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=Results=
=Results=
{|style="margin-left:20px" border="1"
{|style="margin-left:20px" border="1"
|colspan="3"|<html><body><td align="center" width="300px"><A href=#0._Construction_of_Biomolecular_Rocket title="Body"><img src="http://openwetware.org/images/b/b5/BM.jpg" border=0 width=310 height=240></a></td></body></html>
|colspan="3"|<html><body><A href=#0._Construction_of_Biomolecular_Rocket title="Body"><img src="http://openwetware.org/images/b/b5/BM.jpg" border=0 width=310 height=240></a></body></html>
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&nbsp;&nbsp;&nbsp;&nbsp;'''Construction of Biomolecular Rocket'''<br><br>
&nbsp;&nbsp;&nbsp;&nbsp;'''Construction of Biomolecular Rocket'''<br><br>
*We constructed Biomolecular Rocket composed of a micrometer-sized body and many catalytic engines. The catalytic engines were conjugated to the body using DNA-baed linkers in a spatially selective manner.<br><br>
*We constructed Biomolecular Rocket composed of a micrometer-sized body and many catalytic engines. The catalytic engines were conjugated to the body using DNA-bead linkers in a spatially selective manner.<br><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Biomod/2012/Titech/Nano-Jugglers/Results#0._Construction_of_Biomolecular_Rocket|Shown in detail below]]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Biomod/2012/Titech/Nano-Jugglers/Results#0._Construction_of_Biomolecular_Rocket|Shown in detail below]]
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{|style="margin-left:20px" border="1"
{|style="margin-left:20px" border="1"
|<html><body><A href=#1._Power_supply_for_the_rail-free_movement title="Rail-free"><img src="http://openwetware.org/images/7/7f/Rail-free%E3%80%80movement_kinesin.jpg" border=0 width=310 height=220></a></body></html><br>'''Power supply for the rail-free movement'''<br><br>
|<html><body><A href=#1._Power_supply_for_the_rail-free_movement_of_the_Biomolecular_Rocket title="Rail-free"><img src="http://openwetware.org/images/7/7f/Rail-free%E3%80%80movement_kinesin.jpg" border=0 width=310 height=220></a></body></html><br>'''Power supply for the rail-free movement of the Biomolecular Rocket'''<br>
|<html><body><A href=#2._Increasing_driving_force_for_the_high-speed_movement title="High-speed"><img src="http://openwetware.org/images/8/89/High-speed_movement.jpg" border=0 width=310 height=220></a></body></html><br>'''Increasing driving force for the high-speed movement'''
|<html><body><A href=#2._Realization_of_the_high-speed_movement_of_the_Biomolecular_Rocket title="High-speed"><img src="http://openwetware.org/images/8/89/High-speed_movement.jpg" border=0 width=310 height=220></a></body></html><br>'''Realization of high-speed movement of the Biomolecular Rocket'''
|<html><body><A href=#3._Introduction_of_a_photo-switchable_DNA_system_for_the_directional_control title="Control"><img src="http://openwetware.org/images/d/dd/Control_image.jpg" border=0 width=310 height=220></a></body></html><br>'''Introduction of a photo-switchable DNA system for the directional control'''
|<html><body><A href=#3._Introduction_of_a_photo-switchable_DNA_system_for_the_directional_control title="Control"><img src="http://openwetware.org/images/d/dd/Control_image.jpg" border=0 width=310 height=220></a></body></html><br>'''Introduction of a photo-switchable DNA system for the directional control'''
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*We realized rail-free movement by power generation with catalytic reactions of platinum and catalase.<br><br><br><br><br>
*We realized the rail-free movement by power generation with catalytic reactions of platinum and catalase.<br><br><br><br><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Biomod/2012/Titech/Nano-Jugglers/Results#1._Power_supply_for_the_rail-free_movement|Shown in detail below]]  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Biomod/2012/Titech/Nano-Jugglers/Results#1._Power_supply_for_the_rail-free_movement_of_the_Biomolecular_Rocket|Shown in detail below]]  
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*We realized the high-speed movement by power generation with catalytic reactions of platinum and catalase, and analyzed the speed.
*We realized the high-speed movement by power generation with catalytic reactions of platinum and catalase, and analyzed the speed.
*We carried out numerical simulations of the high-speed movement of Biomolecular Rockets.<br>
*We carried out numerical simulations of the high-speed movement of the Biomolecular Rockets.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Biomod/2012/Titech/Nano-Jugglers/Results#2._Increasing_driving_force_for_the_high-speed_movement|Shown in detail below]]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Biomod/2012/Titech/Nano-Jugglers/Results#2._Realization_of_the_high-speed_movement_of_the_Biomolecular_Rocket|Shown in detail below]]
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*We developed photo-switchable DNA for the control of Bimolecular Rocket using UV light irradiation.
*We developed a photo-switchable DNA system for controlling of the Bimolecular Rocket using UV light irradiation.
*We investigated directional control of Biomolecular Rocket in the simulation.<br><br><br>
*We investigated directional control of the Biomolecular Rocket in the simulations.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Biomod/2012/Titech/Nano-Jugglers/Results#3._Introduction_of_a_photo-switchable_DNA_system_for_the_directional_control|Shown in detail below]]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Biomod/2012/Titech/Nano-Jugglers/Results#3._Introduction_of_a_photo-switchable_DNA_system_for_the_directional_control|Shown in detail below]]
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=<font color="green">0. Construction of Biomolecular Rocket</font>=
=<font color="green">0. Construction of Biomolecular Rocket</font>=
{|style="margin-left:35px" width="930px"
{|style="margin-left:35px" width="930px"
|&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We constructed Biomolecular Rocket with a microbead, catalysts, and designed DNAs.</font></body></html><br>
|<html><body><font size="5">We constructed Biomolecular Rocket with a microbead, catalysts, and designed DNAs.</font></body></html><br>
&nbsp;&nbsp;&nbsp;&nbsp;Biomolecular Rocket is composed of a micrometer-sized body and many catalytic engines. The body consists of a microbead with a diameter of 10 μm, and catalytic engines consist of platinum nanoparticles or catalase molecules. The catalytic engines are conjugated to the body using a DNA-based linker in a spatially selective manner.<br>
&nbsp;&nbsp;&nbsp;&nbsp;Biomolecular Rocket is composed of a micrometer-sized body and many catalytic engines. The body consists of a microbead with a diameter of 10 μm, and catalytic engines consist of platinum nanoparticles or catalase molecules. The catalytic engines are conjugated to the body using a DNA-based linker in a spatially selective manner.<br>
&nbsp;&nbsp;&nbsp;&nbsp;We constructed the Biomolecular Rocket through the following four steps.
&nbsp;&nbsp;&nbsp;&nbsp;We constructed the Biomolecular Rocket through the following four steps.
{|width="730px" border="3"
{|width="730px" border="3"
|
|<html><body><ol>
1. The microbead body was selectively coated by vapor deposition of metals (Au and Cr).<br>
<li>The microbead body was selectively coated by vapor deposition of metals (Au and Cr).<br>
2. We designed DNA sequences for spatially-selective hybridization of catalytic engines.<br>
<li>We designed DNA sequences for spatially-selective hybridization of catalytic engines.<br>
3. The DNA molecules were conjugated to a designated metal surface of the microbead body.<br>
<li>The DNA molecules were conjugated to a designated metal surface of the microbead body.<br>
4. Catalyst engines were attached to the microbead body with selective hybridization of DNAs<br>
<li>Catalyst engines were attached to the microbead body with selective hybridization of DNAs we designed.</ol></body></html>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;we designed.
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&nbsp;&nbsp;&nbsp;&nbsp;>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods_of_Biomolecular_Rocket|methods of construction of Biomolecular Rocket]]
&nbsp;&nbsp;&nbsp;&nbsp;>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods_of_Biomolecular_Rocket|methods]]
<div align = "right" style="padding-right:20px">[[#TOP|↑Page Top]]</div><br>
<br>
|<html><body><td align="center"><img src="http://openwetware.org/images/4/4d/Charts.jpg" border=0 width=200 height=440></a></td></body></html>
|<html><body><td align="center"><img src="http://openwetware.org/images/4/4d/Charts.jpg" border=0 width=200 height=440></a></td></body></html>
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==0.1. Selective coating of the body==
==0.1. Selective coating of the body==
:{|
:{|
|<br>&nbsp;&nbsp;&nbsp;&nbsp;<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>
|<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 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 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 result, we conclude that selective coating of microbeads for Biomolecular Rocket.
:&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"
{|style="margin-left:30px" width="930px"position:fixed;z-index:-9999;top:0;left:0;min-width:100%;min-height:100%"" border="1"
|40 μm<br>silica<br>beads
|&nbsp;&nbsp;<html><body><nobr>40 μm silica beads</nobr></body></html>
|&nbsp;&nbsp;'''a'''&nbsp;&nbsp;[[Image:BIOMODTNJPVDR1.jpg|40 μm silica beads|240px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''<br>[[Image:BIOMODTNJPVDR1.jpg|40 μm silica beads|240px]]
|&nbsp;&nbsp;'''b'''&nbsp;&nbsp;[[Image:BIOMODTNJPVDR3.jpg|After first deposition|240px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''b'''<br>[[Image:BIOMODTNJPVDR3.jpg|After first deposition|240px]]
|&nbsp;&nbsp;'''c'''&nbsp;&nbsp;[[Image:BIOMOD_VD.jpg‎ |After second deposition|240px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''c'''<br>[[Image:BIOMOD_VD.jpg‎ |After second deposition|240px]]
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|10 μm<br>polystyrene<br>beads
|&nbsp;&nbsp;<html><body><nobr>10 μm polystyrene beads</nobr></body></html>&nbsp;&nbsp;
|&nbsp;&nbsp;'''d'''&nbsp;&nbsp;[[Image:10umbfAuVD.jpg|10 μm polystyrene beads|240px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''d'''<br>[[Image:10umbfAuVD.jpg|10 μm polystyrene beads|240px]]
|&nbsp;&nbsp;'''e'''&nbsp;&nbsp;[[Image:10umafAuVD.jpg|After first deposition|240px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''e'''<br>[[Image:10umafAuVD.jpg|After first deposition|240px]]
|&nbsp;&nbsp;'''f'''&nbsp;&nbsp;[[Image:10umafCrVD.jpg|After second deposition|240px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''f'''<br>[[Image:10umafCrVD.jpg|After second deposition|240px]]
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|Image<br>of<br>micro-beads
|&nbsp;&nbsp;<html><body><nobr>Image of micro-beads</nobr></body></html>
|&nbsp;&nbsp;<html><body><img src="http://openwetware.org/images/d/d5/Polystyrene.jpg" border=0 width=240 height=180></body></html>
|<html><body><img src="http://openwetware.org/images/d/d5/Polystyrene.jpg" border=0 width=240 height=180></body></html>
|&nbsp;&nbsp;<html><body><img src="http://openwetware.org/images/4/41/After_first_deposition.jpg" border=0 width=240 height=180></body></html>
|<html><body><img src="http://openwetware.org/images/4/41/After_first_deposition.jpg" border=0 width=240 height=180></body></html>
|&nbsp;&nbsp;<html><body><img src="http://openwetware.org/images/3/30/After_second_deposition.jpg" border=0 width=240 height=180></body></html>
|<html><body><img src="http://openwetware.org/images/3/30/After_second_deposition.jpg" border=0 width=240 height=180></body></html>
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|colspan="4"|'''Fig. 0.1''' Selective coating of micro-beads by vapor deposition.
|colspan="4"|&nbsp;&nbsp;&nbsp;&nbsp;Fig. 0.1 Selective coating of micro-beads by vapor deposition.
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==0.2. Design of linker DNA strands==
==0.2. Design of linker DNA strands==
:&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We designed linker DNA strands that can stably hybridize.</font></body></html>
:<html><body><font size="5">We designed DNA sequences for the linkers to attach catalytic engines to the microbead body.</font></body></html>
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/DNA_Design|methods]]
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/DNA_Design|methods]]
{|style="margin-left:35px" width="920px"
{|style="margin-left:35px" width="920px"
