Dynamics of superhelical DNA studied by photon correlation spectroscopy

Langowski, Jörg; Giesen, Ursula; Lehmann, Christina

doi:10.1016/0301-4622(86)87010-7

Cited by 40 publications

(22 citation statements)

References 30 publications

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“…In light scattering studies, D S ͞D C ϭ 1.251 was reported for a 3.7-kbp DNA molecule (44) and D S ͞D C ϭ 1.18 and D S ͞D L ϭ 1.46 were reported for ColE 1 DNA (18). Photon correlation spectroscopy has also been used to study a 2.7-kbp molecule, and a ratio of D S ͞D L ϭ 1.48 was reported (45). Sedimentation ratios have been measured as well, finding S 0 S ͞ S 0 C ϭ 1.26 and S 0 S ͞S 0 L ϭ 1.56 for ColE 1 DNA (18) and S 0 S ͞S 0 C ϭ 1.25 and S 0 S ͞S 0 L ϭ 1.38 for polyoma DNA (46).…”

Section: Resultsmentioning

confidence: 99%

Diffusion of isolated DNA molecules: Dependence on length and topology

Robertson

Laib

Smith

2006

Proc. Natl. Acad. Sci. U.S.A.

253

320

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The conformation and dynamics of circular polymers is a subject of considerable theoretical and experimental interest. DNA is an important example because it occurs naturally in different topological states, including linear, relaxed circular, and supercoiled circular forms. A fundamental question is how the diffusion coefficients of isolated polymers scale with molecular length and how they vary for different topologies. Here, diffusion coefficients D for relaxed circular, supercoiled, and linear DNA molecules of length L ranging from Ϸ6 to 290 kbp were measured by tracking the Brownian motion of single molecules. A topology-independent scaling law D ϳ L ؊ was observed with L ‫؍‬ 0.571 ؎ 0.014, C ‫؍‬ 0.589 ؎ 0.018, and S ‫؍‬ 0.571 ؎ 0.057 for linear, relaxed circular, and supercoiled DNA, respectively, in good agreement with the scaling exponent of Х 0.588 predicted by renormalization group theory for polymers with significant excluded volume interactions. Our findings thus provide evidence in support of several theories that predict an effective diameter of DNA much greater than the Debye screening length. In addition, the measured ratio DCircular͞ DLinear ‫؍‬ 1.32 ؎ 0.014 was closer to the value of 1.45 predicted by using renormalization group theory than the value of 1.18 predicted by classical Kirkwood hydrodynamic theory and agreed well with a value of 1.31 predicted when incorporating a recently proposed expression for the radius of gyration of circular polymers into the Zimm model. circular ͉ polymer ͉ polyelectrolyte ͉ hydrodynamics ͉ excluded volume W hile many eukaryotic genomes are linear, prokaryotic genomes and most cloned DNA constructs are circular (1). Indeed, a commonly stated motivation for theoretical calculations on circular polymers is that they may be applicable to understanding the behavior of DNA. However, four of the five previously reported studies on the diffusion of circular polymers have used synthetic polymers, and only two of these, both using synthetic polymers, examined the dependence of the diffusion coefficient on molecular length. The dependence of D on length for relaxed circular DNA has never been measured. Here, we examine linear, relaxed circular, and supercoiled DNA molecules covering a wide range of lengths (Ϸ6 to 290 kbp).For long linear polymers in a good solvent, where excluded volume effects are appreciable, polymer physics theory (2) predicts D ϳ 1͞R G ϳ L Ϫ with Х 0.588, where R G is radius of gyration. The same scaling exponent has been calculated for both dynamic (D ϳ L Ϫ ) and static (R G ϳ L ) quantities, with nearly identical results determined by using a wide range of methods. Static scaling has been examined by using Monte Carlo simulations (3), bead-rod simulations (4), and cylindrical selfavoiding polygon models (5). Renormalization group theory methods have been used in both static (3, 6) and dynamic (7) calculations, and bond-fluctuation simulations (8) were used to measure and compare both scaling relationships. The predicted scaling exponent is close ...

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Section: Resultsmentioning

confidence: 99%

Diffusion of isolated DNA molecules: Dependence on length and topology

Robertson

Laib

Smith

2006

Proc. Natl. Acad. Sci. U.S.A.

253

320

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“…3,4,[17][18][19][20][21][22][23][24] The diffusion coefficients measured in the present work were corrected to the standard temperature of 20°C using eq. (7).…”

Section: Resultsmentioning

confidence: 99%

Measuring the translational diffusion coefficients of small DNA molecules by capillary electrophoresis

et al. 2001

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“…As a control, we measured the DLS of another pK plasmid carrying a non-curved insert (pKlA108) and, in addition, compared our measurements with earlier data from two other superhelical plasmids with no specifically designed inserts (pUC18 and pACL29; Langowski et al, 1986;Langowski and Giesen, 1989). Although these superhelical plasmids have smaller a2/(a2 + al) amplitudes than pK3A108, the a2/(a2 + al) values of all control plasmids are larger than those of the plasmids with curved inserts (see Figure 3a).…”

Section: Resultsmentioning

confidence: 99%

“…In these experiments, however, the superhelical DNA is transferred to the surface of the electron microscope grid, a process which might change the appearance of the molecule, especially for a structure as flexible as a long DNA molecule. We had shown previously that DLS studies yield information on the structure and internal motion of DNA in solution (Langowski et al, 1986;Langowski, 1987;Langowski and Giesen, 1989;Langowski and Bryan, 1991). This method analyzes the Brownian motion of macromolecules in solution through the fluctuations of the scattered light intensity (Berne and Pecora, 1976).…”

Section: Introductionmentioning

confidence: 98%

DNA curvature influences the internal motions of supercoiled DNA.

et al. 1993

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We present evidence that short curved DNA segments can act as mediators for the ordering of large domains in superhelical DNA. Using a non‐invasive solution method (dynamic light scattering), we investigated the effect of permanently curved inserts on the solution structure and on the internal motions of superhelical plasmid DNA. We find that the dynamics of superhelical DNA are strongly influenced by sequence‐ or protein‐induced bending: in superhelical plasmids containing curved inserts the amplitude of the internal motion is lower than that of non‐curved controls. Furthermore, the relative arrangement of curved sequences in the plasmids can influence the overall shape of the superhelical DNA. On linearized forms of the plasmids, these effects are not observed.

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Dynamics of superhelical DNA studied by photon correlation spectroscopy

Cited by 40 publications

References 30 publications

Diffusion of isolated DNA molecules: Dependence on length and topology

Diffusion of isolated DNA molecules: Dependence on length and topology

Measuring the translational diffusion coefficients of small DNA molecules by capillary electrophoresis

DNA curvature influences the internal motions of supercoiled DNA.

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