Team:HokkaidoU Japan/Notebook/aggregation Week 5

From 2012.igem.org

(Difference between revisions)
Line 16: Line 16:
<p>
<p>
I think that the E. coli which we use transformation is BL21(DE3)pLysS.
I think that the E. coli which we use transformation is BL21(DE3)pLysS.
-
So, the E. coli could multiplication increase on LBC plate.<br />
+
So, the E. coli could grow on LBC plate.<br />
I'm going to do transformation , use DH5&alpha;.
I'm going to do transformation , use DH5&alpha;.
Line 40: Line 40:
#Added 2 ml of LBK into culture tubes.
#Added 2 ml of LBK into culture tubes.
#Resuspended colonies.
#Resuspended colonies.
-
#Incubated the tubes at 37C for  
+
#Incubated the tubes at 37C for 18 hrs.
</p>
</p>
Line 51: Line 51:
==Plasmid extraction==
==Plasmid extraction==
<p>
<p>
-
mini-prep of pT7-RBS-Ag43-dT which had been incubated from yesterday. We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.
+
Mini-prep of pT7-RBS-Ag43-dT which had been incubated from yesterday. We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.
[[image:HokkaidoU2012 120801 pt7-rbs-ag43-dt.jpg|thumb|mini-prep result]]
[[image:HokkaidoU2012 120801 pt7-rbs-ag43-dt.jpg|thumb|mini-prep result]]
</p>
</p>
Line 57: Line 57:
==Digestion==
==Digestion==
<p>
<p>
-
'''pT7-RBS(20 ng/ul) '''=9
+
'''pT7-RBS(20 ng/ul) '''=No. 9
-
SpeI 10xH  
+
SpeI using 10xH  
  {|class="hokkaidou-table-digestion"
  {|class="hokkaidou-table-digestion"
   |-
   |-
Line 78: Line 78:
   |}
   |}
-
SpeI 10xM  
+
SpeI using 10xM
  {|class="hokkaidou-table-digestion"
  {|class="hokkaidou-table-digestion"
   |-
   |-
Line 98: Line 98:
-
'''pT7-RBS(30 ng/ul) '''=10
+
'''pT7-RBS(30 ng/ul) '''=No. 10
-
SpeI 10xH  
+
SpeI using 10xH  
  {|class="hokkaidou-table-digestion"
  {|class="hokkaidou-table-digestion"
   |-
   |-
Line 119: Line 119:
   |}
   |}
-
SpeI 10xM  
+
SpeI using 10xM
  {|class="hokkaidou-table-digestion"
  {|class="hokkaidou-table-digestion"
   |-
   |-
Line 140: Line 140:
[[image:HokkaidoU2012 120801 pt7-rbs-digS.jpg|thumb|digestion result]]
[[image:HokkaidoU2012 120801 pt7-rbs-digS.jpg|thumb|digestion result]]
-
We couldn't cut them exactry so we cut once more time.
+
We couldn't digested them exactly, so we tried to digest once more time.
-
'''pT7-RBS(20 ng/ul) '''=9
+
'''pT7-RBS(20 ng/ul) '''=No. 9
SpeI 10xH  
SpeI 10xH  
  {|class="hokkaidou-table-digestion"
  {|class="hokkaidou-table-digestion"
Line 163: Line 163:
   
