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0.Construction of Biomolecular Rocket

Selective coating by vapor deposition

    In order to have a positional specificity, We made metal-deposited beads. Hemispherical part of polystyrene bead was covered with Cr, 1/4 part of spere was covered with Au and the other part was polystyrene. First, deposited Au on the half of polystyrene beads. Second, deposited Cr on the half of polystyrene beads.

DNA conjugation to polystyrene surface

    Carboxyl (COOH) microparticles can be used for covalent coupling of proteins by activating the carboxyl group with water-soluble carbodiimide. The carbodiimide reacted with the carboxyl group to create an active ester that was reactive toward primary amines on the DNA.
    First, carboxyl group of polystyrene beads and EDAC reacted with each other. Next, carboxyl group became active intermediate. Then DNA coupled to polystyrene beads.

DNA conjugation to metal surface

    When we mix thiol-modified DNA and Pt or Au, they will be self assembly. Thiol-modified DNA and Au or Pt are organized naturally. Using this characteristic, attached two kinds of DNA with Pt and bond another kind of DNA with Au.

Catalyst conjugation


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0.1. Selective coating of the body

1st Deposition

2nd Deposition


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0.2. Design of linker DNA strands

    We used DNA strands for bonding between a body of Biomolecular Rocket and platinum particles. DNA strands must be designed 4 DNA strands to hybridize at room temperature stably. DNA strands are categorize into two types, one type was a DNA strand for conjugation to polystyrene surface and its cDNA, and another type was a DNA strand for conjugation to gold surface and its cDNA. Each cDNA conjugated to platinum particles.
    In this section, we explain how we design DNA strands. There are three steps to design DNA strands, first step is selection of DNA strands , second step is adjustment of the number of bases and final step is design of cDNA strand. We used NUPACK[1] for these processes of DNA design. NUPACK is a software for the analysis and design of nucleic acid systems.
    First, we chosed DNA strands from a treatise[2]. In this step, we analyzed whether DNA could easily hybridize at room temperature stably. Then we selected two DNA strands. Secondly, we adjusted number of bases in order to make easily dissociated when they introduced photo-switching systems. Finally, we design c of each cDNA strands, and modify amino group and thiol group as necessary.
    [1] NUPACK nucleic acid package.
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0-3.DNA conjugation

0.3.1. Selective conjugation of DNA to polystyrene surface area

    We bond polystyrene-beads with DNA using EDAC. EDAC is known as water-soluble carbodiimide (WSC) and is used as coupling agent to form amide bond. EDAC crosslinks nucleic acids to the surfaces, which have carboxy group. In this project, we used this method to conjugate amino-modified DNA onto carboxylated polystyrene-beads. EDAC reacted with carboxylated polystyrene-beads to form active intermediate on the body. Then it reacted to amino-modified DNA. The beads are coupled by nucleic acid. We divide the body into three parts including polystyrene surface, so it is possible to connect each DNA with position classification. By using this method, we were able to connect platinum to aircraft body part of polystyrene in a region-specific manner.

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0.3.2. Selective conjugation of DNA to metal surface area




SAM conjugation onto gold
    Thiolated compound and gold substrate are one of the most famous research of SAMs[3]. Thiol modified DNA was conjugate to gold particles by this chemical reaction. Initially, substrate gold were cleaned by water or acid-base buffer in order to washout organic impurities. Gold particles were dissolved in 10mM phosphate buffer pH8, 10μM thiol modified DNA. Then in addition to NaCl, intended to raise the concentration of NaCl every 2 hours after 24 hours of incubation for 6 hours, then incubate more 16 hoursraise up to 0.7M salt concentration (Salt aging process).Last,clean up again by proper buffer and dry. This reaction was also used ​​with platinum.

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0.4. Catalyst attachment with DNA hybridization

    We attached the catalyst to our rocket body with DNA hybridization. cDNA had adhered to the corresponding parts of the rocket body, so it enabled to attach catalyst engines in that we designed these DNA were thermodynamically stable when they hybridized.


