Biomod/2012/Titech/Nano-Jugglers/Project

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{{Titech/Nano-Jugglers/HEAD}}
{{Titech/Nano-Jugglers/HEAD}}
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=Goals=
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{|style="margin-left:30px"
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=Project=
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==1.Goals==
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{|style="margin-left:80px"
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|[[Image:Goals.jpg|300px]]
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|<html><body><td align="center"><img src="http://openwetware.org/images/8/88/HOME.jpg" border=0 width=300 height=240></a></td></body></html>
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|'''We have set 3 goals'''<br>
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Rail-free
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&nbsp;&nbsp;&nbsp;&nbsp;Our goal is to build the unprecedented Biomolecular Rocket that achieves the following system functions.<br>
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High-speed
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*'''Rail-free movement of the Biomolecular Rocket, whose journey is not restricted by the pre-determined rail'''
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Control
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*'''Extremely high-speed movement of the micrometer-sized Biomolecular Rocket, accomplished by accumulating nanometer-scale catalytic reactions'''
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*'''Directional control, based on a photo-switchable DNA system as a steering gear'''
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==2.Background==
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=Background=
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:&nbsp;&nbsp;&nbsp;&nbsp;Break through the limits of speed― It is one of the most difficult goal, and we are attracted on it. As well as its own attractive, speeding up is also greatly benefit to our lives, such as mass transport and signal transduction.
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{|style="margin-left:35px"
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|&nbsp;&nbsp;&nbsp;&nbsp;It is the same in molecular world. When we desire to have control of substances at nano scale, someone uses bio molecular robots such as DNA spider. However, the speed is limited. Compared to DNA spider, kinesin can move much faster(0.8~2μm/s). Kinesin  has a shape and function to maximize speed and efficiency, and therefore it is utilized throughout our bodies as the fastest motor protein.
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|[[Image:Kinesin100.gif|right|150px]]
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|}
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:&nbsp;&nbsp;&nbsp;&nbsp;'''To exceed the speed of kinesin, we decided to work on the development of a completely new molecular robot,'Biomolecular Rocket'.'''<div align = "right" style="padding-right:200px">[[#TOP|↑]]</div>
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==3.Idea==
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:{|
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{|style="margin-left:35px"
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|&nbsp;&nbsp;&nbsp;&nbsp;'''Rocket Idea'''
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|&nbsp;&nbsp;&nbsp;&nbsp;Speeding-up is always on demand. In DNA nanotechnology, some synthetic molecular motors, such as a DNA spider, were proposed to execute nano- to micro-meter scale tasks including  molecular tranportation. However, the speed of their movement is slow, compared to a kinesin that is one of the fastest natural molecular motor. Therefore, we decided to challenge the construction of a moleculer vehicle, that can exceed the speed of the kinesin.<br>
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&nbsp;&nbsp;&nbsp;&nbsp;Rocket is one of the most fastest vehicle that can be controlled, and not only these features,rocket has innovative features, 'Rail-Free'. That means, rocket can move around freely in a long distance, while other molecular robots need rails to move, so their movement is limited. Concept of rail-free enable rocket to move freely without being bound to the rails. In addition, combined with the fast-moving that, rocket allowed the long-distance movement.
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&nbsp;&nbsp;&nbsp;&nbsp;Among the vehicles that human beings have so far constructed, a rocket is the fastest one. In addition, a rocket can freely travel across the universe. So, we set our goal to construct a high-speed and remotely controllable molecular vehicle that does not require any rail system, limiting its travelling route.  
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|[[Image:Rocket Idea.png|right|300px]]
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|<html><img src="http://openwetware.org/images/9/91/Compare.jpg" border=0 width=300 height=240></html>
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:&nbsp;&nbsp;&nbsp;&nbsp;'''1, 'Rail-free''''... Energy production for rail-free movement
 