   
</p>
</p>
 +
==Liquid culture==
==Liquid culture==
<p>
<p>
Line 183: Line 184:
Our competent cell Protocol
Our competent cell Protocol
-
#Single colony isolation on LB plate
+
#Single colony isolation on LB plate.
-
#incubated the plate for 15-19 hours at 37C
+
#Incubated the plate for 15-19 hours at 37C.
-
#lift colony of E. coli into 2 ml LB
+
#Lift colony of E. coli into 2 ml LB
-
#cultured cells at 37C for 12-16 hours at 180-200 rpm
+
#Incubate at 37C for 12-16 hours at 180-200 rpm
-
#transfered 30 ul, 100 ul, 300 ul of the culture into 100 ml of LB , respectively
+
#Transfer 30 ul, 100 ul, 300 ul of the culture into 100 ml of LB.
-
#cultured cells at 20C (for 24 hours over) at 140 rpm
+
#Incubate cells at 20C (for 24 hours over) at 140 rpm
-
#selected culture by measuring OD 600
+
#Select culture by measuring OD 600.(OD 600=0.5)
-
#left the 300 ml flask for 10 min on ice
+
#Incubate the 300 ml flask for 10 min on ice
-
#transfered the culture into two 50 ml Falcon tube
+
#Transfer the culture into two 50 ml Falcon tube
-
#centrifuged 3000 rpm at 4C for 20 min (TOMY LX-120 rotor), and discard sup
+
#Centrifuge at 3000 rpm, 4C for 20 min (TOMY LX-120 rotor), and discard sup.
-
#suspended the pellet in ice-cold 15 ml of TB (Transformation Buffer)(7.5 ml/tube)
+
#Suspend the pellet in ice-cold 15 ml of TB (Transformation Buffer).(7.5 ml/tube)
-
#collected them to one tube
+
#Collect them to one tube.
-
#centrifuged 3000 rpm at 4C for 20 min (TOMY LX-120 rotor), and discard sup
+
#Centrifuge at 3000 rpm, 4C for 20 min (TOMY LX-120 rotor), and discard sup.
-
#suspended the pellet in ice-cold 3.2 ml of TB
+
#Suspend the pellet in ice-cold 3.2 ml of TB.
-
#Instiled 0.24 ml of DMSO in precipitant
+
#Instill 0.24 ml of DMSO in precipitant.
-
#left the 50 ml Falcon tube for 10 min on ice
+
#Incubate the 50 ml Falcon tube for 10 min on ice.
-
#divide 50 ul of solutions in each 0.5 ml tubes
+
#Divide 50 ul of solutions in each 0.5 ml tubes.
-
#Freezed the suspension in liquid nitrogen
+
#Freezed the suspension by liquid nitrogen.
-
#stored at –80C
+
#Stored at –80C.
Line 208: Line 209:
==Electrophoresis==
==Electrophoresis==
<p>
<p>
-
Electrophoresis of digestion result of yesterday(pT7-RBS on pSB1K3 cut with SpeI)
+
Electrophoresis of digestion result of August 1st.(pT7-RBS on pSB1K3 digested by SpeI)
[[image:HokkaidoU2012 120802 pT7-RBS on pSB1K3 SpeI.jpg|thumb|Electrophoresis result]]
[[image:HokkaidoU2012 120802 pT7-RBS on pSB1K3 SpeI.jpg|thumb|Electrophoresis result]]
Line 216: Line 217:
==Digestion==
==Digestion==
<p>
<p>
-
Digestion of pT7-RBS on pSB1K3(more fresh one)
+
Digestion of pT7-RBS on pSB1K3 (more fresh one)
  {|class="hokkaidou-table-digestion"
  {|class="hokkaidou-table-digestion"
   |-
   |-
Line 244: Line 245:
==Electrophoresis==
==Electrophoresis==
<p>
<p>
-
Electrophoresis for the result of digestion(see the yesterday notebook).
+
Electrophoresis for the result of digestion.
[[image:HokkaidoU2012 120803 pt7-rbs-dspe1.jpg|thumb|Electrophoresis result]]
[[image:HokkaidoU2012 120803 pt7-rbs-dspe1.jpg|thumb|Electrophoresis result]]
</p>
</p>
Line 311: Line 312:
#Plate 300 ul of the transformation onto first dish and spread.
#Plate 300 ul of the transformation onto first dish and spread.
#Added 900 ul of LB to 100 ul of the transformation and plated 300 ul of it onto second dish and spread.  
#Added 900 ul of LB to 100 ul of the transformation and plated 300 ul of it onto second dish and spread.  
-
#Incubated the plates at 37C for 15 hrs 45 min (20:45~12:30).
+
#Incubated the plates at 37C for 15 hrs 45 min.
</p>
</p>
Line 335: Line 336:
|5 ul
|5 ul
|-
|-
-
|Forward Primer(Ag43-f4 primer)
+
|Ag43-f4 primer
|1 ul
|1 ul
|-
|-
-
|Reverse Primer(PS-R primer)
+
|PS-R primer
|1 ul
|1 ul
|-
|-
Line 381: Line 382:
[[image:HokkaidoU2012 120803 Ag43 PCR(Forward=ag43-f4 Reverse=PS-R).jpg|thumb|PCR result]]
[[image:HokkaidoU2012 120803 Ag43 PCR(Forward=ag43-f4 Reverse=PS-R).jpg|thumb|PCR result]]
-
From this result, we could see that the ag43-f4 primer had worked and DNA of last 500~600 bp of ag43 to BioBrick suffix were amplified.
+
From this result, we could see that the ag43-f4 primer had worked and DNA of last 500~600 bp of ag43 to BioBrick suffix were increased.
</p>
</p>
Line 472: Line 473:
==Plasmid extraction==
==Plasmid extraction==
<p>
<p>
-
mini-prep of incubated medium from yesterday. We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.
+
Mini-prep of incubated medium from yesterday. We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.
[[image:HokkaidoU2012 120805 pt7-rbs-ag43-dt.jpg|thumb|mini-prep results]]
[[image:HokkaidoU2012 120805 pt7-rbs-ag43-dt.jpg|thumb|mini-prep results]]
Line 479: Line 480:
==Digestion==
==Digestion==
<p>
<p>
-
Digestion of pT7-RBS on pSB1K3 and pT7-RBS (once digestioned with SpeI) with speI.
+
Digested pT7-RBS on pSB1K3 and pT7-RBS (once digestioned with SpeI) with speI.
Line 541: Line 542:
[[image:HokkaidoU2012 120805 pT7-RBS digestion SpeI (no.jpg|thumb|digestion result]]
[[image:HokkaidoU2012 120805 pT7-RBS digestion SpeI (no.jpg|thumb|digestion result]]
-
From this result the bottom band was misdigested band and middle band was digested band we thought. Was the above band something contaminated in the DNA solution?
+
From this result, the bottom band was misdigested band and middle band was digested band we thought. Was the above band something contaminated in the DNA solution?
</p>
</p>
==Gel extraction==
==Gel extraction==
<p>
<p>
-
Gel extraction of middle band (see the image of digestion reult). We thought this band would be the exactly digested DNA fragment. We used FastGene Gel&PCR extraction kit(NipponGenetics)and got 50 ul of DNA solution.   
+
Gel extraction of middle band. We thought this band would be the exactly digested DNA fragment. We used FastGene Gel&PCR extraction kit(NipponGenetics)and got 50 ul of DNA solution.   
</p>
</p>
==Sequencing==
==Sequencing==
<p>
<p>
-
Sequencing to confirm what kind of DNA we synthesized.
+
Sequencing to confirm what kind of DNA we made.
Line 611: Line 612:
|5 ul
|5 ul
|-
|-
-
|Primer(1pmol/ul)
+
|Primer(1 pmol/ul)
|1.5 ul
|1.5 ul
|-
|-
Line 645: Line 646:
To purify the PCR product, we did ethanol precipitation.
To purify the PCR product, we did ethanol precipitation.
-
 