|&nbsp;&nbsp;&nbsp;&nbsp;We designed 2 types of DNA duplex that can hybridize stably by NUPACK. We called the longer one as DNA sequence L, and the shorter one as DNA sequence S. We called their complementary strands as DNA sequence L<sup>*</sup> and DNA sequence S<sup>*</sup>.
|&nbsp;&nbsp;&nbsp;&nbsp;We designed two kinds of DNA sequences with different stability. One is DNA sequence L. This sequence forms a very stable duplex with its complementary sequence L<sup>*</sup> at a room temperature. Another is DNA sequence S. The duplex of DNA sequence S and S<sup>*</sup> has less stability than DNA sequence L and L<sup>*</sup> but is stable at a room temperature.
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|
{|width="460px" border="1"
{|width="475px" border="1"
|'''DNA sequence L <br>
|&nbsp;&nbsp;'''DNA sequence L <br>
5’-CGTCTATTGCTTGTCACTTCCCC-3'
&nbsp;&nbsp;<html><body><nobr>5’-CGTCTATTGCTTGTCACTTCCCC-3'&nbsp;&nbsp;</nobr></body></html>
|'''DNA sequence S<br>
|&nbsp;&nbsp;'''DNA sequence S<br>
5’-AATACCCAGCC-3’
&nbsp;&nbsp;<html><body><nobr>5’-AATACCCAGCC-3’&nbsp;&nbsp;</nobr></body></html>
|-
|-
|'''DNA sequence  L<sup>*</sup><br>
|&nbsp;&nbsp;'''DNA sequence  L<sup>*</sup><br>
5'-GGGGAAGTGACAAGCAATAGACG-3'
&nbsp;&nbsp;<html><body><nobr>5'-GGGGAAGTGACAAGCAATAGACG-3'&nbsp;&nbsp;</nobr></body></html>
|'''DNA sequence S<sup>*</sup> <br>
|&nbsp;&nbsp;'''DNA sequence S<sup>*</sup> <br>
5’-GGCTGGGTATT-3’
&nbsp;&nbsp;<html><body><nobr>5’-GGCTGGGTATT-3'&nbsp;&nbsp;</nobr></body></html>
|}
|}
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:In both Figure 0.2a and 0.2b, ''T''<sub>m</sub> is far from ''R''<sub>t</sub>. So, we achieved DNA design that can hybridize stably.
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 0.2a and 0.2b show calculated melting profiles of duplexes L-L<sup>*</sup> and S-S<sup>*</sup>, respectively. Calculated melting temperatures of these duplexes were higher than  a room temperature.
{|style="margin-left:35px" border="1"
{|style="margin-left:35px" border="1"
|&nbsp;&nbsp;'''a'''<br>[[Image:SeqA&seqAc2_melt.png|DNA Tm|450px]]
|&nbsp;&nbsp;'''a'''<br>[[Image:SeqA&seqAc2_melt.png|DNA Tm|450px]]
|&nbsp;&nbsp;'''b'''<br>[[Image:SeqB&seqBc_melt.png|Photoresponsive DNA Tm|450px]]
|&nbsp;&nbsp;'''b'''<br>[[Image:SeqB&seqBc_melt.png|Photoresponsive DNA Tm|450px]]
|-
|-
|colspan="2"|'''Fig. 0.2''' Analysis of melting temperature of hybridization with each DNA strands.
|style="padding:10px" colspan="2" |Fig. 0.2. (a) The melting profile of duplex L-L<sup>*</sup>. (b) The melting profile of duplex S-S<sup>*</sup>. RT and ''T''<sub>m</sub> indicate a room temperature (24°C) and a melting temperature, respectively. We calculated the melting profiles using NUPACK software.
'''a'''&nbsp;&nbsp;Melting profile of DNA sequence L and L<sup>*</sup> duplex&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''b'''&nbsp;&nbsp;Melting profile of DNA sequence S and S<sup>*</sup> duplex<br>
Red line shows ''T''<sub>m</sub> (melting temperature), and Blue line shows ''R''<sub>t</sub> (Room temperature, 24 °C).
|}
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==0.3. DNA conjugation==
==0.3. Selective DNA conjugation to the microbead body of Biomolecular Rocket==
===0.3.1. Selective conjugation of DNA to polystyrene surface area===
===0.3.1. Selective conjugation of DNA to polystyrene surface area===
:<hr>
:<hr>
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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>
|&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We succeeded in DNA conjugation to polystyrene surface area by using EDAC.</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;For visualizing the results of DNA conjugation to polystyrene surface area, we hybridized fluorescent complementary DNA and observed them under blue light by microscope.
&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 images of 10 μm selective coated beads under visible light. Figure 0.3.1a', b', and c' are images of 10 μm selective coated beads under blue light. Figure 0.3.1a anda' shows selective coated beads after conjugated DNA to polystyrene area and hybridize fluorescent cDNA. Figure 0.3.1b and b' shows selective coated beads after conjugated DNA to polystyrene area. Figure 0.3.1c and c' shows selective coated beads after mixing fluorescent DNA. Selective coated beads exhibit fluorescence because fluorescent cDNA was excited by blue light. From these results, we conclude that selective conjugation of DNA to polystyrene surface area.
:&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"
:{| border="1"
|Under<br>visible<br>light
|&nbsp;&nbsp;<html><body><nobr>Bright-field microscope images</nobr></body></html>&nbsp;&nbsp;
|'''a'''[[Image:BIOMOD-TNJ-CrAu_1_2.jpg|DNA conjugated beads and FAM|280px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:BIOMOD-TNJ-CrAu_1_2.jpg|DNA conjugated beads and FAM|220px]]
|'''b'''[[Image:BIOMOD-TNJ-CrAu_2.jpg|DNA conjugated beads|280px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''b'''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:BIOMOD-TNJ-CrAu_2.jpg|DNA conjugated beads|220px]]
|'''c'''[[Image:BIOMOD-TNJ-CrAu_3.jpg|Beads and FAM|280px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''c'''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:BIOMOD-TNJ-CrAu_3.jpg|Beads and FAM|220px]]
|-
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|Under blue light
|&nbsp;&nbsp;<html><body><nobr>Fluorescence microscope images</nobr></body></html>&nbsp;&nbsp;
|'''a''''[[Image:BIOMOD-TNJ-CrAu_1_2_2s.jpg|DNA conjugated beads and FAM|280px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''a''''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:BIOMOD-TNJ-CrAu_1_2_2s.jpg|DNA conjugated beads and FAM|220px]]
|'''b''''[[Image:BIOMOD-TNJ-CrAu_2_2s.jpg|DNA conjugated beads|280px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''b''''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:BIOMOD-TNJ-CrAu_2_2s.jpg|DNA conjugated beads|220px]]
|'''c''''[[Image:BIOMOD-TNJ-CrAu_3_2s.jpg|Beads and FAM|280px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''c''''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:BIOMOD-TNJ-CrAu_3_2s.jpg|Beads and FAM|220px]]
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|conditions
|&nbsp;&nbsp;<html><body><nobr>Experimental conditions<nobr></body></html>&nbsp;&nbsp;
|<html><body><img src="http://openwetware.org/images/d/d3/EDACBEADS1.JPG" border=0 width=280 height=150></a></body></html>
|<html><body><img src="http://openwetware.org/images/d/d3/EDACBEADS1.JPG" border=0 width=220 height=120></a></body></html>
|<html><body><img src="http://openwetware.org/images/3/38/EDACBEADS2.JPG" border=0 width=280 height=150></a></body></html>
|<html><body><img src="http://openwetware.org/images/3/38/EDACBEADS2.JPG" border=0 width=220 height=120></a></body></html>
|<html><body><img src="http://openwetware.org/images/2/23/EDACBEADS3.JPG" border=0 width=280 height=150></a></body></html>
|<html><body><img src="http://openwetware.org/images/2/23/EDACBEADS3.JPG" border=0 width=220 height=120></a></body></html>
|-
|-
|colspan="4"|'''Fig. 0.3.1''' &nbsp;&nbsp;Images of DNA conjugation to polystyrene surface area by fluorescence complementary DNA strand.<br>
|style="padding:10px" colspan="4"|Fig. 0.3.1 Microscope images of the microbead bodies of Biomolecular Rocket. (a) and (a') Selectively DNA-conjugated microbeads with complementary fluorophore-modified DNA. (b) and (b') Selectively DNA-conjugated microbeads without complementary fluorophore-modified DNA. (c) and (c') non-DNA-conjugated microbeads with complementary fluorophore-modified DNA.
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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>
|&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We succeeded in DNA conjugation onto Au surface area by the reaction of SAM.</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;For visualizing the results of DNA conjugation to metal surface area, we hybridized linker DNA to Au plate surface.
&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;Figure 0.3.2a is a images of Au plate that linker DNA conjugated partially. Figure 0.3.2b is a images after soaking up DNA buffer of Au plate. Figure 0.3.2a is a images after washing away of partially DNA conjugated Au plate. Final concentration of phosphate and NaCl buffer are the same in these spot. But 1, 2 and 3 are added NaCl concentration immediately after 24 hours of incubation, the other hand 4, 5, and 6 are added NaCl as salt aging process. Au plate reveals partially hydrophilic, this is because physical property of Au surface was assimilated to physical property of DNA. From these result, we conclude that selective conjugation of DNA to metal surface area.
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 0.3.2a shows the Au glass plate with a non-DNA spot (1), a non-thiol-modified DNA spot (2), and a thiol-modified DNA spot (3). Only at the spot (3), residual water was observed. The water remained by the wetting property of the spot (3); the higher wetting property of spot (3) than those of spots (1) and (2) was expected to be caused by the Au surface with thiol-modified DNA conjugation. Therefore, we conclude that selective conjugation of thiol-modified DNA to the Au surface area of the microbead body was also achieved.
{|style="margin-left:35px" border="1"
{|style="margin-left:80px" width="800px" border="1"
|&nbsp;&nbsp;'''a'''[[Image:金板１.jpg|After incubation for 24h|300px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:金板３.jpg|Au plate|400px]]
|&nbsp;&nbsp;'''b'''[[Image:金板２.jpg|After sucking out|300px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''b'''&nbsp;&nbsp;&nbsp;&nbsp;<br>[[Image:%E8%A7%A3%E8%AA%AC.jpg|condition|400px]]
|&nbsp;&nbsp;'''c'''[[Image:金板３.jpg|After washing|300px]]
|-
|-
|&nbsp;&nbsp;'''d'''<html><body><img src="http://openwetware.org/images/1/1a/Auplate1.jpg" border=0 width=300 height=160></a></body></html>
|colspan="2"|&nbsp;&nbsp;&nbsp;&nbsp;'''c'''<br><html><body><img src="http://openwetware.org/images/1/1a/Auplate1.jpg" border=0 width=800 height=150></a></body></html>
|&nbsp;&nbsp;'''e'''<html><body><img src="http://openwetware.org/images/1/12/Auplate2.jpg" border=0 width=300 height=160></a></body></html>
|&nbsp;&nbsp;'''f'''<html><body><img src="http://openwetware.org/images/f/fd/Auplate3.jpg" border=0 width=300 height=160></a></body></html>
|-
|-
|&nbsp;&nbsp;'''g'''[[Image:%E8%A7%A3%E8%AA%AC.jpg|condition|300px]]
|style="padding:10px" colspan="2"|Fig. 0.3.2. (a) An Au glass plate with a non-DNA spot (1), a non-thiol-modified DNA spot (2), and a thiol-modified DNA spot (3). <br>(b) A layout drawing of the spots (1)-(3). <br>(c) Experimental condition for the spots (1)-(3).
|colspan="2"|&nbsp;&nbsp;&nbsp;&nbsp;'''Fig. 0.3.2'''&nbsp;&nbsp;&nbsp;&nbsp;Confirmation of DNA conjugation to metal area <br>
&nbsp;&nbsp;&nbsp;&nbsp;'''a'''&nbsp;&nbsp;Incubated for 48 hours at a gold plate<br>
&nbsp;&nbsp;&nbsp;&nbsp;'''b'''&nbsp;&nbsp;Soaked up the water after incubation<br>
&nbsp;&nbsp;&nbsp;&nbsp;'''c'''&nbsp;&nbsp;Washed away gold plate surface by 3 × SSC  after soaking up the water<br>
&nbsp;&nbsp;&nbsp;&nbsp;'''d'''&nbsp;&nbsp;Image of spot 1, 4<br>
&nbsp;&nbsp;&nbsp;&nbsp;'''e'''&nbsp;&nbsp;Image of spot 2, 5<br>
&nbsp;&nbsp;&nbsp;&nbsp;'''f'''&nbsp;&nbsp;Image of spot 3, 6<br>
&nbsp;&nbsp;&nbsp;&nbsp;'''g'''&nbsp;&nbsp;Condition of gold plate
|}
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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">We tried to attach catalyst to the body of Biomolecular Rocket with DNA hybridization.</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>
&nbsp;&nbsp;&nbsp;&nbsp;DNA hybridization enable us to attach each materials in that DNA strand transits to take  thermodynamically stable forms.
>>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;To verificate this experiments, we tried to attach Pt particles to Au plate (instead of Au deposited beads) , but there is a few difference between DNA conjugated materials and natural materials. So, We must prove the technology of attaching catalyst. DNA strands are nano-scale, and to conjugate micro-scale beads and platinum engines was difficult.
:&nbsp;&nbsp;&nbsp;&nbsp;We also design DNA strands of DNA sequence L  and DNA sequence S that have the first 15 bases from 5' end as a linker (TTTTTTTTTTTTTTT). This DNA was also designed not to make unexpected structures. Probably, this linker part will allow much leeway for attaching the body, in that decrease the effect of steric hindrance.
:{|border="1"
|Poly T linked DNA sequence L
|5’-TTTTTTTTTTTTTTTCGTCTATTGCTTGTCACTTCCCC-3'
|-
|Poly T linked DNA sequence S
|5’-TTTTTTTTTTTTTTTAATACCCAGCC-3’
|}
|}
:&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.
<br><br>
<br><br>
<div align = "right" style="padding-right:20px">[[#TOP|↑Page Top]]</div>
<hr>
<hr>


