Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite

Abstract

We have characterized the polymer physics of single-stranded DNA ͑ssDNA͒ using atomic force microscopy. The persistence length ᐉ p of circular ssDNA adsorbed on a modified graphite surface was determined independently of secondary structure. At a very low ionic strength we obtained ᐉ p = 9.1 nm from the bond correlation function. Increasing the salt concentration lead to a decrease in ᐉ p ; at 1 mM NaCl we found ᐉ p = 6.7 nm, while at 10 mM NaCl a value ᐉ p = 4.6 nm was obtained. The persistence length was also extracted from the root-mean-square end-to-end distance and the end-to-end distance distribution function. Finally, we have investigated the scaling behavior using the two latter quantities, and found that on long length scales ssDNA behaves as a two-dimensional self-avoiding walk.

Dynamics and Statics of DNA-Programmable Nanoparticle Self-Assembly and Crystallization

“…In converting to real units, σ ∼ 2nm, R ∼ 3σ = 6nm and n l = 3, corresponding to ∼ 20 linkers, consistent with experiments [4] as well as the measured Kuhn length for ssDNA [6]. Unless otherwise stated N GN P = 54, and the system consists of N GN P /2 A-GNPs and B-GNPs with A and B containing linkers with bases complementary to each other.…”

Universal bond correlation function for two-dimensional polymer rings

“…In many realistic situations, the BCF exhibits more interesting and complicated features, and its physical interpretation should be carefully made. Several studies have considered particular cases of polymers such as in melts [15], at the Θ-point [16,17] or with short-range repulsion [18], but these studies so far seem mostly devoted to linear chain systems, and do not help resolve recent experimental data on circular DNA [19,20].…”

Sensing Viruses by Mechanical Tension of DNA in Responsive Hydrogels

“…In contrast to dense DNA fibers [37], here we can neglect DNA-DNA interactions because the intermolecular separations exceed the diameter of a typical virus, 2R ∼ 50-100 nm, and the electrostatic forces between individual DNA chains are well screened. Performing simulations of a free chain, we checked that the effective ssDNA persistence length in this model agrees well with the known estimate of l p ¼ 1-4 nm [83,84], and the chain gyration radius follows the Flory law, hR 2 g i ∼ n 6=5 , for an excluded-volume or self-avoiding polymer as a function of the number n of monomers. The inset in Fig.…”