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1.1. DNA hybridization in solution of H2O2

    H2O2 has strong corrosion. There was a risk that DNA strand is denatured by H2O2[1]. So, we had to ensure that the hybridization of DNA is not suffer from H2O2. We guessed that if DNA had been destroyed, then molecular mass would decrease in that DNA can't hybridize. Visualizing the relative magnitude of the molecular weight by electrophoresis, we are able to examine whether DNA can hybridize or not.
    This time, we have to examine the state of the DNA in the time we need to steer rocket, set the time to soak and concentration of H2O2. We used PAGE electrophoresis to ascertain the stability of DNA duplex in thin H₂O₂ solution 1%-5%. PAGE electrophoresis shows the difference of molecular weight that comes from dissociation or hybridization in the form of bands.

[1]Natacha Driessens, Soetkin Versteyhe, Chiraz Ghaddhab, Agne`s Burniat, Xavier De Deken, Jacqueline Van Sande, Jacques-Emile Dumont, Franc¸oise Miot, Bernard Corvilain,Endocrine-Related Cancer 16 845–856(2009)
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1.2. Power supply for rail-free movement by using catalase catalytic engine

    For supplying power of Biomolecular Rocket, we experimented with another catalytic engine[1],[2],[3]. Catalase is known as a enzyme that catalyzes the hydrogen peroxide solution. And we expected that this enzyme will be new catalytic engine of the Biomolecular Rocket because a enzyme activity of this enzyme is 100,000 times stronger than that of platinum. In this experiment, we deposited Au for half surface of polystyrene beads and catalase conjugated onto polystyrene side. In addition, we observed a behavior of the beads in diluted H2O2 solution.

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1.3. Power supply for rail-free movement by using platinum catalytic engine

    The driving force of Biomolecular Rocket is catalytic engine of platinum. This catalytic engine become more powerful[1],[2], increasing the surface of platinum. Biomolecular Rocket has numerous platinum particles to increase the surface of platinum. In this experiment, we deposit chromium to 1µm beads which are covered platinum and we make half platinum beads[3]. In addition, we observe a behavior of the beads in 3% H2O2 solution. From this experiment, we are able to investigate whether Surface area of platinum is related to the speed.
[1]Rustem F. Ismagilov, Alexander Schwartz, Ned Bowden, George M. Whitesides.;Chem. Int. 652-654(2002)
[2]Jonathan R. Howse, Richard A. L. Jones, Anthony J. Ryan, Tim Gough, Reza Vafabakhsh, Ramin Golestanian,;Phys. Rev. Lett. 99, 048102 (2007)
[3]J. G. Gibbs, Y.-P. Zhao,;Appl. Phys. Lett. 94, 163104 (2009)
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2.1. Analyses of the speed of platinum in solution of H2O2 by High-speed camera

  • 1.produced in concurrence with the generation of bubbles
  • 2.produced as the bubbles are destructed
  • 3.produced as the bubbles detach
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3.1. Design of photoresponsive DNA

    We incorporated 4 azobenzene units into photoresponsive DNA[1] strand so that we can quickly dissociated DNA duplex. We called it as Photoresponsive DNA sequence S.[5'-AATXACXCCXAGXCC-3' (X=Azobenzene)]

Photoresponsive DNA sequence S



Photoresponsive DNA sequence S*

  • 5’-(HS)-GGCTGGGTATT-3’

1.This 11 bases DNA are a complementary sequence of photoresponsive DNA sequence S.

    And then, we confirmed that photoresponsive DNA could hybridize stably. For verifying hybridization, we use the value of absorbance.
[1]Hiroyuki Asanuma, Xingguo Liang, Takayuki Yoshida, and Makoto Komiyama,;CHEMBIOCHEM 2, 39-44(2001)
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3.2. Directional control with photo-switchable DNA system


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