A dynamic light scattering study of four DNA restriction fragments

Sorlie, Susan S.; Pecora, R.

doi:10.1021/ma00204a022

Cited by 114 publications

(123 citation statements)

References 2 publications

(3 reference statements)

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“…3,4,[17][18][19][20][21][22][23][24] The diffusion coefficients measured in the present work were corrected to the standard temperature of 20°C using eq. (7).…”

Section: Resultsmentioning

confidence: 99%

Measuring the translational diffusion coefficients of small DNA molecules by capillary electrophoresis

et al. 2001

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“…3,4,[17][18][19][20][21][22][23][24] The diffusion coefficients measured in the present work were corrected to the standard temperature of 20°C using eq. (7).…”

Section: Resultsmentioning

confidence: 99%

Measuring the translational diffusion coefficients of small DNA molecules by capillary electrophoresis

et al. 2001

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“…Smith et al 3 found that the diffusivity of TOTO-1 stained DNA needed to be scaled by (1.75) 2/5 to bring it into line with the native DNA fragments of Sorlie and Pecora. 29 They also reported that this correction factor decreased to (1.32) 2/5 when YOYO-1 stain was used. 5 Using the data of Smith et al, 3 L Ϫ3/5 , that the Kuhn length of TOTO-1 stained DNA increased by a factor of 1.75 relative to the native DNA value of b k ϭ0.106 m, while, for YOYO-1 stained DNA, the Kuhn length increased by a factor of 1.32.…”

Section: Simulationmentioning

confidence: 97%

“…For YOYO-1 stained 21 m -phage DNA in a 43.3 cP solvent at 23 C, we have available experimental values 5 of the equilibrium stretch ͑1.5 m͒, and relaxation time ͑4.1 s͒. We also have available diffusivity data for native DNA fragments ͑Ͻ1 m͒ obtained from light-scattering data 29 and diffusivity data for TOTO-1 stained fragmented and concatenated -phage DNA ͑2-140 m͒ in a 0.95 cP solvent. 3 The diffusivity data for the stained DNA can be scaled to correspond to native DNA in an solvent of arbitrary viscosity, , by the scaling Dϳ Ϫ1 , and correcting for the change in persistence length due to dye intercalation.…”

Section: Simulationmentioning

confidence: 99%

Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions

Jendrejack

Pablo

Graham

2002

The Journal of Chemical Physics

271

364

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We present a fully parametrized bead-spring chain model for stained -phage DNA. The model accounts for the finite extensibility of the molecule, excluded volume effects, and fluctuating hydrodynamic interactions ͑HI͒. Parameters are determined from equilibrium experimental data for 21 m stained -phage DNA, and are shown to quantitatively predict the non-equilibrium behavior of the molecule. The model is then used to predict the equilibrium and nonequilibrium behavior of DNA molecules up to 126 m. In particular, the HI model gives results that are in quantitative agreement with experimental diffusivity data over a wide range of molecular weights. When the bead friction coefficient is fit to the experimental relaxation time at a particular molecular weight, the stretch in shear and extensional flows is adequately predicted by either a free-draining or HI model at that molecular weight, although the fitted bead friction coefficients for the two models differ significantly. In shear flow, we find two regimes at high shear rate (␥ ) that follow different scaling behavior. In the first, the viscosity and first normal stress coefficient scale roughly as ␥ Ϫ6/11 and ␥ Ϫ14/11 , respectively. At higher shear rates, these become ␥ Ϫ2/3 and ␥ Ϫ4/3 . These regimes are found for both free-draining and HI models and can be understood based on scaling arguments for the diffusion of chain ends.

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“…While there has been a number of DLS reports on the properties of DNA solutions (see, for example Refs. [71][72][73][74]), studies involving interactions between DNA and cationic amphiphiles are in a very limited number [18,24,75].…”

Section: A Dynamic Light Scattering Studymentioning

confidence: 99%

DNA and surfactants in bulk and at interfaces

Dias

Pais

Miguel

et al. 2004

Colloids and Surfaces A: Physicochemical and Engineering Aspect

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Recent investigations of the DNA interactions with cationic surfactants and catanionic mixtures are reviewed. Several techniques have been used such as fluorescence microscopy, dynamic light scattering, electron microscopy, and Monte Carlo simulations.The conformational behaviour of large DNA molecules in the presence of cationic surfactant was followed by fluorescence microscopy and also by dynamic light scattering. These techniques were in good agreement and it was possible to observe a discrete transition from extended coils to collapsed globules and their coexistence for intermediate amphiphile concentrations. The dependence on the surfactant alkyl chain was also monitored by fluorescence microscopy and, as expected, lower concentrations of the more hydrophobic surfactant were required to induce DNA compaction, although an excess of positive charges was still required.Monte Carlo simulations on the compaction of a medium size polyanion with shorter polycations were performed. The polyanion chain suffers a sudden collapse as a function of the concentration of condensing agent, and of the number of charges on the polycation molecules. Further increase in the concentration increases the degree of compaction. The compaction was found to be associated with the polycations promoting bridging between different sites of the polyanion. When the total charge of the polycations was lower than that of the polyanion, a significant translational motion of the compacting agent along the polyanion was observed, producing only a small-degree of intrachain segregation, which can explain the excess of positive charges necessary to compact DNA.Dissociation of the DNA-cationic surfactant complexes and a concomitant release of DNA was achieved by addition of anionic surfactants. The unfolding of DNA molecules, previously compacted with cationic surfactant, was shown to be strongly dependent on the anionic surfactant chain length; lower amounts of a longer chain surfactant were needed to release DNA into solution. On the other hand, no dependence on the hydrophobicity of the compacting agent was observed. The structures of the aggregates formed by the two surfactants, after the interaction with DNA, were imaged by cryogenic transmission electron microscopy. It is possible to predict the structure of the aggregates formed by the surfactants, like vesicles, from the phase behaviour of the mixed surfactant systems.Studies on the interactions between DNA and catanionic mixtures were also performed. It was observed that DNA does not interact with negatively charged vesicles, even though they carry positive amphiphiles; however, in the presence of positively charged vesicles, DNA molecules compact and adsorb on their surface.Finally Monte Carlo simulations were performed on the adsorption of a polyelectrolyte on catanionic surfaces. It was observed that the mobile charges in the surface react to the presence of the polyelectrolyte enabling a strong degree of adsorption even though the membrane was globally neutral. Our observati...

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A dynamic light scattering study of four DNA restriction fragments

Cited by 114 publications

References 2 publications

Measuring the translational diffusion coefficients of small DNA molecules by capillary electrophoresis

Measuring the translational diffusion coefficients of small DNA molecules by capillary electrophoresis

Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions

DNA and surfactants in bulk and at interfaces

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