Ethanol precipitation for sequencing.
Ethanol precipitation for sequencing.
Line 655: Line 655:
-
Then run a sequencing machine (ByoDye Terminator v3.1 Cycle Sequencing Kit)
+
Then run a sequencing machine.(ByoDye Terminator v3.1 Cycle Sequencing Kit)
-
Result..Falue.
+
We could not get the sequencing data.
</p>
</p>
==Digestion==
==Digestion==
<p>
<p>
-
Digestion of Ag43-dT (digested with SpeI and XbaI) with HindIII.
+
Digesting of Ag43-dT (digested by SpeI and XbaI) by HindIII.
  {|class="hokkaidou-table-digestion"
  {|class="hokkaidou-table-digestion"
Line 684: Line 684:
[[image:HokkaidoU2012 120805 Ag43-dT on pSB1AK3(d+ with XbaI &amp; SpeI) digestion with HindIII.jpg|thumb|digestion result]]
[[image:HokkaidoU2012 120805 Ag43-dT on pSB1AK3(d+ with XbaI &amp; SpeI) digestion with HindIII.jpg|thumb|digestion result]]
-
From this result we confirmed that the pSB1AK3 was successfully digested with HindIII.
+
From this result, we confirmed that the pSB1AK3 was successfully digested by HindIII.
</p>
</p>

