Difference between revisions of "Biomod/2012/Titech/Nano-Jugglers/Results"

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(2. Realization of the high-speed movement of the Biomolecular Rocket)
 
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:    Figure 0.1a, b and c are microscope images of 40 μm microbeads. Figure 0.1a shows microbeads before vapor deposition of metals. Figure 0.1b shows microbeads after vapor deposition of Au (gold) on the microbeads. Figure 0.1c shows microbeads after additional vapor deposition of Cr (chromium) on the Au-deposited microbeads. The microbeads had three types of surface areas because the angular alignment of the beads was changed when Cr was deposited on the Au-deposited microbeads.
 
:    Figure 0.1a, b and c are microscope images of 40 μm microbeads. Figure 0.1a shows microbeads before vapor deposition of metals. Figure 0.1b shows microbeads after vapor deposition of Au (gold) on the microbeads. Figure 0.1c shows microbeads after additional vapor deposition of Cr (chromium) on the Au-deposited microbeads. The microbeads had three types of surface areas because the angular alignment of the beads was changed when Cr was deposited on the Au-deposited microbeads.
:    Similarly, Figure 0.1e, f and g are microscope images of 10 μm microbeads. Figure 0.1e shows microbeads before vapor deposition of metals. Figure 0.1f shows microbeads after vapor deposition of Au on the microbeads. Figure 0.1g shows microbeads after additional vapor deposition of Cr on the Au-deposited microbeads. The 10 μm microbeads probably had three types of surface areas. From these results, we conclude that selective coating of microbeads for Biomolecular Rocket was achieved.
+
:    Similarly, Figure 0.1e, f and g are microscope images of 10 μm microbeads. Figure 0.1e shows microbeads before vapor deposition of metals. Figure 0.1f shows microbeads after vapor deposition of Au on the microbeads. Figure 0.1g shows microbeads after additional vapor deposition of Cr on the Au-deposited microbeads. The 10 μm microbeads probably had three types of surface areas. From these results, we conclude that selective coating of microbeads for the Biomolecular Rocket was achieved.
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|&nbsp;&nbsp;<html><body><nobr>40 μm silica beads</nobr></body></html>
 
|&nbsp;&nbsp;<html><body><nobr>40 μm silica beads</nobr></body></html>
 
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''<br>[[Image:BIOMODTNJPVDR1.jpg|40 μm silica beads|240px]]
 
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''<br>[[Image:BIOMODTNJPVDR1.jpg|40 μm silica beads|240px]]
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:&nbsp;&nbsp;&nbsp;&nbsp;Figure 0.3.1a, b, and c are bright-field microscope images of selectively-coated microbead bodies (10 μm in diameter). Figure 0.3.1a', b', and c' are fluorescence microscope images of the selectively-coated microbead bodies. Figure 0.3.1a and a' shows selectively DNA-L<sup>*</sup>-conjugated microbeads with fluorophore-modified DNA L. Fluorescence of L was observed only where the polystyrene surface was exposed after the vapor deposition of metal. Figure 0.3.1b and b' shows selectively DNA-L<sup>*</sup>-conjugated microbeads without fluorophore-modified DNA L, and no fluorescence was observed. Figure 0.3.1c and c' shows non-DNA-conjugated microbeads with fluorophore-modified DNA L, and no fluorescence was observed. From these results, we conclude that selective conjugation of DNA L<sup>*</sup> to polystyrene surface area of the microbead bodies was achieved.
 
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 0.3.1a, b, and c are bright-field microscope images of selectively-coated microbead bodies (10 μm in diameter). Figure 0.3.1a', b', and c' are fluorescence microscope images of the selectively-coated microbead bodies. Figure 0.3.1a and a' shows selectively DNA-L<sup>*</sup>-conjugated microbeads with fluorophore-modified DNA L. Fluorescence of L was observed only where the polystyrene surface was exposed after the vapor deposition of metal. Figure 0.3.1b and b' shows selectively DNA-L<sup>*</sup>-conjugated microbeads without fluorophore-modified DNA L, and no fluorescence was observed. Figure 0.3.1c and c' shows non-DNA-conjugated microbeads with fluorophore-modified DNA L, and no fluorescence was observed. From these results, we conclude that selective conjugation of DNA L<sup>*</sup> to polystyrene surface area of the microbead bodies was achieved.
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|&nbsp;&nbsp;<html><body><nobr>Bright-field microscope images</nobr></body></html>&nbsp;&nbsp;
 
|&nbsp;&nbsp;<html><body><nobr>Bright-field microscope images</nobr></body></html>&nbsp;&nbsp;
 
