Separation of DNA Using Ferrofluid Array Electrophoresis

1996 ◽  
Vol 463 ◽  
Author(s):  
Pascal Mayer ◽  
Jerôme Bibette ◽  
J. L. Viovy
Keyword(s):  
Magnetic Field ◽  
Computer Simulations ◽  
Molecular Mechanisms ◽  
Electrophoretic Separation ◽  
Dna Molecules ◽  
Size Fractionation ◽  
Lambda Phage ◽  
Regular Array ◽  
Recent Computer ◽  
Dna Size

ABSTRACTWe present a new method for electrophoretic separation of DNA, Ferro fluid Array Electrophoresis (FAE). The method uses a stabilized suspension of an hydrophobic ferrofluid in aqueous buffer as the separating medium. When this suspension is placed in a slab cell and submitted to a magnetic field perpendicular to the slab plane, it organizes into a regular array of columns with micron-sized spacing. DNA migrating in this maze leads to size-fractionation. Resolution of lambda phage (48.5 kbp) and T4 (140 kbp) DNA molecules in 30 mn is achieved. The motion of individual DNA molecules during FAE is observed using fluorescence videomicroscopy, and the molecular mechanisms responsible for separation are discussed in the light of recent computer simulations. During migration, large DNA molecules temporarily wrap around the impenetrable ferrofluid columns. They disengage by slippage, like a rope on a pulley, and the dependence of the disengagement time upon DNA size is responsible for the size-fractionation.

Contact Value Formulae for the Density Profiles of the Electric Double Layer

2008 ◽  
Vol 73 (4) ◽  
pp. 558-574 ◽  
Author(s):  
Douglas J. Henderson ◽  
Lutful B. Bhuiyan
Keyword(s):  
Computer Simulations ◽  
Density Profile ◽  
Physical Interpretation ◽  
Electric Double Layer ◽  
Reasonable Agreement ◽  
Hard Wall ◽  
Density Profiles ◽  
Sum Rule ◽  
Recent Computer ◽  
Local Expression

An exact sum rule, due to Henderson, Blum, and Lebowitz, for the contact value of the density profile of ions in a primitive model electrolyte next to a planar, nonpolarizable charged hard wall, has been known for some years. This result has a pleasing physical interpretation and is local. It has been useful in assessing the accuracy of theoretical approximations. However, a sum rule for the contact value of the charge profile for the same system has, until recently, not been known. A few years ago, Boda and Henderson proposed what they thought might be a useful, but approximate, local expression for the contact value of the charge profile at a weakly charged electrode. Very recent computer simulations indicate that this expression may well be exact at low electrode charge. Recently, Holovko, Badiali, and di Caprio have obtained a more general, but nonlocal, sum rule for the contact value of the charge profile that is valid for all electrode charge. In this paper, we develop an alternative, nonlocal, but nonrigorous expression for this quantity. Both the expression of Holovko et al. and our new expression are examined by means of computer simulations. The Holovko et al. expression is exact and, within numerical uncertainties, seems supported by our simulations. Although admittedly nonrigorous, our simpler expression is in seemingly reasonable agreement with simulation and thus appears to be useful. The relation between the two expressions has not been established.

Involvement of the host initiator function dnaA in the replication of coliphage lambda.

Genetics ◽  
1995 ◽  
Vol 139 (4) ◽  
pp. 1469-1481 ◽  
Author(s):  
G Wegrzyn ◽  
A Wegrzyn ◽  
I Konieczny ◽  
K Bielawski ◽  
G Konopa ◽  
...  
Keyword(s):  
Dna Replication ◽  
High Yield ◽  
Dna Molecules ◽  
Lambda Phage ◽  
Initiation Of Replication ◽  
Phage Dna ◽  
Theta Replication ◽  
Lambdoid Prophage ◽  
Coliphage Lambda ◽  
Lambda Dna

Abstract We demonstrate that the initiation of coliphage lambda DNA replication is dependent on the host initiator function dnaA, provided that the lambdoid prophage Rac is absent. Presence of Rac compensated the absence of dnaA function, causing initiation of replication. In dnaAts rac+ cells at 43 degrees, most of parental phage DNA molecules, after one round of theta replication, switched to a replication with features of the sigma mode and produced progeny at high yield. Initiation of replication of the lambda Pts1 mutant at 43 degrees was blocked by dnaA function; however, under dnaA-rac+ conditions all parental phage DNA molecules, after one round of theta replication, switched to the sigma mode and produced progeny at high yield. Taking into account our recent finding that transcriptional activation of ori lambda seems to be dnaA-regulated (to be published elsewhere), we suggest that the DnaA-lambda Pts1 incompatibility occurs at the insertion of the ori lambda-bound lambda O-lambda P-DnaB preprimosome between the complementary lambda DNA strands. The role of Rac and the mechanism of the switch from theta to sigma mode of lambda phage DNA replication are discussed.

