Electrophoretic dynamics of large DNA stars in polymer solutions and gels

Heuer, Daniel M.; Saha, Sourav; Archer, Lynden A.

doi:10.1002/elps.200305606

Cited by 17 publications

(31 citation statements)

References 36 publications

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“…On this basis they suggested that the transition from U-to I-shaped motion could be induced by the degree of entanglement among polymer chains. In our previous study [17] we found that starbranched DNA also undergoes a series of conformational changes which were somewhat similar to the U-to I-shape transition observed for linear DNA in semidilute polymer solution. Whereas in fixed networks, star-branched DNA is observed to become trapped near the well, a consequence of the branch point [17].…”

Section: Videomicroscopymentioning

confidence: 66%

“…Electrophoretic mobility of large linear and star DNA was measured using a custom-made visualization cell [17]. Measurements of the steady-state center-of-mass velocity v of fluorescently labeled DNA in semidilute LPA solutions were obtained using an intensified CCD camera (Video Scope Maxicam 3000) and image processing software (Image Pro).…”

Section: Methodsmentioning

confidence: 99%

“…A series of videomicroscopy studies [17,[40][41][42][43][44][45] of large linear DNA in polymer solutions has revealed that the DNA molecule undergoes significant conformational changes during electrophoretic migration. Carlsson et al [43] and Morris and co-workers [44,45] in their visualization studies found that, although the dynamics of DNA migrating through polymer solutions have some characteristics similar to that of DNA migrating in gels, the apex of the U-shape conformation for linear DNA migrates in polymer solution whereas in gels the apex remains stationary.…”

Section: Videomicroscopymentioning

confidence: 99%

“…3-Arm star DNA (N Arm = 48.5 kbp) was synthesized using a similar procedure to that reported in [17] except the 3-arm star core is formed using selfassembly of three 72 bp single-stranded oligonucleotides as shown in Fig. 1.…”

Section: Linear and Star Dnamentioning

confidence: 99%

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Electrophoretic mobility of linear and star‐branched DNA in semidilute polymer solutions

2006

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Electrophoresis of large linear T2 (162 kbp) and 3-arm star-branched (N(Arm) = 48.5 kbp) DNA in linear polyacrylamide (LPA) solutions above the overlap concentration c* has been investigated using a fluorescence visualization technique that allows both the conformation and mobility mu of the DNA to be determined. LPA solutions of moderate polydispersity index (PI approximately 1.7-2.1) and variable polymer molecular weight Mw (0.59-2.05 MDa) are used as the sieving media. In unentangled semidilute solutions (c* < c < c(e)), we find that the conformational dynamics of linear and star-branched DNA in electric fields are strikingly different; the former migrating in predominantly U- or I-shaped conformations, depending on electric field strength E, and the latter migrating in a squid-like profile with the star-arms outstretched in the direction opposite to E and dragging the branch point through the sieving medium. Despite these visual differences, mu for linear and star-branched DNA of comparable size are found to be nearly identical in semidilute, unentangled LPA solutions. For LPA concentrations above the entanglement threshold (c > c(e)), the conformation of migrating linear and star-shaped DNA manifest only subtle changes from their unentangled solution features, but mu for the stars decreases strongly with increasing LPA concentration and molecular weight, while mu for linear DNA becomes nearly independent of c and Mw. These findings are discussed in the context of current theories for electrophoresis of large polyelectrolytes.

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Section: Videomicroscopymentioning

confidence: 66%

Section: Methodsmentioning

confidence: 99%

Section: Videomicroscopymentioning

confidence: 99%

Section: Linear and Star Dnamentioning

confidence: 99%

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Electrophoretic mobility of linear and star‐branched DNA in semidilute polymer solutions

2006

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“…Subsequent staining using an intercalating cyanine dye, YoYo-1 (Molecular Probes), permits direct visualization of the branched DNA molecules. 24,25 In the approach used by Heuer et al, 25 DNA branched structures are synthesized using immobile nucleic acid junctions. These junctions are DNA structures where three or more double-helical strands branch out from a central point.…”