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:BIOMOD-TNJ-CrAu_1_2.jpg|DNA conjugated beads and FAM|220px]]
 
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:BIOMOD-TNJ-CrAu_1_2.jpg|DNA conjugated beads and FAM|220px]]
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:<html><body><font size="5">We succeeded in high speed movement with platinum catalytic engines.</font></body></html>
 
:<html><body><font size="5">We succeeded in high speed movement with platinum catalytic engines.</font></body></html>
 
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/High-speed_camera|methods and full length movie]]<br><br>
 
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/High-speed_camera|methods and full length movie]]<br><br>
:&nbsp;&nbsp;&nbsp;&nbsp;Movie 2.1.1a shows the movement of 0.15-0.40 μm platinum particles in 3% H<sub>2</sub>O<sub>2</sub> solution. Movie 2.1.1b is the movement of platinum particles observed by a high-speed camera (the upper left of the movie) and its analyzed results (the right of the movie). The analyzed results show the values of acceleration (top), velocity (the second from the top), coordinate x (third), and coordinate y (bottom) of platinum movement. From the results, we found the relationships between the bubble radius growth and the speed of platinum. Using the relationships and the kinetic parameters, we did numerical simulations of the movement of the Biomolecular Rocket (see Section 2.2).
+
:&nbsp;&nbsp;&nbsp;&nbsp;Movie 2.1.1a shows the movement of 0.15-0.40 μm platinum particles in 3% H<sub>2</sub>O<sub>2</sub> solution. Movie 2.1.1b is the movement of platinum particles observed by a high-speed camera (the upper left of the movie) and its analyzed results (the right of the movie). The analyzed results show the values of acceleration (top), velocity (the second from the top), coordinate x (third), and coordinate y (bottom) of platinum movement. From the results, we found the relationships between the growth of bubble radius and the speed of platinum. Using the relationships and the kinetic parameters, we did numerical simulations of the movement of the Biomolecular Rocket (see Section 2.2).
:&nbsp;&nbsp;&nbsp;&nbsp;Figure. 2.1.2 shows the graph of the mean square displacement of the platinum particle. From this data, we calculated that the value of diffusion constant was 80.3 mm<sup>2</sup>/s<sup>2</sup>, and the mean velocity was 9.0 mm/s. Platinum particles moved at about '''''9,000 time’s faster speed than kinesin.'''''
+
:&nbsp;&nbsp;&nbsp;&nbsp;Figure. 2.1.2 shows the graph of the mean square displacement of the platinum particle. We can calculate mean speed of platinum particle by making a quadratic curve fitting and calculating square root of coefficient of the curve.  We calculated that the value of quadratic coefficient was 115.5 mm<sup>2</sup>/s<sup>2</sup>, and the average speed was calculated as 10.7 mm/s. Assuming that kinesin moves at 1μm/s, Platinum particles in H<sub>2</sub>O<sub>2</sub> solution can moved at about '''''10,000 time’s faster speed than kinesin.'''''
  
 
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|-
 
|-
 
|style="padding:10px" colspan="2"|Movie. 2.1.1&nbsp;&nbsp;&nbsp;&nbsp;Analyses of the speed of platinum in solution of H<sub>2</sub>O<sub>2</sub>.<br>
 
|style="padding:10px" colspan="2"|Movie. 2.1.1&nbsp;&nbsp;&nbsp;&nbsp;Analyses of the speed of platinum in solution of H<sub>2</sub>O<sub>2</sub>.<br>
(a)&nbsp;&nbsp;Platinum movement in solution of H<sub>2</sub>O<sub>2</sub>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(b)&nbsp;&nbsp;Analises of the speed of plutinum by High-speed camera
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(a)&nbsp;&nbsp;Platinum movement in solution of H<sub>2</sub>O<sub>2</sub>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(b)&nbsp;&nbsp;Analyses of the speed of plutinum by High-speed camera
 