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:&nbsp;&nbsp;&nbsp;&nbsp;Upon building Biomolecular Rocket, in order to product energy for rail-free movement, we looked at the function of the platinum catalyst. Platinum decompose H<small>2</small>O<small>2</small> and emit H<small>2</small>O and O<small>2</small> bubbles. The dissolved O<small>2</small> surrounding a bubble continues to diffuse into the bubble causing it to grow while the buoyancy force and surface adhesion compete against one another. While O<small>2</small> detached from platinum surface, a momentum change which induces a driving force away from the surface. So, by placing the platinum on the back of the rocket body, platinum will move forward.  A new bubble will be generated and released as long as hydrogen peroxide is present, and so the platinum is continuously propelled in the solution. Since the driving force created by divergence of bubbles, and rocket proceeds by dissociation of oxygen, rail does not require.
 
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<br>
 
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:&nbsp;&nbsp;&nbsp;&nbsp;'''2, 'High-speed'''' ...Energy production for high-speed movement
 
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:&nbsp;&nbsp;&nbsp;&nbsp;In order to further accelerate the Biomolecular Rocket, we conjugated numerous platinum catalytic engines to a micro-sized rocket body by taking advantage of DNA hybridization and denaturation. Platinum hemisphere emit sufficient amount of bubbles to move forward in a dilute H<small>2</small>O<small>2</small> solution. Emission of the bubbles depends on the surface area of catalyst. If the catalytic surface area is expanded, it is obvious that our rocket will be able to emit more bubbles and speeding up. Compared to the surface area of platinum hemisphere, we can increase the surface area of platinum for the reaction with H<small>2</small>O<small>2</small>, by conjugating numerous catalytic engine. So our rocket is speeding up in that we can increase the emission of O<small>2</small> bubbles from the rocket.
 
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<br>
 
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:&nbsp;&nbsp;&nbsp;&nbsp;'''3, 'Control'''' ...Directional control of Biomolecular Rocket
 
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:&nbsp;&nbsp;&nbsp;&nbsp;Direction of the rail-free movement of our rocket can be controlled, since we designed the photoresponsive DNA. Photoresponsive DNA structure is changed by UV light irradiation, then denaturation of double strand DNA will happen. This reaction allows the detachment of the engines from the body upon the UV light irradiation in a region-specific manner. Difference in the amount of bubbles are generate at the position of the body. So, we can change the direction of our rocket by only irradiating UV light.
 
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<br>
 
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[[Image:Goals.jpg|center|500px]]
 
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:&nbsp;&nbsp;&nbsp;&nbsp;'''Based on the above contents, we have created the most simplest rocket that combines these three features.'''
 
