shaped viruses [28] and of DNA [51,52] yielded curved plots also for lower agarose concentrations.…”

Section: General 521mentioning

confidence: 99%

“…Eq. (A1) can be adjusted to accommodate the evaluation of nonlinear Ferguson plots [38,50,52] in 1-D electrophoresis. Curve-fitting algorithms for nonlinear Ferguson plots are also part of program ElphoFit.…”

Section: Mapping Proceduresmentioning

confidence: 99%

Computer‐assisted 2‐D agarose electrophoresis of Haemophilus influenzae type B meningitis vaccines and analysis of polydisperse particle populations in the size range of viruses: A review

Tietz

2007

Electrophoresis

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When protein-polysaccharide conjugated vaccines were first developed for the immunization of small children against meningitis caused by infection with Haemophilus influenzae type b (Hib), the vaccine preparations varied in immunogenicity. Testing for immunogenicity was time-consuming and alternative analytical procedures for determining vaccine quality were unsatisfactory. For example, due to the very high molecular weight of the vaccine particles, immunogens could only be physically characterized as a fraction in the void volume of Sepharose gel filtration. In search of better analytical methods, a computer-assisted electrophoretic technique for analyzing such vaccines was developed in the period from 1983 to 1995. This new approach made it possible to analyze highly negatively charged particles as large as or larger than intact viruses. 2-D gel patterns were generated that varied depending on the conditions of the particular vaccine preparation and were therefore characteristic of each vaccine sample. Thus, vaccine particle populations with a continuous size variation over a wide range (polydisperse) could be characterized according to size and free mobility (related to particle surface net charge density). These advances are reviewed in this article, since the developed methods are still a promising tool for vaccine quality control and for predicting immunogen effectiveness in the production of vaccines. The technique is potentially beneficial for Hib immunogens and other high-molecular-mass vaccines. Additional biomedical applications for this nondenaturing electrophoretic technique are briefly discussed and detailed information about computational and mathematical procedures and theoretical aspects is provided in the Appendices.

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“…The DNA-particle complexes were then examined by electrophoresis using 0.8% agarose gels running in 1 3 TAE buffer (40 mM Tris acetate, 1 mM EDTA, pH 8.0) at 100 V for 2 h. The 0.2 lm pore size of such gels was small enough to block migration of the particles but not individual DNA chains on the particles by physical adsorption. 44 Preparation of Aminated Coverslips Clean coverslips were prepared through several washing steps. 45,46 First, each coverslip was thoroughly washed in acetone and ethanol in an ultrasonic bath for 30 min, respectively.…”

Section: Fluorescence Image Of Sa-modified Microparticles By Confocalmentioning

confidence: 99%

Synthesis and application of streptavidin functionalized organosilica microparticles

Hou

Zhang

Wang

et al. 2014

J of Applied Polymer Sci

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This article reports on the chemical synthesis, functionalization and application of streptavidin (SA)-coated organosilica microparticles. Thiol-functionalized organosilica microparticles are synthesized via a two-step approach involving acid-catalyzed hydrolysis and condensation of 3-mercaptopropyl trimethoxysilane (MPS), followed by base-catalyzed condensation. The surfaces of these particles are modified with 3-aminopropyltriethoxysilane (APS), and characterized by FTIR, XPS, and TGA. Then, APSfunctionalized microparticles are covalently coated with SAs by using glutaraldehyde as a coupling agent, and characterized by FTIR, SEM, and AFM. Immobilization of biotinylated k DNA onto microparticles via SA-biotin immuoreaction is confirmed by confocal microscopy. The results show that these SA-functionalized organosilica microparticles are useful carriers for DNA manipulation at the single molecule level.

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Concave ferguson plots of DNA fragments and convex ferguson plots of bacteriophages: Evaluation of molecular and fiber properties, using desktop computers

Cited by 46 publications

References 35 publications

DNA electrophoresis in polymer solutions: Ogston sieving, reptation and constraint release

DNA electrophoresis in polymer solutions: Ogston sieving, reptation and constraint release

Computer‐assisted 2‐D agarose electrophoresis of Haemophilus influenzae type B meningitis vaccines and analysis of polydisperse particle populations in the size range of viruses: A review

Synthesis and application of streptavidin functionalized organosilica microparticles

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