Biomod/2011/TeamJapan/Sendai/Strategy

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Contents

Project summary

Designing a molecular robot is one of the most interesting and challenging targets in biomolecular design. This year, two teams from Japan and one from Denmark propose the first “molecular race” over a defined track made with DNA origami. We are now making a molecular robot for the race.

Our molecular robot and its mechanism for movement are based on the molecular spider developed by Lund et al. (Nature, 2010). In the original design, the spider body consisted of the streptavidin protein, and three DNA-based legs are attached to it. The walking movement of the spider is random, thus the robot must be controlled by means of the patterned course on the Origami.

To win the race, we want to substantially improve the robot performance. For this purpose, we make the whole structure of our robot with DNA, which allows us to design arbitrary geometry of the body. Also, we can assign different base sequence to each leg and scaffold on the Field. These new parameters give us freedom to optimize our robot design.

We have been developing a stochastic dynamics simulation model in order to evaluate the movement of different types of molecular robots, searching for the optimal design. In the final report, we will show our optimal design and the experimental results including walking motion of the robot captured by a video-rate AFM.

Molecular Robot Race

Rules

Our molecular robot race is based on the following rules:

  • The task for the molecular robot is to move from the start region to the goal region as fast as possible.
  • The Field is placed on a cleaved mica surface using counter ion method.
  • No restriction is defined for the solution environment, as long as the Field and the movement of robot are observable by fast scanning AFM.
  • No restriction is defined as a material for the robot.
Figure 1. Parameters, start point and goal point of the molecular race
Figure 1. Parameters, start point and goal point of the molecular race


Our strategy

We want to get to the goal in a more efficient way. This involves a more faster robot.
Now, what should you do to make a robot arrive at the goal more quickly?

First, let us think the problem at the macroscopic scale.. what makes an athlete win the competition?

  1. Striding with longer legs
  2. Reducing useless motions such as deviating from the route
  3. Increasing steps rate

Analogously, at the molecular scale:

  1. Increasing the body’s size and legs
  2. Suppressing the random motion
  3. Improving the DNAzyme activity mechanism

But, how to achieve these solutions?

  1. Making a larger robot body than streptavidin by using DNA origami method
  2. Using a special combination of DNA sequences for the legs and substrate to reduce random motion

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