Microscopy of DNA in Dilute Polymer Solutions

Sunada, Wade M.; Blanch, Harvey W.

doi:10.1021/bp980063+

Cited by 18 publications

(18 citation statements)

References 21 publications

(43 reference statements)

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“…We believe these perturbations arise because linear and star DNA in a high molecular weight polymer solution entangle with the polymer chains for longer times than they do in low-molecularweight polymer solutions, resulting in greater and longerlasting conformational changes that can be observed on time scales accessible to videomicroscopy. These observations are also consistent with previously observed conformational dynamics of T4 DNA (166 kbp) in HEC [28].…”

Section: Concentration Dependencesupporting

confidence: 93%

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Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in polymer solutions

Saha¹,

Heuer

Archer

2004

Electrophoresis

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We study the effect of matrix chain molecular weight Mw and concentration c on the electrophoretic mobility micro of large linear and star-like, branched DNA in polymer solutions. Polyethylene oxide (PEO) with narrow molecular weight distributions form the main focus of this study. For PEO concentrations ranging from one half the overlap concentration, c*, to 3c*, the effective drag coefficient, zeta is identical with (mu0/mu) - 1, satisfies the following approximate scaling relationship, zeta approximately cMw(0.7). Here, mu0 is the electrophoretic mobility in free solution. While the concentration dependence is consistent with predictions from the transient entanglement coupling (TEC) model, the molecular weight dependence is significantly weaker. Although a similar dependence of mobility on Mw can be predicted when nonentangling collisions are the dominant source of drag, a model based on these collisions alone cannot reproduce the experimental observations. We also find that the architecture of large DNA does not affect either the concentration dependence or molecular weight dependence of the electrophoretic mobility.

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Section: Concentration Dependencesupporting

confidence: 93%

“…conformation of large DNA as observed using epifluorescence microscopy [11,[26][27][28]. Therefore, entangling collisions should play a significant role in the electrophoretic migration of large DNA and might explain why the TEC model has been found to fit data well for large DNA [24].…”

Section: Nucleic Acidsmentioning

confidence: 99%

Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in polymer solutions

Saha¹,

Heuer

Archer

2004

Electrophoresis

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“…7). This behavior is similar to what has been observed for linear DNA in polymer solutions [33,34]. Figure 7.…”

Section: Semidilute and Entangled Solutionssupporting

confidence: 87%

“…Another complication arises from the dragging of the matrix chains by the analyte as it moves through and entangles with matrix polymers in solution. These effects have been observed for linear DNA in semidilute solutions [33,34]. The linear DNA was observed to move with a U-shaped configuration, indicating that matrix chains are dragged along with migrating molecules.…”

Section: Semidilute and Entangled Solutionsmentioning

confidence: 56%

Electrophoretic dynamics of large DNA stars in polymer solutions and gels

2003

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We have developed a procedure for synthesizing large stable branched DNA structures that enables visualization via fluorescence microscopy. Using this procedure we have synthesized large DNA stars and observed their electrophoretic behavior in polymer solutions and gels. In dilute polyacrylamide solutions, the DNA stars move as random coils and appear to experience only brief collisions with the polymer chains in solution. The effect of polymer solution concentration on the electrophoretic mobility of stars in the dilute regime is found to be in good accord with predictions of the transient entanglement coupling (TEC) model. In semidilute polymer solutions, the star arms extend in the field direction and drag the core through the matrix. The star arms form several U-shaped conformations as they collide and engage with polyacrylamide chains. The U-shaped conformations occasionally evolve into J-shaped conformations as the star arms slide off the matrix chains they engage during electrophoretic migration. In concentrated polymer solutions, the arms of the star extend and form V-shaped structures with the core as the apex. The arms then pull the core through the matrix. These V-shaped conformations are much longer-lived than U-shaped ones and, unlike the latter, do not transform to J-shaped conformations. In polyacrylamide and agarose gels, where matrix entanglements are fixed, DNA stars become trapped when entanglements with matrix molecules prevent the core from being pulled through the matrix by the extended arms. This trapping was observed at all gel concentrations and electric fields studied.

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“…The separation is based on the interactions between the GNPPs and DNA molecules. Using high-molecularweight (HMW) GNPPs (.2.0 6 10 8 g/particle) that have a very small electrophoretic mobility (7.01 6 10 25 cm 2 /V?s), DNA migration is retarded by interactions (collisions) with the GNPPs [24,25]. Additionally, core-shell-type globular nanoparticles have been applied in microchip CE to the separation of DNA fragments having sizes ranging from 1 to 15 kbp [23].…”

Section: Introductionmentioning

confidence: 99%

Nanoparticle‐filled capillary electrophoresis for the separation of long DNA molecules in the presence of hydrodynamic and electrokinetic forces

Tseng¹,

Huang²,

Huang³

et al. 2005

Electrophoresis

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We report the analysis of long DNA molecules by nanoparticle-filled capillary electrophoresis (NFCE) under the influences of hydrodynamic and electrokinetic forces. The gold nanoparticle (GNP)/polymer composites (GNPPs) prepared from GNPs and poly(ethylene oxide) were filled in a capillary to act as separation matrices for DNA separation. The separations of lambda-DNA (0.12-23.1 kbp) and high-molecular-weight DNA markers (8.27-48.5 kbp) by NFCE, under an electric field of -140 V/cm and a hydrodynamic flow velocity of 554 microm/s, were accomplished within 5 min. To further investigate the separation mechanism, the migration of lambda-DNA was monitored in real time using a charge-coupled device (CCD) imaging system. The GNPPs provide greater retardation than do conventional polymer media when they are encountered during the electrophoretic process. The presence of interactions between the GNPPs and the DNA molecules is further supported by the fluorescence quenching of prelabeled lambda-DNA, which occurs through an energy transfer mechanism. Based on the results presented in this study, we suggest that the electric field, hydrodynamic flow, and GNPP concentration are the three main determinants of DNA separation in NFCE.

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Microscopy of DNA in Dilute Polymer Solutions

Cited by 18 publications

References 21 publications

Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in polymer solutions

Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in polymer solutions

Electrophoretic dynamics of large DNA stars in polymer solutions and gels

Nanoparticle‐filled capillary electrophoresis for the separation of long DNA molecules in the presence of hydrodynamic and electrokinetic forces

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