Biomod/2012/Titech/Nano-Jugglers/Methods - Revision history

Kensuke Hoshi: /* 3.2. Directional control with photo-switchable DNA system */

2012-10-26T17:37:04Z

3.2. Directional control with photo-switchable DNA system

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-	==3.2. Directional control with photo-switchable DNA system==	+	==3.2. Directional control with photo-switchable DNA system==
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Kensuke Hoshi: /* 3.1. Design of photoresponsive DNA */

2012-10-26T17:36:05Z

3.1. Design of photoresponsive DNA

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	1.This 11 bases DNA are a complementary sequence of photoresponsive DNA sequence S.		1.This 11 bases DNA are a complementary sequence of photoresponsive DNA sequence S.
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-	:    And then, we confirmed that photoresponsive DNA could hybridize stably. For verifying hybridization, we ~~use~~ the value of absorbance.<br>	+	:    And then, we confirmed that photoresponsive DNA could hybridize stably. For verifying hybridization, we used the value of absorbance.<br>
	:    In spectroscopy, a relational expression about absorbance can be expressed as follows.		:    In spectroscopy, a relational expression about absorbance can be expressed as follows.
	:[[Image:Math.png\|center\|200px]]		:[[Image:Math.png\|center\|200px]]

Kensuke Hoshi: /* 2.1. Analyses of the speed of platinum in solution of H2O2 by High-speed camera */

2012-10-26T17:35:18Z

2.1. Analyses of the speed of platinum in solution of H2O2 by High-speed camera

←Older revision		Revision as of 17:35, 26 October 2012
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-	==2.1. ~~Analyses of the~~ speed of platinum ~~in solution of H<sub>2</sub>O<sub>2</sub> by High-speed camera~~==	+	==2.1. Power supply for high-speed movement with platinum catalytic engines==
-	:    By using highspeed camera, we studied how the catalytic engine produce the driving force.In this study, we had 3 inference. Driving force is<br>	+	:    By using highspeed camera, we studied how the catalytic engine produce the driving force.In this study, we had 3 inference. Driving force was<br>
	:*1.produced in concurrence with the generation of bubbles		:*1.produced in concurrence with the generation of bubbles
	:*2.produced as the bubbles are destructed		:*2.produced as the bubbles are destructed
	:*3.produced as the bubbles detach		:*3.produced as the bubbles detach
	:    To research these problems, we analyzed when the moving speed of platinum beads and the acceleration of that would change by using "Highspeed microscope VW-9000".		:    To research these problems, we analyzed when the moving speed of platinum beads and the acceleration of that would change by using "Highspeed microscope VW-9000".
-	::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#2.1.~~_Analyses_of_the_speed_of_platinum_in_solution_of_H2O2_by_High~~-~~speed_camera~~\|Results]]	+	::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#2.1._Power_supply_for_high-speed_movement_with_platinum_catalytic_engines\|Results]]
-	~~<br><br>~~	+

	==3.1. Design of photoresponsive DNA==		==3.1. Design of photoresponsive DNA==

Kensuke Hoshi: /* 0.4. Catalyst attachment with DNA hybridization */

2012-10-26T17:34:39Z

0.4. Catalyst attachment with DNA hybridization

←Older revision		Revision as of 17:34, 26 October 2012
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	::::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#0.4._Catalyst_attachment_with_DNA_hybridization\|Results]]		::::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#0.4._Catalyst_attachment_with_DNA_hybridization\|Results]]
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		+	<div align = "right" style="padding-right:200px">[[#TOP\|↑Page Top]]</div>
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Kensuke Hoshi: /* 1.3. Power supply for rail-free movement by using platinum catalytic engine */