Magnetic field draping in the comet Halley coma: Comparison of Vega observations with computer simulations

1987 ◽  
Vol 14 (6) ◽  
pp. 640-643 ◽  
Author(s):  
K. Schwingenschuh ◽  
W. Riedler ◽  
Ye. Yeroshenko ◽  
J. L. Phillips ◽  
C. T. Russell ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Computer Simulations ◽  
Comet Halley

scholarly journals A Compass To Boost Navigation: Cell Biology of Bacterial Magnetotaxis

2020 ◽  
Vol 202 (21) ◽  
Author(s):  
Frank D. Müller ◽  
Dirk Schüler ◽  
Daniel Pfeiffer
Keyword(s):  
Magnetic Field ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Magnetotactic Bacteria ◽  
Genetically Engineered ◽  
Model Organisms ◽  
Complex Cell ◽  
Magnetite Biomineralization ◽  
Directed Motility ◽  
The Impact

ABSTRACT Magnetotactic bacteria are aquatic or sediment-dwelling microorganisms able to take advantage of the Earth’s magnetic field for directed motility. The source of this amazing trait is magnetosomes, unique organelles used to synthesize single nanometer-sized crystals of magnetic iron minerals that are queued up to build an intracellular compass. Most of these microorganisms cannot be cultivated under controlled conditions, much less genetically engineered, with only few exceptions. However, two of the genetically amenable Magnetospirillum species have emerged as tractable model organisms to study magnetosome formation and magnetotaxis. Recently, much has been revealed about the process of magnetosome biogenesis and dedicated structures for magnetosome dynamics and positioning, which suggest an unexpected cellular intricacy of these organisms. In this minireview, we summarize new insights and place the molecular mechanisms of magnetosome formation in the context of the complex cell biology of Magnetospirillum spp. First, we provide an overview on magnetosome vesicle synthesis and magnetite biomineralization, followed by a discussion of the perceptions of dynamic organelle positioning and its biological implications, which highlight that magnetotactic bacteria have evolved sophisticated mechanisms to construct, incorporate, and inherit a unique navigational device. Finally, we discuss the impact of magnetotaxis on motility and its interconnection with chemotaxis, showing that magnetotactic bacteria are outstandingly adapted to lifestyle and habitat.

scholarly journals DNA translocation to giant unilamellar vesicles during electroporation is independent of DNA size

Soft Matter ◽  
2019 ◽  
Vol 15 (45) ◽  
pp. 9187-9194
Author(s):  
Shaurya Sachdev ◽  
Aswin Muralidharan ◽  
Dipendra K. Choudhary ◽  
Dayinta L. Perrier ◽  
Lea Rems ◽  
...  
Keyword(s):  
Electrophoretic Mobility ◽  
Dna Delivery ◽  
Dna Molecules ◽  
Dna Translocation ◽  
Giant Unilamellar Vesicles ◽  
Unilamellar Vesicles ◽  
Dna Size

DNA delivery into GUVs during electroporation is governed by bulk electrophoretic mobility implying a mechanism in which DNA molecules enter in their coiled conformation, as opposed to stochastic threading, through electro-pores.

scholarly journals DNA size in confined environments

2019 ◽  
Vol 21 (23) ◽  
pp. 12566-12575 ◽  
Author(s):  
Marco Zoli
Keyword(s):  
Dna Molecules ◽  
Site Specific ◽  
Twist Conformation ◽  
End Distance ◽  
End To End ◽  
Crowded Environments ◽  
Dna Size ◽  
Macroscopic Parameters

For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders.

scholarly journals Static magnetic field regulates Arabidopsis root growth via auxin signaling

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yue Jin ◽  
Wei Guo ◽  
Xupeng Hu ◽  
Mengmeng Liu ◽  
Xiang Xu ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Root Growth ◽  
Static Magnetic Field ◽  
Molecular Mechanisms ◽  
Biological Significance ◽  
Auxin Signaling ◽  
Biological Processes ◽  
Root Tips ◽  
The North ◽  
Living Organisms

Abstract Static magnetic field (SMF) plays important roles in biological processes of many living organisms. In plants, however, biological significance of SMF and molecular mechanisms underlying SMF action remain largely unknown. To address these questions, we treated Arabidopsis young seedlings with different SMF intensities and directions. Magnetic direction from the north to south pole was adjusted in parallel (N0) with, opposite (N180) and perpendicular to the gravity vector. We discovered that root growth is significantly inhanced by 600 mT treatments except for N180, but not by any 300 mT treatments. N0 treatments lead to more active cell division of the meristem, and higher auxin content that is regulated by coordinated expression of PIN3 and AUX1 in root tips. Consistently, N0-promoted root growth disappears in pin3 and aux1 mutants. Transcriptomic and gene ontology analyses revealed that in roots 85% of the total genes significantly down-regulated by N0 compared to untreatment are enriched in plastid biological processes, such as metabolism and chloroplast development. Lastly, no difference in root length is observed between N0-treated and untreated roots of the double cryptochrome mutant cry1 cry2. Taken together, our data suggest that SMF-regulated root growth is mediated by CRY and auxin signaling pathways in Arabidopsis.

Model and computer simulations of the motion of DNA molecules during pulse field gel electrophoresis

Biochemistry ◽  
1991 ◽  
Vol 30 (21) ◽  
pp. 5264-5274 ◽  
Author(s):  
Steven B. Smith ◽  
Christoph Heller ◽  
Carlos Bustamante
Keyword(s):  
Computer Simulations ◽  
Gel Electrophoresis ◽  
Pulse Field ◽  
Dna Molecules ◽  
Pulse Field Gel Electrophoresis
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