Team:HokkaidoU Japan/Notebook/aggregation Week 11

From 2012.igem.org

(Difference between revisions)
Line 138: Line 138:
<p>
<p>
#Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
#Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
-
#Centrifuged in 14000 rpm, 30 min at 4C.
+
#Centrifuged at 14000 rpm, 30 min at 4C.
#Remove supernatant and added 220 ul of 70% ethanol.
#Remove supernatant and added 220 ul of 70% ethanol.
-
#Centrifuged in 15000 rpm, 15 min at 4C.
+
#Centrifuged at 15000 rpm, 15 min at 4C.
-
#Remove supernatant and air drying in room temperature then added 5 ul of DW.  
+
#Remove supernatant and air drying at room temperature then added 5 ul of DW.  
Line 292: Line 292:
==Aggregation check of pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28==
==Aggregation check of pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28==
<p>
<p>
-
Aggregation check for No.5,6 colonies selected by colony PCR in 11th.
+
Aggregation check for No.5,6 colonies selected by colony PCR at 11th.
#Prepared 5 ml LBA into glass tubes.
#Prepared 5 ml LBA into glass tubes.
#Re-suspended 2 colony mixture (No.2 and No.5 respectively).  
#Re-suspended 2 colony mixture (No.2 and No.5 respectively).  
Line 379: Line 379:
<p>
<p>
#Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
#Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
-
#Centrifuged in 15000 rpm, 15 min at 4C.
+
#Centrifuged at 15000 rpm, 15 min at 4C.
#Remove supernatant and added 220 ul of 70% ethanol.
#Remove supernatant and added 220 ul of 70% ethanol.
-
#Centrifuged in 15000 rpm, 10 min at 4C.
+
#Centrifuged at 15000 rpm, 10 min at 4C.
-
#Remove supernatant and air drying in room temperature then added 10 ul of DW.  
+
#Remove supernatant and air drying at room temperature then added 10 ul of DW.  
Line 624: Line 624:
[[image:HokkaidoU2012 120914 Digestion Insert Vector.jpg|thumb|digestion result]]
[[image:HokkaidoU2012 120914 Digestion Insert Vector.jpg|thumb|digestion result]]
-
We suppose the Insert DNA (RBS-phaB-RBS-eYFP-dT) has contained Vector-dimer DNA as contamination. But desired DNA fragment (about 1600 bp) bond also appeared in the result of migration. We picked up the fragment and extracted from migrated TBE gel.
+
We suppose the Insert DNA (RBS-phaB-RBS-eYFP-dT) has contained Vector-dimer DNA as contamination. But desired DNA fragment (about 1600 bp) bond also appeared in the result of migration. We picked up the fragment and extracted from gel.
</p>
</p>

Revision as of 09:55, 26 September 2012

Contents

September 10th

Digestion of eCFP-RBS-pSB1A2 and pBAD-RBS-pSB1A2

To make a construct of pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28 by 3piece ligation, we digested pBAD-RBS-eCFP-RBS-pSB1A2 with EcoRI & SpeI, Ag43-dT-pSB1AK3 (previously digested with HindIII) with XbaI & NotI and pSTV28 with EcoRI and NotI. Then we digested pT7-RBS-pSB1C3 with XbaI & SpeI as a control for confirmation of the ability of restriction enzyme. Insert1 (pBAD-RBS-eCFP-RBS-pSB1A2)

DNA solution ( 35ng/ul) 17 ul
EcoRI 1 ul
SpeI 1 ul
10xH buffer 3 ul
DW 8 ul
Total 30 ul


Insert2 (Ag43-dT-pSB1AK3)

DNA solution ( 35ng/ul) 25 ul
XbaI 1 ul
NotI 1 ul
10xK buffer 1.5 ul
100xBSA 0.3ul
DW 1.5 ul
Total 30 ul



Vector(pSTV28)

