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| | =Experiment= |
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| =Our Labo Note=
| | Please click on the section you want to learn more about. |
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| | ==Dynamic System== |
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| We conducted a lot of experiments at Komaba Research Campus.
| | <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> |
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| ==September 12th== | | ==DNA Origami== |
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| ===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> |
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| We made a solution of DNA origami.
| | ==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> |
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| :(µL)
| | =Lab Notes= |
| :{|
| |
| !
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| ! M13
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| ! Staple Mix
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| ! TAE 10x
| |
| ! Mg2+
| |
| ! mQ
| |
| ! Total Amount
| |
| |-
| |
| | A
| |
| |3.00
| |
| |7.20
| |
| |1.80
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| |2.25
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| |3.75
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| |20.00
| |
| |-
| |
| | B
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| |3.00
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| |3.60
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| |1.80
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| |2.25
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| |7.35
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| |20.00
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| |-
| |
| | C
| |
| |3.00
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| |10.80
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| |1.80
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| |2.25
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| |0.15
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| |20.00
| |
| |}
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| | <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> |
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| ==September 13th==
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| ===DNA Origami===
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| We observed DNA origami which we made September 12th by AFM.
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| | ==Glossary== |
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|
| *AFM image of A
| | ===Buffers=== |
| [[Image:Biomod_2012_UTokyo_UT-Komaba_Experiment_origami-AFM-1.jpg|300px]] [[Image:Biomod_2012_UTokyo_UT-Komaba_Experiment_origami-AFM-2.jpg|300px]]
| |
|
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|
| | | {| class="tdleft" |
| *AFM image of C
| | ! TAE |
| [[Image:Biomod_2012_UTokyo_UT-Komaba_Experiment_origami-AFM-3.jpg|300px]]
| | | Essential buffer for making origami, which contains TAE |
| | |
| | |
| | |
| ==September 19th==
| |
| | |
| ===DNA Origami===
| |
| We prepared two types of DNA origami solution.
| |
| The purpose of the experiment was to compare the different result from the different concentration of the solutions.
| |
| | |
| :(µL)
| |
| :{|
| |
| !
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| ! Staple Mix
| |
| ! M13
| |
| ! TAE 10x
| |
| ! Mg2+
| |
| ! mQ
| |
| ! Total Amount
| |
| |-
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| | A
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| |8.00
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| |3.33
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| |2.00
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| |0.25
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| |6.42
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| |20.00
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| |-
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| | B
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| |12.00
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| |5.00
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| |2.00
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| |0.25
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| |0.75
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| |20.00
| |
| |}
| |
| | |
| | |
| ===DNA Origami with Enzymes===
| |
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| We use enzymes in bistable system, therefore we make sure that the enzymes do not destroy the DNA origami.
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| We put nickase, polymerase and exnuclease with DNA origami and left them in the PCR.
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| The concentration of original DNA origami was 10x and 15x.
| |
| | |
| :(µL)
| |
| :{|
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| !
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| !BST
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| !NBI
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| !tt-RecJ
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| !DTT
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| !BSA
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| !Smix
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| !DNA origami
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| !mQ
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| !Total Amount
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| |-
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| |DNA origami 10x
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| |0.20
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| |0.80
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| |0.30
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| |0.20
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| |0.20
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| |5.00
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| |10.00
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| |3.30
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| |20.00
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| |-
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| |DNA origami 15x
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| |0.20
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| |0.80
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| |0.30
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| |0.20
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| |0.20
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| |5.00
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| |10.00
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| |3.30
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| |20.00
| |
| |}
| |
| | |
| ===DNA Origami with BSA===
| |
| We are also worried if BSA interrupt the AFM and we can not get clear images of DNA origami.
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| Therefore, we prepare the solution for September 20th.
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| The concentration of original DNA origami was 10x and 15x.
| |
| | |
| :(µL)
| |
| :{|
| |
| !
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| !DNA origami
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| !Smix 4x
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| !BSA
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| !mQ
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| !Total Amount
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| |-
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| |DNA origami 10x
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| |2.00
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| |5.00
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| |2.00
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| |11.00
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| |20.00
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| |-
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| |DNA origami 15x
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| |2.00
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| |5.00
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| |2.00
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| |11.00
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| |20.00
| |
| |}
| |
| | |
| ===Bistable System===
| |
| We wanted to know the best concentration for the bistable system.
