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

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(1.1. Power supply for rail-free movement by using catalase catalytic engine)
 
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:{|
 
:{|
 
|<html><body><font size="5">We succeeded in selective coating of a micrometer-sized bead by vapor deposition of Au and Cr.</font></body></html><br>
 
|<html><body><font size="5">We succeeded in selective coating of a micrometer-sized bead by vapor deposition of Au and Cr.</font></body></html><br>
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/selective_coating|methods]]<br><br>
+
>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/selective_coating|methods]]<br><br>
 
|<html><body><td align="center"><img src="http://openwetware.org/images/a/a5/Vapor_deposition.jpg" border=0 width=330 height=110></a></td></body></html>
 
|<html><body><td align="center"><img src="http://openwetware.org/images/a/a5/Vapor_deposition.jpg" border=0 width=330 height=110></a></td></body></html>
 
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:&nbsp;&nbsp;&nbsp;&nbsp;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 on the Au-deposited microbeads. The microbeads had three types of surface areas because the angular alignment of the beads was changed when Cr (chromium) was deposited on the Au-deposited microbeads.
+
:&nbsp;&nbsp;&nbsp;&nbsp;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.
:&nbsp;&nbsp;&nbsp;&nbsp;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.
+
:&nbsp;&nbsp;&nbsp;&nbsp;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.
{|style="margin-left:30px" width="930px" border="1"
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{|style="margin-left:30px" width="930px"position:fixed;z-index:-9999;top:0;left:0;min-width:100%;min-height:100%"" border="1"
 
|&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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{|width="475px" border="1"
 
{|width="475px" border="1"
 
|&nbsp;&nbsp;'''DNA sequence L <br>
 
|&nbsp;&nbsp;'''DNA sequence L <br>
&nbsp;&nbsp;5’-CGTCTATTGCTTGTCACTTCCCC-3'&nbsp;&nbsp;
+
&nbsp;&nbsp;<html><body><nobr>5’-CGTCTATTGCTTGTCACTTCCCC-3'&nbsp;&nbsp;</nobr></body></html>
 
|&nbsp;&nbsp;'''DNA sequence S<br>
 
|&nbsp;&nbsp;'''DNA sequence S<br>
&nbsp;&nbsp;5’-AATACCCAGCC-3’&nbsp;&nbsp;
+
&nbsp;&nbsp;<html><body><nobr>5’-AATACCCAGCC-3’&nbsp;&nbsp;</nobr></body></html>
 
|-
 
|-
 
|&nbsp;&nbsp;'''DNA sequence  L<sup>*</sup><br>
 
|&nbsp;&nbsp;'''DNA sequence  L<sup>*</sup><br>
&nbsp;&nbsp;5'-GGGGAAGTGACAAGCAATAGACG-3'&nbsp;&nbsp;
+
&nbsp;&nbsp;<html><body><nobr>5'-GGGGAAGTGACAAGCAATAGACG-3'&nbsp;&nbsp;</nobr></body></html>
 
|&nbsp;&nbsp;'''DNA sequence S<sup>*</sup> <br>
 
|&nbsp;&nbsp;'''DNA sequence S<sup>*</sup> <br>
&nbsp;&nbsp;5’-GGCTGGGTATT-3’&nbsp;&nbsp;
+
&nbsp;&nbsp;<html><body><nobr>5’-GGCTGGGTATT-3'&nbsp;&nbsp;</nobr></body></html>
 
|}
 
|}
 
|}
 
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|<html><body><td align="center"><img src="http://openwetware.org/images/f/f5/Polystyrene_EDAC.jpg" border=0 width=300 height=240></a></td></body></html>
 
|<html><body><td align="center"><img src="http://openwetware.org/images/f/f5/Polystyrene_EDAC.jpg" border=0 width=300 height=240></a></td></body></html>
 
|<html><body><font size="5">We succeeded in selective DNA conjugation to the polystyrene surface area  of the microbead body.</font></body></html><br>
 
|<html><body><font size="5">We succeeded in selective DNA conjugation to the polystyrene surface area  of the microbead body.</font></body></html><br>
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Polystyrene_conjugation|methods]]<br><br>
+
>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Polystyrene_conjugation|methods]]<br><br>
 
&nbsp;&nbsp;&nbsp;&nbsp;We conjugated amino-modified DNA sequence L<sup>*</sup> to the calboxylated polystyrene surface area of the microbead body with amide binding. To investigate the selective conjugation of L<sup>*</sup>, we hybridized a fluorophore-modified DNA sequence L with L* on the body and observed the DNA-conjugated microbead bodies.
 