DNA solution ( 15ng/ul) 9 ul
EcoRI 1 ul
NotI 1 ul
10xH buffer 2 ul
10xBSA 0.2ul
DW 7 ul
Total 20 ul


control (pT7-RBS-pSB1C3)

DNA solution (30~40 ng/ul) 10 ul
XbaI 1 ul
SpeI 1 ul
10xM buffer 2 ul
DW 6 ul
Total 20 ul


Number Degree Minute
1 37 120
2 70 20
3 4 HOLD


digestion result

Ethanol precipitation of ptet-RBS-eYFP-dT-pSB1A2 and pSTV28

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged at 14000 rpm, 30 min at 4C.
  3. Remove supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged at 15000 rpm, 15 min at 4C.
  5. Remove supernatant and air drying at room temperature then added 5 ul of DW.
ethanol precipitation result

We confirmed that the concentration of Insert1 DNA solution is 50 ng/ul, Insert2 DNA solution is 10~15 ng/ul and Vector DNA solution is 10 ng/ul.

Ligation of pBAD-RBS-eCFP-RBS, Ag43-dT and pSTV28

Vector DNA (10 ng/ul) 4 ul
Insert1 DNA (50 ng/ul) 2 ul
Insert2 DNA (10~15 ng/ul) 4 ul
Ligation Mighty Mix 10 ul
Total 20 ul


Ligation reaction time was in detail below.

Degree Minute
16 30
65 10
4 Hold

Transformation of pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28

Transformation of DH5α.

  1. Mixed 2 ul pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28 ligation product to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30 min.
  3. Mixed 350 ul of LB.
  4. Incubated for 2 hrs to get the resistance to Chloramphenicol.
  5. Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBC).
  6. Plated 300 ul of the culture onto first dish and spread.
  7. Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
  8. Incubated the plates at 37C for 14 hours.


September 11th

Colony PCR of pBAD-RBS-eCFP-RBS-pSB1A2

DNA solution 4 ul
Kapa-Taq(Taq polymerase) 5 ul
Forward Primer(pbad-f2 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 53.3 30
4 72 60
5 72 60
6 4 HOLD

Cycle:2~4 x 35

  • We noticed that this step was actually 68.9 degree after reaction.

We used N1 (DW only) and N2(pBAD-RBS-Ag43-dT-pSB1A2)as controls. Desired product is about 542bp.

Colony PCR result


Because of mis-setting the PCR program, we failed to amplify desired DNA fragment so we retried the colony PCR in same reagent, correct PCR machine program.

Colony PCR result


We noticed that the ligated DNA contains at least Ag43-dT-BioBrick_Suffix complex. We selected No.2,4 for incubation for mini-prep and No.5,6 for Aggregation check (see details below).


September 12th

Analysis nucleotide sequence

We analyzed the nucleotide sequence of pBAD-RBS-Ag43-dT on pSB1AK3 and pSB1C3. We used these 6 kinds of primers. 100b up EX-F primer, pBAD-f1 primer, pBAD-f2 primer, Ag43-f1 primer, Ag43-f2 primer, Ag43-f3 primer, Ag43-f4 primer, 200b down PS-R primer

Aggregation check of pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28

Aggregation check for No.5,6 colonies selected by colony PCR at 11th.

  1. Prepared 5 ml LBA into glass tubes.
  2. Re-suspended 2 colony mixture (No.2 and No.5 respectively).
  3. Incubated at 37C for hrs.

Digestion of RBS-phaB-pSB1A2 as Vector and RBS-eYFP-dT as Insert

To make a construct of RBS-phaB-RBS-eYFP-dT-pSB1A2, we digested RBS-phaB-pSB1A2 with SpeI & PstI, RBS-eYFP-dT with XbaI & PstI.