=<font color="red">1. Power supply for the rail-free movement</font>=
=<html><body><font color="red">1. Power supply for the rail-free movement of the Biomolecular Rocket</font></body></html>=
:<html><body><font size="5">We achieved the power supply for the rail-free movement of the Biomolecular Rocket.</font></body></html>
{|style="margin-left:35px"
{|style="margin-left:35px"
|
|&nbsp;&nbsp;&nbsp;&nbsp;We utilized H<sub>2</sub>O<sub>2</sub> for fuel and catalysts of H<sub>2</sub>O<sub>2</sub> for catalytic engines to realize the rail-free movement of the Biomolecular Rocket. Catalysts such as platinum and catalase catalyze the decomposition of H<sub>2</sub>O<sub>2</sub> into H<sub>2</sub>O and O<sub>2</sub>; emitted bubbles of O<sub>2</sub> launch Biomolecular Rocket.
&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We achieved the power supply for the rail-free movement.</font></body></html><br><br>
&nbsp;&nbsp;&nbsp;&nbsp;Here, we investigated the following points to realize the power supply for the rail-free movement of the Biomolecular Rocket.<br>
&nbsp;&nbsp;&nbsp;&nbsp;Biomolecular Rocket can move  straightforward by emitting bubbles. Platinum and catalase catalysts decompose H<sub>2</sub>O<sub>2</sub> and emit H<sub>2</sub>O and O<sub>2</sub> bubbles. When the O<sub>2</sub> bubble is emitted from the surface of Biomolecular Rocket, the momentum changes induces a driving force to put the bubble away from the surface, and rail-free movement is accomplished. <br>
&nbsp;&nbsp;&nbsp;&nbsp;We achieved Power supply for the rail-free movement through the following parts.  
{|border="3" width="690px"
{|border="3" width="690px"
|<html><body><ol>
<li>We found that catalase molecules as catalytic engines could emit sufficient amount of bubbles for the rail-free movement.
<li>We found that platinum particles as a catalytic engines could emit sufficient amount of bubbles for rail-free movement.
<li>We found that the H<sub>2</sub>O<sub>2</sub> did not affect the stability of DNA linkers for attaching catalytic engines to the body in the H<sub>2</sub>O<sub>2</sub> solution.
</ol></body></html>
|}
|<html><body><td align="center"><img src="http://openwetware.org/images/b/b3/WikiRFBM.jpg" border=0 width=240 height=240></a></td></body></html>
|}
==1.1. Power supply for rail-free movement by using catalase catalytic engine==
:<html><body><font size="5">We succeeded in the rail-free movement by O<sub>2</sub> bubble emission with catalase.</font></body></html>'''<br>
:&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>
:&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"
|
|
1. DNA hybridization is not affected damage and denaturate that comes from H<sub>2</sub>O<sub>2</sub><br>
{|width="320px" border="1"
2. Platinum catalyst can supply efficient energy for rail-free movement<br>
|<html><body><img src="http://openwetware.org/images/1/1b/Crf.jpg" border=0 width=420 height=315></body></html>
3. Catalase catalyst can supply efficient energy for rail-free movement
|-
|style="padding:10px"|Fig. 1.1&nbsp;&nbsp;Image of a microbead with a hemispherical Au surface and a hemispherical polystyrene surface in 3% H<sub>2</sub>O<sub>2</sub> solution.
|}
|}
|<html><body><td align="center"><img src="http://openwetware.org/images/b/b3/WikiRFBM.jpg" border=0 width=240 height=240></a></td></body></html>
|
|}<div align = "right" style="padding-right:20px">[[#TOP|↑Page Top]]</div>
{|border="1" width="420px"
<br><br>
|<HTML><iframe width="420" height="315" src="http://www.youtube.com/embed/Ie2dUHcwZN0" frameborder="0" allowfullscreen></iframe></HTML>
==1.1. DNA hybridization in solution of H<sub>2</sub>O<sub>2</sub>==
:&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We succeeded in DNA hybridization in 1%-5% H<sub>2</sub>O<sub>2</sub> solution stably.</font></body></html><br>
:&nbsp;&nbsp;&nbsp;To visualize the stability of DNA duplex in 1%-5% H<sub>2</sub>O<sub>2</sub> solution, we use PAGE electrophoresis. It shows the difference of molecular weight of nucleic acid that comes from denaturetion or hybridization in the form of bands.<br>
:&nbsp;&nbsp;&nbsp;>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/DNA_hybridization|methods]]<br><br>
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 1.1 is a image of DNA hybridization after immersing in solution of H<sub>2</sub>O<sub>2</sub>. Lane 1, 2, 3, and 8 shows dsDNA, that is hybridized after immersing in solution of 0%-5% H<sub>2</sub>O<sub>2</sub> for 90 minutes. Lane 4, 5, 6, and 7 shows ssDNA, after immersing in solution of 0%-5% H<sub>2</sub>O<sub>2</sub> for 90 minutes. Influence of H<sub>2</sub>O<sub>2</sub> solution within 90 minutes was few for DNA hybridizing, because the line of dsDNA appear in the same positions. Also influence of H<sub>2</sub>O<sub>2</sub> solution within 90 minutes was few for ssDNA in that the line of ssDNA appear in the same positions. From this results, we achieved DNA hybridization in solution of H<sub>2</sub>O<sub>2</sub>.
:{|style="margin-left:100px" width="700px" border="1"
|[[Image:BIOMODTNJEPR 04.JPG|Electrophoresis|700px]]
|-
|-
|'''Fig. 1.1'''&nbsp;&nbsp;&nbsp; Results of DNA hybridization after immersing in solution of H<sub>2</sub>O<sub>2</sub><br>
|style="padding:10px"|Movie. 1.1&nbsp;&nbsp;&nbsp;The real-time video of the moving 10 μm bead with a catalase-conjugated hemisphere area in 3% H<sub>2</sub>O<sub>2</sub> solution.  
&nbsp;&nbsp;&nbsp;&nbsp;dsDNA bands show in lane 1, 2, 3 & 8. In lane 4, 5, 6 & 7 show ssDNA bands. Lane 1 & 8 are the same, lane 2 & 3 are immersed in  H<sub>2</sub>O<sub>2</sub> solution (1% and 5%) for 90 minutes. In lane 5 & 7 show the results of ssDNA in solution of H<sub>2</sub>O<sub>2</sub>. In lane 4 & 6 are the control bands of ssDNA.
|}
|}
==1.2. Power supply for rail-free movement by using catalase catalytic engine==
{|
|<html><body><td><img src="http://openwetware.org/images/1/1b/Crf.jpg" border=0 width=240 height=180></a></td></body></html>
|&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We scceeded in rail-free movement by taking advantage of catalase catalytic ability.</font></body></html>'''<br>
Catalase has Catalytic ability of decomposing H<sub>2</sub>O<sub>2</sub>, like platinum. We conjugated catalase to the polystyrene hemisperical area, so this catalase hemispherical bead moves by emission of O<sub>2</sub> bubbles without rails.<br>
&nbsp;&nbsp;&nbsp;&nbsp;>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Varification_catalase|methods]]
|}
|}
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 1.2 reveals the movement of 10 μm catalase hemisphere movement in solution of 3% H<sub>2</sub>O<sub>2</sub>. We can easily distinguish catalase conjugated bead or natural bead in that their movement in solution of 3% H<sub>2</sub>O<sub>2</sub> is very different. Natural beads didn't move at all, on the other hand catalase hemisphere emitted bubbles and moved quickly. From this results, we conclude that power supply for rail-free movement by using catalase catalytic engine.


