Methods to electrophoretically stretch DNA: microcontractions, gels, and hybrid gel-microcontraction devices

Randall, Greg; Schultz, Kelly M.; Doyle, Patrick S.

doi:10.1039/b515326c

Cited by 83 publications

(132 citation statements)

References 56 publications

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“…47 Finally, in direct linear analysis, 48,49 DNA collisions with posts may be a useful way of preconditioning DNA configurations before attempting to completely stretch DNA in an elongational flow [48][49][50] or electric field. 28,51 …”

Section: Discussionmentioning

confidence: 99%

Collision of a DNA Polymer with a Small Obstacle

2006

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Using single molecule fluorescence microscopy, we study the dynamics of an electric-field-driven DNA molecule colliding with a single stationary post. The radius of the obstacle is small compared to the contour length of the molecules. Molecules that achieve hooked configurations which span the obstacle were chosen for study. Four different types of hooked configurations were found: symmetric hairpins with constant extension during unhooking, asymmetric hairpins with constant extension during unhooking, asymmetric hairpins with increasing extension during unhooking, and rare multiply looped entangled configurations. The important physics describing the unhooking dynamics for each classification differ and models are proposed to predict unhooking times. Surprisingly, we find that most collisions do not follow classic rope-on-pulley motion but instead form hairpins with increasing total extension during the unhooking process (called X collisions). Last, we show that unraveling to form a hairpin and center-of-mass motion during unhooking affect the overall center of mass holdup time during a collision process.

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Section: Discussionmentioning

confidence: 99%

Collision of a DNA Polymer with a Small Obstacle

2006

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“…The electrophoretic strain rate ˙is nearly constant in much of the contraction, 18,19 and the nominal strain accumulated by a molecule moving down the centerline of the device is Ϸ ln͑w 1 / w 2 ͒ = 4. The electric field gradient in the contraction can be approximated using the scaling ٌE Ϸ͑E 2 − E 1 ͒ / ᐉ c = ͓E 1 ͑w 1 / w 2 −1͔͒ / ᐉ c where E 1 and E 2 are the electric field strengths at the inlet and the outlet of the channel, respectively.…”

Section: Device Geometrymentioning

confidence: 99%

“…15,16 In DLA devices, the molecules are typically stretched by field gradients in microcontractions. 2,3,[17][18][19][20] However, in these strain-limited devices, molecular individualism 21 leads to a large population of molecules that do not reach full extension. Recent studies have shown that the effects of molecular individualism can be mitigated by "preconfiguring" the initial conformation of a molecule before it is stretched.…”

Section: Introductionmentioning

confidence: 99%

“…Recent studies have shown that the effects of molecular individualism can be mitigated by "preconfiguring" the initial conformation of a molecule before it is stretched. 18,20,22 Several different methods to preconfigure molecules have been shown to increase the uniformity of stretch, including preshearing 22 and passing through a gel matrix. 18 A promising technique is placing a microfabricated obstacle array just before the contraction to induce molecular collisions with the obstacles 4,20 ͓see Fig.…”

Section: Introductionmentioning

confidence: 99%

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Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning

Trahan

Doyle

2009

Biomicrofluidics

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Recently our group has reported experiments using an obstacle array to precondition the conformations of DNA molecules to facilitate their stretch in a microcontraction. Based upon previous successes simulating electrophoretic stretching in microcontractions without obstacles, we use our simulation model to study the deformation of DNA chains in a microcontraction preceded by an array of cylindrical obstacles. We compare our data to the experimental results and find good qualitative, and even quantitative, agreement concerning the behavior of the chains in the array; however, the simulations overpredict the mean stretch of the chains as they leave the contraction. We examine the amount of stretch gained between leaving the array and reaching the end of the contraction and speculate that the differences seen are caused by nonlinear electrokinetic effects that become important in the contraction due to a combination of field gradients and high field strengths.

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“…1,2 The potential for the use of small-channel devices in DNA mapping [3][4][5][6][7] and separation, [8][9][10][11][12][13] single biomolecule manipulation, 12 and even ion separation 14,15 has inspired interest in the static and dynamic response of individual molecules to confinement. [16][17][18] The proximity of the bounding walls offers a very powerful method to change the polymer equilibrium conformation through steric interactions as well as the polymer dynamics through modulation of hydrodynamic interactions (HI).…”

Section: Introductionmentioning

confidence: 99%

Double-Stranded DNA Diffusion in Slitlike Nanochannels

et al. 2006

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We present an experimental study of double-stranded DNA diffusion in slitlike channels. The channel heights span the regime from moderate confinement (height ∼ bulk radius of gyration of the DNA) to strong confinement (height ∼ persistence length). Scalings of diffusivity with channel height differ from blob model predictions. The diffusivity scales inversely with molecular weight when the channel height is smaller than the bulk radius of gyration. This scaling is indicative of hydrodynamic screening. A scaling analysis shows that the screening of hydrodynamic interactions arises from a combination of two mechanisms. After using a Zimm preaverage approximation, the unique symmetry of the thin-slit disturbance velocity and the isotropic nature of the polymer conformation together cause a cancellation of hydrodynamic interactions due to symmetry. We also find that the algebraic decay of the far-field velocity magnitude is sufficient to eliminate large-length scale hydrodynamic cooperativity in diffusion of quasi-two-dimensional polymers in good solvents.

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Methods to electrophoretically stretch DNA: microcontractions, gels, and hybrid gel-microcontraction devices

Cited by 83 publications

References 56 publications

Collision of a DNA Polymer with a Small Obstacle

Collision of a DNA Polymer with a Small Obstacle

Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning

Double-Stranded DNA Diffusion in Slitlike Nanochannels

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