Biomod/2012/UTokyo/UT-Komaba/Experiment: Difference between revisions
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=Experiment= | =Experiment= | ||
== | Please click on the section you want to learn more about. | ||
==Dynamic System== | |||
<html> | <html> | ||
<a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Normal_Bistable"><img src="http://openwetware.org/images/3/31/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_NormalBistable.png" width="250px" height="110px" /></a> | <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Normal_Bistable"><img src="http://openwetware.org/images/3/31/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_NormalBistable.png" width="250px" height="110px" alt="Normal Bistable" /></a> | ||
<a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Indirect_Bistable"><img src="http://openwetware.org/images/7/79/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_IndirectBistable.png" width="250px" height="110px" /></a> | <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Indirect_Bistable"><img src="http://openwetware.org/images/7/79/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_IndirectBistable.png" width="250px" height="110px" alt="Indirect Bistable" /></a> | ||
<a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Trioscillate_System"><img src="http://openwetware.org/images/ | <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Trioscillate_System"><img src="http://openwetware.org/images/8/88/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_TrioscillatorSystem.png" width="250px" height="110px" alt="Trioscillate System" /></a> | ||
</html> | </html> | ||
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<html> | <html> | ||
<a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Original_Origami"><img src="http://openwetware.org/images/7/76/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_OriginalOrigami.png" width="250px" height="110px" /></a> | <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Original_Origami"><img src="http://openwetware.org/images/7/76/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_OriginalOrigami.png" width="250px" height="110px" /></a> | ||
<a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Compatibility_with_Bistable"><img src="http://openwetware.org/images/8/8b/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_Compatibility_with_Bistable.png" width="250px" height="95px" /></a> | |||
<a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Modified_Origami"><img src="http://openwetware.org/images/3/3a/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_ModifiedOrigami.png" width="250px" height="110px" /></a> | <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Modified_Origami"><img src="http://openwetware.org/images/3/3a/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_ModifiedOrigami.png" width="250px" height="110px" /></a> | ||
</html> | </html> | ||
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<a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/DNA_Tablet"><img src="http://openwetware.org/images/7/72/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_DNATablet.png" width="250px" height="110px" /></a></html> | <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/DNA_Tablet"><img src="http://openwetware.org/images/7/72/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_DNATablet.png" width="250px" height="110px" /></a></html> | ||
= | =Lab Notes= | ||
<html> | <html> | ||
<a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Lab_Notes"><img src="http://openwetware.org/images/b/b7/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_LabNotes.png" width="250px" height="110px" /></a></html> | <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Lab_Notes"><img src="http://openwetware.org/images/b/b7/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_LabNotes.png" width="250px" height="110px" /></a></html> | ||
= | |||
==Glossary== | |||
===Buffers=== | |||
{| class="tdleft" | |||
! TAE | |||
| Essential buffer for making origami, which contains TAE | |||
|- | |||
! Mg2+ | |||
| Essential for keeping the shape of origami | |||
|- | |||
! Smix | |||
| Buffer contains a lot of essential chemicals | |||
|- | |||
! DTT | |||
| Buffer which contains DTT | |||
|- | |||
! dTTP | |||
| Buffer which contains dTTP | |||
|- | |||
! BSA | |||
| Buffer which contains BSA | |||
|- | |||
! mQ | |||
| Pure water | |||
|} | |||
===Enzymes=== | |||
{| class="tdleft" | |||
! NBI | |||
| Buffer which contains DNA nickase | |||
|- | |||
! Bst | |||
| Buffer which contains DNA polymerase | |||
|- | |||
! tt-RecJ | |||
| Buffer which contains DNA exonuclease | |||
|- | |||
|} | |||
===DNAs=== | |||
{| class="tdleft" | |||
! M13 | |||
| Scaffold strand | |||
|- | |||
! VII | |||
| Strand for Dynamic system | |||
|- | |||
! XII | |||
| Strand for Dynamic system | |||
|- | |||
! DII | |||
| Strand for Dynamic system | |||
|- | |||
! NII | |||
| Strand for Dynamic system | |||
|- | |||
! inhV | |||
| Inhibitor to VII-autocatalisys | |||
|- | |||
! inhX | |||
| Inhibitor to XII-autocatalisys | |||
|- | |||
! inhQ | |||
| Inhibitor to QII-autocatalisys | |||
|} | |||
===Templates=== | |||
{| class="tdleft" | |||
! CvII | |||
| Autocatalysis template for VII | |||
|- | |||
