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=Experiment=


=Our Labo Note=
Please click on the section you want to learn more about.


==Dynamic System==


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>


==September 12th==
==DNA Origami==


===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>


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>


:(µL)
=Lab Notes=
:{|
!
! M13
! Staple Mix
! TAE 10x
! Mg2+
! mQ
! Total Amount
|-
| A
|3.00
|7.20
|1.80
|2.25
|3.75
|20.00
|-
| B
|3.00
|3.60
|1.80
|2.25
|7.35
|20.00
|-
| C
|3.00
|10.80
|1.80
|2.25
|0.15
|20.00
|}


<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>


==September 13th==


===DNA Origami===
We observed DNA origami which we made September 12th by AFM.


==Glossary==


*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]]


 
{| 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
 
|-
 
! Mg2+
 
| Essential for keeping the shape of origami
==September 19th==
|-
 
! Smix  
===DNA Origami===
| Buffer contains a lot of essential chemicals
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)
:{|
!
! Staple Mix
! M13
! TAE 10x
! Mg2+
! mQ
! Total Amount
|-
| A
|8.00
|3.33
|2.00
|0.25
|6.42
|20.00
|-
| B
|12.00
|5.00
|2.00
|0.25
|0.75
|20.00
|}
 
 
===DNA Origami with Enzymes===
 
We use enzymes in bistable system, therefore we make sure that the enzymes do not destroy the DNA origami.
We put nickase, polymerase and exnuclease with DNA origami and left them in the PCR.
The concentration of original DNA origami was 10x and 15x.
 
:(µL)
:{|
!
!BST
!NBI
!tt-RecJ
!DTT
!BSA
!Smix
!DNA origami
!mQ
!Total Amount
|-
|DNA origami 10x
|0.20
|0.80
|0.30
|0.20
|0.20
|5.00
|10.00
|3.30
|20.00
|-
|DNA origami 15x
|0.20
|0.80
|0.30
|0.20
|0.20
|5.00
|10.00
|3.30
|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.
Therefore, we prepare the solution for September 20th.
The concentration of original DNA origami was 10x and 15x.
 
:(µL)
:{|
!
!DNA origami
!Smix 4x
!BSA
!mQ
!Total Amount
|-
|DNA origami 10x
|2.00
|5.00
|2.00
|11.00
|20.00
|-
|DNA origami 15x
|2.00
|5.00
|2.00
|11.00
|20.00
|}
 
===Bistable System===
We wanted to know the best concentration for the bistable system.
Two different DNA strands, "XII" and "VII", were used for the experiment.
We searched the best concentration of CvII and CxII separately.<br/>
CvII is the template for doubling V, and CxII is the one of X.
"X to inhV" is the template for making inhV DNA from X, and "V to inhX" is the one of V.
We change the concentration of CvII and CxII in order to find out the best concentration of them.
We keep PCR in 42℃.
 
*The Experiment of VII
 
:(µL)
:{|
  !
  !Bst
  !NBI
  !tt-RecJ
  !DTT
  !BSA
  !Smix 4x
  !V to inhX
  !X to inhV
  !dTTP
  !VII
  !CvII
  !mQ
  !Total Amount
  |-
  |5x
  |0.21
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.42
  |0.21
  |0.11
  |0.11
  |12.69
  |21.00
  |-
  |10x
  |0.21
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.42
  |0.21
  |0.11
  |0.21
  |12.59
  |21.00
  |-
  |15x
  |0.21
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.42
  |0.21
  |0.11
  |0.32
  |12.48
  |21.00
  |-
  |20x
  |0.21
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.42
  |0.21
  |0.11
  |0.43
  |12.37
  |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
  |0.21
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.42
  |0.21
  |0.11
  |0.11
  |12.69
  |21.00
  |-
  |10x
  |0.21
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.42
  |0.21
  |0.11
  |0.21
  |12.59
  |21.00
  |-
  |15x
  |0.21
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.42
  |0.21
  |0.11
  |0.32
  |12.48
  |21.00
  |-
  |20x
  |0.21
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.42
  |0.21
  |0.11
  |0.43
  |12.37
  |21.00
  |}
 
When several hours passed after keeping these tubes in 42℃, we injected XII 0.4µL in each VII tubes and VII 0.4µL in each XII tubes.
Then we kept these tubes in 42℃ for about 1 day.
==September 24th==
 
===Bistable System===
 
We change the condition of the bistable experiment and put some tubes in PCR.
The concentration of Bst and X to inhV were different from the same experiment of September 19th.
We kept these tubes in 42℃.
 
