Biomod/2011/TeamJapan/Sendai/Strategy: Difference between revisions

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***gel:24% Poly-Acrylamide Gel
***gel:24% Poly-Acrylamide Gel
***buffer:1×TAE
***buffer:1×TAE
***sample:Legs and substrate is contained in sample. First, 1xTA is contained in 1 and 5. Second, 1xTA Mg2+ is contained to 2 and 6. Third, 1xTA Zn2+ (1mM) is contained in 3 and 7.　Forth, 1xTA Mg2+ Zn2+ (1mM) is contained in 4 and 8.  
***sample:Legs and substrate is contained in sample. First, 1xTA is contained in 1 and 5. Second, 1xTA Mg2+ is contained to 2 and 6. Third, 1xTA Zn2+ (1mM) is contained in 3 and 7.　Forth, 1xTA Mg2+ Zn2+ (1mM) is contained in 4 and 8. 1, 2, 3, and 4 are immediately after putting in buffer. 5, 6, 7 and 8 have passes 15min after putting in buffer. The more time passes, the more it turns out that the quantity of cut substrates increases because we can check that substrates of 2, 4, 6, and 8 are cut the band of the right figure.
1, 2, 3, and 4 are immediately after putting in buffer. 5, 6, 7 and 8 have passes 15min after putting in buffer. The more time passes, the more it turns out that the quantity of cut substrates increases because we can check that substrates of 2, 4, 6, and 8 are cut the band of the right figure.




Revision as of 20:32, 5 October 2011

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<ul id="verticalmenu" class="glossymenu"> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai">Home</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Strategy">Strategy</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Design">Design</a></li> <li><a href="#">Experiments</a> 

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   <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Results/Electrophoresis">Electrophoresis</a> 
   <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Results/Atomic_Force_Microscope">AFM</a> 
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</li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Computational_design/Simulation" >Simulation</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Notes">Notes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Team">Team</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Resources">Resources</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Sitemap">Sitemap</a></li>


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Abstract

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

Our molecular robot is designed based on the DNA spider (Lund et al., Nature, 2010). In the original design, the body of DNA spider is made of a protein (streptavidin), and three DNA legs are attached to the body. The walking movement of the DNA spider is random, thus the robot must be controlled by means of the patterned course on the Origami. Consequently, the movement of the spider is slow and inefficient.

To win the race, we want to substantially improve the performance of the robot. For this purpose, we make the whole structure of our robot with DNA, which allows us to design arbitrary geometry of the body and to increase the number of legs. 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 different types of robot, searching for the optimal design. In the final report, we will show our optimal design and the details of experimental results including its walking motion captured by a video-rate AFM.

DNA sequence

Opened-up cube　ｔriangular prism robot

We make Triangular prism robot by folding up the developed view of the above figure and legs by extension of red staples.

Experiment

AFM

coming soon…

Electrophoresis

  • the check method of structure
    • triangular prism
      • gel:1.4% agarose gel
      • buffer:1×TAE Mg2+
      • sample:
    • the stick robot
      • gel:1.4% agarose gel
      • buffer:1×TAE Mg2+
      • sample:


  • the check method of cutting legs and substrates
legs and substrate attached fluorescence protein
    • legs and substrate attached fluorescence protein
      • gel:24% Poly-Acrylamide Gel
      • buffer:1×TAE
      • sample:Legs and substrate is contained in sample. First, 1xTA is contained in 1 and 5. Second, 1xTA Mg2+ is contained to 2 and 6. Third, 1xTA Zn2+ (1mM) is contained in 3 and 7.　Forth, 1xTA Mg2+ Zn2+ (1mM) is contained in 4 and 8. 1, 2, 3, and 4 are immediately after putting in buffer. 5, 6, 7 and 8 have passes 15min after putting in buffer. The more time passes, the more it turns out that the quantity of cut substrates increases because we can check that substrates of 2, 4, 6, and 8 are cut the band of the right figure.




legs and substrate unattached fluorescence protein
    • legs and substrate unattached fluorescence protein
      • gel:24% Poly-Acrylamide Gel
      • buffer:1×TAE
      • sample:①②③④にはlegとsubstrateが入っており，⑤にはsubstrateのみが入っており，⑥にはlegのみが入っている．また，①にはbufferとして1×TE Mg2+ Zn2+(1mM)，②にはbufferとして1×TE Zn2+(1mM)，③にはbufferとして1×TE Mg2+，④にはbufferとして1×TE，⑤⑥にはbufferとして1×TEが入っており，sampleはすべてbufferを入れてから15min経過している．右図のバンドから①②③が切断されていることが確認できる．また今回②において切断が確認できた理由としてはサーマルサイクラーを使って二重螺旋を組ませたためであると考えられる．




  • the duplicate of M13 by PCR
    • gel:
    • buffer:
    • sample:

Brainstorming

  • Hexagonal Prism
    • melit
      • First, a maximum of 72 legs can be attached. Second, The robot don't retreat. Third, it can walk forward efficiently.
    • demelit
      • First, It is difficult to check whether robot structure is made. Second, it costs a lot of time the robot to be annealed. Third, the structure is too complicated because it has many kinds of staples.
  • Wall runner
    • melit
      • First, this robot can go to one way. Second, how to move is novel.
    • demelit
      • First, This robot may fall at the time of observation by AFM. Second, it is difficult to make a wall.
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