DNA In Polymer Solutions Research Articles

Electrophoretic Mobility of Double-Stranded DNA in Polymer Solutions and Gels with Tuned Structures

We report a systematic experimental study on the migration behavior of double-stranded DNA (dsDNA) in polymer networks with precisely controlled network structures. The electrophoretic mobility (μ) appeared to be a power law function of the number of base pairs (n), μ ∼ n–γ, with 0.36 < γ < 1.46. The variance in γ has been commonly explained using the reptation model with constraint release or using the entropic trapping (ET) model. However, our results indicated that the μ values were expressed as products of a power law function and an exponential function of n, which differs from any of the existing models. The power law function terms corresponded to the existing models, the Rouse model or the reptation model. In polymer gels, we observed a crossover from the Rouse to the reptation model with an increase in n, while the migration behavior in polymer solutions always obeyed the Rouse model. These results revealed that the continuous change in γ was accommodated by the exponential function terms.

Stretching and migration of DNA by solvent elasticity in an oscillatory flow

A model with solution viscoelasticity is proposed to explain the ratchetlike stretching of DNA by a symmetric ac electric field in polymer solutions. In this model, DNA is stretched by the interaction between the fluid elasticity and the oscillatory flow induced by DNA. Predictions of the model are confirmed by DNA stretching experiments performed in various polymer solutions and the corresponding rheological measurements of the solutions. In particular, experiments have verified that a net migration of stretched DNA in polymer solutions can be induced by a zero-mean asymmetric ac electric field. This last finding cannot be explained by other existing models.

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

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.

Theory for the capillary electrophoretic separation of DNA in polymer solutions

We present a mathematical model based on the models of Hubert et al. [Macromolecules 29 (1996) 1006] and Sunada and Blanch [Electrophoresis, 19 (1998) 3128] to describe the electrophoretic mobility of DNA by a transient entanglement coupling mechanism. The proposed model takes into account the interactions between molecules in the capillary and the cross-section of collision between DNA and polymer molecules. The results show that the calculated values agree remarkably well with our electrophoretic mobility data.

Separation of double-stranded and single-stranded DNA in polymer solutions: I. Mobility and separation mechanism.

We have studied the separation of single-stranded and double-stranded DNA in a matrix of entangled, linear poly-N,N-dimethylacrylamide. Our results give better insight into the mechanisms involved during separations in polymer solutions. The dependence of different parameters on DNA size, electric field, pore size and the polymer chain length are evaluated and compared to theoretical predictions. Striking differences between experimental data and predicted scaling laws are found. Our data should help to optimize DNA separation in capillary electrophoresis and to improve existing models for DNA separation in porous matrices.

Separation of double-stranded and single-stranded DNA in polymer solutions: II. Separation, peak width and resolution.

The electrophoretic separation of single-stranded and double-stranded DNA has been examined, using a matrix of linear poly-N,N-dimethylacrylamide (pDMA). The dependence of peak spacing, peak width and resolution on important parameters such as polymer concentration, polymer chain length and electric field strength, has been studied. This work complements our systematic study on electrophoretic mobility under different conditions (C. Heller, Electrophoresis 1999, 20, 1962-1977), and will help to further optimize and improve high performance DNA separation in capillary electrophoresis with entangled polymer solutions.

A theory for the electrophoretic separation of DNA in polymer solutions.

We present a mathematical model of DNA capillary electrophoresis in polymer solutions based on nonentangling collisions between DNA and polymer molecules. Using videomicroscopy images of DNA migrating through polymer solutions, we propose a modified transient entanglement coupling mechanism for DNA separations that includes nonentangling DNA/polymer collisions. We show that a mathematical model based on individual nonentangling DNA/polymer collisions is able to predict the mobilities of DNA in solutions of low molecular mass polymer. We compare the model predictions to mobility data for separations of DNA in a range of concentrations for solutions of both hydroxypropylcellulose (Mw 100,000) and hydroxyethylcellulose (Mw 139,000). The model relies on one fitted parameter, the time constant for the interaction between the DNA and polymer molecules, which is based on the physical properties of DNA and polymers.

Microscopy of DNA in dilute polymer solutions.

The mechanism of separation of DNA in polymer solutions is not well understood. In this paper we use epifluorescence videomicroscopy to investigate the dynamic behavior of DNA electrophoresing through dilute polymer solutions. DNA collides with polymer obstacles, which cause the conformation of DNA to change from the globular, random coil conformation it takes in free solution. There are two main types of DNA-polymer collisions: U-shape collisions and brief collisions. In U-shape collisions, the DNA collides with a polymer obstacle, extends into a U-shape, and then slides around the polymer obstacle like a pulley. There are occasionally multiple entanglement points, causing the DNA to take more complex conformations, such as W-shapes. In the brief collision process, the DNA collides with a polymer obstacle and begins to extend but then collapses back into its globular conformation before a full U-shape is formed. The frequency of these interactions increases as the DNA size increases, and it also increases when the polymer size or concentration increases. These data support the transient entanglement coupling mechanism of separation of DNA, which states that entanglements between DNA and polymer molecules result in the separation of DNA.

Systematic study of field and concentration effects in capillary electrophoresis of DNA in polymer solutions

A systematic study of the separation of double-stranded DNA in hydroxypropylcellulose (HPC) with a molecular mass of 10 6 was undertaken, using a variety of concentrations (from 0.1 to 1%) and different electric fields (from 6 to 540 V/cm). The data show that a high polymer concentrations (⩾0.4%) and low fields, the separation mechanism is similar to that occurring in gels. The results are in good agreement with theoretical models, and in particular with a recently proposed theory for gels with a pore size smaller than the persistence length of DNA. For more dilute solutions and high fields, however, the separation pattern cannot be explained by existing theories. The existence of an original mechanism was confirmed by the direct observation of the conformation of double-stranded DNA molecules in the polymer solution by fluorescence videomicroscopy. Practical conclusions for the capillary electrophoretic separation of duplex DNA are drawn.

A transition to a compact form of DNA in polymer solutions.

In the presence of over-threshold concentrations of simple neutral polymers and salts, DNA undergoes a cooperative change in its solution structure. Sedimentation studies at low DNA concentrations show that phage DNA molecules collapse into particles approaching the compactness of the contents of phage heads. The interaction between DNA and polymers is thought to be nonspecifically replusive.