Low angle light scattering studies on whole, half, and quarter molecules of T2 bacteriophage DNA

Harpst, J.A.; Dawson, Jeffrey R.

doi:10.1016/s0006-3495(89)82919-4

Cited by 15 publications

(33 citation statements)

References 56 publications

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“…Other techniques such as static light scattering were considered, but such measurements are extremely difficult for long molecules and become virtually impossible for molecules longer than Ϸ60 m (38). Therefore, although there is no apparent way to directly measure R G for our entire range of molecular lengths, we can still examine whether our data are consistent with theories that relate R G and D. The hydrodynamic radius R H can be calculated from D by using the Stokes-Einstein relation D ϭ k B T͞6p R H , where k B is Boltzmann's constant, T is temperature (Х297 K), and is solvent viscosity (Х1.2 cPa).…”

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.

252

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.

252

320

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“…This potentially alters the persistence length and effective diameter of native dsDNA, and nominally increases the contour length by as much as 50% (ref. 45). Of the experimental measurements discussed in Section 1, Strychalski et al…”

Section: Fluorescent Dyesmentioning

confidence: 99%

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

et al. 2015

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There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency.Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations.An understanding of the many factors influencing the size of dsDNA under nanoscale confinement is highly relevant to rationally designing measurement technologies for genomic sequencing and medical sensing and for accurately describing crowding effects on dsDNA organization in living systems. Consequently, there have been many recent theoretical and experimental studies of this phenomenon. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] In particular, it has been possible for two decades to image individual fluorescently labeled dsDNA under conditions of nanoscale confinement in nanofluidic devices with slit-like geometries. In this way, the in-plane radius of gyration of dsDNA as a function of slit height has been recently measured. Fig. 1 summarizes the results of these experimental measurements, which exhibit a puzzling scatter under nominally similar experimental conditions. Scaling arguments and continuum chain models have dominated the majority of the recent theoretical treatments of this problem, which generally ignore polymer-surface interactions and hav...

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“…In the case of the DNA studies presented here, we note the following. In some studies, the polydispersity is either not explicitly reported 44,55,56 …”

Section: Polydispersity Effectmentioning

confidence: 99%

The intrinsic viscosity of linear DNA

2011

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We measured the intrinsic viscosity of very small synthetic DNA molecules, of 20-395 base pairs, and incorporated them in a nearly complete picture for the whole span of molecular weights reported in the literature to date. A major transition is observed at M approximately 2 × 10(6) . It is found that in the range of approximately 7 × 10(3) ≤ M ≤ 2 × 10(6) , the intrinsic viscosity scales as [η] approximately M(1.05) , suggesting that short DNA chains are not as rigid as generally thought. The corresponding scaling for the range of 2 × 10(6) ≤ M ≤ 8 × 10(10) is [η] approximately M(0.69) . A comparison of our results with existing equations, for much narrower data distributions, is made, and the agreement is very satisfactory considering the huge range of data analyzed here. Experimental concerns such as the effect of ionic strength, polydispersity, temperature, and shear rate are discussed in detail. Some issues concerning the Huggins coefficient, polymer chain stiffness, and the relationship between the Mark-Houwink constants K, α are also presented; it is found that log K = 1.156 - 6.19α.

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Low angle light scattering studies on whole, half, and quarter molecules of T2 bacteriophage DNA

Cited by 15 publications

References 56 publications

Diffusion of isolated DNA molecules: Dependence on length and topology

Diffusion of isolated DNA molecules: Dependence on length and topology

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

The intrinsic viscosity of linear DNA

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