Biomod/2012/UTokyo/UT-Komaba/Experiment: Difference between revisions

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=Experiment=
=Experiment=


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==Dynamic System==
==Dynamic System==


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<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/b/bf/Biomod_2012_UTokyo_UT-Komaba_Experiment_Icon_TrioscillateSystem.png" width="250px" height="110px" /></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>
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<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>
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<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 09:15, 28 October 2012

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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


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