Biomod/2012/Titech/Nano-Jugglers/Project

From OpenWetWare

Jump to: navigation, search



Project

1.Goals

We have set 3 goals

Rail-free High-speed Control

2.Background

    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.
    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.
    To exceed the speed of kinesin, we decided to work on the development of a completely new molecular robot,'Biomolecular Rocket'.

3.Idea

    Rocket Idea

    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.

    1, 'Rail-free'... Energy production for rail-free movement
    Upon building Biomolecular Rocket, in order to product energy for rail-free movement, we looked at the function of the platinum catalyst. Platinum decompose H2O2 and emit H2O and O2 bubbles. The dissolved O2 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 O2 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.


    2, 'High-speed' ...Energy production for high-speed movement
    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 H2O2 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 H2O2, by conjugating numerous catalytic engine. So our rocket is speeding up in that we can increase the emission of O2 bubbles from the rocket.


    3, 'Control' ...Directional control of Biomolecular Rocket
    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.


    Based on the above contents, we have created the most simplest rocket that combines these three features.


    Why DNA?
    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.
    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.
    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
    This study embodies the concept to utilize and control non-biological reactions by designing biomolecules for achieving novel functions implemented by synthetic molecular systems.


4.Project Overview

0.Body construction

    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.


1,Energy production for rail-free movement of Biomolecular Rocket

    DNA spider moves forward by controlling of Brownian motion and kinesin motor gains energy of ATP hydrolysis. These movements are carried out through the rails. In other words, power and direction of these movements are bound by rails.
    Energy production of Biomolecular Rocket isn’t depended on rails. Our rocket utilizes H2O and O2 that is included in the solution. Platinum particles and catalase are catalysts that have the ability to decompose hydrogen peroxide into oxygen and water. Since the driving force created by divergence of bubbles, and rocket proceeds by dissociation of oxygen, rail does not require.


2,Speeding up of Biomolecular Rocket

    Platinum hemisphere emit sufficient amount of bubbles to move forward in a dilute H2O2 solution. Emission of the bubbles depends on the surface area of catalyst. If the surface area is expanded, it is obvious that our rocket will be able to emit more bubbles and speeding up. So, we conjugated numerous catalytic engines to a rocket body with the use of DNA in order to expend surface area of catalyst.
    We conjugate between 10 μm polystyrene beads and 0.15 ~ 0.40 μm sized platinum. In this condition, approximately 2000 of platinum particles can be conjugated to the hemisphere. This suggests that comparison the value of platinum surface area, platinum particles enable to get more surface than equally size of platinum hemisphere. Our rocket got of the surface area 3.6 times in the calculation
    That means, we can significantly increase the surface area of the catalytic reaction.

3,Directional control of Biomolecular Rocket

    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.

4-1 BODY

The body is made of polystyrene beads, Pt beads and DNA. Polystyrene beads are processed to conjugate different kinds of DNA.
Vapor deposition

    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.
1.Deposit Au on the half of polystyrene beads.
2.Deposit Cr on the half of polystyrene beads like the left picture.


Amino modified DNA and polystyrene conjugation
    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.
1.Carboxyl group of polystyrene beads and EDAC react with each other
2.Carboxyl group become active intermediate
3.DNA coupled to Polystyrene beads



SAM(Self-assembled Monolayer)
    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.


    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.

4-2 DRIVING FORCE

Image:BIOMODTNJBUB.png

    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.


4-3 CONTROL

Photo switching system

    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.


    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.


Personal tools