&nbsp;&nbsp;&nbsp;&nbsp;We conjugated amino-modified DNA sequence L<sup>*</sup> to the calboxylated polystyrene surface area of the microbead body with amide binding. To investigate the selective conjugation of L<sup>*</sup>, we hybridized a fluorophore-modified DNA sequence L with L* on the body and observed the DNA-conjugated microbead bodies.
 
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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.
:{| border="1" width="930px"
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:{| border="1"
 
|&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><td align="center" width="150px"><img src="http://openwetware.org/images/8/87/Metal_SAM.jpg" border=0 width=300 height=240></a></td></body></html>
 
|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/8/87/Metal_SAM.jpg" border=0 width=300 height=240></a></td></body></html>
 
|<html><body><font size="5">We succeeded in selective DNA conjugation to the Au surface area of the microbead body.</font></body></html><br>
 
|<html><body><font size="5">We succeeded in selective DNA conjugation to the Au surface area of the microbead body.</font></body></html><br>
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Metal_area|methods]]<br><br>
+
>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Metal_area|methods]]<br><br>
 
&nbsp;&nbsp;&nbsp;&nbsp;We conjugated thiol-modified DNA sequence S<sup>*</sup> to the Au surface area of the microbead body with Au-thiol bonding. To confirm the selective conjugation of S<sup>*</sup> to an Au surface, we observed an Au-deposited cover glass after DNA conjugation instead of selectively Au-coated microbeads after DNA conjugation. We investigated the wetting properties of the Au surface before and after DNA conjugation because the wetting investigation showed the selective conjugation of DNA more clearly than the fluorescence observation like Fig. 0.3.1.
 
&nbsp;&nbsp;&nbsp;&nbsp;We conjugated thiol-modified DNA sequence S<sup>*</sup> to the Au surface area of the microbead body with Au-thiol bonding. To confirm the selective conjugation of S<sup>*</sup> to an Au surface, we observed an Au-deposited cover glass after DNA conjugation instead of selectively Au-coated microbeads after DNA conjugation. We investigated the wetting properties of the Au surface before and after DNA conjugation because the wetting investigation showed the selective conjugation of DNA more clearly than the fluorescence observation like Fig. 0.3.1.
 
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|-
 
|-
 
|<html><body><td align="center"><img src="http://openwetware.org/images/1/19/Conjugation_catalyst.jpg" border=0 width=300 height=230></a></td></body></html>
 
|<html><body><td align="center"><img src="http://openwetware.org/images/1/19/Conjugation_catalyst.jpg" border=0 width=300 height=230></a></td></body></html>
|&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">Catalyst engines are attached to the microbead body of Biomolecular Rocket with DNA hybridization reactions between L and L<sup>*</sup>, and S and S<sup>*</sup>.</font></body></html><br>
+
|<html><body><font size="5">Catalyst engines are attached to the microbead body of Biomolecular Rocket with DNA hybridization reactions between L and L<sup>*</sup>, and S and S<sup>*</sup>.</font></body></html><br>
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Conjugation_catalyst|methods]]<br><br>
+
>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Conjugation_catalyst|methods]]<br><br>
 
|}
 
|}
 
:&nbsp;&nbsp;&nbsp;&nbsp;From the results of sections 0.1 and 0.3, a selectively DNA-conjugated microbead body of Biomolecular Rocket is constructed. In addition, we prepared catalytic engines with DNA-tag sequences (L and S) that are complementary to the DNA sequences (L<sup>*</sup> and S<sup>*</sup>) on the body. Therefore, by mixing the DNA-tagged catalytic engines and selectively DNA-conjugated body, Biomolecular Rocket would be constructed in a self-assembled manner. Experiments are currently in progress.
 
