Osmotic Pressure of DNA Solutions and Effective Diameter of the Double Helix

Yarmola, Elena G.; Zarudnaya, M. I.; Lazurkin, Yu. S.

doi:10.1080/07391102.1985.10507614

Cited by 33 publications

(20 citation statements)

References 9 publications

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“…The agreement is excellent for the results of one study (14) and fair for those of the other (15). An independent measure of the Na+ dependence of knotting probability by Shaw and Wang (33) …”

Section: Discussionsupporting

confidence: 51%

“…Two other estimations of the dependence of deff on NaCl concentration have been made based on the osmotic pressure of concentrated DNA solutions (14,15). The agreement is excellent for the results of one study (14) and fair for those of the other (15).…”

Section: Discussionmentioning

confidence: 82%

“…electrically charged DNA. Because DNA is a highly charged polyelectrolyte, electrostatic repulsion can make the effective diameter much greater than the geometrical diameter (13)(14)(15). Computer simulations show that the probability of a knot in a randomly cyclized polymer strongly depends on the effective chain diameter.…”

mentioning

confidence: 99%

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Probability of DNA knotting and the effective diameter of the DNA double helix.

Rybenkov

Cozzarelli

Vologodskii

1993

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

375

435

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During the random cyclization of long polymer chains, knots of different types are formed. We investigated experimentally the distribution ofknot types produced by random cyclization of phage P4 DNA via its long cohesive ends. The simplest knots (trefoils) predominated, but more complex knots were also detected. The fraction of knots greatly diminished with decreasing solution Na+ concentration. By comparing these experimental results with computer simulations of knotting probability, we calculated the effective diameter ofthe DNA double helix. This important excluded-volume parameter is a measure of the electrostatic repulsion between segments of DNA molecules. The calculated effective DNA diameter is a sensitive function of electrolyte concentration and is several times larger than the geometric diameter in solutions of low monovalent cation concentration.A classic problem in polymer physics is the probability that the random cyclization of a polymer produces a knot of a particular topology. The issues were formulated more than 30 years ago by Frisch and Wasserman (1) and by Delbruck (2). The initial solution was provided by a Monte Carlo simulation in 1974 (3), and since then several computational analyses of the knotting probability of polymer chains have appeared (reviewed in refs. 4 and 5).Experimental measures of knotting frequency have not been made, however, despite the considerable interest in these forms. Ever since the production oflinked hydrocarbon rings, organic chemists have striven to synthesize knotted molecules. These attempts have recently come to fruition with the elegant and complete synthesis of a hydrocarbon knot by Dietrich-Buchecker and Sauvage (6). A distinct synthetic route based on the properties of nucleic acids has been used by Seeman's group to synthesize different types of knots (7).Knots made of DNA, first identified in 1976 (8), are much easier to synthesize and to analyze than other knotted polymers. Knotted DNA has been identified in numerous in vitro and in vivo experiments (9, 10). The topology of the knots is diagnostic of the mechanism of the enzymes that produce them and of the structure of the DNA substrates (9). The experimental studies of DNA knots have been guided by the development of mathematical methods for analyzing DNA topology (11,12).DNA is thus the most suitable polymer for the experimental investigation of the probability of knotting. The measurement of the probability of knotting duplex DNA is of special interest because it provides an excellent means for determining the effective diameter of DNA. This important parameter characterizes the excluded volume of DNA. The effective diameter of DNA is the diameter of an uncharged polymer chain that mimics the conformational properties of actualThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. electrically charged DNA. Because DNA is a highly charge...

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Section: Discussionsupporting

confidence: 51%

Section: Discussionmentioning

confidence: 82%

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Probability of DNA knotting and the effective diameter of the DNA double helix.