==1.3. Power supply for rail-free movement by using platinum catalytic engine==
==1.2. Power supply for rail-free movement by using platinum catalytic engine==
:{|
:<html><body><font size="5">We achieved bubble emissions with platinum micro-particles in solution of H<sub>2</sub>O<sub>2</sub>.</font></body></html><br>
:&nbsp;&nbsp;&nbsp;&nbsp;We provided 1 μm platinum particles, and Cr coating to create platinum hemispherical area. Then added 3% H<sub>2</sub>O<sub>2</sub> solution and observed their movement.
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Varification_platinum|methods]]<br><br>
:&nbsp;&nbsp;&nbsp;&nbsp;Movie 1.2 reveals the catalytic reaction of 3% H<sub>2</sub>O<sub>2</sub> and 1 μm beads that have platinum hemispherical area. We can recognize that bubbles are emitted in H<sub>2</sub>O<sub>2</sub> solution. These bubbles are emitted from 1 μm beads that have platinum hemispherical area by decomposing H<sub>2</sub>O<sub>2</sub>. From this result, we conclude that power supply for rail-free movement by using platinum catalytic engine was achieved.
{|style="margin-left:35px"
|
{|width="420px" border="1"
|<html><body><img src="http://openwetware.org/images/8/89/Simple_beads.jpg" border=0 width=420 height=315></a></body></html>
|-
|-
|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/8/89/Simple_beads.jpg" border=0 width=240 height=180></a></td></body></html>
|style="padding:10px"|Fig. 1.2 Image of a microbead with a hemispherical Cr surface and a hemispherical platinum surface in 3% H<sub>2</sub>O<sub>2</sub> solution.
|}
|
|
&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We tried to verify whether platinum hemisphere moves forward in solution of H<sub>2</sub>O<sub>2</sub>.</font></body></html><br>
{|border="1" width="420"
&nbsp;&nbsp;&nbsp;&nbsp;We provide 1 μm platinum particles, and Cr coating to create platinum hemisphere. Then added 3% H<sub>2</sub>O<sub>2</sub> solution and observed their movement.
|
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Varification_platinum|methods]]
<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.
|}
|}
|}
<br><br>
 
