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

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==October 2nd==
==October 2nd==
===Bistable System===
===Bistable System===
hoge
We  lowered the concentratinons of DtoX, and NtoY.
Today, we conducted eperiments in order to find out the ideal concentration of "X to unhV"
 
*Experiment of VII
 
:(µL)
:{| border="2"
  |
  |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
  |}

Revision as of 02:35, 13 October 2012

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Our Labo Note

We conducted a lot of experiments at Komaba Research Campus.

September 13th

DNA Origami

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


  • AFM image of A


  • AFM image of C

September 12th

DNA Origami

We made a solution of DNA origami.

(µL)
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


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)
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.
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 "Vto inhX" is the one of V.

  • 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

October 2nd

Bistable System

We lowered the concentratinons of DtoX, and NtoY. Today, we conducted eperiments in order to find out the ideal concentration of "X to unhV"

  • 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
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