*The Experiment of VII
 
:(µL)
:{| border="2"
  !
  !Bst
  !NBI
  !tt-RecJ
  !dTTP
  !BSA
  !Smix 4x
  !V to inhX
  !X to inhV
  !DTTP
  !VII
  !CvII
  !mQ
  !Total Amount
  |-
  |5x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.11
  |0.11
  |12.83
  |21.00
  |-
  |10x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.11
  |0.21
  |12.73
  |21.00
  |-
  |15x
  |0.17
  |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
  |}
 
 
*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
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.11
  |0.11
  |12.83
  |21.00
  |-
  |10x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.11
  |0.21
  |12.73
  |21.00
  |-
  |15x
  |0.17
  |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 0.4µL in each VII tubes and VII 0.4µL in each XII tubes.
Then we kept these tubes in 42℃ 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 also kept these tubes in 42℃.
 
*The Experiment of VII
 
:(µL)
:{|
  !
  !Bst
  !NBI
  !tt-RecJ
  !dTTP
  !BSA
  !Smix 4x
  !V to inhX
  !X to inhV
  !D to V
  !N to X
  !dTTP
  !VII
  !CvII
  !mQ
  !Total Amount
  |-
  |5x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.21
  |0.21
  |0.11
  |0.11
  |12.41
  |21.00
  |-
  |10x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.21
  |0.21
  |0.11
  |0.21
  |12.31
  |21.00
  |-
  |15x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.21
  |0.21
  |0.11
  |0.32
  |12.20
  |21.00
  |-
  |20x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.21
  |0.21
  |0.11
  |0.43
  |12.09
  |21.00
  |}
 
 
*The Experiment of XII
 
:(µL)
:{|
  !
  !Bst
  !NBI
  !tt-RecJ
  !DTT
  !BSA
  !Smix 4x
  !V to inhX
  !X to inhV
  !D to V
  !N to X
  !dTTP
  !XII
  !CxII
  !mQ
  !Total Amount
  |-
  |5x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.21
  |0.21
  |0.11
  |0.11
  |12.41
  |21.00
  |-
  |10x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.21
  |0.21
  |0.11
  |0.21
  |12.31
  |21.00
  |-
  |15x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.21
  |0.21
  |0.11
  |0.32
  |12.20
  |21.00
  |-
  |20x
  |0.17
  |0.84
  |0.32
  |0.21
  |0.21
  |5.25
  |0.42
  |0.32
  |0.21
  |0.21
  |0.21
  |0.11
  |0.43
  |12.09
  |21.00
  |}
 
 
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.
After putting DNAs, we kept them in PCR.
 
==October 1st==
 
===Bistable 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.
 
*Tubes which start from "X"
 
:(µL)
:{|
! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! VtoinhX !! Xtoinhv !! DTTP !! XII !! CXII !! CVII !! mQ !! Total Amount
|-
|-
| 0.168 || 0.84 || 0.315 || 0.21 || 0.21 || 5.25 || 0.42 || 0.21 || 0.21 || 0.105 || 0.105 || 0.42 || 12.537 || 21
! DTT
| Buffer which contains DTT
|-
|-
| 0.168 || 0.84 || 0.315 || 0.21 || 0.21 || 5.25 || 0.42 || 0.245 || 0.21 || 0.105 || 0.105 || 0.42 || 12.502 || 21
! dTTP
| Buffer which contains dTTP
|-
|-
| 0.168 || 0.84 || 0.315 || 0.21 || 0.21 || 5.25 || 0.42 || 0.28 || 0.21 || 0.105 || 0.105 || 0.42 || 12.467 || 21
! BSA
| Buffer which contains BSA
|-
|-
| 0.168 || 0.84 || 0.315 || 0.21 || 0.21 || 5.25 || 0.42 || 0.315 || 0.21 || 0.105 || 0.105 || 0.42 || 12.432 || 21
! mQ
| Pure water
|}
|}
:injection: VII 0.6µL each


*Tubes which start from "V"