Revision as of 13:15, 26 September 2012

Contents

July 30th

digestion

I tried to digest the mini-prep products again, and after Ethanol precipitation, we did electrophoresis.

digestion result

transformation

I think that the E. coli which we use transformation is BL21(DE3)pLysS. So, the E. coli could grow on LBC plate.
I'm going to do transformation , use DH5α. Transformation of plasmid DNA ligated at 25th (pT7-RBS-Ag43-dT on pSB1K3) in DH5α.

  1. Added 2 ul of plasmid DNA to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30 min.
  3. Added 200 ul of LB then incubated the cells for 2 hours at 37C.
  4. Prepared and Labeled two petri dishes with LBK.
  5. Plate 200 ul of the transformation onto first dish and spread.
  6. Added 450 ul of LB to 50 ul of the transformation and plated 200 ul of it onto second dish and spread.
  7. Incubated the plates at 37C for 14 hours.


July 31th

liquid culture

Liquid culture for pT7-RBS-Ag43-dT on pSB1K3.

  1. Added 2 ml of LBK into culture tubes.
  2. Resuspended colonies.
  3. Incubated the tubes at 37C for 18 hrs.


August 1st

Plasmid extraction

Mini-prep of pT7-RBS-Ag43-dT which had been incubated from yesterday. We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.

mini-prep result

Digestion

pT7-RBS(20 ng/ul) =No. 9 SpeI using 10xH

DNA solution 4.5 ul
SpeI 1 ul
10xH buffer 1 ul
DW 3.5 ul
Total 10 ul

SpeI using 10xM

DNA solution 4.5 ul
SpeI 1 ul
10xM buffer 1 ul
DW 3.5 ul
Total 10 ul


pT7-RBS(30 ng/ul) =No. 10

SpeI using 10xH

DNA solution 3 ul
SpeI 1 ul
10xH buffer 1 ul
DW 5 ul
Total 10 ul

SpeI using 10xM

DNA solution 3 ul
SpeI 1 ul
10xM buffer 1 ul
DW 5 ul
Total 10 ul
digestion result

We couldn't digested them exactly, so we tried to digest once more time.

pT7-RBS(20 ng/ul) =No. 9 SpeI 10xH

DNA solution 4.5 ul
SpeI 1 ul
10xM buffer 2 ul
DW 12.5 ul
Total 20 ul

Liquid culture

Liquid culture for pBAD-RBS on pSB1K3.

  1. Added 2 ml of LBK into culture tube.
  2. Scraped the surface of glycerol stock of construct.
  3. Incubated the tube at 33C.


August 2nd

Preparing chemical competent cell

Preparing chemical competent cell of BL21, JM109 and DH5α. Chemical competent cell made in each E. coli strains.