Rybenkov

Cozzarelli

Vologodskii

1993

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

375

435

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“…18,55 Since, as discussed above, the electrostatic diameter of DNA in physiological conditions is closer to 5nm, it seems quite unlikely that the productive synapse could pass through a supercoil (as in Figure 3). [59][60][61] Brownian dynamics simulations of site juxtaposition support these findings. 62 Additionally, the probability of one duplex (linear) invading a supercoiled domain has been shown to be quite low, by both experiments and MMC simulations.…”

Section: Evidence For Assumptionsupporting

confidence: 73%

Predicting Knot or Catenane Type of Site-Specific Recombination Products

Buck¹,

Flapan²

2007

Journal of Molecular Biology

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Site-specific recombination on supercoiled circular DNA yields a variety of knotted or catenated products. We develop a model of this process, and give extensive experimental evidence that the assumptions of our model are reasonable. We then characterize all possible knot or catenane products that arise from the most common substrates. We apply our model to tightly prescribe the knot or catenane type of previously uncharacterized data.

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“…He found w not very sensitive to these values. This prediction of w has been verified by various studies using sedimentation, 16 osmotic pressure, 17 and measurement of the probability of trefoil knots of DNA during cyclization. 18,19 The most well-known analytical prediction of the electrostatic persistence length (p el ) of a semiflexible chain was given by Odijk, 20 and Skolnick and Fixman 21 (OSF).…”

mentioning

confidence: 88%

Ionic Effects on the Equilibrium Dynamics of DNA Confined in Nanoslits

2008

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The ionic effects on the dynamics and conformation of DNA in silt-like confinement are investigated. Confined λ-DNA is considered as a model polyelectrolyte, and its longest relaxation time, diffusivity, and size are measured at a physiological ionic strength between 1.7-170 mM. DNA properties change drastically in response to the varying ionic environment, and these changes can be explained by blob theory with an electrostatically mediated effective diameter and persistence length. In the ionic range we investigate, the effective diameter of DNA that represents the electrostatic repulsion between remote segments is found to be the main driving force for the observed change in DNA properties. Our results are useful for understanding the manipulation of biomolecules in nanofluidic devices.With the advance of nanotechnology, new devices have been created to manipulate biomolecules. Many such applications, including DNA separation 1 and gene mapping, 2 rely on the confinement-induced change in molecular properties. Several studies have been devoted to the investigation of those confinement effects on DNA and have had fruitful progress.3-6 On the other hand, the ionic environment is also known to have a strong influence on biomolecule properties and can be readily manipulated in experiments. However, the compound effects of confinement and ionic environment, critical for many applications, are yet to be fully understood.Several studies have investigated the ionic effects on confined DNA conformation in rectangular channels (height (h) ≈ width (d)).2,7,8 DNA extension was found to increase with decreasing ionic strength. This observation was explained either by de Gennes' blob theory (h and d > p (persistence length)) 9,10 or by Odijk's deflection chain theory (h and d < p). 11Although the finding is promising, we find that the buffer ionic strengths reported in these studies are somewhat inaccurate especially at low salt concentration due to neglect of the ionic contribution of antiphotobleaching agents. Furthermore, it is not clear how ionic environment will influence DNA dynamics and whether the above theories can be applied. In the current study, we investigate the ionic effects on both conformation and dynamics of DNA confined in nanoslits with better control on buffer ionic strength. We show that our analysis can be used to explain the ionic effects on both confined and unconfined DNA, providing a consistent picture for this highly debated issue of DNA/polyelectrolytes.To understand the physical origin of the ionic effects on polyelectrolytes, we first consider the conformation of neutral polymers. From the Flory theory, 12 the equilibrium size (R bulk ) of an unconfined, semiflexible polymer in good solvents can be expressed as:

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Osmotic Pressure of DNA Solutions and Effective Diameter of the Double Helix

Cited by 33 publications

References 9 publications

Probability of DNA knotting and the effective diameter of the DNA double helix.

Probability of DNA knotting and the effective diameter of the DNA double helix.

Predicting Knot or Catenane Type of Site-Specific Recombination Products

Ionic Effects on the Equilibrium Dynamics of DNA Confined in Nanoslits

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