:&nbsp;&nbsp;&nbsp;&nbsp;From the results of sections 0.1 and 0.3, a selectively DNA-conjugated microbead body of Biomolecular Rocket is constructed. In addition, we prepared catalytic engines with DNA-tag sequences (L and S) that are complementary to the DNA sequences (L<sup>*</sup> and S<sup>*</sup>) on the body. Therefore, by mixing the DNA-tagged catalytic engines and selectively DNA-conjugated body, Biomolecular Rocket would be constructed in a self-assembled manner. Experiments are currently in progress.
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:&nbsp;&nbsp;&nbsp;&nbsp;We utilized the catalase for catalytic engines, which catalyzes the decomposition of H<sub>2</sub>O<sub>2</sub> into H<sub>2</sub>O and O<sub>2</sub>. Here, we conjugated the catalase to the polystyrene area of a microbead with a hemispherical Au surface and a hemispherical polystyrene surface (Fig. 1.1).
 
:&nbsp;&nbsp;&nbsp;&nbsp;We utilized the catalase for catalytic engines, which catalyzes the decomposition of H<sub>2</sub>O<sub>2</sub> into H<sub>2</sub>O and O<sub>2</sub>. Here, we conjugated the catalase to the polystyrene area of a microbead with a hemispherical Au surface and a hemispherical polystyrene surface (Fig. 1.1).
 
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Varification_catalase|methods]]<br><br>
 
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Varification_catalase|methods]]<br><br>
:&nbsp;&nbsp;&nbsp;&nbsp;Movie 1.1 shows the rail-free movement of a 10 μm microbead with a hemispherical Au surface and a hemispherical polystyrene surface by O2 bubble emission with catalase. The 10 μm beads without catalase did not move at all (Movie 1.2). Thus, we conclude that we succeeded in the rail-free movement by O<sub>2</sub> bubble emission with catalase.
+
:&nbsp;&nbsp;&nbsp;&nbsp;Movie 1.1 shows the rail-free movement of a 10 μm microbead with a hemispherical Au surface and a hemispherical polystyrene surface by O<sub>2</sub> bubble emission with catalase. The 10 μm beads without catalase did not move at all (Movie 1.2). Thus, we conclude that we succeeded in the rail-free movement by O<sub>2</sub> bubble emission with catalase.
 
{|style="margin-left:35px"
 
{|style="margin-left:35px"
 
|
 
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<HTML><iframe width="420" height="300" src="http://www.youtube.com/embed/gPNaMMd3NP4" frameborder="0" allowfullscreen></iframe></HTML>
 
<HTML><iframe width="420" height="300" src="http://www.youtube.com/embed/gPNaMMd3NP4" frameborder="0" allowfullscreen></iframe></HTML>
 
|-
 
|-
|style="padding:10px"|Movie. 1.2 &nbsp;&nbsp;&nbsp;&nbsp;Image of the catalytic reaction of 3% H<sub>2</sub>O<sub>2</sub> and 1 μm beads that have platinum hemispherical area
+
|style="padding:10px"|Movie. 1.2 &nbsp;&nbsp;&nbsp;&nbsp;Image of the catalytic reaction of 3% H<sub>2</sub>O<sub>2</sub> and 1 μm beads that have platinum hemispherical area.
 
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|[[Image:BIOMODTNJEPR 04.JPG|Electrophoresis|700px]]
 
|[[Image:BIOMODTNJEPR 04.JPG|Electrophoresis|700px]]
 
|-
 
|-
|style="padding:10px|Fig. 1.3&nbsp;&nbsp;&nbsp; A gel image of a native PAGE of DNA in H<sub>2</sub>O<sub>2</sub> solutions. Lanes 1-3, 8: a double stranded DNA (D+R) in diluted H<sub>2</sub>O<sub>2</sub> solutions eith concentrations 0% (lanes 1 and 8), 1% (lane 2), and 5% (lane 3). In lanes 4-7, single stranded DNAs in 0% and 5% H<sub>2</sub>O<sub>2</sub> solutions were shown. DNA sequences R and D are shown at the top right of the image.
+
|style="padding:10px"|Fig. 1.3&nbsp;&nbsp;&nbsp; A gel image of a native PAGE of DNA in H<sub>2</sub>O<sub>2</sub> solutions. Lanes 1-3, 8: a double stranded DNA (D+R) in diluted H<sub>2</sub>O<sub>2</sub> solutions eith concentrations 0% (lanes 1 and 8), 1% (lane 2), and 5% (lane 3). In lanes 4-7, single stranded DNAs in 0% and 5% H<sub>2</sub>O<sub>2</sub> solutions were shown. DNA sequences R and D are shown at the upper right of the image.
 
