Temperature dependence of DNA persistence length

Geggier, Stephanie; Kotlyar, Alexander; Vologodskii, Alexander

doi:10.1093/nar/gkq932

Cited by 140 publications

(126 citation statements)

References 45 publications

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“…At low gel concentration (M  0.010 gm/mL) where long range interactions dominate, good agreement between theory and experiment is achieved if the persistence length, P, of DNA is taken to be 65 nm and the gel fiber radius, r g , of agarose is taken to be 2.5 nm. A persistence length of this magnitude is consistent with independent studies [44]. Also, a gel fiber radius of 2.5 nm is consistent with earlier modeling studies of DNA diffusion [16] as well as the electrophoresis of Au nanoparticles [15] in agarose gels.…”

Section: Discussionsupporting

confidence: 91%

“…In the absence of a gel,  1 exp is best fit by setting P = 65 nm in modeling. This value is in good agreement with experiment when the comparatively low salt conditions of the experiment are factored in [44]. Under physiological salt conditions, a value of P of around 50 nm is expected.…”

Section: Experimental Section: Rotational Relaxation Of Dna In a Dilusupporting

confidence: 86%

“…Unless the duplex DNA is very short, however, it is better to model the DNA as a wormlike chain of persistence length P (contour length equal to L and axial radius equal to R) rather than a right circular cylinder. For DNA, P is typically in the 50 nm size range, but this varies with ionic strength [43,44]. As an illustrative example, L = 211.5 nm for 622 bp DNA which is more than 4 persistence lengths long.…”

Section: R For the Right Circular Cylinder In An Em Withmentioning

confidence: 99%

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Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Twahir

Davis

et al. 2011

Polymers

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Abstract:In this work, the retarding influence of a gel on the rotational motion of a macromolecule is investigated within the framework of the Effective Medium (EM) model. This is an extension of an earlier study that considered the effect of a gel on the translational motion of a macromolecule [Allison, S. et al. J. Phys. Chem. B 2008, 112, 5858-5866]. The macromolecule is modeled as an array of non-overlapping spherical beads with no restriction placed on their size or configuration. Specific applications include the rotational motion of right circular cylinders and wormlike chains modeled as strings of identical touching beads. The procedure is then used to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. At low gel concentration (M  0.010 gm/mL), good agreement between theory and experiment is achieved if the persistence length of DNA is taken to be 65 nm and the gel fiber radius of agarose is taken to be 2.5 nm. At higher gel concentrations, the EM model substantially underestimates the rotational relaxation time of DNA and this can be attributed to the onset of direct interactions that become significant when the effective particle size becomes comparable to the mean gel fiber spacing. OPEN ACCESSPolymers 2011, 3 847

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Section: Discussionsupporting

confidence: 91%

Section: Experimental Section: Rotational Relaxation Of Dna In a Dilusupporting

confidence: 86%

Section: R For the Right Circular Cylinder In An Em Withmentioning

confidence: 99%

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Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Twahir

Davis

et al. 2011

Polymers

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“…1 can be usefully described in terms of temperature-dependent elastic constants.) Recent measurements by the Vologodskii group [32] report that the persistence length l p of ds DNA decreases by about 30% from 5 C to 60 C, which corresponds to a roughly 15% decrease in B ¼ kTl p . The present experiment is unsuitable to measure these effects [and they are not included in the analysis; for instance, in Eq.…”

Section: Discussionmentioning

confidence: 99%

Critical Torque for Kink Formation in Double-Stranded DNA

Wang

Tseng

et al. 2011

Phys. Rev. X

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We measure the bending energy of double-stranded DNA in the nonlinear (sharply bent) regime. The measurements are obtained from the melting curves of stressed DNA ring molecules. The nonlinear elastic behavior is captured by a single parameter: the critical torque c at which the molecule develops a kink. In this regime, the elastic energy is linear in the kink angle. This phenomenology is the same as for the previously reported case of nicked DNA. For the sequences examined, we find c ¼ 31 pN Â nm. This critical torque corresponds to a characteristic energy scale ð =2Þ c ¼ 12 kT room relevant for molecular biology processes associated with DNA bending.

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“…This increase in the centre-tocentre distance arises possibly from the stiffening of the central junctions and to the increase of the persistence length as the system is cooled down [48].…”

Section: A Single Tetramer Conformationmentioning

confidence: 99%

Accurate phase diagram of tetravalent DNA nanostars

Rovigatti

Bomboi

Sciortino

2014

The Journal of Chemical Physics

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We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarsegrained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA. We find that, as the system is cooled down, tetramers undergo a gas-liquid phase separation in a region of concentrations which, if the difference in salt concentration is taken into account, is comparable with the recently measured experimental phase diagram [S. Biffi et al, Proc. Natl. Acad. Sci, 110, 15633 (2013)]. We also present a meanfield free energy for modelling the phase diagram based on the bonding contribution derived by Wertheim in his studies of associating liquids. Combined with mass-action law expressions appropriate for DNA binding and a numerically evaluated reference free energy, the resulting free energy qualitatively reproduces the numerical data. Finally, we report information on the nanostar structure, e.g. geometry and flexibility of the single tetramer and of the collective behaviour, providing a useful reference for future small angle scattering experiments, for all investigated temperatures and concentrations.

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Temperature dependence of DNA persistence length

Cited by 140 publications

References 45 publications

Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Critical Torque for Kink Formation in Double-Stranded DNA

Accurate phase diagram of tetravalent DNA nanostars

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