Crowding-facilitated macromolecular transport in attractive micropost arrays

Abstract

Our study of DNA dynamics in weakly attractive nanofabricated post arrays revealed crowding enhances polymer transport, contrary to hindered transport in repulsive medium. The coupling of DNA diffusion and adsorption to the microposts results in more frequent cross-post hopping and increased long-term diffusivity with increased crowding density. We performed Langevin dynamics simulations and found maximum long-term diffusivity in post arrays with gap sizes comparable to the polymer radius of gyration. We found that macromolecular transport in weakly attractive post arrays is faster than in non-attractive dense medium. Furthermore, we employed hidden Markov analysis to determine the transition of macromolecular adsorption-desorption on posts and hopping between posts. The apparent free energy barriers are comparable to theoretical estimates determined from polymer conformational fluctuations.

Three Regimes of Polymer Surface Dynamics under Crowded Conditions

“…Crowding effects play a crucial role in applications including biosensing, nanorheology, chromatography, multicomponent material synthesis, confined polymer crystallization, and biointerfaces. − The few experiments conducted at high surface coverage either have neglected the effects of bulk-mediated diffusion, which is now established as a dominant mode of interfacial transport, , or have focused narrowly on specific conditions relevant to a particular application . For example, increased mobility was observed for crowded DNA chains; however, the behavior was uniquely related to the structural characteristics of the DNA . Recent studies investigated the effect of concentration on protein surface residence times , but did not investigate interfacial mobility.…”

“…18 For example, increased mobility was observed for crowded DNA chains; however, the behavior was uniquely related to the structural characteristics of the DNA. 23 Recent studies investigated the effect of concentration on protein surface residence times 24,25 but did not investigate interfacial mobility. In sum, the influence of molecular crowding on interfacial polymer mass transport remains poorly understood.…”

A novel assessment of the traction forces upon settlement of two typical marine fouling invertebrates using PDMS micropost arrays

“…Because of the advantages in mechanical application and quantitative measurements, PDMS micropost arrays have been employed in a wide spectrum of biological and chemical studies, including assessing macromolecular transport ( Chien et al, 2017 ) and designing dielectrophoretic trapping ( Mohammadi et al, 2016 ). Comparable studies were performed to assess the mechanics of adhesive mammalian cells and to clarify the correlation of biochemical and mechanical signals ( Beussman et al, 2016 ; Rodriguez et al, 2014 ; Tan et al, 2003 ; Saez et al, 2007 ).…”