! CxII | |||
| Autocatalysis template for XII | |||
|- | |||
! V to inhX | |||
| Template which produces inhibitor to XII-autocatalisys from VII | |||
|- | |||
! V to inhQ | |||
| Template which produces inhibitor to QII-autocatalisys from VII | |||
|- | |||
! X to inhV | |||
| Template which produces inhibitor to VII-autocatalisys from XII | |||
|- | |||
! X to inhQ | |||
| Template which produces inhibitor to QII-autocatalisys from XII | |||
|- | |||
! Q to inhV | |||
| Template which produces inhibitor to VII-autocatalisys from QII | |||
|- | |||
! Q to inhX | |||
| Template which produces inhibitor to XII-autocatalisys from QII | |||
|- | |||
! D to V | |||
| Template which produces VII from DII | |||
|- | |||
! N to X | |||
| Template which produces XII from NII | |||
|} | |||
__NOEDITSECTION__ |
Latest revision as of 02:15, 28 October 2012
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<div id="title"><img src="http://openwetware.org/images/4/47/Biomod_2012_UTokyo_UT-Komaba_Top.png" alt="DNA tablet" width="800" height="120" onClick="this.src='http://openwetware.org/images/7/7d/BIOMOD_2012_UTokyo_UT-Komaba_title-animation.gif'"/></div>
<div id="navi"> <ul>
<li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba">Home</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Idea">Idea</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Simulation">Simulation</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment">Experiment</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Progress">Progress</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Episode">Episode</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Team">Team</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Supplementary">Supplementary</a></li>
</ul> </div>
</html>
Experiment
Please click on the section you want to learn more about.
Dynamic System
<html> <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Normal_Bistable"><img src="http://openwetware.org/images/3/31/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_NormalBistable.png" width="250px" height="110px" alt="Normal Bistable" /></a> <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Indirect_Bistable"><img src="http://openwetware.org/images/7/79/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_IndirectBistable.png" width="250px" height="110px" alt="Indirect Bistable" /></a> <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Trioscillate_System"><img src="http://openwetware.org/images/8/88/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_TrioscillatorSystem.png" width="250px" height="110px" alt="Trioscillate System" /></a> </html>
DNA Origami
<html> <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Original_Origami"><img src="http://openwetware.org/images/7/76/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_OriginalOrigami.png" width="250px" height="110px" /></a> <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Compatibility_with_Bistable"><img src="http://openwetware.org/images/8/8b/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_Compatibility_with_Bistable.png" width="250px" height="95px" /></a> <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Modified_Origami"><img src="http://openwetware.org/images/3/3a/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_ModifiedOrigami.png" width="250px" height="110px" /></a> </html>
DNA Tablet
<html> <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/DNA_Tablet"><img src="http://openwetware.org/images/7/72/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_DNATablet.png" width="250px" height="110px" /></a></html>
Lab Notes
<html> <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment/Lab_Notes"><img src="http://openwetware.org/images/b/b7/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_LabNotes.png" width="250px" height="110px" /></a></html>
Glossary
Buffers
TAE | Essential buffer for making origami, which contains TAE |
---|---|
Mg2+ | Essential for keeping the shape of origami |
Smix | Buffer contains a lot of essential chemicals |
DTT | Buffer which contains DTT |
dTTP | Buffer which contains dTTP |
BSA | Buffer which contains BSA |
mQ | Pure water |
Enzymes
NBI | Buffer which contains DNA nickase |
---|---|
Bst | Buffer which contains DNA polymerase |
tt-RecJ | Buffer which contains DNA exonuclease |
DNAs
M13 | Scaffold strand |
---|---|
VII | Strand for Dynamic system |
XII | Strand for Dynamic system |
DII | Strand for Dynamic system |
NII | Strand for Dynamic system |
inhV | Inhibitor to VII-autocatalisys |
inhX | Inhibitor to XII-autocatalisys |
inhQ | Inhibitor to QII-autocatalisys |
Templates
CvII | Autocatalysis template for VII |
---|---|
CxII | Autocatalysis template for XII |
V to inhX | Template which produces inhibitor to XII-autocatalisys from VII |
V to inhQ | Template which produces inhibitor to QII-autocatalisys from VII |
X to inhV | Template which produces inhibitor to VII-autocatalisys from XII |
X to inhQ | Template which produces inhibitor to QII-autocatalisys from XII |
Q to inhV | Template which produces inhibitor to VII-autocatalisys from QII |
Q to inhX | Template which produces inhibitor to XII-autocatalisys from QII |
D to V | Template which produces VII from DII |
N to X | Template which produces XII from NII |