==1.3. DNA hybridization in solution of H<sub>2</sub>O<sub>2</sub>==
:<html><body><font size="5">We revealed that diluted H<sub>2</sub>O<sub>2</sub> solutions did not affect DNA hybridization and a H<sub>2</sub>O<sub>2</sub> solution was suitable for a fuel for the Biomolecular Rocket. </font></body></html><br>
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/DNA_hybridization|methods]]<br><br>
:&nbsp;&nbsp;&nbsp;We confirmed that DNA duplexes were stably formed in diluted H<sub>2</sub>O<sub>2</sub> solutions by the native polyacrylamide gel electrophoresis (PAGE). Figure 1.3 shows the gel image of the PAGE. As shown in the lanes 1-3, a double-stranded DNA was formed in 1% and 5% H<sub>2</sub>O<sub>2</sub> solutions.
:{|style="margin-left:100px" width="700px" border="1"
|[[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 upper right of the image.
|}
<br><br><div align = "right" style="padding-right:20px">[[#TOP|↑Page Top]]</div>
<hr>
<hr>


=<font color="blue">2. Increasing driving force for the high-speed movement</font>=
=<font color="blue">2. Realization of the high-speed movement of the Biomolecular Rocket</font>=
:<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, 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.
&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">Biomolecular Rocket achieved high-speed movement by increasing catalytic surface area.</font></body></html><br>
&nbsp;&nbsp;&nbsp;&nbsp;Catalytic engine produced sufficient energy to move quickly, but further accelerate the Biomolecular Rocket, we conjugated numerous platinum catalytic engines to a micro-sized rocket body. Emission of bubbles depends on the surface area of catalyst, so if the catalytic surface area is expanded, it is obvious that our rocket will be able to emit more bubbles and speeding up.<br>
&nbsp;&nbsp;&nbsp;&nbsp;Increasing driving force for the high-speed movement, we attained through the following parts.
{|border="3" width="630px"
{|border="3" width="630px"
|
|<html><body><ol>
1. Analyses of the speed of platinum to get data of the relationship between<br>
<li>Observations of the movement of platinum particles using a high-speed camera and analyses of the speed
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;bubble conditions and platinum behavior<br>
<li>Numerical simulations of the movement of the Biomolecular Rocket</ol></body></html>
2. Compare the speed of kinesin, platinum hemisphere and Biomolecular Rocket to<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dictate which is the fastest one.
|}
|}


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<html><body><img src="http://openwetware.org/images/2/26/Hst.jpg" width=300 height=230></body></html>
<html><body><img src="http://openwetware.org/images/2/26/Hst.jpg" width=300 height=230></body></html>
|}
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<div align = "right" style="padding-right:20px">[[#TOP|↑Page Top]]</div>
==2.1. Power supply for the high-speed movement with platinum catalytic engines==
:<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>
:&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. 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.'''''


==2.1. Analyses of the speed of platinum in solution of H<sub>2</sub>O<sub>2</sub> by High-speed camera==
:&nbsp;&nbsp;&nbsp;&nbsp;'''We succeeded in analyses of the speed of plutinum in solution of H<sub>2</sub>O<sub>2</sub> by High-speed camera.'''
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/High-speed_camera|methods]]
:{|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/E1rtI0mS5Zs" 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>
|-
|-
|colspan="2"|'''Fig. 2.1'''&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
|}
{|style="margin-left:200px" width="500px" border="1"
|[[Image:Calculation speed.jpg|500px|]]
|-
|&nbsp;&nbsp;Fig. 2.1.2 The mean square displacement of a platinum particle.
|}
 
==2.2. Numerical estimation of the speed of the Biomolecular Rocket==
:<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]]
:&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"
|[[Image:Hi_speed.png|Simulation of high-speed|700px]]
|-
|style="padding:10px"|Fig. 2.2 &nbsp;&nbsp;&nbsp;Image of each molecular motor’s instantaneous speed with time
|}
|}
:&nbsp;&nbsp;&nbsp;&nbsp;Figure 2.1b disclosed the values of ''Acceleration'', ''Velocity'', ''Coordinate x'', and ''Coordinate y'' of platinum movement. Not only that, by observation of these values, we could determine relationships between bubble radius growth and the speed of platinum, so we were able to simulate of movement of our rocket.


==2-2.Simulation for speeding-up of Biomolecular Rocket movement==
:&nbsp;&nbsp;&nbsp;&nbsp;'''From our numerical simurations of high-speed.We carried out numerical simulations of the high-speed movement of Biomolecular Rockets.
::<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/f/f0/Simulation_speed.jpg" border=0 width=240 height=180></a></td></body></html>
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=<font color="orange">3. Introduction of a photo-switchable DNA system for the directional control</font>=
=<font color="orange">3. Introduction of a photo-switchable DNA system for the directional control</font>=
:<html><body><font size="5">We developed a photo-switchable DNA system for the directional control with a photoresponsive DNA.</font></body></html><br>
{|style="margin-left:35px"
{|style="margin-left:35px"
|
|
&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We realized a photo-switchable DNA system for directional control by photoresponsive DNA.</font></body></html><br>
&nbsp;&nbsp;&nbsp;&nbsp;The photo-switchable DNA system consists of an azobenzene-based photoresponsive DNA. The structure of the photoresponsive DNA is changed by UV light irradiation, then the photoresponsive DNA duplex is dissociated into DNA single strands. By the dissociation of DNA, catalytic engines are dissociated from the body of Biomolecular Rocket. As a result, the directional change of the force generated by O<sub>2</sub> bubble is caused, and the direction of the Biomolecular Rocket is changed. Here, we developed and investigated the photo-switchable DNA system by the following experiments and simulations.
&nbsp;&nbsp;&nbsp;&nbsp;Photoresponsive DNA structure is changed by UV light irradiation, then dissociation of double strand DNA will happen. Take advantage of this reaction in region-specific manner, we can control the direction of our rocket.
{|width="620px" border="3"
&nbsp;&nbsp;&nbsp;&nbsp;In order to realize Directional control of our rocket, we conducted the following parts.
|<html><body><ol>
{|width="600px" border="3"
<li>Design of a photo-switchable DNA system for the directional control
|
<li>Investigation of the dissociation rate of the photo-switchable DNA duplex by UV light irradiation experiments
1. Introduction of a photo-switchable DNA system for the directional control<br>
<li>Investigation of the directional control of Biomolecular Rocket with the photo-switchable DNA system by numerical simulations
2. Research the relationship between the strength of UV light and the time<br>
</ol></body></html>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;of dissociation to determine the valid time<br>
3. Verification of the relationship between the movement of Biomolcular <br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Rocket and dissociation of catalyst engines
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==3.1. Design of photoresponsive DNA==
==3.1. Design of photoresponsive DNA==
:{|
:{|
|-
|-
|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/4/45/Photo_design.jpg" border=0 width=210 height=210></a></td></body></html>
|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/4/45/Photo_design.jpg" border=0 width=210 height=210></a></td></body></html>
|&nbsp;&nbsp;&nbsp;&nbsp;<html><body><font size="5">We designed photoresponsive DNA strands in order to control the direction 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>
&nbsp;&nbsp;&nbsp;&nbsp;In this project, we ensured that photoresponsive DNA could hybridize their cDNA by Abs. Numerical values of Abs depends on the concentration of material corresponding to the absorption wavelength. <br>
>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Design_of_photoresponsive_DNA|methods]]<br><br>
&nbsp;&nbsp;&nbsp;&nbsp;>>see more [[Biomod/2012/Titech/Nano-Jugglers/Methods/Design_of_photoresponsive_DNA|methods]]
&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 called DNA as A:Photoresponsive DNA sequence S, and B:Photoresponsive DNA sequence S<sup>*</sup>. Figure 3.1 reveals that Abs of A+B around 260nm was below those of A and B, and also Abs of A+B around 330 nm was less than that of A. This is because the concentration of azobenzene decreased by hybridization of A with B.<br>
{|style="margin-left:200px" width="500px" border = "1"
:&nbsp;&nbsp;&nbsp;&nbsp;Calculation an average absorbance of A and B Abs around 260 nm, theorical value of A+B was 0.168. Compared to this, measured value of absorbance is 22.6% lower. We thought this difference comes from that DNA formed duplex and interactions between base pairs, so decrease the UV absorbance relative to single strands.
|
:&nbsp;&nbsp;&nbsp;&nbsp;In this point, we believe that the complementary photo-responsive DNAs can form duplex. So, we concluded that these results mean A and B hybridized successfully.
[[Image:TNJ-figure3-azobenzene.png|Spectrum analysis|500px]]
{|style="margin-left:35px" border = "1"
|'''a'''<br>
&nbsp;&nbsp;&nbsp;&nbsp;[[Image:TNJ-figure3-azobenzene.png|Spectrum analysis|400px]]
|'''b'''<br>
&nbsp;&nbsp;&nbsp;&nbsp;[[Image:TNJ-figure2-azobenzene.png|aroundWave length around 260 nm|400px]]
|-
|-
|colspan="2"|'''Fig.3.1'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Abs of photoresponsive DNA results, wave length around 260 nm reveals the concentration of DNA. Around 330 nm reveals the concentration of trans-formed azobenzene.  
|style="padding:10px"|Fig.3.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Absorbance spectra of DNA strands (A) photoresponsive DNA sequence S*, (B) DNA sequence S, and (A+B) the duplex of them at a room temperature.
|}
|}