Insert (RBS-eYFP-dT)

DNA solution ( 40ng/ul) 25 ul
XbaI 1 ul
NotI 1 ul
10xK buffer 1.5 ul
100xBSA 0.3ul
DW 1.5 ul
Total 30 ul



Vector(RBS-phaB-pSB1A2)

DNA solution ( 35ng/ul) 6 ul
SpeI 1 ul
PstI 1 ul
10xH buffer 2 ul
DW 10 ul
Total 20 ul


Number Degree Minute
1 37 120
2 60 15
3 4 HOLD


digestion result

</p>

Ethanol precipitation of ptet-RBS-eYFP-dT-pSB1A2 and pSTV28

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged at 15000 rpm, 15 min at 4C.
  3. Remove supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged at 15000 rpm, 10 min at 4C.
  5. Remove supernatant and air drying at room temperature then added 10 ul of DW.
ethanol precipitation result

We confirmed that the concentration of Insert DNA solution is 40 ng/ul and Vector DNA solution is 30 ng/ul.

Ligation of pBAD-RBS-eCFP-RBS, Ag43-dT and pSTV28

Vector DNA (40 ng/ul) 3 ul
Insert DNA (30 ng/ul) 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


September 13th

Transformation of RBS-phaB-RBS-eYFP-dT-pSB1A2

Transformation of JM109.

  1. Mixed 2 ul ligation product to 50 ul of thawed competent cells (JM109) on ice.
  2. Incubated on ice for 30 min.
  3. Mixed 350 ul of LB.
  4. Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBA).
  5. Plated 300 ul of the culture onto first dish and spread.
  6. Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
  7. Incubated the plates at 37C for 14 hours.

Aggregation Check of pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28

  1. Mixed 25 ul Arabinose solution (20 %) to 5 ml LBC in glass tube.
  2. Incubated for 24 hrs at 37C.
Result: The construct has aggregated not forming large cluster but small dot cluster, and the supernatant has muddiness.

Colony PCR of RBS-phaB-RBS-eYFP-dT-pSB1A2

DNA solution 4 ul
Kapa-Taq(Taq polymerase) 10 ul
Forward Primer(pbad-f2 primer: 10 ng/ul) 0.8 ul
Reverse Primer(PS-R down primer: 10 ng/ul) 0.8 ul
DW 4.4 ul
Total 20 ul


Number Degree Second
1 95 120
2 95 30
3 64.4 30
4 72 180
5 72 120
6 4 HOLD

Cycle:2~4 x 35


We used N1 (DW only) and N2(RBS-phaB-pSB1A2)as controls. Desired product is about 1800~2000bp.

Colony PCR result


We noticed the ligated DNA contains phaB-something-SP sequence and the length is about 1600~1800bp, at least over 1000 bp. We selected No.1,2 for incubation for mini-prep and No.3,4 for stock at 4C.


Incubation of RBS-phaB-RBS-eYFP-dT-pSB1A2 for mini-prep

  1. Prepared 2 ml LBC into culture tubes.
  2. Re-suspended 2 colony mixture (No.1 and No.2 respectively).
  3. Incubated at 37C for 14 hrs.


September 14th

Digestion of eCFP-RBS-pSB1A2 and pBAD-RBS-pSB1A2

To make a construct of RBS-phaC-RBS-phaA-RBS-phaB-RBS-dT-pSB1A2, we digested RBS-phaC-RBS-phaA with SpeI & PstI, RBS-phaB-RBS-eYFP-pSB1A2 with XbaI & PstI. Insert (RBS-phaB-RBS-eYFP-dT)

DNA solution ( 30ng/ul) 21 ul
XbaI 1 ul
PstI 1 ul
10xM buffer 3 ul
DW 4 ul
Total 30 ul


Vector(RBS-phaC-RBS-phaA-pSB1A2)

DNA solution (about 30~40 ng/ul) 6 ul
SpeI 1 ul
PstI 1 ul
10xH buffer 2 ul
DW 10 ul
Total 20 ul


Number Degree Minute
1 37 180
2 60 15
3 4 HOLD


Number Degree Minute
1 37 120
2 70 20
3 4 HOLD


digestion result

We suppose the Insert DNA (RBS-phaB-RBS-eYFP-dT) has contained Vector-dimer DNA as contamination. But desired DNA fragment (about 1600 bp) bond also appeared in the result of migration. We picked up the fragment and extracted from gel.