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==2.2. Numerical estimation of the speed of Biomolecular Rocket==
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==2.2. Numerical estimation of the speed of the Biomolecular Rocket==
:<html><body><font size="5">The numerical simulation revealed that Biomolecular Rocket can move at ten times faster than kinesin moves.</font></body></html><br>
+
:<html><body><font size="5">The numerical simulation revealed that the Biomolecular Rocket can move ten times faster than kinesin.</font></body></html><br>
 
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Simulation|simulation models]]
 
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Simulation|simulation models]]
:&nbsp;&nbsp;&nbsp;&nbsp;The simulation also demonstrated that Biomolecular Rocket with many platinum catalysts on the body can move twice faster than a microbead with a hemispherical platinum surface moves because of the difference in the catalytic surface areas between them (Fig. 2.2).
+
:&nbsp;&nbsp;&nbsp;&nbsp;The simulation also demonstrated that the Biomolecular Rocket with many platinum catalysts on the body can move twice faster than a microbead with a hemispherical platinum surface moves because of the difference in the catalytic surface areas between them (Fig. 2.2).
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 2.2 shows instantaneous speed at each time steps of kinesin motor, 10 μm beads with a hemispherical platinum surface (catalytic motor without DNA), and 10 μm of Biomolecular Rocket. We take the average of instantaneous speed of each molecular motor at 100 time steps and make a comparison among them.
+
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 2.2 shows instantaneous speed at each time steps of kinesin motor, 10 μm beads with a hemispherical platinum surface (catalytic motor without DNA), and 10 μm of the Biomolecular Rocket. We take the average of 100 time step's instantaneous speed of each molecular motor and make a comparison among them.
:&nbsp;&nbsp;&nbsp;&nbsp;As a result, the average speed of Biomolecular Rocket is calculated as 11.2 μm/s, and the average speed of catalytic motor without DNA is 6.8 μm/s. We assumed that Kinesin moves straightforward at 1.0 μm/s all the time, Kinesin's average speed is calculated as 1.0 μm/s.  
+
:&nbsp;&nbsp;&nbsp;&nbsp;As a result, the average speed of the Biomolecular Rocket is calculated as 11.2 μm/s, and the average speed of catalytic motor without DNA is 6.8 μm/s. We assumed that Kinesin moves straightforward at 1.0 μm/s all the time, Kinesin's average speed is calculated as 1.0 μm/s.  
:&nbsp;&nbsp;&nbsp;&nbsp;Therefore, we estimate that biomolecular rocket moves faster than kinesin, and surface enlargement of catalyst increases the speed of Biomolecular Rocket.
+
:&nbsp;&nbsp;&nbsp;&nbsp;Therefore, we estimate that the Biomolecular Rocket moves faster than kinesin. Moreover, the Biomolecular Rocket can get more speed by surface enlargement of catalyst with DNA.
 
:{|style="margin-left:100px" border="1"
 
:{|style="margin-left:100px" border="1"
 
|[[Image:Hi_speed.png|Simulation of high-speed|700px]]
 
|[[Image:Hi_speed.png|Simulation of high-speed|700px]]
 
|-
 
|-
|style="padding:10px"|Fig. 2.2 &nbsp;&nbsp;&nbsp;Image of each molecular motor’s speed with time
+
|style="padding:10px"|Fig. 2.2 &nbsp;&nbsp;&nbsp;Image of each molecular motor’s instantaneous speed with time
 
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|<html><body><ol>
 
|<html><body><ol>
 
<li>Design of a photo-switchable DNA system for the directional control
 
<li>Design of a photo-switchable DNA system for the directional control
<li>Investigation of the dissociation rate of the photo-switchahble DNA duplex by UV light irradiation experiments
+
<li>Investigation of the dissociation rate of the photo-switchable DNA duplex by UV light irradiation experiments
 
<li>Investigation of the directional control of Biomolecular Rocket with the photo-switchable DNA system by numerical simulations
 
<li>Investigation of the directional control of Biomolecular Rocket with the photo-switchable DNA system by numerical simulations
 
</ol></body></html>
 
</ol></body></html>
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|<html><body><font size="5">We designed photoresponsive DNA strands for a photo-switchable DNA system to achieve the directional control of Biomolecular Rocket.</font></body></html><br>
 
|<html><body><font size="5">We designed photoresponsive DNA strands for a photo-switchable DNA system to achieve the directional control of Biomolecular Rocket.</font></body></html><br>
 
>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Design_of_photoresponsive_DNA|methods]]<br><br>
 
