Team:HokkaidoU Japan/Notebook/aggregation Week 10
From 2012.igem.org
(Incubation of eCFP-RBS-pSB1A2 for mini-prep) |
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#Re-suspended 2 colony mixture (No.2 and No.5 respectively). | #Re-suspended 2 colony mixture (No.2 and No.5 respectively). | ||
#Incubated at 37C for hrs. | #Incubated at 37C for hrs. | ||
+ | </p> | ||
+ | |||
+ | ==Digestion of eCFP-RBS-pSB1A2 and pBAD-RBS-pSB1A2== | ||
+ | <p> | ||
+ | To make a construct of pBAD-RBS-eCFP-RBS-pSB1A2, we digested eCFP-RBS-pSB1A2 with XbaI & PstI and pBAD-RBS-pSB1A2 with SpeI & PstI. And we digested eCFP-pSB1A2 with XbaI & SpeI as a control for confirmation of the ability to digest. | ||
+ | |||
+ | Insert (eCFP-RBS-pSB1A2) | ||
+ | {|class="hokkaidou-table-digestion" | ||
+ | |- | ||
+ | |DNA solution ( 35ng/ul) | ||
+ | |11 ul | ||
+ | |- | ||
+ | |EcoRI | ||
+ | |1 ul | ||
+ | |- | ||
+ | |SpeI | ||
+ | |1 ul | ||
+ | |- | ||
+ | |10xH buffer | ||
+ | |2 ul | ||
+ | |- | ||
+ | |DW | ||
+ | |5 ul | ||
+ | |- | ||
+ | |Total | ||
+ | |20 ul | ||
+ | |} | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | Vector(pBAD-RBS-pSB1A2) | ||
+ | {|class="hokkaidou-table-digestion" | ||
+ | |- | ||
+ | |DNA solution ( 29ng/ul) | ||
+ | |6 ul | ||
+ | |- | ||
+ | |EcoRI | ||
+ | |1 ul | ||
+ | |- | ||
+ | |XbaI | ||
+ | |1 ul | ||
+ | |- | ||
+ | |10xM buffer | ||
+ | |2 ul | ||
+ | |- | ||
+ | |DW | ||
+ | |10 ul | ||
+ | |- | ||
+ | |Total | ||
+ | |20 ul | ||
+ | |} | ||
+ | |||
+ | |||
+ | control (pT7-RBS-pSB1C3) | ||
+ | {|class="hokkaidou-table-digestion" | ||
+ | |- | ||
+ | |DNA solution (30 ng/ul) | ||
+ | |6 ul | ||
+ | |- | ||
+ | |XbaI | ||
+ | |1 ul | ||
+ | |- | ||
+ | |10xM buffer | ||
+ | |2 ul | ||
+ | |- | ||
+ | |100x BSA | ||
+ | |0.2 | ||
+ | |- | ||
+ | |DW | ||
+ | |11 ul | ||
+ | |- | ||
+ | |Total | ||
+ | |20 ul | ||
+ | |} | ||
+ | |||
+ | |||
+ | |||
+ | {|class="hokkaidou-table-digestion" | ||
+ | |- | ||
+ | |Number | ||
+ | |Degree | ||
+ | |Minute | ||
+ | |- | ||
+ | |1 | ||
+ | |37 | ||
+ | |120 | ||
+ | |- | ||
+ | |2 | ||
+ | |60 | ||
+ | |15 | ||
+ | |- | ||
+ | |3 | ||
+ | |4 | ||
+ | |HOLD | ||
+ | |} | ||
+ | |||
+ | |||
+ | [[image:HokkaidoU2012 120902 Digestion I-+ V-+ C(XbaI)-+.jpg|thumb|digestion result]] | ||
+ | |||
+ | |||
+ | From this image, we confirmed that DNA were digested into fragments and all of restriction enzyme worked. | ||
+ | </p> | ||
+ | |||
+ | ==Estimation of concentration of eCFP, pT7-RBS-Ag43-dT-pSB1C3 and Ag43-dT-pSB1AK3== | ||
+ | <p> | ||
+ | No.2,5 means the colony number of colony PCR of eCFP-RBS-pSB1A2. | ||
+ | |||
+ | |||
+ | [[image:.jpg|thumb|electrophoresis result]] | ||
+ | |||
+ | |||
+ | We estimated the concentration of pT7-RBS-Ag43-dT-pSB1C3 is 31 ng/ul and Ag43-dT-pSB1AK3 is 35ng/ul. | ||
+ | </p> | ||
+ | |||
+ | ==Ethanol precipitation of digestion products (eCFP and RBS-pSB1A2) and estimation of concentration== | ||
+ | <p> | ||
+ | #Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol. | ||
+ | #Centrifuged in 14000 rpm, 30 min at 4C. | ||
+ | #Remove supernatant and added 220 ul of 70% ethanol. | ||
+ | #Centrifuged in 15000 rpm, 15 min at 4C. | ||
+ | #Remove supernatant and air drying in room temperature then added 5 ul of DW. | ||
+ | |||
+ | |||
+ | [[image:HokkaidoU2012 120902 Ethapre V I.jpg|thumb|ethanol precipitation result]] | ||
+ | |||
+ | We estimated the concentration of ethanol presipitation products.The concentration of Insert DNA solution is about 20 ng/ul and Vector DNA solution is about 37 ng/ul. | ||
+ | </p> | ||
+ | |||
+ | ==Ligation of eCFP and RBS-pSB1A2== | ||
+ | <p> | ||
+ | {|class="hokkaidou-table-ligation" | ||
+ | |- | ||
+ | |Vector DNA (37 ng/ul) | ||
+ | |1 ul | ||
+ | |- | ||
+ | |Insert DNA (20 ng/ul | ||
+ | |4 ul | ||
+ | |- | ||
+ | |Ligation Mighty Mix | ||
+ | |6 ul | ||
+ | |- | ||
+ | |Total | ||
+ | |11 ul | ||