Ethanol precipitation of RBS-phaB-RBS-eYFP-dT and RBS-phaC-RBS-phaA-pSB1A2

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged in 14000 rpm, 30 min at 4C.
  3. Remove supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged in 15000 rpm, 15 min at 4C.
  5. Remove supernatant and air drying in room temperature then added 5 ul of DW.
ethanol precipitation result

We confirmed that the concentration of Insert DNA solution is 20 ng/ul and Vector DNA solution is about 50~60 ng/ul.

Ligation of RBS-phaB-RBS-eYFP-dT and RBS-phaC-RBS-phaA-pSB1A2

Insert DNA (20 ng/ul) 4 ul
Vector DNA (50~60 ng/ul) 1.5 ul
Ligation Mighty Mix 6 ul
DW 0.5 ul
Total 20 ul


Ligation reaction time was in detail below.

Degree Minute
16 30
65 10
4 Hold

Transformation of RBS-phaC-RBS-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2

Transformation of JM109.

  1. Mixed 2 ul RBS-phaC-RBS-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2 ligation product to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30 min.
  3. Mixed 350 ul of LB.
  4. Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBA).
  5. Plated 300 ul of the culture onto first dish and spread.
  6. Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
  7. Incubated the plates at 37C for 13 hours.
We succeeded to transform the cells but noticed that we have used wrong DNA solution. We'll try this DNA synthesis again tomorrow.


September 15th

Digestion of eCFP-RBS-pSB1A2 and pBAD-RBS-pSB1A2

To make a construct of RBS-phaC-RBS-phaA-RBS-phaB-RBS-dT-pSB1A2, we digested RBS-phaC-RBS-phaA with SpeI & PstI, RBS-phaB-RBS-eYFP-pSB1A2 with XbaI & PstI. Insert (RBS-phaB-RBS-eYFP-dT)

DNA solution ( 30ng/ul) 21 ul
XbaI 1 ul
PstI 1 ul
10xM buffer 3 ul
DW 4 ul
Total 30 ul


Vector(RBS-phaC-RBS-phaA-pSB1A2)

DNA solution (about 30~40 ng/ul) 6 ul
SpeI 1 ul
PstI 1 ul
10xH buffer 2 ul
DW 10 ul
Total 20 ul


Number Degree Minute
1 37 120
2 60 15
3 4 HOLD


Number Degree Minute
1 37 120
2 70 20
3 4 HOLD


digestion result

Ethanol precipitation of RBS-phaB-RBS-eYFP-dT and RBS-phaC-RBS-phaA-pSB1A2

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged in 14000 rpm, 30 min at 4C.
  3. Remove supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged in 15000 rpm, 15 min at 4C.
  5. Remove supernatant and air drying in room temperature then added 5 ul of DW.
ethanol precipitation result

We confirmed that the concentration of Insert DNA solution is 20 ng/ul and Vector DNA solution is about 50~60 ng/ul.

Ligation of RBS-phaB-RBS-eYFP-dT and RBS-phaC-RBS-phaA-pSB1A2

Insert DNA (20 ng/ul) 4 ul
Vector DNA (50~60 ng/ul) 1.5 ul
Ligation Mighty Mix 6 ul
DW 0.5 ul
Total 20 ul


Ligation reaction time was in detail below.

Degree Minute
16 30
65 10
4 Hold

Transformation of RBS-phaC-RBS-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2

Transformation of JM109.

  1. Mixed 2 ul RBS-phaC-RBS-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2 ligation product to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30 min.
  3. Mixed 350 ul of LB.
  4. Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBA).
  5. Plated 300 ul of the culture onto first dish and spread.
  6. Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
  7. Incubated the plates at 37C for 17 hours.


