Diffusion coefficient of DNA molecules during free solution electrophoresis

Nkodo, Axel Ekani; Garnier, J M; Tinland, B.; Ren, Hongji; Desruisseaux, Claude; McCormick, Laurette C.; Drouin, Guy; Slater, Gary W.

doi:10.1002/1522-2683(200107)22:12<2424::aid-elps2424>3.0.co;2-1

Cited by 195 publications

(184 citation statements)

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“…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].…”

supporting

confidence: 44%

“…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: -2mentioning

confidence: 99%

“…We are grateful to Dr. B. Tinland for making accessible data of Ref. [7] and to K. Birkenfeld for her invaluable assistance with DNA samples.…”

Section: -2mentioning

confidence: 99%

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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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Section: -2mentioning

confidence: 99%

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Diffusion and Segmental Dynamics of Double-Stranded DNA

et al. 2006

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“…However, a detailed physical understanding of surface transport of DNA is currently not available. 3 For example, it is commonly known that the diffusion coefficient of DNA decreases with increase in DNA size in free solution 4 and under two-dimensional confinement. 5 However, a recent experimental study on electrophoresis of DNA on an atomic force microscopy surface showed the faster movement of longer DNA in a thin pure water film.…”

mentioning

confidence: 99%

Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface

Park

Aluru

2010

Applied Physics Letters

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In this paper, we investigate, using molecular dynamics simulations, the conformation and diffusion of longer and shorter single-strand DNA ͑ssDNA͒ as a function of water film thickness. While the conformation of the shorter ssDNA is significantly affected and the diffusion is suppressed with reduction in water film thickness, the conformation and diffusion of the longer DNA is not influenced. We explain our observations by considering the competition between stacking interaction of bases and solvation tendency of ssDNA. This paper suggests an approach to control the surface motion of ssDNA in nanoscale water films using film thickness. © 2010 American Institute of Physics. ͓doi:10.1063/1.3366725͔ DNA separation is an essential technique for gene sequencing and DNA fingerprinting. The development of accurate and versatile DNA separation technique is currently a significant issue in nanobiotechnology. 1 Recently, Pernodet et al. 2 reported separation of DNA chains on a surface without any topological restrictions or any solution sieving media. This can be a significant benefit over conventional separation methods. However, a detailed physical understanding of surface transport of DNA is currently not available. 3 For example, it is commonly known that the diffusion coefficient of DNA decreases with increase in DNA size in free solution 4 and under two-dimensional confinement. 5 However, a recent experimental study on electrophoresis of DNA on an atomic force microscopy surface showed the faster movement of longer DNA in a thin pure water film. 6 According to the Nernst-Einstein relation between mobility and diffusion, this implies that the longer DNA has higher diffusion than the shorter DNA.To understand the reasons behind the ambiguities in the physics of surface transport of DNA, in this paper, we investigate, using extensive molecular dynamics ͑MD͒ simulations, the diffusion of DNA in nanometer-thick water films by considering DNA of various sizes. As shown in the schematic in Fig. 1͑a͒, a single-strand DNA ͑ssDNA͒ was solvated in a pure water film on a solid surface. Following the experiment, 6 the surface was made by grafting the poly͑eth-ylene glycol͒-silanes ͑PEG-silanes͒ on a solid substrate. The size of the surface is 20ϫ 20 nm 2 and it consists of 1600 PEG-silane molecules. The PEG-silane has 32 atoms and it is attached to the substrate atom ͓see Fig. 1͑b͔͒. The initial configuration and the atomic partial charges of PEG-silane molecule were obtained from PRODRG ͑Ref. 7͒ using GRO-MOS forcefield and charge. The substrate atoms were assumed frozen and their atomic charges were adjusted to make the entire system neutral. We considered two small ssDNAs fragments with 6 and 12 bases. Although recent DNA sequencing technologies utilize tens of millions of small DNA fragments, 8 efficient separation of such small fragments is still challenging. 9 The longer 12-base ssDNA of 5Ј − CGCGAATTCGCG− 3Ј was prepared by unzipping the well-known Dickerson's B-DNA dodecamer ͑double stranded͒, 10 while the shorter 6-bas...

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“…The gel was stained with SYBR Gold and imaged using a UV trans-illuminator. 51 52 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 …”

Section: Affinity Measurementmentioning

confidence: 99%

Probing and quantifying DNA–protein interactions with asymmetrical flow field-flow fractionation

Ashby

Schachermeyer

Duan

et al. 2014

Journal of Chromatography A

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Tools capable of measuring binding affinities as well as amenable to downstream sequencing analysis are needed for study of DNA-protein interaction, particularly in discovery of new DNA sequences with affinity to diverse targets. Asymmetrical flow field-flow fractionation (AF4) is an open-channel separation technique that eliminates interference from column packing to the non-covalently bound complex and could potentially be applied for study of macromolecular interaction. The recovery and elution behaviors of the poly(dA) n strand and aptamers in AF4 were investigated. Good recovery of ssDNAs was achieved by judicious selection of the channel membrane with consideration of the membrane pore diameter and the radius of gyration (R g ) of the ssDNA, which was obtained with the aid of a Molecular Dynamics tool. The R g values were also used to assess the folding situation of aptamers based on their migration times in AF4. The interactions between two ssDNA aptamers and their respective protein components were investigated. Using AF4, near-baseline resolution between the free and protein-bound aptamer fractions could be obtained. With this information, dissociation constants of ~16nM and ~57 nM were obtained for an IgE aptamer and a streptavidin aptamer, respectively. In addition, free and protein-bound IgE aptamer was extracted from the AF4 eluate and amplified, illustrating the potential of AF4 in screening ssDNAs with high affinity to targets.Our results demonstrate that AF4 is an effective tool holding several advantages over the existing techniques and should be useful for study of diverse macromolecular interaction systems.

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Diffusion coefficient of DNA molecules during free solution electrophoresis

Cited by 195 publications

References 31 publications

Diffusion and Segmental Dynamics of Double-Stranded DNA

Diffusion and Segmental Dynamics of Double-Stranded DNA

Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface

Probing and quantifying DNA–protein interactions with asymmetrical flow field-flow fractionation

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