2012-10-26T17:34:04Z

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

←Older revision		Revision as of 17:34, 26 October 2012
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	==1.3. Power supply for rail-free movement by using platinum catalytic engine==		==1.3. Power supply for rail-free movement by using platinum catalytic engine==
-	:    The driving force of Biomolecular Rocket is catalytic engine of platinum. This catalytic engine ~~become~~ more powerful<sup>[1],[2]</sup>, increasing the surface of platinum. Biomolecular Rocket ~~has~~ numerous platinum particles to increase the surface of platinum. In this experiment, we ~~deposit~~ chromium to 1µm beads which are covered platinum and we make half platinum beads<sup>[3]</sup>. ~~In addition~~, we ~~observe~~ a behavior of the beads in 3% H<sub>2</sub>O<sub>2</sub> solution. From this experiment, we are able to investigate whether Surface area of platinum is related to the speed.<br>	+	:    The driving force of Biomolecular Rocket is catalytic engine of platinum. This catalytic engine became more powerful<sup>[1],[2]</sup>, increasing the surface of platinum. Biomolecular Rocket had numerous platinum particles to increase the surface of platinum. In this experiment, we deposited chromium to 1µm beads which are covered platinum and we make half platinum beads<sup>[3]</sup>. Then, we observed a behavior of the beads in 3% H<sub>2</sub>O<sub>2</sub> solution. From this experiment, we are able to investigate whether Surface area of platinum was related to the speed.<br>
	[[Image:Make platinum hemisphere.png\|center\|300px]]		[[Image:Make platinum hemisphere.png\|center\|300px]]
	:Reference		:Reference

Kensuke Hoshi: /* 1.2. Power supply for rail-free movement by using catalase catalytic engine */

2012-10-26T17:33:00Z

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

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	\|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/5/5a/Catalase_image.jpg" border=0 width=300 height=240></a></td></body></html>		\|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/5/5a/Catalase_image.jpg" border=0 width=300 height=240></a></td></body></html>
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-	For supplying power of Biomolecular Rocket, we ~~experiment~~ with another catalytic engine<sup>[1],[2],[3]</sup>. Catalase is known as a enzyme that catalyzes the hydrogen peroxide solution. And we ~~expect~~ that this enzyme will be new catalytic engine of the Biomolecular Rocket because a enzyme activity of this enzyme is 100,000 times stronger than that of platinum. In this experiment, we ~~deposit~~ Au for half surface of polystyrene beads and catalase conjugated onto polystyrene side. In addition, we ~~observe~~ a behavior of the beads in diluted H<small>2</small>O<small>2</small> solution.<br>	+	For supplying power of Biomolecular Rocket, we experimented with another catalytic engine<sup>[1],[2],[3]</sup>. Catalase is known as a enzyme that catalyzes the hydrogen peroxide solution. And we expected that this enzyme will be new catalytic engine of the Biomolecular Rocket because a enzyme activity of this enzyme is 100,000 times stronger than that of platinum. In this experiment, we deposited Au for half surface of polystyrene beads and catalase conjugated onto polystyrene side. In addition, we observed a behavior of the beads in diluted H<small>2</small>O<small>2</small> solution.<br>
	[[Image:Make catalase rocket.png\|center\|350px]]		[[Image:Make catalase rocket.png\|center\|350px]]
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Kensuke Hoshi: /* 1.1. DNA hybridization in solution of H2O2 */