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=Design principles=
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::&nbsp;&nbsp;&nbsp;&nbsp;'''Why DNA?'''
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:{|style="margin-left:35px"
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::&nbsp;&nbsp;&nbsp;&nbsp;There are three reasons of using DNA. First of all, we can connect Platinum particles with Rocket body in a region-specific because DNA has complementarity. If we bind DNA single strand to the target point, the target molecular which has the complementary DNA, would hybridize and connect with the target point naturally.
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::&nbsp;&nbsp;&nbsp;&nbsp;For the second, it is necessary to detach catalytic engine in a region-specific manner. While there are a variety of ways, using the denaturation of photoresponsive DNA can be done very easily than others.
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::&nbsp;&nbsp;&nbsp;&nbsp;Thirdly, there is a merit that we can conjugate each material with use of only one way.If we use several ways to conjugate in response to each material, it is difficult for each conjugation to stay one another because their suitable conditions are different, such as pH and temperature.However, by using DNA, we can conjugate various materials at time due to the DNA’s characteristic, because DNA’s conjugation depends on the base sequences. So, if we design DNA’s base sequences, it enables each conjugation at the time
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::&nbsp;&nbsp;&nbsp;&nbsp;This study embodies the concept to utilize and control non-biological reactions by designing biomolecules for achieving novel functions implemented by synthetic molecular systems.
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<div align = "right" style="padding-right:200px">[[#TOP|↑]]</div>
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==4.Overview ==
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===0.Body construction ===
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:&nbsp;&nbsp;&nbsp;&nbsp;Biomolecular Rocket is consisted of 10μm beads, platinum or catalase, and DNA. By using DNA, platinum or catalase particles are conjugated to 10μm beads. Beads have been addressed by the deposition of gold and chromium, so DNA was able to conjugate to beads region-specific. In addition, we designed the photoresponsive DNA for allowing detachment of the engines from the Biomolecular rocket’s body upon the UV light irradiation in a region-specific manner.
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:The body is made of polystyrene beads, Pt beads and DNA. Polystyrene beads are processed to conjugate different kinds of DNA.
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{|style="margin-left:80px"
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|[[Image:BIOMODTNJPVD.png|300px]]
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|'''Vapor deposition'''<br>
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&nbsp;&nbsp;&nbsp;&nbsp;In order to have a positional specificity, We make metal-deposited beads. Hemispherical part of polystyrene bead is covered with Cr,1/4 part of spere is covered with Au and the other part is polystyrene.<br>
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1.Deposit  Au on the half of polystyrene beads.<br>
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2.Deposit  Cr on the half of polystyrene beads like the left picture.
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<br>
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{|style="margin-left:80px"
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|[[Image:BIOMODTNJEDAC.png|300px]]
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|<html><body><td align="center"><img src="http://openwetware.org/images/1/1f/Background.jpg" border=0 width=300 height=240></a></td></body></html>
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'''Amino modified DNA and polystyrene conjugation'''<br>
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&nbsp;&nbsp;&nbsp;&nbsp;The Biomolecular Rocket consists of a micrometer-sized bead as its body, submicrometer-sized beads or nanometer-sized catalases as its catalytic engines, and DNA as its steering gear. The rail-free movement is accomplished by taking advantage of bubble propulsion like jet engines. To realize the high-speed movement of our rocket, we conjugated numerous catalytic engines by utilizing sequence-specific DNA hybridization. As a consquence, the directional control of our rocket movement is acheived by triggering region-specific DNA denaturation. As a proof of concept, we constructed a simple version of the Bimomolecular Rocket, as described below.
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&nbsp;&nbsp;&nbsp;&nbsp;Carboxyl (COOH) microparticles can be used for covalent coupling of proteins by activating the carboxyl group with water-soluble carbodiimide. The carbodiimide reacts with the carboxyl group to create an active ester that is reactive toward primary amines on the DNA.<br>
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1.Carboxyl group of polystyrene beads and EDAC react with each other<br>
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2.Carboxyl group become active intermediate<br>
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3.DNA coupled to Polystyrene beads
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<br>
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==1. Power supply for the rail-free movement==
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{|style="margin-left:80px"
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:{|
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|<html><body><td align="center"><img src="http://openwetware.org/images/f/f8/13494300320MEbInRZtgnIFp3_1349430019.gif" border=0 width=300 height=240></a></td></body></html>
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[[Image:BIOMODTNJSAM3.png|300px]]<br>
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&nbsp;&nbsp;&nbsp;&nbsp;'''Biomolecular Rocket moves straightforward by emitting bubbles.'''<br> <br>  
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[[Image:BIOMODTNJSAM.png|300px]]