>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Design_of_photoresponsive_DNA|methods]]<br><br>
&nbsp;&nbsp;&nbsp;&nbsp;We designed a photoresponsive DNA strand based on DNA sequence S<sup>*</sup>; four azobenzene molecules were introduced into S<sup>*</sup>. Figure 3.1.1 shows that absorbance spectra of DNA strands (A) photoresponsive DNA sequence S<sup>*</sup>, (B) DNA sequence S, and (A+B) the duplex of them at a room temperature. The absorbance of A+B around 260nm was less than those of A and B. This indicated that the hybridization of A with B was stable at a room temperature.
+
&nbsp;&nbsp;&nbsp;&nbsp;We designed a photoresponsive DNA strand based on DNA sequence S<sup>*</sup>; four azobenzene molecules were introduced into S<sup>*</sup>. Figure 3.1.1 shows that absorbance spectra of DNA strands (A) photoresponsive DNA sequence S<sup>*</sup>, (B) DNA sequence S, and (A+B) the duplex of them at a room temperature. The absorbance of (A+B) around 260nm was less than those of (A) and (B). This indicated that the hybridization of (A) with (B) was stable at a room temperature.
 
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<html><body><font size="5">We have succeeded in development of a photo-switchable DNA system.</font></body></html><br>
 
<html><body><font size="5">We have succeeded in development of a photo-switchable DNA system.</font></body></html><br>
 
>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Dissociation_of_photoresponsive_DNA|methods]]<br><br>
 
>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Dissociation_of_photoresponsive_DNA|methods]]<br><br>
&nbsp;&nbsp;&nbsp;&nbsp;We introduce the photo-switching DNA system into Biomolecular Rocket in order to control its moving direction.
+
&nbsp;&nbsp;&nbsp;&nbsp;We introduced the photo-switching DNA system into Biomolecular Rocket in order to control its moving direction.
 
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:&nbsp;&nbsp;&nbsp;To investigate the relationship between the strength of UV light and the irradiation time for dissociation of the photoresponsive DNA and determine the valid time for UV light irradiation, we examined two types of strength of UV light.
 
:&nbsp;&nbsp;&nbsp;To investigate the relationship between the strength of UV light and the irradiation time for dissociation of the photoresponsive DNA and determine the valid time for UV light irradiation, we examined two types of strength of UV light.
:&nbsp;&nbsp;&nbsp;Figure 3.2.1a represents the absorbance spectra in the condition of UV-light irradiation with the strength of 30 mW/cm<sup><small>2</small></sup>. The absorbance of the DNA duplex A+B at the wavelength of 260 nm gradually increased from 0 minutes to 5 minutes (Fig. 3.2.1b). This result means that the DNA duplex A+B was dissociated after 5 minutes irradiation of UV light. Moreover, the absorbance of the DNA duplex A+B at 330 nm decreased from 0 minutes to 5 minutes (Fig. 3.2.1b). This means that the trans-formed azobenzene changed its form to cis-formation. Therefore, we conclude that the dissociation of the photoresponsive DNA can be achieved by 5 minutes irradiation of UV-light (30 mW/cm<sup><small>2</small></sup>).
+
:&nbsp;&nbsp;&nbsp;Figure 3.2.1a represents the absorbance spectra in the condition of UV-light irradiation with the strength of 30 mW/cm<sup><small>2</small></sup>. The absorbance of the DNA duplex (A+B) at the wavelength of 260 nm gradually increased from 0 minutes to 5 minutes (Fig. 3.2.1b). This result means that the DNA duplex (A+B) was dissociated after 5 minutes irradiation of UV light. Moreover, the absorbance of the DNA duplex (A+B) at 330 nm decreased from 0 minutes to 5 minutes (Fig. 3.2.1b). This means that the trans-formed azobenzene changed its form to cis-formation. Therefore, we conclude that the dissociation of the photoresponsive DNA can be achieved by 5 minutes irradiation of UV-light (30 mW/cm<sup><small>2</small></sup>).
 
