Active, motor-driven mechanics in a DNA gel

Abstract

Cells are capable of a variety of dramatic stimuli-responsive mechanical behaviors. These capabilities are enabled by the pervading cytoskeletal network, an active gel composed of structural filaments (e.g., actin) that are acted upon by motor proteins (e.g., myosin). Here, we describe the synthesis and characterization of an active gel using noncytoskeletal components. We use methods of base-pair-templated DNA self assembly to create a hybrid DNA gel containing stiff tubes and flexible linkers. We then activate the gel by adding the motor FtsK50C, a construct derived from the bacterial protein FtsK that, in vitro, has a strong and processive DNA contraction activity. The motors stiffen the gel and create stochastic contractile events that affect the positions of attached beads. We quantify the fluctuations of the beads and show that they are comparable both to measurements of cytoskeletal systems and to theoretical predictions for active gels. Thus, we present a DNA-based active gel whose behavior highlights the universal aspects of nonequilibrium, motor-driven networks.

Fig. 1.

Components and synthesis of an active DNA gel. (A) Schematic of gel synthesis and activation, in which base-pair-programmed self-assembly is used first to create two types of rigid DNA nanotubes decorated with sticky ends then to cross-link the tubes with long linker DNAs. The gel is activated by addition of the motor protein construct FtsK50C. (B) Confocal fluorescent image of a DNA gel. The gel contains two types of nanotubes containing, respectively, red and green dyes. (C) Sketch and data demonstrating the contractile activity of FtsK50C on a single, stretched DNA strand; data shown are adapted from ref. .

Fig. 2.

Trajectories of a bead attached to a passive and active DNA gel. (A) Sketch of experimental geometry, in which a DNA gel is attached to a glass surface and a 1 μm diameter bead, and the bead’s position is tracked over time. (B) Representative x, y, and z trajectories of a bead attached to the same gel fragment before and after activation by the motor FtsK50C. To simplify the comparison of fluctuations, the passive and active trajectories are offset to share the same baseline value. (C) Highlight of one second of trajectory showing the sawtooth shape of an individual motor-induced bead excursion.

Fig. 3.

Van Hove correlation functions, P(Δr(τ)), of active and passive gel fluctuations in each dimension, r = x, y, or z. P(Δr(τ)) was calculated from the three-dimensional trajectory of a bead attached to the same gel in both the passive and active state. The gray lines show the best fits to either the normal distribution (passive data) or a summed normal/exponential distribution (active data).

Fig. 4.

Dynamics of the active and passive gel. (A) Mean-squared displacement vs. lag time, τ, for a bead attached to a passive (blue) and active (red) gel. The small-τ active gel data are fit to a power law (gray lines), with the best-fit exponent noted. (B) Power spectral density of the positions of the same bead. The dashed line is an overlay (not a fit) indicating the 1/f² behavior expected for a freely diffusing particle.