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| Two different DNA strands, "XII" and "VII", were used for the experiment.
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| We searched the best concentration of CvII and CxII separately.<br/>
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| CvII is the template for doubling V, and CxII is the one of X.
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| "X to inhV" is the template for making inhV DNA from X, and "V to inhX" is the one of V.
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| We change the concentration of CvII and CxII in order to find out the best concentration of them.
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| We keep PCR in 42°C.
| |
| | |
| *The Experiment of VII
| |
| | |
| :(µL)
| |
| :{|
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| !
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| !Bst
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| !NBI
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| !tt-RecJ
| |
| !DTT
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| !BSA
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| !Smix 4x
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| !V to inhX
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| !X to inhV
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| !dTTP
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| !VII
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| !CvII
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| !mQ
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| !Total Amount
| |
| |-
| |
| |5x
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| |0.21
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.42
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| |0.21
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| |0.11
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| |0.11
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| |12.69
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| |21.00
| |
| |-
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| |10x
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| |0.21
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.42
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| |0.21
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| |0.11
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| |0.21
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| |12.59
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| |21.00
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| |-
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| |15x
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| |0.21
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.42
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| |0.21
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| |0.11
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| |0.32
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| |12.48
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| |21.00
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| |-
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| |20x
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| |0.21
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.42
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| |0.21
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| |0.11
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| |0.43
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| |12.37
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| |21.00
| |
| |}
| |
| | |
| | |
| *The Experiment of XII
| |
| | |
| :(µL)
| |
| :{|
| |
| !
| |
| !Bst
| |
| !NBI
| |
| !tt-RecJ
| |
| !DTT
| |
| !BSA
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| !Smix 4x
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| !V to inhX
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| !X to inhV
| |
| !dTTP
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| !XII
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| !CxII
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| !mQ
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| !Total Amount
| |
| |-
| |
| |5x
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| |0.21
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| |0.84
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| |0.32
| |
| |0.21
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| |0.21
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| |5.25
| |
| |0.42
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| |0.42
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| |0.21
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| |0.11
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| |0.11
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| |12.69
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| |21.00
| |
| |-
| |
| |10x
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| |0.21
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| |0.84
| |
| |0.32
| |
| |0.21
| |
| |0.21
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| |5.25
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| |0.42
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| |0.42
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| |0.21
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| |0.11
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| |0.21
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| |12.59
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| |21.00
| |
| |-
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| |15x
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| |0.21
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.42
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| |0.21
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| |0.11
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| |0.32
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| |12.48
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| |21.00
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| |-
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| |20x
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| |0.21
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.42
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| |0.21
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| |0.11
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| |0.43
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| |12.37
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| |21.00
| |
| |}
| |
| | |
| When several hours passed after keeping these tubes in 42°C, we injected XII 0.40µL in each VII tubes and VII 0.40µL in each XII tubes.
| |
| Then we kept these tubes in 42°C for about 1 day.
| |
|
| |
| ==September 24th==
| |
| | |
| ===Bistable System===
| |
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| We change the condition of the bistable experiment and put some tubes in PCR.
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| The concentration of Bst and X to inhV were different from the same experiment of September 19th.
| |
| We kept these tubes in 42°C.
| |
| | |
| *The Experiment of VII
| |
| | |
| :(µL)
| |
| :{| border="2"
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| !
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| !Bst
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| !NBI
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| !tt-RecJ
| |
| !dTTP
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| !BSA
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| !Smix 4x
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| !V to inhX
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| !X to inhV
| |
| !DTTP
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| !VII
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| !CvII
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| !mQ
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| !Total Amount
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| |-
| |
| |5x
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| |0.17
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.32
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| |0.21
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| |0.11
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| |0.11
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| |12.83
| |
| |21.00
| |
| |-
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| |10x
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| |0.17
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.32
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| |0.21
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| |0.11
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| |0.21
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| |12.73
| |
| |21.00
| |
| |-
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| |15x
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| |0.17
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.32
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| |0.21
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| |0.11
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| |0.32
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| |12.62
| |
| |21.00
| |
| |-
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| |20x
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| |0.17
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| |0.84
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| |0.32
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| |0.21
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| |0.21
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| |5.25
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| |0.42
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| |0.32
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| |0.21
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| |0.11
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| |0.43
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| |12.51
| |
| |21.00
| |
| |}
| |
| | |
| | |
| *The Experiment of XII
| |
| | |
| :(µL)
| |
| :{|
| |
| !