September 16th

Digestion of pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28 and pT7-RBS-pSB1C3

To make a construct of pBAD-RBS-eCFP-RBS-Ag43-dT-pSB1C3, we digested pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28 with EcoRI & SpeI, and pT7-RBS-pSB1C3 with EcoRI & SpeI. As a control, we digested pT7-RBS-pSB1C3 with only EcoRI to confirm the digestibility of This DNA (The digestibility with SpeI has confirmed in August 26th). Insert (pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28)

DNA solution (about 35ng/ul) 41 ul
EcoRI 1 ul
SpeI 1 ul
10xH buffer 5 ul
DW 2 ul
Total 50 ul


Vector(pT7-RBS-pSB1C3)

DNA solution (about 30~40 ng/ul) 2 ul
EcoRI 1 ul
SpeI 1 ul
10xH buffer 2 ul
DW 14 ul
Total 20 ul


control (pT7-RBS-pSB1C3)

DNA solution (about 30~40 ng/ul) 2 ul
EcoRI 1 ul
10xH buffer 1 ul
DW 6 ul
Total 10 ul


Number Degree Minute
1 37 120
2 60 15
3 4 HOLD


digestion result

We confirmed 4 bonds in the result of Inset DNA digestion. A Bond which shows the highest concentration and places about 8k ~ 10k bp area would be pBAD-RBS-eCFP-RBS-Ag43-pSTV28 construct. We considered about it bond whether remained from digestion, or at first formed dimer and separated by digestion. In either case, our target product has about 5200 bp and there is appropriate bond. We extracted the target bond from TBE gel and went next step.

Ethanol precipitation of pBAD-RBS-eCFP-RBS-Ag43-dT--pSB1C3

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged in 15000 rpm, 15 min at 4C.
  3. Remove supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged in 15000 rpm, 10 min at 4C.
  5. Remove supernatant and air drying in room temperature then added 5 ul of DW.
ethanol precipitation result

Ligation of pBAD-RBS-eCFP-RBS-Ag43-dT and pSB1C3

Insert DNA 4 ul
Vector DNA 1 ul
Ligation Mighty Mix 5 ul
Total 10 ul


Ligation reaction time was in detail below.

Degree Minute
16 30
65 10
4 Hold

Transformation of pBAD-RBS-eCFP-RBS-Ag43-dT-pSB1C3

Transformation of DH5α.

  1. Mixed 2 ul pBAD-RBS-eCFP-RBS-Ag43-dT--pSB1C3 ligation product to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30 min.
  3. Mixed 350 ul of LB.
  4. Incubated for 2 hrs to get the resistance to Chloramphenicol.
  5. Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBC).
  6. Plated 300 ul of the culture onto first dish and spread.
  7. Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
  8. Incubated the plates at 37C for 13 hours.

Colony PCR of RBS-phaC-RBs-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2

DNA solution 4 ul
Kapa-Taq(Taq polymerase) 10 ul
Forward Primer(phaA-1083bp-F primer: 10 ng/ul) 0.8 ul
Reverse Primer(PS-R down primer: 10 ng/ul) 0.8 ul
DW 4.4 ul
Total 20 ul


Number Degree Second
1 95 120
2 95 30
3 68.9 30
4 72 180
5 72 120
6 4 HOLD

Cycle:2~4 x 35


We used N1 (DW only) and N2(RBS-phaC-RBS-phaA-RBS-phaB-dT-pSB1A2)as controls. Desired product is about 1800~2000bp.

Colony PCR result


We noticed the ligated DNA contains phaB-something-SP sequence and the length is about 1600~1800bp, at least over 1000 bp. We selected No.1,2 for incubation for mini-prep and No.3,4 for stock at 4C.

Incubation of RBS-phaB-RBS-eYFP-dT-pSB1A2 for mini-prep

  1. Prepared 2 ml LBA into culture tubes.
  2. Re-suspended 2 colony mixture (No.1 and No.2 respectively).
  3. Incubated at 37C for hrs.


Retrieved from "http://2012.igem.org/Team:HokkaidoU_Japan/Notebook/aggregation_Week_11"