Probing single DNA mobility with fluorescence correlation microscopy

Tatarkova, Svetlana A.; Berk, David A.

doi:10.1103/physreve.71.041913

Cited by 17 publications

(23 citation statements)

References 20 publications

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“…FCS has also been used to probe the dynamic fluctuations of fluorescently labeled DNA [4,5]. Recently Shusterman and co-workers [6] probed the dynamics of the end monomer in single-stranded (ss) and double-stranded (ds) DNA using FCS.…”

Section: Introductionmentioning

confidence: 99%

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Internal Mechanical Response of a Polymer in Solution

Cohen

Moerner

2007

Phys. Rev. Lett.

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We observed single molecules of fluorescently labeled double-stranded (ds) λ DNA held in an antiBrownian electrokinetic trap. From the measured density fluctuations we extract the density-density response function of the molecule over times >4.5 ms and distances >250 nm, i.e., how a perturbation in density in one part of the molecule propagates through the rest of the molecule. We find a nonmonotonic radial dependence of the relaxation time. In contrast with earlier measurements on freely diffusing dsDNA, we observe clear signs of internal hydrodynamic interactions.Thermal fluctuations agitate molecules in solution over a broad range of times and distances. By passively watching the shape fluctuations of a thermally driven biopolymer, one can infer properties of the underlying interactions that determine the motion.Dynamic light scattering (DLS) and fluorescence correlation spectroscopy (FCS) each probe specific low-dimensional correlation functions of the shape fluctuations; these can be compared to predictions of Rouse, Zimm, or other hydrodynamic models [1]. The two techniques are complementary in that DLS probes fluctuations at a fixed k vector and FCS at a fixed position vector. Both techniques are also limited in the time scales they can probe: very fast fluctuations occur over distances too short to be detected optically, and very slow fluctuations are masked by translational diffusion.DLS has been used to measure the few longest relaxation times of DNA, and much theory has been devoted to predicting scattering functions for different polymer models [2,3]. FCS has also been used to probe the dynamic fluctuations of fluorescently labeled DNA [4,5]. Recently Shusterman and co-workers [6] probed the dynamics of the end monomer in single-stranded (ss) and double-stranded (ds) DNA using FCS. They observed Zimm dynamics in the ssDNA, but, surprisingly, Rouse dynamics in the dsDNA on time scales <10 ms. In contrast, the translational diffusion of dsDNA obeys Zimm scaling to high accuracy [7]. Shusterman et al. argued that a semiflexible partially draining polymer should show Rouse dynamics on short time scales and Zimm dynamics on long time scales. However, the observation times required to detect Zimm dynamics in dsDNA are longer than can be achieved with FCS.Here we directly measure the underlying time-dependent conformations of individual dsDNA molecules over times >4.5 ms and distances >250 nm. FCS-like and DLS-like correlation functions are special cases of the density-density covariance obtained from our data. Our experiment lacks the short-time resolution of DLS and FCS, but probes long-time dynamics (milliseconds to seconds) that are masked by translational diffusion in the other techniques. The data presented here provide the first detailed spatial picture of the fluctuating dynamics within a single conformationally relaxed polymer molecule. To study a single molecule in equilibrium, one would like to eliminate the motion of the center of mass (c.m.), without affecting internal motions. We used ...

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Section: Introductionmentioning

confidence: 99%

“…Fluctuations in D should lead to a nonzero value of the 4th order correlation function of the pseudofree trajectory: (5) where Δx(t) ≡ x(t + δt) -x(t) is the Brownian hop along the x axis in the interframe interval, δt (Fig. 5).…”

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confidence: 99%

Internal Mechanical Response of a Polymer in Solution

Cohen

Moerner

2007

Phys. Rev. Lett.

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“…We used an additional laser source (488 nm) and a home-built detection unit to carry out the spectroscopic measurements. More details of optical setting could be found in [5].…”

Section: Methodsmentioning

confidence: 99%

Characterization of Liposomes for Cancer Cell Transfection

Tatarkova¹,

Khaira²

2007

TOBEJ

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“…In particular, diffusion (translational and rotational) has been studied in a wide range of environments including the cytoplasm of cells [1], concentrated suspensions [2], gels or hydrogels [3][4][5][6][7][8][9][10][11][12][13], and mucus [14]. The diffusion of a host particle through a rigid gel matrix is reduced, relative to diffusion in "free solution", by long range hydrodynamic interaction and short range steric effects.…”

Section: Introductionmentioning

confidence: 99%

Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Twahir

Davis

et al. 2011

Polymers

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Abstract:In this work, the retarding influence of a gel on the rotational motion of a macromolecule is investigated within the framework of the Effective Medium (EM) model. This is an extension of an earlier study that considered the effect of a gel on the translational motion of a macromolecule [Allison, S. et al. J. Phys. Chem. B 2008, 112, 5858-5866]. The macromolecule is modeled as an array of non-overlapping spherical beads with no restriction placed on their size or configuration. Specific applications include the rotational motion of right circular cylinders and wormlike chains modeled as strings of identical touching beads. The procedure is then used to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. At low gel concentration (M  0.010 gm/mL), good agreement between theory and experiment is achieved if the persistence length of DNA is taken to be 65 nm and the gel fiber radius of agarose is taken to be 2.5 nm. At higher gel concentrations, the EM model substantially underestimates the rotational relaxation time of DNA and this can be attributed to the onset of direct interactions that become significant when the effective particle size becomes comparable to the mean gel fiber spacing. OPEN ACCESSPolymers 2011, 3 847

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Probing single DNA mobility with fluorescence correlation microscopy

Cited by 17 publications

References 20 publications

Internal Mechanical Response of a Polymer in Solution

Internal Mechanical Response of a Polymer in Solution

Characterization of Liposomes for Cancer Cell Transfection

Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

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