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&nbsp;&nbsp;&nbsp;&nbsp;We utilized the submicrometer-sized platinum beads or nanometer-sized catalases that catalyze decomposition of H<sub>2</sub>O<sub>2</sub> into H<sub>2</sub>O and O<sub>2</sub>. The generated O<sub>2</sub> gas forms a bubble. The dissolved O<sub>2</sub> gas surrounding a bubble continues to diffuse into the bubble, causing it to grow while the buoyancy force and surface adhesion compete against one another. When the O<sub>2</sub> bubble is emitted from the surface of platinum beads, the accompanying momentum change induces a driving force to put the bubble away from the surface. Therefore, by placing the catalytic engines on the back of the rocket body, the Biomolecular Rocket moves straightforward to the opposite direction, and thus, the rail-free movement is accomplished.<br>
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'''SAM(Self-assembled Monolayer)'''<br>
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&nbsp;&nbsp;&nbsp;&nbsp;When we mix thiol-modified DNA and Pt or Au, they will be self assembly. SH group of thiol-modified DNA and Au or Pt are organized naturally. Using this characteristic, bond two kinds of DNA with Pt and bond another kind of DNA with Au.
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[[Image:BIOMODTNJBUB.png|catalytic reaction|center|300px]]
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<!--[[Image:BIOMODTNJSAM2.png|300px]]-->
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==2. Increasing driving force for the high-speed movement==
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{|
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{|style="margin-left:80px"
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|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/7/7f/Energy_production.gif" border=0 width=300 height=240></a></td></body></html>
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|&nbsp;&nbsp;&nbsp;&nbsp;'''Biomolecular Rocket gets stronger driving force by increasing catalytic surface area.'''<br><br>
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&nbsp;&nbsp;&nbsp;&nbsp;Since the driving force generated upon emission of bubbles depends on the surface area of catalyst, it is expected to speed our rocket up by increasing the surface area of platinum beads and enable it to emit more bubbles. For setting a high-speed record of the Biomolecular Rocket, we attached numerous catalytic engines to a micrometer-sized rocket body, instead of the conventional strategy to use a hemisphere of a bead as a rocket body for the catalytic suface. According to our strategy, the total surface area of the catalytic engines of our rocket is estimated approximately 3.6 times larger than that of a bead hemisphere.
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[[Image:BIOMODTNJSAM4.png|300px]]
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{|style="margin-left:100px"
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&nbsp;&nbsp;&nbsp;&nbsp;Bond photoresponsive DNA with Au and bond normal DNA with Polystyrene.When we add Pt which has complementary DNA,we can connect JET's BODY with Pt regiospecifically.
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|[[Image:Surface_area.png|Compare surface|300px]]
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|&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Image:Calculation image.jpg|Calculation|400px]]
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===4-2 DRIVING FORCE===
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==3. Introduction of a photo-switchable DNA system for the directional control==
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{|
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::[[Image:BIOMODTNJBUB.png]]
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|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/2/27/Control_gif.gif" border=0 width=300 height=240></a></td></body></html>
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&nbsp;&nbsp;&nbsp;&nbsp;Hydrogen peroxide is decomposed into water and oxygen by the catalyst, and platinum and catalase cause the decomposition reaction. This reaction creates a high concentration of oxygen gas on the catalyst surface. The bubble continues to grow until it reaches the detachment radius and is released from the surface. The detachment induces a driving force from the catalyst surface.
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|&nbsp;&nbsp;&nbsp;&nbsp;'''Direction of the rail-free movement of our rocket can be changed by the UV light irradiation.'''<br> <br>
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&nbsp;&nbsp;&nbsp;&nbsp;Hybridization and dissociation between a photo-responsive DNA and its complement can be switched upon UV light irradiation. By introducing this photo-switchable DNA hybridzation system into the Biomolecular Rocket, detachment of the catalytic engines can be triggered by UV light. In addition, when the photo-switchable DNA hybridzation system is introduced only at specific regions, the direction of the driving force is also changed upon the photo-triggered detachment of the catalytic engines. Therefore, we can remotely control the direction of the rail-free movement of our Biomolecular Rocket by irradiating UV light.  
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===4-3 CONTROL===
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{|style="margin-left:80px"
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|[[Image:BIOMODTNJAZOBENZEN.png|300px]]
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'''Photo switching system'''
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&nbsp;&nbsp;&nbsp;&nbsp;The formation of DNA which includes azobenzen can be changed by UV light irradiation. When we irradiate UV light on photoresponsive DNA, DNA will be dissociated. By adjusting the position of photoresponsive DNA, we can control the direction of biomolecular rocket’s moving. We bond photoresponsive DNA with Au, and normal DNA with polystyrene and also each complementary DNAs with Pt.
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<div align = "right" style="padding-right:20px">[[#TOP|Page Top]]</div>
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[[Image:BIOMODTNJUV.png|center]]
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&nbsp;&nbsp;&nbsp;&nbsp;When we irradiate UV light on biomolecular rocket, Pt beads are cut off from Au and the power from Au side disappears and finally, the direction of JET’s power would be changed.
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<br>
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<div align = "right" style="padding-right:200px">[[#TOP|]]</div>
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Current revision