| |
| !Bst
| |
| !NBI
| |
| !tt-RecJ
| |
| !DTT
| |
| !BSA
| |
| !Smix 4x
| |
| !V to inhX
| |
| !X to inhV
| |
| !dTTP
| |
| !XII
| |
| !CxII
| |
| !mQ
| |
| !Total Amount
| |
| |-
| |
| |5x
| |
| |0.17
| |
| |0.84
| |
| |0.32
| |
| |0.21
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| |0.21
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| |5.25
| |
| |0.42
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| |0.32
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| |0.21
| |
| |0.11
| |
| |0.11
| |
| |12.83
| |
| |21.00
| |
| |-
| |
| |10x
| |
| |0.17
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| |0.84
| |
| |0.32
| |
| |0.21
| |
| |0.21
| |
| |5.25
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| |0.42
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| |0.32
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| |0.21
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| |0.11
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| |0.21
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| |12.73
| |
| |21.00
| |
| |-
| |
| |15x
| |
| |0.17
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| |0.84
| |
| |0.32
| |
| |0.21
| |
| |0.21
| |
| |5.25
| |
| |0.42
| |
| |0.32
| |
| |0.21
| |
| |0.11
| |
| |0.32
| |
| |12.62
| |
| |21.00
| |
| |-
| |
| |20x
| |
| |0.17
| |
| |0.84
| |
| |0.32
| |
| |0.21
| |
| |0.21
| |
| |5.25
| |
| |0.42
| |
| |0.32
| |
| |0.21
| |
| |0.11
| |
| |0.43
| |
| |12.51
| |
| |21.00
| |
| |}
| |
| | |
| | |
| When several hours had passed since we put them in PCR, we injected XII 0.40µL in each VII tubes and VII 0.40µL in each XII tubes.
| |
| Then we kept these tubes in 42°C for about 1 day as the bistable experiment we did before.
| |
| | |
| ==September 28th==
| |
| | |
| ===Bistable System===
| |
| We could not get a good result of the bistable system so that we change several part of the system.
| |
| We introduce two types of DNA, "DII" and "NII", and two types of templates, "D to V" and "N to X" in the system.
| |
| We change the concentration of "D to V" and "N to X", which are always the saame concentration.
| |
| We also kept these tubes in 42°C.
| |
| | |
| *The Experiment of XII
| |
| | |
| :(µL)
| |
| :{|
| |
| ! !!BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! XII !! CxII !! CvII !! D to V !! N to X !! mQ !! Total Amount
| |
| |- | | |- |
| | 2.5nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.05 || 0.05 || 12.20 ||21.00 | | ! Mg2+ |
| | | Essential for keeping the shape of origami |
| |- | | |- |
| | 5.0nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.11 || 0.11 || 12.08 ||21.00 | | ! Smix |
| | | Buffer contains a lot of essential chemicals |
| |- | | |- |
| | 7.5nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.16 || 0.16 || 11.98 ||21.00 | | ! DTT |
| | | Buffer which contains DTT |
| |- | | |- |
| | 10.0nM ||0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.21 || 0.21 || 11.88 ||21.00
| | ! dTTP |
| |}
| | | Buffer which contains dTTP |
| | |
| *The Experiment of VII
| |
| | |
| :(µL)
| |
| :{|
| |
| ! !!BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! VII !! CxII !! CvII !! D to V !! N to X !! mQ !! Total Amount
| |
| |- | |
| | 2.5nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.05 || 0.05 || 12.20 ||21.00
| |
| |-
| |
| | 5.0nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.11 || 0.11 || 12.08 ||21.00
| |
| |- | | |- |
| | 7.5nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.16 || 0.16 || 11.98 ||21.00 | | ! BSA |
| | | Buffer which contains BSA |
| |- | | |- |
| | 10.0nM ||0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.21 || 0.21 || 11.88 ||21.00 | | ! mQ |
| | | Pure water |
| |} | | |} |
|
| |
|
|
| |
|
| When several hours had passed since we put these tubes in PCR, we put DII in tubes of X and NII in that of V so that the concentration of X or V might not change radically.