Section: Visualizing Relaxation Dynamics Of Molecules Near Surfacesmentioning

confidence: 99%

Tethered Lubricants for Small Systems

Archer¹

2006

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The objective of this research project is two-fold. First, to fundamentally understand friction and relaxation dynamics of polymer chains near surfaces; and second, to develop novel self-lubricated substrates suitable for MEMS devices. During the last three years of the study the PI and his students have executed all tasks promised in the grant proposal. Details of research accomplishments in each area of the project are described in the next sections. Research A. Interfacial Friction and Dynamics of Alkylsilane SAMsThe main hypothesis that guides our work is that molecular-scale disorder in monolayer films tethered to substrates enhances molecular freedom and improves lubrication and ware properties of thin films. Self-assembled monolayers (SAMs) are in most cases the first choice for creating self-lubricated substrates for small systems (e.g. MEMS and NEMS). SAMs are attractive as lubricating coatings for a variety of reasons.1-3 If the SAMs are created using low surface energy molecules (e.g. alkane or fluorinated alkanes), for example, they reduce interfacial adhesion between substrates to which they are attached, which reduces the interfacial friction coefficient. SAMs can also reduce adhesion by preventing adsorption of stiction promoting species such as water to the substrate. Furthermore, because molecules comprising the SAM are chemically bonded to the substrate, a well-designed SAM coating can retain its lubricating properties through multiple cycles of interfacial shear. The thickness of most SAM coatings is rarely greater than a few nanometers, making these systems ideal for lubricating small mechanical systems such as in MEMs and NEMs. Boundary lubrication properties of several SAM systems, including alkanethiols (CH 3 (CH 2 ) n-1 SH) on Au, Ag, and Cu, and alkyltrichlorosilanes (CH 3 (CH 2 ) n-1 SiCl 3 ) on SiO 2 and mica, have been studied primarily by experiment to establish connections between SAM order, chemistry, and lubrication properties. A important finding is that SAMs formed by long alkylsilane or alkenethiol molecules (chain length >10) provide the best lubrication.2,4 It has been asserted in the literature, without proof, that greater disorder within SAMs comprised of shorter molecules (chain length <10) yields more energy dissipation modes, which increases interfacial friction. 3,5 This assertion contradicts the notion that molecular-scale disorder in monolayer films enhances dynamics and improves lubrication properties.Zhang and Archer recently used Lateral force Atomic Force Microscopy, dynamic contact angle measurements, infrared spectroscopy, and theory to study the interfacial properties of alkyl silane SAMs with varying amounts of disorder.6 Disorder was introduced in the SAMs by mixing two self-assembling components with different molecular weights in varying amounts. Mixed twocomponent (C n /C 18 ) alkylsilane SAMs formed in this manner were confirmed to possess greater levels of orientation disorder using infrared spectroscopy and hexadecane contact angle measurements. 6 Signi...

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Topological effects on the electrophoretic mobility of rigid rodlike DNA in polyacrylamide gels

2003

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The electrophoretic migration of rigid rodlike DNA structures with well defined topologies has been investigated in polyacrylamide (PA) hydrogels prepared by copolymerization of acrylamide and N, N'-methylenebisacrylamide. Previous studies have reported structural and dynamic characteristics of linear and branched DNA during electrophoresis in PA gels using a variety of experimental parameters. However, a thorough investigation aimed at establishing specific relationships between topological features of rigid rodlike DNA structures and their electrophoretic behavior is still needed. In order to study these topological effects on mobility, an intensive examination of the electrophoretic mobility of small linear and starlike DNA was performed. A series of model DNA structures with well-defined branched topologies were synthesized with varying molecular parameters, such as number of arms surrounding the branch point and arm length. The electrophoretic mobility of these structures was then contrasted with a series of data obtained using linear DNA of comparable molecular size. When large DNA stars (M >/= 60 bp) were compared with linear DNA of identical molecular weight, the Ferguson plots were quite different. However, small DNA stars (24-32 bp) and linear analogues had identical Ferguson plots. This indicates that a different motional mode or greater interaction with the gel exists for the larger DNA stars. When the total molecular weight of the DNA stars was held constant and the number of arms varied, the Ferguson plots for all the stars were identical. Additionally, a critical pore size was reached when the ratio of linear DNA mobility to star DNA mobility increased dramatically. Thus, while the incorporation of a single branch point can produce a large reduction in mobility, above a critical molecular size, the incorporation of additional branch points does not appear to provide further reduction in mobility. This finding is consistent with the transport properties of large synthetic star polymers, where a large reduction in their diffusion coefficient is observed when a single branch is added. When additional arms are incorporated, large synthetic stars do not display an appreciable further reduction in diffusion coefficient. The effect of arm length on mobility for rigid rod DNA stars was also studied. For four-arm DNA stars, the mobility was found to scale as an exponential function of the arm length. Finally, a recently proposed phenomenological model was used to successfully fit the mobility data for linear rigid rod DNA at various concentrations of PA.

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Electrophoretic dynamics of large DNA stars in polymer solutions and gels

Cited by 17 publications

References 36 publications

Electrophoretic mobility of linear and star‐branched DNA in semidilute polymer solutions

Electrophoretic mobility of linear and star‐branched DNA in semidilute polymer solutions

Tethered Lubricants for Small Systems

Topological effects on the electrophoretic mobility of rigid rodlike DNA in polyacrylamide gels

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