==3.2. Dissociation of photoresponsive DNA by UV-light irradiation==
==3.2. Achievement of the photo-switchable DNA system==
:{|
:{|
|-
|-
|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/f/f3/Azobenzene_image_dissociation.jpg" border=0 width=240 height=180></a></td></body></html>
|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/f/f3/Azobenzene_image_dissociation.jpg" border=0 width=240 height=180></a></td></body></html>
|
|
&nbsp;&nbsp;&nbsp;&nbsp;'''We have scceeded in dissociation of photo-switchable DNA by UV-light irradiation'''.<br><br>
<html><body><font size="5">We have succeeded in development of a photo-switchable DNA system.</font></body></html><br>
&nbsp;&nbsp;&nbsp;&nbsp;Photo-switchable DNA duplex can easily dissociate its duplex by irradiating UV-light. We put this switching system in the rocket in order to control our rocket. To concirm the dissociation of photo-switchable DNA duplex, we checked Abs.
>>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]]
&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 time of dissociation to determine the valid time, we examine 2 type 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;Fig.3-2.1 represents spctrum of Abs in condition of UV-light(30 mW/cm<sup><small>2</small></sup>) irradiation. Abs of A+B around 260 nm was increasing gradually from 0 minutes to 5 minutes. This result means dsDNA was completely dissociated after irradiating UV-light for 5 minutes. Moreover, Abs of A+B around 330 nm was decreasing from 0 minutes to 5 minutes. This means trans-formed azobenzene changed its form to cis-formation. Therefore, we achieved photoresponsive DNA which was designed by us would be dissociated by irradiating UV-light for 5 minutes.
:&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" border = "1"
{|style="margin-left:35px" width="800px" border = "1"
|'''a'''<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Image:Azo figure3.jpg|Spectrum analysis|400px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''<br>[[Image:Azo figure3.jpg|Spectrum analysis|400px]]
|'''b'''<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Image:TNJ-figure4-azobenzene.png|Wave length around 260 nm and 330 nm|400px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''b'''<br>[[Image:TNJ-figure4-azobenzene.png|Wave length around 260 nm and 330 nm|400px]]
|-
|-
|colspan="2"|'''Fig.3.2.1'''&nbsp;&nbsp;&nbsp;&nbsp;Spectrum analysis of photoresponsive DNA duplex(A+B) in condition of UV-light(30 mW/cm<sup><small>2</small></sup>) irradiation
|style="padding:10px" colspan="2"|Fig. 3.2.1. (a)&nbsp;&nbsp;&nbsp;&nbsp;Absorbance spectra of photoresponsive DNA duplex (A+B) in condition of UV light irradiation (30 mW/cm<sup><small>2</small></sup>). (b) Time course of the absorbance change during UV light irradiation.
|}
|}
:&nbsp;&nbsp;&nbsp;Then, we tested the dissociation of photoresponsive DNA under the condition of different strength of UV-light(180 mW/cm<sup><small>2</small></sup>).
<br>
:nbsp;&nbsp;&nbsp;&nbsp;Fig.3-2.2 shows photoresponsive dsDNA was dissociated completely after the irradiation of UV-light for 50 seconds. There are three evidences.<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;First, from Fig.b), we could find that dsDNA was dissociated gradually from 0 seconds to 50 seconds because maximum Abs around 260 nm was increasing. Second, Fig.c) shows that trans-formed azobenzene decreased because Abs around 330 nm was decreasing from irradiation for 0 seconds to 50 seconds. Finally, Fig.d) shows cis-formed azobenzene increased. As we did experiences for many times, we noticed that there was maximum wave length around 480 nm. By researching, we reached the fact that Abs around 480 nm shows the existence of cis-formed azobenzene. So, we can say that cis-formed azobenzene increased because Abs around 480 nm was increasing from irradiation for 0 seconds to 50 seconds.
{|style="margin-left:35px" width="800px" border = "1"
:&nbsp;&nbsp;&nbsp;&nbsp;'''So, we concluded that photo-seichable DNA system achieved after 50 seconds irradiation of UV-light(180 mW/cm<sup><small>2</small></sup>).'''
|&nbsp;&nbsp;&nbsp;&nbsp;'''a'''<br>[[Image:TNJ-figure5-azobenzene.png|Spectrum analysis|400px]]
{|style="margin-left:35px" border = "1"
|&nbsp;&nbsp;&nbsp;&nbsp;'''b'''<br>[[Image:TNJ-figure6-azobenzene.png|Wave lengte around 260 nm|400px]]
|'''a'''<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Image:TNJ-figure5-azobenzene.png|Spectrum analysis|400px]]
|'''b'''<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Image:TNJ-figure6-azobenzene.png|Wave lengte around 260 nm|400px]]
|-
|-
|'''c'''<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Image:TNJ-figure8-azobemzene.png|Wave lengte around 330 nm|400px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''c'''<br>[[Image:TNJ-figure8-azobemzene.png|Wave lengte around 330 nm|400px]]
|'''d'''<br>&nbsp;&nbsp;&nbsp;&nbsp;[[Image:TNJ-figure7-azobenzene.png|Wave lengte around 480 nm|400px]]
|&nbsp;&nbsp;&nbsp;&nbsp;'''d'''<br>[[Image:TNJ-figure7-azobenzene.png|Wave lengte around 480 nm|400px]]
|-
|-
|colspan="2"|'''Fig.3.2.2'''&nbsp;&nbsp;&nbsp;&nbsp;Spectrum analysis of photoresponsive DNA duplex(A+B) in condition of UV-light(180 mW/cm<sup><small>2</small></sup>) irradiation
|style="padding:10px" colspan="2"|Fig. 3.2.2&nbsp;&nbsp;&nbsp;&nbsp;Spectrum analysis of photoresponsive DNA duplex(A+B) in condition of UV-light(180 mW/cm<sup><small>2</small></sup>) irradiation
|}
|}


==3-3.Simulation for directional control of Biomolecular Rocket==
==3.3. Directional control of the Biomolecular Rocket by the photo-switchable DNA system==
::sss
:&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>
<div align = "right" style="padding-right:200px">[[#TOP|↑Page Top]]</div>
:>>see more [[Biomod/2012/Titech/Nano-Jugglers/Simulation|Simulation Models]]
:If you want to see all of our methods, click [[Biomod/2012/Titech/Nano-Jugglers/Methods|here]]
:&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"
|[[Image:ControlResult画像.png|Control simulation|600px]]
|-
|style="padding:10px"|Fig. 3.3 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.
|}
 
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} </style> </head> <BODY> <div id="biomodlink"> <<a href="http://openwetware.org/wiki/Biomod">BIOMOD</a>|<a href="http://openwetware.org/wiki/Biomod/2012">2012</a>|Titech Nano-Jugglers </div> <div id="header"> <div id="navigation"> <div id="menu"> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers"><br>Home<br><br></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Team/Students"><br>Team<br><br></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Project"><br>Project<br><br></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Results">Results<br>&<br>Methods</a></font></li> <li class="ach"><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Achievements"><br>Achievements<br><br></a> <li class="sup"><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Protocols"><br>Suppl. Info.<br><br></a></li> <li class="none"><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Acknowledgement"><br>Acknowledgements<br><br></a></li> </ul> </div> </div> </div> </BODY> </html>

Results

<html><body><A href=#0._Construction_of_Biomolecular_Rocket title="Body"><img src="http://openwetware.org/images/b/b5/BM.jpg" border=0 width=310 height=240></a></body></html>

    Construction of Biomolecular Rocket

  • We constructed Biomolecular Rocket composed of a micrometer-sized body and many catalytic engines. The catalytic engines were conjugated to the body using DNA-bead linkers in a spatially selective manner.