| | ===Enzymes=== |
| After putting DNAs, we kept them in PCR.
| |
| | |
| ==October 1st== | |
| | |
| ===Bistable System=== | |
| We conducted the same experiment as what we did in September 28th.
| |
| We got enough information about the experiment of VII, so we only conducted that of VII.
| |
| The purpose of the experiment is to find out the best condition of the experiment of XII.
| |
| We changed the concentration of CvII and X to inhV and compared the results.
| |
| | |
| | |
| *The Concentration of X to inhV: 10.00nM.
| |
|
| |
|
| :(µL)
| | {| class="tdleft" |
| :{|
| | ! NBI |
| ! !!BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! XII !! CxII !! CvII !! D to V !! N to X !! mQ !! Total Amount
| | | Buffer which contains DNA nickase |
| |- | | |- |
| | CvII: 20.00nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.20 || 0.20 || 0.10 || 0.10 || 0.40 || 0.20 || 0.20 || 11.54 ||20.00 | | ! Bst |
| | | Buffer which contains DNA polymerase |
| |- | | |- |
| | CvII: 22.50nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.20 || 0.20 || 0.10 || 0.10 || 0.45 || 0.20 || 0.20 || 11.49 ||20.00 | | ! tt-RecJ |
| | | Buffer which contains DNA exonuclease |
| |- | | |- |
| | CvII: 25.00nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.20 || 0.20 || 0.10 || 0.10 || 0.50 || 0.20 || 0.20 || 11.44 ||20.00
| |
| |} | | |} |
|
| |
|
| *The Concentration of X to inhV: 15.00nM
| |
|
| |
|
| :(µL)
| | ===DNAs=== |
| :{|
| | {| class="tdleft" |
| ! !!BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! XII !! CxII !! CvII !! D to V !! N to X !! mQ !! Total Amount | | ! M13 |
| | | Scaffold strand |
| |- | | |- |
| | CvII: 20.00nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.30 || 0.20 || 0.10 || 0.10 || 0.40 || 0.20 || 0.20 || 11.44 ||20.00 | | ! VII |
| | | Strand for Dynamic system |
| |- | | |- |
| | CvII: 22.50nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.30 || 0.20 || 0.10 || 0.10 || 0.45 || 0.20 || 0.20 || 11.39 ||20.00 | | ! XII |
| | | Strand for Dynamic system |
| |- | | |- |
| | CvII: 25.00nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.30 || 0.20 || 0.10 || 0.10 || 0.50 || 0.20 || 0.20 || 11.34 ||20.00
| | ! DII |
| |}
| | | Strand for Dynamic system |
|
| |
| | |
| ==October 2nd==
| |
| | |
| ===Bistable System===
| |
| We lowered the concentratinons of D to V, and N to X.
| |
| Today, we conducted experiments in order to find out the ideal concentration of "X to inhV".
| |
| We kept these tubes in 42°C, and injected once each wells.
| |
| | |
| *The Experiment of XII
| |
| | |
| :(µL)
| |
| :{|
| |
| ! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! XII !! CxII !! CvII !! mQ !! Total Amount
| |
| |- | | |- |
| | 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.21 || 0.21 || 0.11 || 0.11 || 0.42 || 12.54 || 21 | | ! NII |
| | | Strand for Dynamic system |
| |- | | |- |
| | 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.25 || 0.21 || 0.11 || 0.11 || 0.42 || 12.50 || 21 | | ! inhV |
| | | Inhibitor to VII-autocatalisys |
| |- | | |- |
| | 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.28 || 0.21 || 0.11 || 0.11 || 0.42 || 12.47 || 21 | | ! inhX |
| | | Inhibitor to XII-autocatalisys |
| |- | | |- |
| | 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 12.43 || 21 | | ! inhQ |
| | | Inhibitor to QII-autocatalisys |
| |} | | |} |
| :injection: VII 0.6µL each
| |
|
| |
|
| *The Experiment of VII
| |
|
| |
|
| :(µL)
| | ===Templates=== |
| :{|
| |
| ! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! VII !! CxII !! CvII !! mQ !! Total Amount
| |
| |-
| |
| | 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.21 || 0.21 || 0.11 || 0.11 || 0.42 || 12.54 || 21
| |
| |-
| |
| | 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.25 || 0.21 || 0.11 || 0.11 || 0.42 || 12.50 || 21
| |
| |-
| |
| | 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.28 || 0.21 || 0.11 || 0.11 || 0.42 || 12.47 || 21
| |
| |-
| |
| | 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 12.43 || 21
| |
| |}
| |
| :injection: XII 0.6µL each
| |
|
| |
|
| ===Trioscillate System=== | | {| class="tdleft" |
| To investigate ideal condition of trioscillate system, we conducted experiments which checks three parts of this system.