2012-10-26T17:32:16Z

1.1. DNA hybridization in solution of H2O2

←Older revision		Revision as of 17:32, 26 October 2012
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	==1.1. DNA hybridization in solution of H<sub>2</sub>O<sub>2</sub>==		==1.1. DNA hybridization in solution of H<sub>2</sub>O<sub>2</sub>==
-	:    H<sub>2</sub>O<sub>2</sub> has strong corrosion. There was a risk that DNA strand is denatured by H<sub>2</sub>O<sub>2</sub><sup>[1]</sup>. So, we had to ensure that the hybridization of DNA is not suffer from H<sub>2</sub>O<sub>2</sub>. We ~~guess~~ that if DNA had been destroyed, then molecular mass would decrease in that DNA can't hybridize. ~~Measure~~ the relative magnitude of the molecular weight by electrophoresis, we are able to ~~examaine~~ whether DNA can hybridize or not.<br>	+	:    H<sub>2</sub>O<sub>2</sub> has strong corrosion. There was a risk that DNA strand is denatured by H<sub>2</sub>O<sub>2</sub><sup>[1]</sup>. So, we had to ensure that the hybridization of DNA is not suffer from H<sub>2</sub>O<sub>2</sub>. We guessed that if DNA had been destroyed, then molecular mass would decrease in that DNA can't hybridize. Visualizing the relative magnitude of the molecular weight by electrophoresis, we are able to examine whether DNA can hybridize or not.<br>
-	:    This time, we have to examine the state of the DNA in the time we need to steer rocket, set the time to soak and concentration of H<small>2</small>O<small>2</small>. We used PAGE electrophoresis to ascertain the stability of DNA duplex in thin H₂O₂ solution 1%-5%. PAGE electrophoresis shows the difference of molecular weight that comes from ~~denaturetion~~ or hybridization in the form of bands.<br><br>	+	:    This time, we have to examine the state of the DNA in the time we need to steer rocket, set the time to soak and concentration of H<small>2</small>O<small>2</small>. We used PAGE electrophoresis to ascertain the stability of DNA duplex in thin H₂O₂ solution 1%-5%. PAGE electrophoresis shows the difference of molecular weight that comes from dissociation or hybridization in the form of bands.<br><br>
	:Reference<br>		:Reference<br>
	:[1]Natacha Driessens, Soetkin Versteyhe, Chiraz Ghaddhab, Agne`s Burniat, Xavier De Deken, Jacqueline Van Sande, Jacques-Emile Dumont, Franc¸oise Miot, Bernard Corvilain,Endocrine-Related Cancer 16 845–856(2009)<br>		:[1]Natacha Driessens, Soetkin Versteyhe, Chiraz Ghaddhab, Agne`s Burniat, Xavier De Deken, Jacqueline Van Sande, Jacques-Emile Dumont, Franc¸oise Miot, Bernard Corvilain,Endocrine-Related Cancer 16 845–856(2009)<br>

Kensuke Hoshi: /* 0.4. Catalyst attachment with DNA hybridization */

2012-10-26T17:31:19Z

0.4. Catalyst attachment with DNA hybridization

←Older revision		Revision as of 17:31, 26 October 2012
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	'''We attached the catalyst to our rocket body with DNA hybridization.''' cDNA had adhered to the corresponding parts of the rocket body, so it enabled to attach catalyst engines in that we designed these DNA were thermodynamically stable when they hybridized.<br><br>		'''We attached the catalyst to our rocket body with DNA hybridization.''' cDNA had adhered to the corresponding parts of the rocket body, so it enabled to attach catalyst engines in that we designed these DNA were thermodynamically stable when they hybridized.<br><br>
-	First, we prepared DNA-conjugated 10 μm sized polystyrene beads which were deposited 1/4 Au and 1/2 Cr. At the same time we prepared DNA-conjugated 0.15-0.40 μm sized platinum particles. Then, mixed these materials in 3×SSC buffer at ~~90℃~~, and cooled to room temperature slowly over time. Namely, annealing DNA by raising temperature at the first time, next make it easy to hybridize each other by downing to room temperature.	+	First, we prepared DNA-conjugated 10 μm sized polystyrene beads which were deposited 1/4 Au and 1/2 Cr. At the same time we prepared DNA-conjugated 0.15-0.40 μm sized platinum particles. Then, mixed these materials in 3×SSC buffer at 90 °C, and cooled to room temperature slowly over time. Namely, annealing DNA by raising temperature at the first time, next make it easy to hybridize each other by downing to room temperature.
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	::::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#0.4._Catalyst_attachment_with_DNA_hybridization\|Results]]		::::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#0.4._Catalyst_attachment_with_DNA_hybridization\|Results]]
-	~~<br><br>~~
-	~~<div align = "right" style="padding-right:200px">[[#TOP\|↑Page top]]</div>~~
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Kensuke Hoshi: /* 0.3.2. Selective conjugation of DNA to metal surface area */

