A Bipedal DNA Brownian Motor with Coordinated Legs

Abstract

A significant challenge in engineering molecular motors is designing mechanisms to coordinate the motion between multiple domains of the motor so as to bias random motion. For bipedal motors, this challenge takes the form of coordinating the movement of the biped’s legs, so they can move in a synchronized fashion. To address this problem, we have constructed an autonomous DNA bipedal nanorobot that coordinates the action of its two legs by coupling room temperature thermal energy with the catalysis of metastable DNA fuel strand hybrids. This coupling leads to a chemically ratcheted unidirectional walk along a DNA track. By crosslinking aliquots of the walker covalently to its track in successive walking states, we demonstrate that the walker can complete a full walking cycle on a track whose length could be extended for longer walks.

Direct observation of stepwise movement of a synthetic molecular transporter

“…This precisely controlled, long-range transport could lead to the development of systems that could be programmed and routed by instructions encoded in the nucleotide sequences of the track and motor. Such systems might be used to create molecular assembly lines modelled on the ribosome.An effective linear molecular motor must traverse its track without dissociating [1][2][3][4][5][6][7]10,12 and run unidirectionally without external intervention [4][5][6][7][8][9][10][11][12] . Directionality may be imposed by the sequential addition of DNA instructions 1-3 or, for autonomous motors, by modifying the track sites that have been visited 5,6,12 , by coupling motion to a unidirectional reaction cycle 4,9,12 or by coordinating the conformation changes of different parts of the motor 11,12 .…”

“…Directionality may be imposed by the sequential addition of DNA instructions 1-3 or, for autonomous motors, by modifying the track sites that have been visited 5,6,12 , by coupling motion to a unidirectional reaction cycle 4,9,12 or by coordinating the conformation changes of different parts of the motor 11,12 . DNA motors that satisfy all these criteria have typically been demonstrated on tracks that allow only 1-3 steps, although a stochastic DNA 'spider' with many legs has been shown to move longer distances by biased diffusion 17 along a 100 nm track 18 .…”

“…Controlled motion at the nanoscale can be achieved by using Watson-Crick base-pairing to direct the assembly and operation of a molecular transport system consisting of a track, a motor [1][2][3][4][5][6][7][8][9][10][11][12] and fuel [13][14][15] , all made from DNA. Here, we assemble a 100-nm-long DNA track on a two-dimensional scaffold 16 , and show that a DNA motor loaded at one end of the track moves autonomously and at a constant average speed along the full length of the track, a journey comprising 16 consecutive steps for the motor.…”

Self-assembling knots of controlled topology by designing the geometry of patchy templates

“…A beautiful example is provided by the creation of DNA origami [12][13][14] , or of other DNA-based microstructures, such as molecular spiders and nanorobots [15][16][17] . Here various target structures can be achieved by favouring the base pairing of specific DNA regions, which embody the struts of the desired construct.…”

DNA walker circuits: computational potential, design, and verification

“…by theirs, but we consider another setting which also exhibits localised reactions: DNA walker systems [2,7,10,[14][15][16].…”