| | ! CvII |
| | | | Autocatalysis template for VII |
| :(µL)
| |
| :{|
| |
| ! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! inhmix !! dTTP !! XII !! CxII !! mQ !! Total Amount
| |
| |- | | |- |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.10 || 12.44 || 20.00 | | ! CxII |
| | | Autocatalysis template for XII |
| |- | | |- |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.20 || 12.34 || 20.00 | | ! V to inhX |
| | | Template which produces inhibitor to XII-autocatalisys from VII |
| |- | | |- |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.30 || 12.24 || 20.00 | | ! V to inhQ |
| | | Template which produces inhibitor to QII-autocatalisys from VII |
| |- | | |- |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.40 || 12.14 || 20.00 | | ! X to inhV |
| | | Template which produces inhibitor to VII-autocatalisys from XII |
| |- | | |- |
| |}
| | ! X to inhQ |
| :injection: VII 0.80µL each
| | | Template which produces inhibitor to QII-autocatalisys from XII |
| | |
| :(µL)
| |
| :{|
| |
| ! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! inhmix !! dTTP !! VII !! CvII !! mQ !! Total Amount | |
| |- | |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.10 || 12.44 || 20.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.20 || 12.34 || 20.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.30 || 12.24 || 20.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.40 || 12.14 || 20.00
| |
| |-
| |
| |}
| |
| :injection: QII 0.80µL each
| |
| | |
| :(µL)
| |
| :{|
| |
| ! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! inhmix !! dTTP !! QII !! CqII !! mQ !! Total Amount
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.10 || 12.44 || 20.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.20 || 12.34 || 20.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.30 || 12.24 || 20.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.50 || 0.20 || 0.10 || 0.40 || 12.14 || 20.00
| |
| |-
| |
| |}
| |
| :injection: XII 0.80µL each
| |
| | |
| ==October 3rd==
| |
| | |
| ===Bistable System===
| |
| In today's experiment, we investigated the ideal temperature for the bistable system.
| |
| We made two solutions (one starts from "X", and the other from "Y"), and observed at 6 different temperatures - 41.6~47.6℃.
| |
| | |
| :(µL)
| |
| :{|
| |
| ! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! D to V,N to X !! V to inhX !! X to inhv !! dTTP !! XII !! VII !! CxII !! CvII !! mQ !! Total Amount
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 1.50 || 0.40 || 0.30 || 0.20 || 0.10 || 0.00 || 0.10 || 0.40 || 10.34 || 20.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 1.50 || 0.40 || 0.30 || 0.20 || 0.00 || 0.10 || 0.10 || 0.40 || 10.34 || 20.00
| |
| |}
| |
| :injection: XII or VII 0.60µL each
| |
| | |
| ==October 11th==
| |
| ===Trioscillate system===
| |
| Today, we tested whole trioscillate system. To investigate the ideal condition, we tested both direction of inhibition (V-|X-|Q, V-|Q-|X) and each concentration of CxII, CvII, CqII.