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<br><br><div align = "right" style="padding-right:20px">[[#TOP|↑Page Top]]</div>
 
<br><br><div align = "right" style="padding-right:20px">[[#TOP|↑Page Top]]</div>
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:<html><body><font size="5">We confirmed the high-speed movement of the Biomorecular Rocket by bubble emission.</font></body></html><br><br>
 
:<html><body><font size="5">We confirmed the high-speed movement of the Biomorecular Rocket by bubble emission.</font></body></html><br><br>
 
{|style="margin-left:35px"
 
{|style="margin-left:35px"
|&nbsp;&nbsp;&nbsp;&nbsp;Catalytic engines emit large amount of bubbles, and thus, supplies powerful driving force to the Biomolecular Rocket. By the analyses of the movement of platinum particles and numerical simulations, we found that the speed of the Biomolcular Rocket was faster than that of kinesin. We carried out the experiments and simulations as follows.
+
|&nbsp;&nbsp;&nbsp;&nbsp;Catalytic engines emit large amount of bubbles, and thus, supply powerful driving force to the Biomolecular Rocket. By the analyses of the movement of platinum particles and numerical simulations, we found that the speed of the Biomolcular Rocket was faster than that of kinesin. We carried out the experiments and simulations as follows.
 
{|border="3" width="630px"
 
{|border="3" width="630px"
 
|<html><body><ol>
 
|<html><body><ol>
<li>Observations of the movement of platinum particles using a high-speed camera and analyses of the speed.
+
<li>Observations of the movement of platinum particles using a high-speed camera and analyses of the speed
 
<li>Numerical simulations of the movement of the Biomolecular Rocket</ol></body></html>
 
<li>Numerical simulations of the movement of the Biomolecular Rocket</ol></body></html>
 
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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 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 top 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.'''''
  
 
:{|border = "1"
 
:{|border = "1"
|'''a'''<br><HTML><iframe width="440" height="330" src="http://www.youtube.com/embed/7pBw4FWEt3I" frameborder="0" allowfullscreen></iframe></HTML><br>
+
|&nbsp;&nbsp;&nbsp;'''a'''<br><HTML><iframe width="440" height="330" src="http://www.youtube.com/embed/7pBw4FWEt3I" frameborder="0" allowfullscreen></iframe></HTML><br>
|'''b'''<br><HTML><iframe width="440" height="330" src="http://www.youtube.com/embed/R4RsXKiknIs" frameborder="0" allowfullscreen></iframe></HTML><br>
+
|&nbsp;&nbsp;&nbsp;'''b'''<br><HTML><iframe width="440" height="330" src="http://www.youtube.com/embed/R4RsXKiknIs" frameborder="0" allowfullscreen></iframe></HTML><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>
 
|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
+
(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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{|style="margin-left:200px" width="500px" border="1"
 
{|style="margin-left:200px" width="500px" border="1"
 
|[[Image:Calculation speed.jpg|500px|]]
 
|[[Image:Calculation speed.jpg|500px|]]
 
|-
 
|-
|&nbsp;&nbsp;Fig. 2.1.2. The mean square displacement of a platinum particle.
+
|&nbsp;&nbsp;Fig. 2.1.2 The mean square displacement of a platinum particle.
 
|}
 
|}
  
==2.2. Numerical estimation of the speed of Biomolecular Rocket==
+
==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>
:&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 areas between them (Fig. 2.2).
+
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Simulation|simulation models]]
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 2.2 shows mean speed of kinesin motor, 10 μm sized bead that have platinum hemispherical area (catalytic motor without DNA), and 10 μm of Biomolecular Rocket. The speed of Biomolecular Rocket is calculated as 11.2 μm/s, the speed of catalytic motor without DNA is 6.8 μm/s. We assumed that Kinesin will move straightforward at 1.0 μm/s, therefore, we can speculate that biomolecular rocket will move faster than kinesin, and surface enlargement of catalyst will surely increase the speed of Biomolecular Rocket.
+
:&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 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 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 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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{|style="margin-left:200px" width="500px" border = "1"
 
{|style="margin-left:200px" width="500px" border = "1"
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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.
 
|}
 
|}
 
:&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/cm2. 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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|}
 
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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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|}
 
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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>
:&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.
+
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Simulation|Simulation Models]]
 +
:&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]]

Latest revision as of 00:04, 28 October 2012


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