Dynamical Scaling of DNA Diffusion Coefficients

Smith, Douglas E.; Perkins, Thomas T.; Chu, Steven

doi:10.1021/ma951455p

Cited by 284 publications

(331 citation statements)

References 14 publications

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“…Taking the theoretical value of 0.588 for the Flory exponent ν we find an exponent of α = 2ν = 1.18 for this model. If we take the experimentally obtained value for ν of 0.61 [9], we find α = 1.22 -in excellent agreement with our experiments, where we find power law scaling with an exponent of 1.26 ± 0.07.…”

supporting

confidence: 90%

“…Assuming Zimm dynamics (and thus that the solvent inside the coil moves with the polymer), the coil experiences a Stokes drag force of 6πηRv = 6πηR g dR g /dt, which for typical parameters yields a drag force of about 24 pN. This assumption is justified by experiments by Smith et al [9], who found clear evidence for Zimm dynamics for DNA longer than 4.3 kbp. Clearly, in this case the hydrodynamic friction on the part of the polymer outside the pore is the dominant force counteracting the driving force.…”

mentioning

confidence: 94%

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Fast DNA Translocation through a Solid-State Nanopore

et al. 2005

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We report translocation experiments on double-strand DNA through a silicon oxide nanopore. Samples containing DNA fragments with seven different lengths between 2000 to 96000 basepairs have been electrophoretically driven through a 10 nm pore. We find a power-law scaling of the translocation time versus length, with an exponent of 1.26 ± 0.07. This behavior is qualitatively different from the linear behavior observed in similar experiments performed with protein pores. We address the observed nonlinear scaling in a theoretical model that describes experiments where hydrodynamic drag on the section of the polymer outside the pore is the dominant force counteracting the driving. We show that this is the case in our experiments and derive a power-law scaling with an exponent of 1.18, in excellent agreement with our data.

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confidence: 90%

mentioning

confidence: 94%

Fast DNA Translocation through a Solid-State Nanopore

et al. 2005

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“…Within the range of lengths studied, D L ÿ2=3 and r L 2 , and thus the results do not follow the predictions of either the Rouse or Zimm model [1]. At the same time, our data are in a very good agreement with experimental results obtained by other techniques not related to FCS [5][6][7][8] and closely follow the predictions of the semiflexible polymer theory [4]. Therefore, our results clearly demonstrate that in the range of the lengths studied, dsDNA behaves as a semiflexible polymer with strong hydrodynamic interactions [29].…”

Section: -2supporting

confidence: 44%

“…The dynamics of dsDNA in solution has been a subject of a number of experimental investigations carried out by various techniques, including DLS [5], single-molecule fluorescence microscopy [6], electrophoresis [7], and TEB [8]. Fluorescence correlation spectroscopy (FCS) [9], a single-molecule technique that can provide more detailed information on the macromolecular dynamics than the classical ensemble-based methods, has been recently applied to investigation of DNA in solution [10 -12], which has lead to a controversy whether dsDNA dynamics in dilute solution is controlled by hydrodynamic interactions [10,12] or not [11].…”

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confidence: 99%

Diffusion and Segmental Dynamics of Double-Stranded DNA

et al. 2006

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Diffusion and segmental dynamics of the double-stranded -phage DNA polymer are quantitatively studied over the transition range from stiff to semiflexible chains. Spectroscopy of fluorescence fluctuations of single-end fluorescently labeled monodisperse DNA fragments unambiguously shows that doublestranded DNA in the length range of 10 2 -2 10 4 base pairs behaves as a semiflexible polymer with segmental dynamics controlled by hydrodynamic interactions. DOI: 10.1103/PhysRevLett.97.258101 PACS numbers: 87.14.Gg, 82.35.Lr, 87.15.He, 87.15.Vv The dynamic behavior of individual macromolecules in solution is governed by chain connectivity and hydrodynamic interactions [1]. Understanding polymer dynamics and quantitative verification of polymer theories requires detailed information on segmental motion of individual polymer molecules. However, the classical experimental techniques, such as dynamic light scattering (DLS) or transient electric birefringence (TEB), predominantly deliver information on large-scale shape fluctuations of macromolecules, and development of new experimental approaches providing detailed information on internal dynamics of individual molecules is of high importance.Precise experiments in polymer physics are impossible without well-defined monodisperse polymer samples covering a wide range of molecular weights. The recent progress in molecular biotechnology resulted in a variety of techniques to produce monodisperse DNA fragments, which stimulated the use of DNA as a model compound in studies of polymer dynamics in solution [2]. Doublestranded DNA (dsDNA) is a biopolymer characterized by a large persistence length l p 50 nm [3]. As a result, dsDNA fragments exhibit rodlike, semiflexible, or even flexible polymer behavior, depending on their length. Thus, simple generic models of polymer dynamics [1] are not expected to provide a quantitative description of dsDNA behavior, and more advanced models accounting for the persistence of the polymer chain [4] are required.The dynamics of dsDNA in solution has been a subject of a number of experimental investigations carried out by various techniques, including DLS [5], single-molecule fluorescence microscopy [6], electrophoresis [7], and TEB [8]. Fluorescence correlation spectroscopy (FCS) [9], a single-molecule technique that can provide more detailed information on the macromolecular dynamics than the classical ensemble-based methods, has been recently applied to investigation of DNA in solution [10 -12], which has lead to a controversy whether dsDNA dynamics in dilute solution is controlled by hydrodynamic interactions [10,12] or not [11]. Apart from this controversy, for different reasons, none of these FCS-based experiments produced parameters of DNA dynamics. Generally, to the best of our knowledge, no experimental studies were published so far where diffusion and intramolecular dynamics of dsDNA have been simultaneously investigated over the transition range from stiff to semiflexible chains. In the present Letter, we fill this gap and car...

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“…Typical microfluidic flows are several orders of magnitude slower with Re ≪ 1, and the flow residence time in the microchannel (for performing bio-chemical analysis or other experiments) ranges from a few seconds to a few minutes. In contrast, the time required for the chain molecule concentration profile to fully develop scales as For lambda phase DNA (λ-DNA) in water and D ≈ 0.43µm 2 /s [36], the molecule diffuses a distance of O(10) µm in O(10 2 ) s. In order for the chain concentration profile to fully develop, the chain molecules need to diffuse for a much longer time than the typical residence time. To resolve this problem, we propose the use of oscillatory flow in microfluidic devices.…”

Section: Introductionmentioning

confidence: 99%

DNA Molecules in Microfluidic Oscillatory Flow

Chen¹,

Graham²,

Pablo³

et al. 2005

Macromolecules

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The conformation and dynamics of a single DNA molecule undergoing oscillatory pressure-driven flow in microfluidic channels is studied using Brownian dynamics simulations, accounting for hydrodynamic interactions between segments in the bulk and between the chain and the walls. Oscillatory flow provides a scenario under which the polymers may remain in the channel for an indefinite amount of time as they are stretched and migrate away from the channel walls. We show that by controlling the chain length, flow rate and oscillatory flow frequency, we are able to manipulate the chain extension and the chain migration from the channel walls. The chain stretch and the chain depletion layer thickness near the wall are found to increase as the Weissenberg number increases and as the oscillatory frequency decreases.

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Dynamical Scaling of DNA Diffusion Coefficients

Cited by 284 publications

References 14 publications

Fast DNA Translocation through a Solid-State Nanopore

Fast DNA Translocation through a Solid-State Nanopore

Diffusion and Segmental Dynamics of Double-Stranded DNA

DNA Molecules in Microfluidic Oscillatory Flow

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