Analysis of low angle light scattering results from T7 DNA

Harpst, J.A.

doi:10.1016/0301-4622(80)80032-9

Cited by 17 publications

(37 citation statements)

References 32 publications

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“…2,7 However other studies suggest that excluded volume interactions indeed have an impact at similar contour lengths. 8–10 Further confounding the issue, the oft-cited measurements of the diffusion coefficient of concatamers of λ-DNA by Smith et al 11 suggested that dsDNA had already reached a universal limit. However, the work by Smith et al is at odds with recent theoretical work on the draining behavior of wormlike polymer coils 12 and work on DNA in confinement 13 which suggests that the molecular weight required to reach the universal limit for dynamic properties is even larger than the weight required for static properties.…”

Section: Introductionmentioning

confidence: 99%

Is DNA a Good Model Polymer?

et al. 2013

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The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48,500 base pairs) does not exhibit “ideal” scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior.

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Section: Introductionmentioning

confidence: 99%

Is DNA a Good Model Polymer?

et al. 2013

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“…While none of these studies present a direct measurement of coil structure in solution, even static light scattering (SLS) experiments that do measure the structure factor of solutions, reveal a significant 30-40% expansion of 14 m DNA chains [15,16] far exceeding theoretical estimations ($ 4%) [17,18]. A known issue in SLS studies is the very poor scattering by DNA, that requires extrapolation procedures from higher concentrations to measure DNA structure in dilute solutions [16]. SLS is also sensitive to scattering by dust particles, that are not (5) 058102-1 Ó 2013 American Physical Society trivial to remove because of the closeness of their sizes to those of DNA molecules [15].…”

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confidence: 98%

“…In fact, a variety of experimental results actually contradict it: the diffusion coefficient of DNA coils of lengths 2:6 < L < 130 m [12], the segment distribution of DNA of lengths 15 < L < 60 m tethered to a substrate [13], AFM measurements of DNA end-to-end distance distribution for 0:5 < L < 15 m [14]-all reveal the scaling R g / L 0:57-0:59 indicating strong excluded volume interactions. While none of these studies present a direct measurement of coil structure in solution, even static light scattering (SLS) experiments that do measure the structure factor of solutions, reveal a significant 30-40% expansion of 14 m DNA chains [15,16] far exceeding theoretical estimations ($ 4%) [17,18]. A known issue in SLS studies is the very poor scattering by DNA, that requires extrapolation procedures from higher concentrations to measure DNA structure in dilute solutions [16].…”

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confidence: 99%

Structure of DNA Coils in Dilute and Semidilute Solutions

et al. 2013

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We apply scanning fluorescence correlation spectroscopy to study the structure of individual DNA coils in dilute and semidilute solutions. In dilute solutions, over two decades in length, from 0.6 to 46 μm, DNA behave as ideal chains, in agreement with theoretical predictions and in disagreement with prior experiments. In semidilute solutions, up to very high densities, the structures of individual DNA coils are independent of concentration, unlike flexible coils that shrink with increasing density. Our experimental findings are consistent with the marginal solution theory of semiflexible polymers.

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“…The light-scattering method can be applied in a stationary-state mode (Harpst, 1980;Lemaire et al, 1984Lemaire et al, , 1987 or as a function of time (Denk and Schnabel, 1982). The method is more convenient when the scattered light is measured at an angle of 90" to the incident light beam than at a very small angle of 2-7".…”

Section: Methodsmentioning

confidence: 99%