2012-10-26T17:30:28Z

0.3.2. Selective conjugation of DNA to metal surface area

←Older revision		Revision as of 17:30, 26 October 2012
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	SAM conjugation onto gold<br>		SAM conjugation onto gold<br>
-	Thiolated compound and gold substrate are one of the most famous research of SAMs<sup>[3]</sup>. Thiol modified DNA is conjugate to gold particles by this chemical reaction. Initially, substrate gold ~~are~~ cleaned by water or acid-base buffer in order to washout organic impurities. Gold particles ~~are~~ dissolved in 10mM phosphate buffer pH8, 10μM thiol modified DNA. Then in addition to NaCl, intended to raise the concentration of NaCl every 2 hours after 24 hours of incubation for 6 hours, then incubate more 16 hoursraise up to 0.7M salt concentration '''(Salt aging process)'''.Last,clean up again by proper buffer and dry. This reaction is also ~~use~~ with platinum ~~In order to accomplish our project ,we need platinum-DNA and gold-DNA conjugation, so we use thiol modified DNA~~.	+	Thiolated compound and gold substrate are one of the most famous research of SAMs<sup>[3]</sup>. Thiol modified DNA was conjugate to gold particles by this chemical reaction. Initially, substrate gold were cleaned by water or acid-base buffer in order to washout organic impurities. Gold particles were dissolved in 10mM phosphate buffer pH8, 10μM thiol modified DNA. Then in addition to NaCl, intended to raise the concentration of NaCl every 2 hours after 24 hours of incubation for 6 hours, then incubate more 16 hoursraise up to 0.7M salt concentration '''(Salt aging process)'''.Last,clean up again by proper buffer and dry. This reaction was also used with platinum.
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Kensuke Hoshi: /* 0.3.1. Selective conjugation of DNA to polystyrene surface area */

2012-10-26T17:29:29Z

0.3.1. Selective conjugation of DNA to polystyrene surface area

←Older revision		Revision as of 17:29, 26 October 2012
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	\|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/2/2c/BIOMODTNJEDAC.png" border=0 width=300 height=270></a></td></body></html>		\|<html><body><td align="center" width="150px"><img src="http://openwetware.org/images/2/2c/BIOMODTNJEDAC.png" border=0 width=300 height=270></a></td></body></html>
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-	'''We bond polystyrene-beads with DNA using EDAC.''' EDAC is known as water-soluble carbodiimide (WSC) and is used as coupling agent to form amide bond. EDAC crosslinks nucleic acids to the surfaces, which have carboxy group. In this project, we used this method to conjugate amino-modified DNA onto carboxylated polystyrene-beads. EDAC ~~reacts~~ with carboxylated polystyrene-beads to form active intermediate on the body. Then it ~~reacts~~ to amino-modified DNA. The beads are coupled by nucleic acid. We divide the body into three parts including polystyrene surface, so it is possible to connect each DNA with position classification. By using this method, we ~~can~~ connect platinum to aircraft body part of polystyrene in a region-specific manner.	+	'''We bond polystyrene-beads with DNA using EDAC.''' EDAC is known as water-soluble carbodiimide (WSC) and is used as coupling agent to form amide bond. EDAC crosslinks nucleic acids to the surfaces, which have carboxy group. In this project, we used this method to conjugate amino-modified DNA onto carboxylated polystyrene-beads. EDAC reacted with carboxylated polystyrene-beads to form active intermediate on the body. Then it reacted to amino-modified DNA. The beads are coupled by nucleic acid. We divide the body into three parts including polystyrene surface, so it is possible to connect each DNA with position classification. By using this method, we were able to connect platinum to aircraft body part of polystyrene in a region-specific manner.
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	::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#0.3.1._Selective_conjugation_of_DNA_to_polystyrene_surface_area\|Results]]		::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#0.3.1._Selective_conjugation_of_DNA_to_polystyrene_surface_area\|Results]]