        Shown in detail below

<html><body><A href=#1._Power_supply_for_the_rail-free_movement_of_the_Biomolecular_Rocket title="Rail-free"><img src="http://openwetware.org/images/7/7f/Rail-free%E3%80%80movement_kinesin.jpg" border=0 width=310 height=220></a></body></html>
Power supply for the rail-free movement of the Biomolecular Rocket
 <html><body><A href=#2._Realization_of_the_high-speed_movement_of_the_Biomolecular_Rocket title="High-speed"><img src="http://openwetware.org/images/8/89/High-speed_movement.jpg" border=0 width=310 height=220></a></body></html>
Realization of high-speed movement of the Biomolecular Rocket 		<html><body><A href=#3._Introduction_of_a_photo-switchable_DNA_system_for_the_directional_control title="Control"><img src="http://openwetware.org/images/d/dd/Control_image.jpg" border=0 width=310 height=220></a></body></html>
Introduction of a photo-switchable DNA system for the directional control
  • We realized the rail-free movement by power generation with catalytic reactions of platinum and catalase.




      Shown in detail below

  • We realized the high-speed movement by power generation with catalytic reactions of platinum and catalase, and analyzed the speed.
  • We carried out numerical simulations of the high-speed movement of the Biomolecular Rockets.

      Shown in detail below

  • We developed a photo-switchable DNA system for controlling of the Bimolecular Rocket using UV light irradiation.
  • We investigated directional control of the Biomolecular Rocket in the simulations.

      Shown in detail below



0. Construction of Biomolecular Rocket

<html><body><font size="5">We constructed Biomolecular Rocket with a microbead, catalysts, and designed DNAs.</font></body></html>

    Biomolecular Rocket is composed of a micrometer-sized body and many catalytic engines. The body consists of a microbead with a diameter of 10 μm, and catalytic engines consist of platinum nanoparticles or catalase molecules. The catalytic engines are conjugated to the body using a DNA-based linker in a spatially selective manner.
    We constructed the Biomolecular Rocket through the following four steps.

<html><body><ol>

<li>The microbead body was selectively coated by vapor deposition of metals (Au and Cr).<br> <li>We designed DNA sequences for spatially-selective hybridization of catalytic engines.<br> <li>The DNA molecules were conjugated to a designated metal surface of the microbead body.<br> <li>Catalyst engines were attached to the microbead body with selective hybridization of DNAs we designed.</ol></body></html>

    >>see more methods

<html><body><td align="center"><img src="http://openwetware.org/images/4/4d/Charts.jpg" border=0 width=200 height=440></a></td></body></html>

0.1. Selective coating of the body

<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>

>>see more methods

 <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>
    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 the Biomolecular Rocket was achieved.
  <html><body><nobr>40 μm silica beads</nobr></body></html>     a
40 μm silica beads 		    b
After first deposition 		    c
After second deposition
  <html><body><nobr>10 μm polystyrene beads</nobr></body></html>       d
10 μm polystyrene beads 		    e
After first deposition 		    f
After second deposition
  <html><body><nobr>Image of micro-beads</nobr></body></html> <html><body><img src="http://openwetware.org/images/d/d5/Polystyrene.jpg" border=0 width=240 height=180></body></html> <html><body><img src="http://openwetware.org/images/4/41/After_first_deposition.jpg" border=0 width=240 height=180></body></html> <html><body><img src="http://openwetware.org/images/3/30/After_second_deposition.jpg" border=0 width=240 height=180></body></html>
    Fig. 0.1 Selective coating of micro-beads by vapor deposition.

0.2. Design of linker DNA strands

<html><body><font size="5">We designed DNA sequences for the linkers to attach catalytic engines to the microbead body.</font></body></html>
>>see more methods
    We designed two kinds of DNA sequences with different stability. One is DNA sequence L. This sequence forms a very stable duplex with its complementary sequence L* at a room temperature. Another is DNA sequence S. The duplex of DNA sequence S and S* has less stability than DNA sequence L and L* but is stable at a room temperature.
  DNA sequence L

  <html><body><nobr>5’-CGTCTATTGCTTGTCACTTCCCC-3'&nbsp;&nbsp;</nobr></body></html>

  DNA sequence S

  <html><body><nobr>5’-AATACCCAGCC-3’&nbsp;&nbsp;</nobr></body></html>

  DNA sequence L*

  <html><body><nobr>5'-GGGGAAGTGACAAGCAATAGACG-3'&nbsp;&nbsp;</nobr></body></html>

  DNA sequence S*

  <html><body><nobr>5’-GGCTGGGTATT-3'&nbsp;&nbsp;</nobr></body></html>

    Figure 0.2a and 0.2b show calculated melting profiles of duplexes L-L* and S-S*, respectively. Calculated melting temperatures of these duplexes were higher than a room temperature.
  a
DNA Tm 		  b
Photoresponsive DNA Tm
Fig. 0.2. (a) The melting profile of duplex L-L*. (b) The melting profile of duplex S-S*. RT and Tm indicate a room temperature (24°C) and a melting temperature, respectively. We calculated the melting profiles using NUPACK software.

0.3. Selective DNA conjugation to the microbead body of Biomolecular Rocket

0.3.1. Selective conjugation of DNA to polystyrene surface area

<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>

>>see more methods

    We conjugated amino-modified DNA sequence L* to the calboxylated polystyrene surface area of the microbead body with amide binding. To investigate the selective conjugation of L*, we hybridized a fluorophore-modified DNA sequence L with L* on the body and observed the DNA-conjugated microbead bodies.

    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*-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*-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* to polystyrene surface area of the microbead bodies was achieved.
  <html><body><nobr>Bright-field microscope images</nobr></body></html>       a    
DNA conjugated beads and FAM 		    b    
DNA conjugated beads 		    c    
Beads and FAM
  <html><body><nobr>Fluorescence microscope images</nobr></body></html>       a'    
DNA conjugated beads and FAM 		    b'    
DNA conjugated beads 		    c'    
Beads and FAM
  <html><body><nobr>Experimental conditions<nobr></body></html>   <html><body><img src="http://openwetware.org/images/d/d3/EDACBEADS1.JPG" border=0 width=220 height=120></a></body></html> <html><body><img src="http://openwetware.org/images/3/38/EDACBEADS2.JPG" border=0 width=220 height=120></a></body></html> <html><body><img src="http://openwetware.org/images/2/23/EDACBEADS3.JPG" border=0 width=220 height=120></a></body></html>
Fig. 0.3.1 Microscope images of the microbead bodies of Biomolecular Rocket. (a) and (a') Selectively DNA-conjugated microbeads with complementary fluorophore-modified DNA. (b) and (b') Selectively DNA-conjugated microbeads without complementary fluorophore-modified DNA. (c) and (c') non-DNA-conjugated microbeads with complementary fluorophore-modified DNA.

0.3.2. Selective conjugation of DNA to metal surface area

<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>

>>see more methods

    We conjugated thiol-modified DNA sequence S* to the Au surface area of the microbead body with Au-thiol bonding. To confirm the selective conjugation of S* 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.

    Figure 0.3.2a shows the Au glass plate with a non-DNA spot (1), a non-thiol-modified DNA spot (2), and a thiol-modified DNA spot (3). Only at the spot (3), residual water was observed. The water remained by the wetting property of the spot (3); the higher wetting property of spot (3) than those of spots (1) and (2) was expected to be caused by the Au surface with thiol-modified DNA conjugation. Therefore, we conclude that selective conjugation of thiol-modified DNA to the Au surface area of the microbead body was also achieved.
    a    
Au plate 		    b    
condition
    c
<html><body><img src="http://openwetware.org/images/1/1a/Auplate1.jpg" border=0 width=800 height=150></a></body></html>
Fig. 0.3.2. (a) An Au glass plate with a non-DNA spot (1), a non-thiol-modified DNA spot (2), and a thiol-modified DNA spot (3).
(b) A layout drawing of the spots (1)-(3).
(c) Experimental condition for the spots (1)-(3).

0.4. Catalyst attachment with DNA hybridization

<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><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>

>>see more methods

    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* and S*) 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.



