Formation of DNA pearl‐necklace structures on mica surface governed by kinetics and thermodynamics

Abstract

Polyelectrolytes (PEs) possibly occur in the form of a pearl‐necklace structure in poor solvents. This structure, characterized by the form of segregated beads connected by narrow strings, has been extensively studied by scaling analysis and computer simulation, and was believed to be formed by the Rayleigh instability mechanism. However, the structure has not been experimentally well studied, and a complete experimental picture on the necklace formation is still not available. In this study, pearl‐necklace structures of DNA induced by different condensing agents are observed by atomic force microscopy. The results show that the formation of a pearl‐necklace conformation is highly dependent on kinetic factors such as incubation time and thermodynamic factors including the concentration and condensing ability of the agent. If the incubation time is sufficiently short, this conformation can exist as an intermediate state of the DNA coil–globule transition. When agents with weaker crowding effect or screening ability are added, the structure appeared to be thermodynamically stable. The same effect was observed in rather low concentrations of agent. A rods‐on‐a‐string structure, unlike the common characterized spherical beads‐on‐a‐string conformation, was observed and was believed to result from the stiffness of DNA. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017, 55, 971–979

Conformation of a single polyelectrolyte in poor solvents

“…37,59 In contrast, the formation of the new pearl predicted by our theory is achieved by continuously adjusting the curvatures of the existing pearls and strings, which does not necessitate a discontinuous shape transition. The continuous change in the curvature in the conformational transition makes it difficult to identify the PN structures with a different number of pearls, in agreement with both the experimental results using an AFM image [38][39][40][41][42] as well as neutron scattering 41,[53][54][55][56] and the snapshots observed in molecular simulations. 51,52 The conformational transition can be more clearly illustrated by tracking the order parameter of asphericity, as shown in Fig.…”

“…[34][35][36] In addition, Dobrynin, Rubinstein, and Obukhov developed a scaling theory for this pearl-necklace model and predicted a cascade of abrupt transitions between necklaces with different numbers of pearls. 37 The pearl-necklace structure has been supported by AFM images [38][39][40][41][42] and molecular simulations of a polyelectrolyte in implicit solvents. [43][44][45][46][47][48][49][50] However, using molecular dynamics simulations either with an explicit solvent model or a solvent-accessible surface area model where the polymer-solvent interaction is rigorously considered, Yethiraj and co-workers claimed that the pearl-necklace structures were not clearly seen in the snapshots.…”

DNA–Lysozyme Nanoarchitectonics: Quantitative Investigation on Charge Inversion and Compaction

“…A transverse MT setup was built on an inverted microscope (Nikon TE2000U, Tokyo, Japan) for studying the dynamic process of tethering DNA, as shown in Figure 1 A. The detailed description of MT setup was presented in previous works [ 18 , 23 , 31 ]. The procedure for force measurement can be briefly described as follows: one end of DNA molecule is linked to an immobile substrate (the glass sidewalls) and other end is attached to a paramagnetic bead [ 32 ].…”

Reductant-dependent DNA-templated silver nanoparticle formation kinetics

“…Mica sheets (1 cm  1 cm) were used to deposit the samples. 51 The mica surface was first modified with 30 mL of a 0.001%(v/v) APTES solution for adsorption of the DNA. Second, the mica surfaces were cleaned with 20 mL of deionized water and blown dry with a gentle flow of nitrogen gas.…”