| |
| | |
| | |
| : inhibit direction: V-|X-|Q
| |
| :(µL)
| |
| :{|
| |
| ! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! inhmix !! dTTP !! XII !! VII !! CxII !! CvII !! CqII !! mQ !! Total Amount
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.50 || 0.40 || 0.50 || 11.22 || 20.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.50 || 0.40 || 1.00 || 11.72 || 21.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.50 || 0.40 || 1.50 || 12.22 || 22.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.50 || 0.40 || 2.00 || 12.72 || 23.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 1.00 || 0.40 || 0.50 || 14.72 || 24.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 1.00 || 0.40 || 1.00 || 15.22 || 25.00
| |
| |- | | |- |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 1.00 || 0.40 || 1.50 || 15.72 || 26.00 | | ! Q to inhV |
| | | Template which produces inhibitor to VII-autocatalisys from QII |
| |- | | |- |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 1.00 || 0.40 || 2.00 || 16.22 || 27.00 | | ! Q to inhX |
| | | Template which produces inhibitor to XII-autocatalisys from QII |
| |- | | |- |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 1.50 || 0.40 || 0.50 || 18.22 || 28.00 | | ! D to V |
| | | Template which produces VII from DII |
| |- | | |- |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 1.50 || 0.40 || 1.00 || 18.72 || 29.00
| | ! N to X |
| |-
| | | Template which produces XII from NII |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 1.50 || 0.40 || 1.50 || 19.22 || 30.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 1.50 || 0.40 || 2.00 || 19.72 || 31.00 | |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 2.00 || 0.40 || 0.50 || 21.72 || 32.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 2.00 || 0.40 || 1.00 || 22.22 || 33.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 2.00 || 0.40 || 1.50 || 22.72 || 34.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 2.00 || 0.40 || 2.00 || 23.22 || 35.00
| |
| |} | | |} |
|
| |
|
|
| |
|
| | | __NOEDITSECTION__ |
| : inhibit direction: V-|Q-|X
| |
| :(µL)
| |
| :{|
| |
| !BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! inhmix !! dTTP !! XII !! VII !! CxII !! CvII !! CqII !! mQ !! Total Amount
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 0.50 || 0.50 || 11.52 || 20.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 0.50 || 1.00 || 12.02 || 21.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 0.50 || 1.50 || 12.52 || 22.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 0.50 || 2.00 || 13.02 || 23.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 1.00 || 0.50 || 15.02 || 24.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 1.00 || 1.00 || 15.52 || 25.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 1.00 || 1.50 || 16.02 || 26.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 1.00 || 2.00 || 16.52 || 27.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 1.50 || 0.50 || 18.52 || 28.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 1.50 || 1.00 || 19.02 || 29.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 1.50 || 1.50 || 19.52 || 30.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 1.50 || 2.00 || 20.02 || 31.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 2.00 || 0.50 || 22.02 || 32.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 2.00 || 1.00 || 22.52 || 33.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 2.00 || 1.50 || 23.02 || 34.00
| |
| |-
| |
| | 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.10 || 0.11 || 0.11 || 0.10 || 2.00 || 2.00 || 23.52 || 35.00
| |
| |}
| |
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Experiment
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Dynamic System
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DNA Origami
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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/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>
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DNA Tablet
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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>
Lab Notes
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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>
Glossary
Buffers
TAE
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Essential buffer for making origami, which contains TAE
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Mg2+
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Essential for keeping the shape of origami
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Smix
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Buffer contains a lot of essential chemicals
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DTT
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Buffer which contains DTT
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dTTP
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Buffer which contains dTTP
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BSA
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Buffer which contains BSA
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mQ
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Pure water
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Enzymes
NBI
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Buffer which contains DNA nickase
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Bst
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Buffer which contains DNA polymerase
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tt-RecJ
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Buffer which contains DNA exonuclease
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DNAs
M13
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Scaffold strand
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VII
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Strand for Dynamic system
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XII
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Strand for Dynamic system
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DII
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Strand for Dynamic system
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NII
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Strand for Dynamic system
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inhV
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Inhibitor to VII-autocatalisys
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inhX
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Inhibitor to XII-autocatalisys
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inhQ
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Inhibitor to QII-autocatalisys
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Templates
CvII
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Autocatalysis template for VII
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CxII
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Autocatalysis template for XII
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V to inhX
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Template which produces inhibitor to XII-autocatalisys from VII
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V to inhQ
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Template which produces inhibitor to QII-autocatalisys from VII
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X to inhV
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Template which produces inhibitor to VII-autocatalisys from XII
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X to inhQ
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Template which produces inhibitor to QII-autocatalisys from XII
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Q to inhV
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Template which produces inhibitor to VII-autocatalisys from QII
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Q to inhX
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Template which produces inhibitor to XII-autocatalisys from QII
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D to V
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Template which produces VII from DII
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N to X
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Template which produces XII from NII
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