Our competent cell Protocol

  1. Single colony isolation on LB plate.
  2. Incubated the plate for 15-19 hours at 37C.
  3. Lift colony of E. coli into 2 ml LB
  4. Incubate at 37C for 12-16 hours at 180-200 rpm
  5. Transfer 30 ul, 100 ul, 300 ul of the culture into 100 ml of LB.
  6. Incubate cells at 20C (for 24 hours over) at 140 rpm
  7. Select culture by measuring OD 600.(OD 600=0.5)
  8. Incubate the 300 ml flask for 10 min on ice
  9. Transfer the culture into two 50 ml Falcon tube
  10. Centrifuge at 3000 rpm, 4C for 20 min (TOMY LX-120 rotor), and discard sup.
  11. Suspend the pellet in ice-cold 15 ml of TB (Transformation Buffer).(7.5 ml/tube)
  12. Collect them to one tube.
  13. Centrifuge at 3000 rpm, 4C for 20 min (TOMY LX-120 rotor), and discard sup.
  14. Suspend the pellet in ice-cold 3.2 ml of TB.
  15. Instill 0.24 ml of DMSO in precipitant.
  16. Incubate the 50 ml Falcon tube for 10 min on ice.
  17. Divide 50 ul of solutions in each 0.5 ml tubes.
  18. Freezed the suspension by liquid nitrogen.
  19. Stored at –80C.


Electrophoresis

Electrophoresis of digestion result of August 1st.(pT7-RBS on pSB1K3 digested by SpeI)

Electrophoresis result

There were low concentration band in above of thick band. This thick band was same as digestion minus band.

Digestion

Digestion of pT7-RBS on pSB1K3 (more fresh one)

DNA solution 4 ul
SpeI 1 ul
10xM buffer 2 ul
DW 13 ul
Total 20 ul


August 3rd

Electrophoresis

Electrophoresis for the result of digestion.

Electrophoresis result

Gel extraction

Gel extraction for digestion product. We used FastGene Gel&PCR extraction kit(NipponGenetics)and got 50 ul of DNA solution.

Ethanol precipitation

Ethanol precipitation for digestion and gel extraction product.

  1. Added 5ul of NaoAc, 1.5 ul of glycogen and 125ul of 100% ethanol.
  2. Centrifuged at 15000 rpm, 10 min at 4C.
  3. Removed supernatant and added 220ul of 70% ethanol.
  4. Centrifuged at 15000 rpm, 5 min at 4C.
  5. Removed supernatant and air drying at room temperature then added 10 ul of DW.

Ligation

We ligated pT7-RBS on pSB1K3 (digested Spe1) as vector and Ag43-dT (digested Spe1 and Xba1 and HindIII) as insert.

pT7-RBS 2 ul
Ag43-dT 4 ul
Ligation Mighty Mix(TAKARA) 6 ul
Total 12 ul


Ligation reaction time was written below.

Degree Minute
16 30
65 10
4 Hold

Transformation

Transformation of plasmid DNA ligation product (pT7-RBS-Ag43-dT on pSB1K3) in DH5α.

  1. Added 1 ul of plasmid DNA to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30min.
  3. Added 600 ul of LB then incubated the cells for 2 hrs at 37C.
  4. Prepared and Labeled two petri dishes with LBK.
  5. Plate 300 ul of the transformation onto first dish and spread.
  6. Added 900 ul of LB to 100 ul of the transformation and plated 300 ul of it onto second dish and spread.
  7. Incubated the plates at 37C for 15 hrs 45 min.

PCR

PCR to confirm Ag43-f4 primer.

DNA solution 1 ul
KOD-Plus-NEO(Taq polymerase) 1 ul
dNTP 5 ul
MgSO4 3 ul
KOD-Plus-NEO Buffer 5 ul
Ag43-f4 primer 1 ul
PS-R primer 1 ul
DW 33 ul
Total 50 ul


Number Degree Second
1 94 120
2 98 10
3 58 30
4 68 60
5 4 HOLD

Cycle:2~4 x 45


PCR result

From this result, we could see that the ag43-f4 primer had worked and DNA of last 500~600 bp of ag43 to BioBrick suffix were increased.



August 4th

Colony PCR

Colony PCR to confirm that whether the Ag43-dT was successfully ligated with pT7-RBS on pSB1K3 or not.