:(µL)
===Enzymes===
:{|
 
! BST  !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! VtoinhX !! Xtoinhv !! DTTP !! VII !! CXII !! CVII !! mQ !! Total Amount
{| class="tdleft"
|-
! NBI  
| 0.168 || 0.84 || 0.315 || 0.21 || 0.21 || 5.25 || 0.42 || 0.21 || 0.21 || 0.105 || 0.105 || 0.42 || 12.537 || 21
| Buffer which contains DNA nickase
|-
|-
| 0.168 || 0.84 || 0.315 || 0.21 || 0.21 || 5.25 || 0.42 || 0.245 || 0.21 || 0.105 || 0.105 || 0.42 || 12.502 || 21
! Bst
| Buffer which contains DNA polymerase
|-
|-
| 0.168 || 0.84 || 0.315 || 0.21 || 0.21 || 5.25 || 0.42 || 0.28 || 0.21 || 0.105 || 0.105 || 0.42 || 12.467 || 21
! tt-RecJ
| Buffer which contains DNA exonuclease
|-
|-
| 0.168 || 0.84 || 0.315 || 0.21 || 0.21 || 5.25 || 0.42 || 0.315 || 0.21 || 0.105 || 0.105 || 0.42 || 12.432 || 21
|}
|}
:injection: XII 0.6µL each


===Trioscillate System===
To investigate ideal condition of trioscillate system, we conducted experiments which checks three parts of this system.


:(µL)
===DNAs===
:{|
{| class="tdleft"
! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! inhmix !! dTTPs !! XII !! CXII !! mQ !! Total Amount
! M13
| Scaffold strand
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.1 || 12.44 || 20
! VII
| Strand for Dynamic system
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.2 || 12.34 || 20
! XII
| Strand for Dynamic system
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.3 || 12.24 || 20
! DII
| Strand for Dynamic system
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.4 || 12.14 || 20
! NII
| Strand for Dynamic system
|-
|-
! inhV
| Inhibitor to VII-autocatalisys
|-
! inhX
| Inhibitor to XII-autocatalisys
|-
! inhQ
| Inhibitor to QII-autocatalisys
|}
|}
:injection: VII 0.8µL  each


:(µL)
 
:{|
===Templates===
! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! inhmix !! dTTPs !! VII !! CVII !! mQ !! Total Amount
 
|-
{| class="tdleft"
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.1 || 12.44 || 20
! CvII
| Autocatalysis template for VII
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.2 || 12.34 || 20
! CxII
| Autocatalysis template for XII
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.3 || 12.24 || 20
! V to inhX
| Template which produces inhibitor to XII-autocatalisys from VII
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.4 || 12.14 || 20
! V to inhQ
| Template which produces inhibitor to QII-autocatalisys from VII
|-
|-
|}
! X to inhV
:injection: QII 0.8µL  each
| Template which produces inhibitor to VII-autocatalisys from XII
 
:(µL)
:{|
! BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! inhmix !! dTTPs !! QII !! CQII !! mQ !! Total Amount
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.1 || 12.44 || 20
! X to inhQ
| Template which produces inhibitor to QII-autocatalisys from XII
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.2 || 12.34 || 20
! Q to inhV
| Template which produces inhibitor to VII-autocatalisys from QII
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.3 || 12.24 || 20
! Q to inhX
| Template which produces inhibitor to XII-autocatalisys from QII
|-
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 0.5 || 0.2 || 0.1 || 0.4 || 12.14 || 20
! D to V
| Template which produces VII from DII
|-
|-
! N to X
| Template which produces XII from NII
|}
|}
:injection: XII 0.8µL  each


==October 3rd==


===Bistable System===
__NOEDITSECTION__
In today's experiment, we investigated the ideal temperature for the bistable system.
We made two solutions (one is 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  !! DtoV,NtoX !!  VtoinhX  !!  Xtoinhv  !!  dTTPs !!  XII  !! VII !!  CXII  !!  CVII  !!  mQ  !!  total amount
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 1.5 || 0.4 || 0.3 || 0.2 || 0.1 || 0 || 0.1 || 0.4 || 10.34 || 20
|-
| 0.16 || 0.8 || 0.3 || 0.2 || 0.2 || 5 || 1.5 || 0.4 || 0.3 || 0.2 || 0 || 0.1 || 0.1 || 0.4 || 10.34 || 20
|}
:injection: XII or VII 0.6µL each

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

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Lab Notes

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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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