Dataset Information

Investigating the dynamics of surface-immobilized DNA nanomachines.

ABSTRACT: Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface-immobilized nanomachines are significantly different to those of the solution phase reaction, and we attribute this to the effects of intermolecular interactions within the DNA layer. We demonstrate that the dynamics of strand displacement can be manipulated by changing strand length, concentration and G/C content. By inserting mismatched bases it is also possible to tune the rates of the constituent displacement processes (toehold-binding and branch migration) independently, and information can be encoded in the time-dependence of the overall reaction. Our findings will facilitate the rational design of surface-immobilized dynamic DNA nanomachines, including computing devices and track-based motors.

SUBMITTER: Dunn KE

PROVIDER: S-EPMC4937388 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Investigating the dynamics of surface-immobilized DNA nanomachines.

Dunn Katherine E KE Trefzer Martin A MA Johnson Steven S Tyrrell Andy M AM

Scientific reports 20160708

Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface-immobilized nanomachines are significantly different to those of the solution phase reactio ...[more]

PMID: 27387252

Similar Datasets

Project description:High frequency (30 Hz) two-dimensional particle image velocimetry data recorded during a field experiment exploring fire spread from point ignition in hand-spread pine needles under calm ambient wind conditions are analysed in this study. In the initial stages, as the flame spreads approximately radially away from the ignition point in the absence of a preferred wind-forcing direction, it entrains cooler ambient air into the warmer fire core, thereby experiencing a dynamic pressure resistance. The fire-front, comprising a flame that is tilted inward, is surrounded by a region of downdraft. Coherent structures describe the initial shape of the fire-front and its response to local wind shifts while also revealing possible fire-spread mechanisms. Vortex tubes originating outside the fire spiral inward and get stretched thinner at the fire-front leading to higher vorticity there. These tubes comprise circulation structures that induce a radially outward velocity close to the fuel bed, which pushes hot gases outward, thereby causing the fire to spread. Moreover, these circulation structures confirm the presence of counter-rotating vortex pairs that are known to be a key mechanism for fire spread. The axis of the vortex tubes changes its orientation alternately towards and away from the surface of the fuel bed, causing the vortex tubes to be kinked. The strong updraft observed at the location of the fire-front could potentially advect and tilt the kinked vortex tube vertically upward leading to fire-whirl formation. As the fire evolves, its perimeter disintegrates in response to flow instabilities to form smaller fire "pockets". These pockets are confined to certain points in the flow field that remain relatively fixed for a while and resemble the behavior of a chaotic system in the vicinity of an attractor. Increased magnitudes of the turbulent fluxes of horizontal momentum, computed at certain such fixed points along the fire-front, are symptomatic of irregular fire bursts and help contextualize the fire spread. Most importantly, the time-varying transport terms of the turbulent kinetic energy budget equation computed at adjacent fixed points indicate that local fires along the fire-front primarily interact via the horizontal turbulent transport term.

Dataset Information

Investigating the dynamics of surface-immobilized DNA nanomachines.

Publications

Investigating the dynamics of surface-immobilized DNA nanomachines.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets