Team:HokkaidoU Japan/Notebook/aggregation Week 9
From 2012.igem.org
(28th) |
(28th ~ptet-RBs-eYFP-dT transformation) |
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|} | |} | ||
Cycle:2~4 x 35 | Cycle:2~4 x 35 | ||
+ | |||
+ | [[image:|thumb|PCR result]] | ||
</p> | </p> | ||
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<div> | <div> | ||
==mini-prep of pT7-RBS-Ag43-dT on pSB1C3== | ==mini-prep of pT7-RBS-Ag43-dT on pSB1C3== | ||
- | |||
<p> | <p> | ||
+ | Mini-prep of pT7-RBS-Ag43-dT on pSB1C3. We re-suspended No.1,2 colonies and incubated. | ||
[[image:|thumb|mini-prep result]] | [[image:|thumb|mini-prep result]] | ||
</p> | </p> | ||
+ | |||
+ | ==Estimation of Concentration of RBS-eYFP-dT and ptetR-pSB1A2== | ||
+ | <p> | ||
+ | {| | ||
+ | |Solution | ||
+ | |Value(ul) | ||
+ | |- | ||
+ | |1kb ladder | ||
+ | |1 | ||
+ | |- | ||
+ | |Insert | ||
+ | |1 | ||
+ | |- | ||
+ | |Vector | ||
+ | |1 | ||
+ | |- | ||
+ | |} | ||
+ | |||
+ | |||
+ | [[image:|thumb|Electrophoresis result]] | ||
+ | |||
+ | |||
+ | From this result, We estimated that the concentration of Insert DNA solution is about 40mM, and Vector DNA is also about 40mM. | ||
+ | </p> | ||
+ | |||
+ | ==Digestion of ptet-pSB1A2 and RBS-Ag43-dT== | ||
+ | <p> | ||
+ | ptet-pSB1A2(Vector) was digested with SpeI and PstI, and RBS-Ag43-dT(Insert) was cut with XbaI and PstI. | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | Vector | ||
+ | {|class="hokkaidou-table-digestion" | ||
+ | |- | ||
+ | |DNA solution ( 40ng/ul) | ||
+ | |5 ul | ||
+ | |- | ||
+ | |SpeI | ||
+ | |0.5 ul | ||
+ | |- | ||
+ | |PstI | ||
+ | |0.5 ul | ||
+ | |- | ||
+ | |10xH buffer | ||
+ | |2 ul | ||
+ | |- | ||
+ | |DW | ||
+ | |12 ul | ||
+ | |- | ||
+ | |Total | ||
+ | |20 ul | ||
+ | |} | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | Inset | ||
+ | {|class="hokkaidou-table-digestion" | ||
+ | |- | ||
+ | |DNA solution ( 40ng/ul) | ||
+ | |14 ul | ||
+ | |- | ||
+ | |XbaI | ||
+ | |1 ul | ||
+ | |- | ||
+ | |PstI | ||
+ | |1 ul | ||
+ | |- | ||
+ | |10xM buffer | ||
+ | |2 ul | ||
+ | |- | ||
+ | |DW | ||
+ | |2 ul | ||
+ | |- | ||
+ | |Total | ||
+ | |20 ul | ||
+ | |} | ||
+ | |||
+ | |||
+ | |||
+ | {|class="hokkaidou-table-digestion" | ||
+ | |- | ||
+ | |Number | ||
+ | |Degree | ||
+ | |Minute | ||
+ | |- | ||
+ | |1 | ||
+ | |37 | ||
+ | |180 | ||
+ | |- | ||
+ | |2 | ||
+ | |60 | ||
+ | |15 | ||
+ | |- | ||
+ | |3 | ||
+ | |4 | ||
+ | |HOLD | ||
+ | |} | ||
+ | |||
+ | |||
+ | [[image:|thumb|digestion result]] | ||
+ | |||
+ | From this result, we confirmed that Insert and Vector DNA were digested. | ||
+ | </p> | ||
+ | |||
+ | |||
+ | ==Ethanol Precipitation== | ||
+ | <p> | ||
+ | Ethanol precipitation for ptet-pSB1A2 and RBS-eYFP-dT digestion products. | ||
+ | #Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol. | ||
+ | #Centrifuged in 15000 rpm, 15 min at 4C. | ||
+ | #Remove supernatant and added 220 ul of 70% ethanol. | ||
+ | #Centrifuged in 15000 rpm, 10 min at 4C. | ||
+ | #Remove supernatant and air drying in room temperature then added 10 ul of DW. | ||
+ | </p> | ||
+ | ==Ligation== | ||
+ | <p> | ||
+ | Ligation for ptet-pSB1A2 and RBS-eYFP-dT. | ||
+ | We used Ligation Mighty Mix (TAKARA BIO INC.) which contains ligase and buffer. | ||
+ | |||
+ | |||
+ | {|class="hokkaidou-table-ligation" | ||
+ | |- | ||
+ | |Vector DNA | ||
+ | |3 ul | ||
+ | |- | ||
+ | |Insert DNA | ||
+ | |3 ul | ||
+ | |- | ||
+ | |Ligation Mighty Mix | ||
+ | |6 ul | ||
+ | |- | ||
+ | |Total | ||
+ | |12 ul | ||
+ | |} | ||
+ | |||
+ | |||
+ | Ligation reaction time was in detail below. | ||
+ | |||
+ | {|class="hokkaidou-table-ligation" | ||
+ | |- | ||
+ | |Degree | ||
+ | |Minute | ||
+ | |- | ||
+ | |16 | ||
+ | |30 | ||
+ | |- | ||
+ | |65 | ||
+ | |10 | ||
+ | |- | ||
+ | |4 | ||
+ | |Hold | ||
+ | |} | ||
+ | </p> | ||
+ | |||
+ | ==Transformation== | ||
+ | <p> | ||
+ | Transformation for ligation product. We used E.coli strain DH5α. | ||
+ | #Mixed 1 ul of DNA 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 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 15 hours. | ||
+ | </p> | ||
+ | |||
</div></div> | </div></div> | ||
Revision as of 07:34, 29 August 2012
August 27th
Colony PCR
Colony PCR to confirm that whether the pT7-RBS-Ag43-dT on pSB1C3 was successfully ligated or not.
DNA solution | 4 ul |
Kapa-Taq(Taq polymerase) | 5 ul |
Forward Primer(ag43-f4 primer) | 0.5 ul |
Reverse Primer(200bp down primer) | 0.5 ul |
Total | 10 ul |
Number | Degree | Second |
1 | 95 | 120 |
2 | 95 | 30 |
3 | 53.0 | 30 |
4 | 72 | 60 |
5 | 72 | 60 |
6 | 4 | HOLD |
Cycle:2~4 x 35
We used N1 (DW only) and N2 (Ag43-dT on pSB1AK3) as controls. Desired product is about 695bp.
[[image:|thumb|Colony PCR result]]
Incubation for mini-prep of pT7-RBS-Ag43-dT on pSB1C3
Incubation of pT7-RBS-Ag43-dT on pSB1C3 in LBC liquid medium.
- Prepared 2 ml LBC into culture tubes.
- Re-suspended 2 colonies (No.1 and No.2 respectively).
- Incubated at 37C for 15 hrs.
Transformation of ptet-RBS(B0034)-CFP-dT on pSB1A2
- Mixed 1 ul DNA 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 LBC.
- 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 15 hours.
PCR of RBS-YFP-dT
Amplified the construct by 100bp-up-EX primer and 200bp-down-PS primer. Mixed PCR solutions.
Solution | Volume(ul) |
DNA | 1 |
100bp-up-EX | 1 |
200bp-down-PS | 1 |
MgSO4 | 3 |
dNTP | 5 |
10x KOD-Plus-Neo Buffer | 5 |
KOD-Plus-Neo | 1 |
DW | 33 |
Total | 50 |
Number | Degree | Second |
1 | 94 | 120 |
2 | 98 | 10 |
3 | 58.2 | 30 |
4 | 68 | 60 |
5 | 4 | HOLD |
Cycle:2~4 x 35
[[image:|thumb|PCR result]]
August 28th
mini-prep of pT7-RBS-Ag43-dT on pSB1C3
Mini-prep of pT7-RBS-Ag43-dT on pSB1C3. We re-suspended No.1,2 colonies and incubated. [[image:|thumb|mini-prep result]]
Estimation of Concentration of RBS-eYFP-dT and ptetR-pSB1A2
Solution | Value(ul) |
1kb ladder | 1 |
Insert | 1 |
Vector | 1 |
[[image:|thumb|Electrophoresis result]]
From this result, We estimated that the concentration of Insert DNA solution is about 40mM, and Vector DNA is also about 40mM.
Digestion of ptet-pSB1A2 and RBS-Ag43-dT
ptet-pSB1A2(Vector) was digested with SpeI and PstI, and RBS-Ag43-dT(Insert) was cut with XbaI and PstI. Vector
DNA solution ( 40ng/ul) | 5 ul |
SpeI | 0.5 ul |
PstI | 0.5 ul |
10xH buffer | 2 ul |
DW | 12 ul |
Total | 20 ul |
Inset
DNA solution ( 40ng/ul) | 14 ul |
XbaI | 1 ul |
PstI | 1 ul |
10xM buffer | 2 ul |
DW | 2 ul |
Total | 20 ul |
Number | Degree | Minute |
1 | 37 | 180 |
2 | 60 | 15 |
3 | 4 | HOLD |
[[image:|thumb|digestion result]]
From this result, we confirmed that Insert and Vector DNA were digested.
Ethanol Precipitation
Ethanol precipitation for ptet-pSB1A2 and RBS-eYFP-dT digestion products.
- Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
- Centrifuged in 15000 rpm, 15 min at 4C.
- Remove supernatant and added 220 ul of 70% ethanol.
- Centrifuged in 15000 rpm, 10 min at 4C.
- Remove supernatant and air drying in room temperature then added 10 ul of DW.
Ligation
Ligation for ptet-pSB1A2 and RBS-eYFP-dT. We used Ligation Mighty Mix (TAKARA BIO INC.) which contains ligase and buffer.
Vector DNA | 3 ul |
Insert DNA | 3 ul |
Ligation Mighty Mix | 6 ul |
Total | 12 ul |
Ligation reaction time was in detail below.
Degree | Minute |
16 | 30 |
65 | 10 |
4 | Hold |
Transformation
Transformation for ligation product. We used E.coli strain DH5α.
- Mixed 1 ul of DNA 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 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 15 hours.