+ | |} | ||
+ | |||
+ | |||
+ | Ligation reaction time was in detail below. | ||
+ | |||
+ | {|class="hokkaidou-table-ligation" | ||
+ | |- | ||
+ | |Degree | ||
+ | |Minute | ||
+ | |- | ||
+ | |16 | ||
+ | |30 | ||
+ | |- | ||
+ | |65 | ||
+ | |10 | ||
+ | |- | ||
+ | |4 | ||
+ | |Hold | ||
+ | |} | ||
+ | |||
+ | </p> | ||
+ | |||
+ | ==Transformation of eCFP-RBS-pSB1A2== | ||
+ | <p> | ||
+ | #Mixed 2 ul eCFP-RBS-pSB1A2 ligation product to 50 ul of thawed competent cells on ice. | ||
+ | #Incubated on ice for 30 min. | ||
+ | #Mixed 350 ul of LB. | ||
+ | #Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBA). | ||
+ | #Plated 300 ul of the culture onto first dish and spread. | ||
+ | #Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread. | ||
+ | #Incubated the plates at 37C for 19 hours. | ||
</p> | </p> | ||
Revision as of 21:30, 3 September 2012
September 3rd
Colony PCR of eCFP-RBS-pSB1A2
DNA solution | 4 ul |
Kapa-Taq(Taq polymerase) | 5 ul |
Forward Primer(EX-F primer) | 0.5 ul |
Reverse Primer(PS-R down primer) | 0.5 ul |
Total | 10 ul |
Number | Degree | Second |
1 | 95 | 120 |
2 | 95 | 30 |
3 | 68.9 | 30 |
4 | 72 | 60 |
5 | 72 | 60 |
6 | 4 | HOLD |
Cycle:2~4 x 35
We used N1 (DW only) and N2 (ptetR-RBS-eCFP-dT-pSB1A2) as controls. Desired product is about 776bp.
We confirmed that about 70% of ligated DNA formed our desired construct. We selected No.2 and 5 colony for incubation and store No.7 and 8 colony mixture at 4C.
Incubation of eCFP-RBS-pSB1A2 for mini-prep
- Prepared 2 ml LBA into culture tubes.
- Re-suspended 2 colony mixture (No.2 and No.5 respectively).
- Incubated at 37C for hrs.
Digestion of eCFP-RBS-pSB1A2 and pBAD-RBS-pSB1A2
To make a construct of pBAD-RBS-eCFP-RBS-pSB1A2, we digested eCFP-RBS-pSB1A2 with XbaI & PstI and pBAD-RBS-pSB1A2 with SpeI & PstI. And we digested eCFP-pSB1A2 with XbaI & SpeI as a control for confirmation of the ability to digest. Insert (eCFP-RBS-pSB1A2)
DNA solution ( 35ng/ul) | 11 ul |
EcoRI | 1 ul |
SpeI | 1 ul |
10xH buffer | 2 ul |
DW | 5 ul |
Total | 20 ul |
Vector(pBAD-RBS-pSB1A2)
DNA solution ( 29ng/ul) | 6 ul |
EcoRI | 1 ul |
XbaI | 1 ul |
10xM buffer | 2 ul |
DW | 10 ul |
Total | 20 ul |
control (pT7-RBS-pSB1C3)
DNA solution (30 ng/ul) | 6 ul |
XbaI | 1 ul |
10xM buffer | 2 ul |
100x BSA | 0.2 |
DW | 11 ul |
Total | 20 ul |
Number | Degree | Minute |
1 | 37 | 120 |
2 | 60 | 15 |
3 | 4 | HOLD |
From this image, we confirmed that DNA were digested into fragments and all of restriction enzyme worked.
Estimation of concentration of eCFP, pT7-RBS-Ag43-dT-pSB1C3 and Ag43-dT-pSB1AK3
No.2,5 means the colony number of colony PCR of eCFP-RBS-pSB1A2.
We estimated the concentration of pT7-RBS-Ag43-dT-pSB1C3 is 31 ng/ul and Ag43-dT-pSB1AK3 is 35ng/ul.
Ethanol precipitation of digestion products (eCFP and RBS-pSB1A2) and estimation of concentration
- Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
- Centrifuged in 14000 rpm, 30 min at 4C.
- Remove supernatant and added 220 ul of 70% ethanol.
- Centrifuged in 15000 rpm, 15 min at 4C.
- Remove supernatant and air drying in room temperature then added 5 ul of DW.
We estimated the concentration of ethanol presipitation products.The concentration of Insert DNA solution is about 20 ng/ul and Vector DNA solution is about 37 ng/ul.
Ligation of eCFP and RBS-pSB1A2
Vector DNA (37 ng/ul) | 1 ul |
Insert DNA (20 ng/ul | 4 ul |
Ligation Mighty Mix | 6 ul |
Total | 11 ul |
Ligation reaction time was in detail below.
Degree | Minute |
16 | 30 |
65 | 10 |
4 | Hold |
Transformation of eCFP-RBS-pSB1A2
- Mixed 2 ul eCFP-RBS-pSB1A2 ligation product to 50 ul of thawed competent cells on ice.
- Incubated on ice for 30 min.
- Mixed 350 ul of LB.
- Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBA).
- Plated 300 ul of the culture onto first dish and spread.
- Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
- Incubated the plates at 37C for 19 hours.