Is DNA a worm-like chain in Couette flow?:In search of persistence length, a critical review

Abstract

Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of B-DNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.

Single-molecule micromanipulation studies of methylated DNA

“…2). The least-squares fit of combined data for bare construct indicated an average slope corresponding to a persistence length of A = 44+2 nm, quantitatively close to previously reported results [33]. Coefficient estimates are found to be statistically significant at the 5% level, and additional details on coefficient values and significance values can be seen in Table S2.…”

“…Persistence length (A), roughly 50 nm (150 bp) for unmodified double-stranded DNA in physiological buffer conditions, is the property that quantifies polymer stiffness, and corresponds to the average distance along which DNA maintains its direction before deviating from it. The definition of persistence length includes both flexibility and curvature [33] and it is important to highlight that different base pair steps show different susceptibility for helical deformations and deformations induced by slide or shift changes [34].…”

Calculations of flow-induced orientation distributions for analysis of linear dichroism spectroscopy

“…Strictly, DNA is a semi-rigid rod, its persistence length being approximately 50 nm. 33 (We return to this issue in Section 3.3.) FtsZ monomers, within protolaments, are approximately 4.2 nm in length and 5.7 nm wide.…”

“…In this work, we showed how to apply a model of dilute suspensions of rigid, rodlike particles in a steady shear ow with Brownian effects to the analysis of Couette-ow and Fig. 6 Dependence of orientation parameter, S, on DNA length at shear rate 3000 s À1 and temperature 22 C (determined from experimental data in Rittman et al 33 and Simonson and Kubista 40 ), assuming that a ¼ 86 and the average base extinction coefficient is 6600 mol À1 dm 3 cm À1 .…”

“…We used the absorbance of a 0.1 mg mL À1 protein solution (determined from Kelly et al 38 to be $0.015 at 206 nm) to calculate LD r . (b) Orientation parameter, S, of DNA plasmid pC3.1 (100 mM) at 37 C with absorbance determined from assuming an average base extinction coefficient at 260 nm of 6600 mol À1 cm À1 dm 3 (data derived from Rittman et al 33 ). If we assume that FtsZ is sufficiently rigid for the model to be appropriate, we can use the calculated dependence of S on length from the model to understand what is happening in polymerisation experiments.…”