Goals

    Our goal is to build the unprecedented Biomolecular Rocket that achieves the following system functions.

  • Rail-free movement of the Biomolecular Rocket, whose journey is not restricted by the pre-determined rail
  • Extremely high-speed movement of the micrometer-sized Biomolecular Rocket, accomplished by accumulating nanometer-scale catalytic reactions
  • Directional control, based on a photo-switchable DNA system as a steering gear

Background

    Speeding-up is always on demand. In DNA nanotechnology, some synthetic molecular motors, such as a DNA spider, were proposed to execute nano- to micro-meter scale tasks including molecular tranportation. However, the speed of their movement is slow, compared to a kinesin that is one of the fastest natural molecular motor. Therefore, we decided to challenge the construction of a moleculer vehicle, that can exceed the speed of the kinesin.

    Among the vehicles that human beings have so far constructed, a rocket is the fastest one. In addition, a rocket can freely travel across the universe. So, we set our goal to construct a high-speed and remotely controllable molecular vehicle that does not require any rail system, limiting its travelling route.

Design principles

    The Biomolecular Rocket consists of a micrometer-sized bead as its body, submicrometer-sized beads or nanometer-sized catalases as its catalytic engines, and DNA as its steering gear. The rail-free movement is accomplished by taking advantage of bubble propulsion like jet engines. To realize the high-speed movement of our rocket, we conjugated numerous catalytic engines by utilizing sequence-specific DNA hybridization. As a consquence, the directional control of our rocket movement is acheived by triggering region-specific DNA denaturation. As a proof of concept, we constructed a simple version of the Bimomolecular Rocket, as described below.

1. Power supply for the rail-free movement

    Biomolecular Rocket moves straightforward by emitting bubbles.

    We utilized the submicrometer-sized platinum beads or nanometer-sized catalases that catalyze decomposition of H2O2 into H2O and O2. The generated O2 gas forms a bubble. The dissolved O2 gas surrounding a bubble continues to diffuse into the bubble, causing it to grow while the buoyancy force and surface adhesion compete against one another. When the O2 bubble is emitted from the surface of platinum beads, the accompanying momentum change induces a driving force to put the bubble away from the surface. Therefore, by placing the catalytic engines on the back of the rocket body, the Biomolecular Rocket moves straightforward to the opposite direction, and thus, the rail-free movement is accomplished.

catalytic reaction

2. Increasing driving force for the high-speed movement

    Biomolecular Rocket gets stronger driving force by increasing catalytic surface area.

    Since the driving force generated upon emission of bubbles depends on the surface area of catalyst, it is expected to speed our rocket up by increasing the surface area of platinum beads and enable it to emit more bubbles. For setting a high-speed record of the Biomolecular Rocket, we attached numerous catalytic engines to a micrometer-sized rocket body, instead of the conventional strategy to use a hemisphere of a bead as a rocket body for the catalytic suface. According to our strategy, the total surface area of the catalytic engines of our rocket is estimated approximately 3.6 times larger than that of a bead hemisphere.

Compare surface             Calculation

3. Introduction of a photo-switchable DNA system for the directional control

    Direction of the rail-free movement of our rocket can be changed by the UV light irradiation.

    Hybridization and dissociation between a photo-responsive DNA and its complement can be switched upon UV light irradiation. By introducing this photo-switchable DNA hybridzation system into the Biomolecular Rocket, detachment of the catalytic engines can be triggered by UV light. In addition, when the photo-switchable DNA hybridzation system is introduced only at specific regions, the direction of the driving force is also changed upon the photo-triggered detachment of the catalytic engines. Therefore, we can remotely control the direction of the rail-free movement of our Biomolecular Rocket by irradiating UV light.

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