<html><body><font color="red">1. Power supply for the rail-free movement of the Biomolecular Rocket</font></body></html>

<html><body><font size="5">We achieved the power supply for the rail-free movement of the Biomolecular Rocket.</font></body></html>
    We utilized H2O2 for fuel and catalysts of H2O2 for catalytic engines to realize the rail-free movement of the Biomolecular Rocket. Catalysts such as platinum and catalase catalyze the decomposition of H2O2 into H2O and O2; emitted bubbles of O2 launch Biomolecular Rocket.

    Here, we investigated the following points to realize the power supply for the rail-free movement of the Biomolecular Rocket.

<html><body><ol>

<li>We found that catalase molecules as catalytic engines could emit sufficient amount of bubbles for the rail-free movement. <li>We found that platinum particles as a catalytic engines could emit sufficient amount of bubbles for rail-free movement. <li>We found that the H<sub>2</sub>O<sub>2</sub> did not affect the stability of DNA linkers for attaching catalytic engines to the body in the H<sub>2</sub>O<sub>2</sub> solution. </ol></body></html>

<html><body><td align="center"><img src="http://openwetware.org/images/b/b3/WikiRFBM.jpg" border=0 width=240 height=240></a></td></body></html>

1.1. Power supply for rail-free movement by using catalase catalytic engine

<html><body><font size="5">We succeeded in the rail-free movement by O<sub>2</sub> bubble emission with catalase.</font></body></html>
    We utilized the catalase for catalytic engines, which catalyzes the decomposition of H2O2 into H2O and O2. 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 methods

    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 O2 bubble emission with catalase.
<html><body><img src="http://openwetware.org/images/1/1b/Crf.jpg" border=0 width=420 height=315></body></html>
Fig. 1.1  Image of a microbead with a hemispherical Au surface and a hemispherical polystyrene surface in 3% H2O2 solution.
<html><iframe width="420" height="315" src="http://www.youtube.com/embed/Ie2dUHcwZN0" frameborder="0" allowfullscreen></iframe></html>
Movie. 1.1   The real-time video of the moving 10 μm bead with a catalase-conjugated hemisphere area in 3% H2O2 solution.

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

<html><body><font size="5">We achieved bubble emissions with platinum micro-particles in solution of H<sub>2</sub>O<sub>2</sub>.</font></body></html>
    We provided 1 μm platinum particles, and Cr coating to create platinum hemispherical area. Then added 3% H2O2 solution and observed their movement.
>>see more methods

    Movie 1.2 reveals the catalytic reaction of 3% H2O2 and 1 μm beads that have platinum hemispherical area. We can recognize that bubbles are emitted in H2O2 solution. These bubbles are emitted from 1 μm beads that have platinum hemispherical area by decomposing H2O2. From this result, we conclude that power supply for rail-free movement by using platinum catalytic engine was achieved.
<html><body><img src="http://openwetware.org/images/8/89/Simple_beads.jpg" border=0 width=420 height=315></a></body></html>
Fig. 1.2 Image of a microbead with a hemispherical Cr surface and a hemispherical platinum surface in 3% H2O2 solution.

<html><iframe width="420" height="300" src="http://www.youtube.com/embed/gPNaMMd3NP4" frameborder="0" allowfullscreen></iframe></html>

Movie. 1.2     Image of the catalytic reaction of 3% H2O2 and 1 μm beads that have platinum hemispherical area.

1.3. DNA hybridization in solution of H2O2

<html><body><font size="5">We revealed that diluted H<sub>2</sub>O<sub>2</sub> solutions did not affect DNA hybridization and a H<sub>2</sub>O<sub>2</sub> solution was suitable for a fuel for the Biomolecular Rocket. </font></body></html>
>>see more methods

   We confirmed that DNA duplexes were stably formed in diluted H2O2 solutions by the native polyacrylamide gel electrophoresis (PAGE). Figure 1.3 shows the gel image of the PAGE. As shown in the lanes 1-3, a double-stranded DNA was formed in 1% and 5% H2O2 solutions.
Electrophoresis
Fig. 1.3    A gel image of a native PAGE of DNA in H2O2 solutions. Lanes 1-3, 8: a double stranded DNA (D+R) in diluted H2O2 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% H2O2 solutions were shown. DNA sequences R and D are shown at the upper right of the image.



2. Realization of the high-speed movement of the Biomolecular Rocket

<html><body><font size="5">We confirmed the high-speed movement of the Biomorecular Rocket by bubble emission.</font></body></html>

    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.
<html><body><ol>

<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>

<html><body><img src="http://openwetware.org/images/2/26/Hst.jpg" width=300 height=230></body></html>

2.1. Power supply for the high-speed movement with platinum catalytic engines

<html><body><font size="5">We succeeded in high speed movement with platinum catalytic engines.</font></body></html>
>>see more methods and full length movie

    Movie 2.1.1a shows the movement of 0.15-0.40 μm platinum particles in 3% H2O2 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).
    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 mm2/s2, and the average speed was calculated as 10.7 mm/s. Assuming that kinesin moves at 1μm/s, Platinum particles in H2O2 solution can moved at about 10,000 time’s faster speed than kinesin.
   a
<html><iframe width="440" height="330" src="http://www.youtube.com/embed/7pBw4FWEt3I" frameborder="0" allowfullscreen></iframe></html>
    b
<html><iframe width="440" height="330" src="http://www.youtube.com/embed/R4RsXKiknIs" frameborder="0" allowfullscreen></iframe></html>
Movie. 2.1.1    Analyses of the speed of platinum in solution of H2O2.

(a)  Platinum movement in solution of H2O2          (b)  Analyses of the speed of plutinum by High-speed camera

  Fig. 2.1.2 The mean square displacement of a platinum particle.

2.2. Numerical estimation of the speed of the Biomolecular Rocket

<html><body><font size="5">The numerical simulation revealed that the Biomolecular Rocket can move ten times faster than kinesin.</font></body></html>
>>see more simulation models
    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).
    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.
    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.
    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.
Simulation of high-speed
Fig. 2.2    Image of each molecular motor’s instantaneous speed with time



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

<html><body><font size="5">We developed a photo-switchable DNA system for the directional control with a photoresponsive DNA.</font></body></html>

    The photo-switchable DNA system consists of an azobenzene-based photoresponsive DNA. The structure of the photoresponsive DNA is changed by UV light irradiation, then the photoresponsive DNA duplex is dissociated into DNA single strands. By the dissociation of DNA, catalytic engines are dissociated from the body of Biomolecular Rocket. As a result, the directional change of the force generated by O2 bubble is caused, and the direction of the Biomolecular Rocket is changed. Here, we developed and investigated the photo-switchable DNA system by the following experiments and simulations.

<html><body><ol>

<li>Design of a photo-switchable DNA system for the directional control <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 </ol></body></html>

<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/8/8a/DC.jpg" border=0 width=300 height=230></a></td></body></html>

3.1. Design of photoresponsive DNA

<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/4/45/Photo_design.jpg" border=0 width=210 height=210></a></td></body></html> <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>

>>see more methods

    We designed a photoresponsive DNA strand based on DNA sequence S*; four azobenzene molecules were introduced into S*. Figure 3.1.1 shows that absorbance spectra of DNA strands (A) photoresponsive DNA sequence S*, (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.

Spectrum analysis

Fig.3.1     Absorbance spectra of DNA strands (A) photoresponsive DNA sequence S*, (B) DNA sequence S, and (A+B) the duplex of them at a room temperature.

3.2. Achievement of the photo-switchable DNA system

<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/f/f3/Azobenzene_image_dissociation.jpg" border=0 width=240 height=180></a></td></body></html>

<html><body><font size="5">We have succeeded in development of a photo-switchable DNA system.</font></body></html>
>>see more methods

    We introduced the photo-switching DNA system into Biomolecular Rocket in order to control its moving direction.

   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.
   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/cm2).
    a
Spectrum analysis 		    b
Wave length around 260 nm and 330 nm
Fig. 3.2.1. (a)    Absorbance spectra of photoresponsive DNA duplex (A+B) in condition of UV light irradiation (30 mW/cm2). (b) Time course of the absorbance change during UV light irradiation.


    Similarly, we studied the dissociation rate of photoresponsive DNA under the condition of UV light irradiation with the strength of 180 mW/cm2 (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/cm2). From these results, we conclude that the dissociation of photoresponsive DNA by UV-light irradiation was achived.
    a
Spectrum analysis 		    b
Wave lengte around 260 nm
    c
Wave lengte around 330 nm 		    d
Wave lengte around 480 nm
Fig. 3.2.2    Spectrum analysis of photoresponsive DNA duplex(A+B) in condition of UV-light(180 mW/cm2) irradiation

3.3. Directional control of the Biomolecular Rocket by the photo-switchable DNA system

    <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>
>>see more Simulation Models
    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.
Control simulation
Fig. 3.3 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.
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