Dynamic structure factor of semiflexible macromolecules in dilute solution

Harnau, Ludger; Winkler, Roland G.; Reineker, P.

doi:10.1063/1.471297

Cited by 152 publications

(307 citation statements)

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“…In the present Letter, we fill this gap and carry out a study of the solution dynamics of single-end fluorescently labeled dsDNA fragments in the range of lengths L from 10 2 to 2 10 4 base pairs (bp) (L=l p 0:7-140) by following the Brownian motion of the labeled ends of single DNA molecules using fluorescence correlation spectroscopy. Diffusion coefficients of dsDNA fragments obtained from FCS data in a model-independent way, as well as polymer relaxation times obtained by applying the theory of semiflexible polymer dynamics [4] to experimental data, show excellent agreement with both independent experimental data and theory. Our results clearly demonstrate that in this length range dsDNA behaves as a semiflexible polymer with strong hydrodynamic interactions.…”

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confidence: 56%

Section: -2mentioning

confidence: 99%

“…We carry out such a quantitative analysis on the basis of semiflexible polymer theory [4], where we use Eq. (1) with the MSD of the labeled DNA end given by a sum of contributions due to translational diffusion and intramolecular dynamics [4,12]: (2) where T is the temperature, k B the Boltzmann factor, and the viscosity. l L=2 is the value of the lth eigenfunction of a chain of length L at its end,~l is the lth relaxation time in the presence of hydrodynamic interactions, l is the freedraining relaxation time, and D is the translational diffusion coefficient of the macromolecule.…”

Section: -2mentioning

confidence: 99%

“…For long flexible polymers, the Rouse and Zimm models predict the short-time behavior of the MSD of the polymer end to follow a power law t with exponents 1=2 (free-draining regime) and 2=3 (nondraining regime), respectively [1]; for semiflexible polymers, the short-time behavior with 3=4 is expected [4,26]. One should keep in mind, however, that these power laws are valid only for times much shorter than the longest relaxation time of the polymer, whereas at comparable and longer times the intramolecular contribution to the MSD saturates due to the finite size of the polymer coil [ Fig.…”

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confidence: 99%

“…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.…”

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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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supporting

confidence: 56%

Section: -2mentioning

confidence: 99%

Section: -2mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Diffusion and Segmental Dynamics of Double-Stranded DNA

et al. 2006

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Distribution functions and dynamical properties of stiff macromolecules

Winkler¹,

Harnau²,

Reineker³

1997

Macro Theory & Simulations

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SUMMARYAn analytically tractable model for chain molecules with bending stiffness is presented and the dynamical properties of such chains are investigated. The partition function is derived via the maximum entropy principle taking into account the chain connectivity as well as the bending restrictions in form of constraints. We demonstrate that second moments agree exactly with those known from the Kratky-Porod wormlike chain. Moreover, various distribution functions are calculated. In particular, the static structure factor is shown to be proportional to l / q at large scattering vectors q. The equations of motion for a chain in a melt as well as in dilute solution are presented. In the latter case the hydrodynamic interaction is taken into account via the Rotne-Prager tensor. The dynamical equations are solved by a normal mode analysis. In the limit of a flexible chain the model reproduces the well-known Rouse and Zimm dynamics, respectively, on large length scales, whereas in the rod limit the eigenfunctions correspond to bending motion only. In addition, the coherent and incoherent dynamic structure factor is discussed. For melts we show that at large scattering vectors the incoherent dynamic structure factor is a universal function of only the combination q8/3p'/3, where 1/(2p) is the persistence length of the macromolecules. The comparison of the theoretical results with quasielastic neutron and light scattering experiments of various polymers in solution and melt exhibits good agreement. Our investigations show that local stiffness strongly influences the dynamics of macromolecules on small length scales even for long and flexible chains.

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Dynamics of polyethylene melts studied by Monte Carlo simulations on a high coordination lattice

Lin

Mattice

Meerwall

2006

J Polym Sci B Polym Phys

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A detailed comparison is made between the experiment, prior simulations by other groups, and our simulation based on a newly designed dynamic Monte Carlo algorithm, on the dynamics of polyethylene (PE) melts. The new algorithm, namely, noncross random two-bead move has been developed on a high coordination lattice (the 2nnd lattice) for studying the dynamics of realistic polymers. The chain length (molecular weight) in our simulation ranges from C40 (562 Da) to C324 (4538 Da). The effects of finite chain length have been confirmed and significant non-Gaussian statistics evidently results in nonstandard static and dynamic properties of short PE chains. The diffusion coefficients scale with molecular weight (M) to the À1.7 power for short chains and À2.2 for longer chains, which coincides very well with experimental results. No pure Rouse scaling in diffusion has been observed. The transitional molecular weight to the entanglement regime is around 1500 Da. The detailed mean square displacements of middle bead (g1) are presented for several chain lengths. The reptation-like slowdown can be clearly observed only above M $ 2400 Da. The slope 0.25 predicted by the theory for the intermediate regime is missing; instead a slope close to 0.4 appears, indicating that additional relaxation mechanism exists in this transitional region. The relaxation times extracted by fitting the autocorrelation function of end-to-end vectors with reptation model scale with M to 2.5 for long chains, which seemingly conflicts with the scaling of diffusion.

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Dynamic structure factor of semiflexible macromolecules in dilute solution

Cited by 152 publications

References 72 publications

Diffusion and Segmental Dynamics of Double-Stranded DNA

Diffusion and Segmental Dynamics of Double-Stranded DNA

Distribution functions and dynamical properties of stiff macromolecules

Dynamics of polyethylene melts studied by Monte Carlo simulations on a high coordination lattice

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