DNA solution 4 ul
Kapa-Taq(Taq polymerase) 5 ul
Forward Primer(Ag43-f4 primer) 0.5 ul
Reverse Primer(PS-R primer) 0.5 ul
Total 10 ul


Number Degree Second
1 95 120
2 95 30
3 58 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 500~600bp.

Colony PCR result

We thought that No. 5 and 9 colonies were made in exactly transformed in E. coli. and No. 10 colony had high concentration band. Next step, we resuspended these three colonies and cultured.

Liquid culture

Liquid culture of colonies passed the colony PCR test.

  1. Added 2 ml of LBK into culture tubes.
  2. Resuspended 3 colonies.
  3. Incubated the tubes at 37C for 13 hrs.


August 5th

Plasmid extraction

Mini-prep of incubated medium from yesterday. We used FastGene Plasmid Mini Kit(Nippon Genetics) and got 50 ul of DNA solutions.

mini-prep results

Digestion

Digested pT7-RBS on pSB1K3 and pT7-RBS (once digestioned with SpeI) with speI. pT7-RBS on pSB1K3

DNA solution 8 ul
SpeI 2 ul
10xM buffer 2 ul
DW 8 ul
Total 20 ul


pT7-RBS (once digestioned with SpeI)

DNA solution 4 ul
SpeI 1 ul
10xM buffer 1 ul
DW 4 ul
Total 10 ul
DNA solution 4 ul
SpeI 1 ul
10xM buffer 2 ul
DW 13 ul
Total 20 ul


digestion result

From this result, the bottom band was misdigested band and middle band was digested band we thought. Was the above band something contaminated in the DNA solution?

Gel extraction

Gel extraction of middle band. We thought this band would be the exactly digested DNA fragment. We used FastGene Gel&PCR extraction kit(NipponGenetics)and got 50 ul of DNA solution.

Sequencing

Sequencing to confirm what kind of DNA we made.

DNA primer
Ag43 mini-prep product 100bp-up forward primer, ag43-f1, ag43-f2, ag43-f3, ag43-f4
K542009 100bp-up forward primer, ag43-f1, ag43-f2, ag43-f3, ag43-f4
pT7-RBS on pSB1K3 100bp-up forward primer
pT7-RBS on pSB1C3 100bp-up forward primer
Ag43-dT on pSB1AK3 100bp-up forward primer, ag43-f1, ag43-f2, ag43-f3, ag43-f4
Ag43-dT on pSB1T3 100bp-up forward primer, ag43-f1, ag43-f2, ag43-f3, ag43-f4
pT7-RBS on pSB1K3 100bp-up forward primer


Sequencing PCR

template DNA 1 ul
Ready Reaction Premix 1 ul
5x Sequencing Buffer 1.5 ul
H2O 5 ul
Primer(1 pmol/ul) 1.5 ul
Total 10 ul


Number Degree Second
1 96 10
2 50 5
3 60 240
4 4 HOLD

Cycle:1~3 x 25


To purify the PCR product, we did ethanol precipitation.

Ethanol precipitation for sequencing.

  1. Added 10 ul of H2O, 2 ul of NaoAc, 1 ul of glycogen and 50 ul of 100% ethanol.
  2. Centrifuged at 15000 rpm, 15 min at 26C.
  3. Removed supernatant and added 100ul of 70% ethanol.
  4. Centrifuged at 15000 rpm, 5 min at 26C.
  5. Removed supernatant and air drying at room temperature then added 10 ul of Hi-Di.


Then run a sequencing machine.(ByoDye Terminator v3.1 Cycle Sequencing Kit) We could not get the sequencing data.

Digestion

Digesting of Ag43-dT (digested by SpeI and XbaI) by HindIII.

DNA solution 10 ul
HindIII 1 ul
10xM buffer 2 ul
DW 7 ul
Total 20 ul


digestion result

From this result, we confirmed that the pSB1AK3 was successfully digested by HindIII.

Gel extraction

Gel extraction for digestion production. We used FastGene Gel&PCR extraction kit(NipponGenetics)and got 50 ul of DNA solution.