{|style="margin-left:35px" width="800px" border = "1"
 
{|style="margin-left:35px" width="800px" border = "1"
 
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''<br>[[Image:Azo figure3.jpg|Spectrum analysis|400px]]
 
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''<br>[[Image:Azo figure3.jpg|Spectrum analysis|400px]]
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<br>
 
<br>
:&nbsp;&nbsp;&nbsp;&nbsp;Similarly, we studied the dissociation rate of photoresponsive DNA under the condition of UV light irradiation with the strength of 180 mW/cm<sup><small>2</small></sup> (Fig. 3.2.2a). Figure 3.2.2b represents that the DNA duplex A+B was gradually dissociated from 0 seconds to 50 seconds because the maximum absorbance at 260 nm increased. Figure 3.2.2c shows that the trans-formed azobenzene changed to the cis-fomed one by the UV irradiation because the absorbance at 330 nm decreased from 0 seconds to 50 seconds. Figure 3.2.2d shows that the cis-formed azobenzene increased because the absorbance at 480 nm increased from 0 seconds to 50 seconds. In summary, the photo-switchable DNA system worked by 50-second irradiation of UV-light (180 mW/cm<sup><small>2</small></sup>). From these results, we conclude that the dissociation of photoresponsive DNA by UV-light irradiation was achived.
+
:&nbsp;&nbsp;&nbsp;&nbsp;Similarly, we studied the dissociation rate of photoresponsive DNA under the condition of UV light irradiation with the strength of 180 mW/cm<sup><small>2</small></sup> (Fig. 3.2.2a). Figure 3.2.2b represents that the DNA duplex (A+B) was gradually dissociated from 0 seconds to 50 seconds because the maximum absorbance at 260 nm increased. Figure 3.2.2c shows that the trans-formed azobenzene changed to the cis-fomed one by the UV irradiation because the absorbance at 330 nm decreased from 0 seconds to 50 seconds. Figure 3.2.2d shows that the cis-formed azobenzene increased because the absorbance at 480 nm increased from 0 seconds to 50 seconds. In summary, the photo-switchable DNA system worked by 50-second irradiation of UV-light (180 mW/cm<sup><small>2</small></sup>). From these results, we conclude that the dissociation of photoresponsive DNA by UV-light irradiation was achived.
 
{|style="margin-left:35px" width="800px" border = "1"
 
{|style="margin-left:35px" width="800px" border = "1"
 
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''<br>[[Image:TNJ-figure5-azobenzene.png|Spectrum analysis|400px]]
 
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''<br>[[Image:TNJ-figure5-azobenzene.png|Spectrum analysis|400px]]
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==3.3. Directional control of Biomolecular Rocket by the photo-switchable DNA system==
+
==3.3. Directional control of the Biomolecular Rocket by the photo-switchable DNA system==
:&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">By numerical simulations, we found that Biomolecular Rocket changes its direction by the UV light irradiation even though Biomolecular Rocket is affected by the viscous resistance force and Brownian dynamics of water.</font></body></html><br>
+
:&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">By numerical simulations, we found that the Biomolecular Rocket changes its direction by the UV light irradiation even though the Biomolecular Rocket is affected by the viscous resistance force and Brownian dynamics of water.</font></body></html><br>
 
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Simulation|Simulation Models]]
 
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Simulation|Simulation Models]]
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 3.3 shows the trajectories of Biomolecular Rockets of 10 μm in diameter by the numerical simulation. Each trajectory shows the movement of Biomolecular Rocket that detaches catalytic engines after the irradiation of UV light when 10 seconds, 15 seconds, 20 seconds, and 25 seconds passed. This simulation results suggested that Biomolecular Rocket can change its direction immediately after all catalytic engines are dissociated even though the viscous resistance and Brownian movement prevented the controlled movement of Biomolecular Rocket. From these results, we conclude that Biomolecular Rocket changes its direction by UV light irradiation.
+
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 3.3 shows the trajectories of the the Biomolecular Rockets of 10 μm in diameter by the numerical simulation. Each trajectory shows the movement of the Biomolecular Rocket that detaches catalytic engines after the irradiation of UV light when 10 seconds, 15 seconds, 20 seconds, and 25 seconds passed. This simulation results suggested that the Biomolecular Rocket can change its direction immediately after all catalytic engines are dissociated even though the viscous resistance and Brownian movement prevented the controlled movement of the Biomolecular Rocket. From these results, we conclude that the Biomolecular Rocket changes its direction by UV light irradiation.
 
{|style="margin-left:170px" width="600px" border="1"
 
{|style="margin-left:170px" width="600px" border="1"
 
|[[Image:ControlResult画像.png|Control simulation|600px]]
 
|[[Image:ControlResult画像.png|Control simulation|600px]]

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