Team:TU Delft/21 July 2010 content

From 2010.igem.org

(Difference between revisions)
(→Method 1)
(→Assembly of reference construct)
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The transformants that were replated on kanamycin plates produced colonies, indicating that hypothesis II was invalid. To test whether these colonies did contain the proper insert however, a [https://2010.igem.org/Team:TU_Delft#page=protocols/colony_PCR colony PCR] was performed:
The transformants that were replated on kanamycin plates produced colonies, indicating that hypothesis II was invalid. To test whether these colonies did contain the proper insert however, a [https://2010.igem.org/Team:TU_Delft#page=protocols/colony_PCR colony PCR] was performed:
-
[[Image:TU_Delft_scPCR_21-07.png|400px|thumb|left|1% agarose of colony PCR. Gel runned at 100V for 1 hour. Of all samples 5 µL was loaded with 1 µL loadingbuffer. 5 µL was loaded of marker]]
+
[[Image:TU_Delft_lastgel_21Jul10.png|450px|thumb|left|1% agarose of colony PCR. Gel runned at 100V for 1 hour. Of all samples 5 µL was loaded with 1 µL loadingbuffer. 5 µL was loaded of marker]]
Lane description:
Lane description:
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|<font color=limegreen>✓</font>
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|7
|7
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|transformant #1 of ligation mix: E-pSB1AK2-I13401-X (ligation control)
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|transformant #6 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
-
|1173
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|1239
|G00101 + G00101
|G00101 + G00101
|<font color=red>✗</font>
|<font color=red>✗</font>
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|8
|8
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|transformant #2 of ligation mix: E-pSB1AK2-I13401-X (ligation control)
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|transformant #7 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
-
|1173
+
|1239
|G00101 + G00101
|G00101 + G00101
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|<font color=limegreen>✓</font>
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|<font color=red>✗</font>
|
|
|-
|-
|9
|9
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|transformant #3 of ligation mix: E-pSB1AK2-I13401-X (ligation control)
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|transformant #8 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
-
|1173
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|1239
|G00101 + G00101
|G00101 + G00101
|<font color=red>✗</font>
|<font color=red>✗</font>
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|10
|10
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|transformant #1 of digestion mix: E-pSB1AK2-I13401-X (digestion control)
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|transformant #9 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
-
|1173
+
|1239
|G00101 + G00101
|G00101 + G00101
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|<font color=limegreen>✓</font>
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|<font color=red>✗</font>
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|11
|11
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|transformant #2 of digestion mix: E-pSB1AK2-I13401-X (digestion control)
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|transformant #10 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
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|1173
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|1239
|G00101 + G00101
|G00101 + G00101
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|<font color=limegreen>✓</font>
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|<font color=red>✗</font>
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|
|-
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|12
|12
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|transformant #1 of K081005 in pSB1A2
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|transformant #11 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
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|296
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|1239
|G00101 + G00101
|G00101 + G00101
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|<font color=limegreen>✓</font>
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|<font color=red>✗</font>
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|13
|13
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|transformant #2 of K081005 in pSB1A2
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|transformant #12 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
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|296
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|1239
|G00101 + G00101
|G00101 + G00101
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|<font color=limegreen>✓</font>
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|<font color=red>✗</font>
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|-
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|14
|14
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|transformant #3 of K081005 in pSB1A2
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|transformant #13 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
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|296
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|1239
|G00101 + G00101
|G00101 + G00101
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|<font color=limegreen>✓</font>
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|<font color=red>✗</font>
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|15
|15
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|BioRad EZ Load
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|transformant #14 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
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|n/a
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|1239
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|n/a
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|G00101 + G00101
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|16
|16
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|Digested PCR product of E0240, XbaI and PstI
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|transformant #15 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
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|898
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|1239
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|None
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|G00101 + G00101
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|<font color=limegreen>✓</font>
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|<font color=red>✗</font>
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|17
|17
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|Digested PCR product of E0240, XbaI and PstI
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|transformant #16 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
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|898
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|1239
-
|None
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|G00101 + G00101
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|<font color=limegreen>✓</font>
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|<font color=red>✗</font>
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|-
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|18
|18
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|Digested PCR product of E0240, XbaI and PstI
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|transformant #17 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X
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|898
+
|1239
-
|None
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|G00101 + G00101
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|<font color=limegreen>✓</font>
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|<font color=red>✗</font>
 +
|
 +
|-
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|19
 +
|BioRad EZ Load
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|N/A
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|N/A
 +
||<font color=limegreen>✓</font>
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Revision as of 13:16, 13 August 2010

Contents

Lab work

Ordered DNA

The transformations of 19 July containing the different ligations gave colonies (~5 per plate). We picked 5 colonies per plate and performed a colony PCR.

Alkane degradation

Unfortunately there were no transformants on yesterday's plates. This is most likely due to the fact that the ligation didn't work with the small pieces of DNA of the RBSs. Next plan is to cut open the RBS plasmid without removing the RBS (with SpeI and PstI) and insert the gene in this plasmid. We will try this tomorrow.

Salt Tolerance

The overnight ligation was transformed using the standard method and grown up overnight at 37 degrees C.

Emulsifier

2% agarose of colony PCR. Gel runned at 100V for 1 hour. Of all samples 10 μL + 2 μL loadingbuffer was loaded. 5 μL was loaded of marker
There were small colonies on the plates. Pieter picked seven and performed colony PCR on them.

Lane Description

# Description Expected lenght (bp) Primer Status
M1 EZ Ladder n/a n/a n/a
1 B0032 (control) 220 G00100 + G00101 ✓
2 Transformant #1 of ligation mix R0011-B0032 300 G00100 + G00101 ✗
3 Transformant #2 of ligation mix R0011-B0032 300 G00100 + G00101 ✗
4 Transformant #3 of ligation mix R0011-B0032 300 G00100 + G00101 ✗
5 Transformant #4 of ligation mix R0011-B0032 300 G00100 + G00101 ✗
6 Transformant #5 of ligation mix R0011-B0032 300 G00100 + G00101 ✗
7 Transformant #6 of ligation mix R0011-B0032 300 G00100 + G00101 ✗
8 Transformant #7 of ligation mix R0011-B0032 300 G00100 + G00101 ✗

Unfortunately all other lanes were empty or the same as the negative control. So from this gel we conclude that the ligation has failed.

Characterisation of Anderson RBS sequences

Assembly of reference construct

Method 1

Hypothesis II The transformants that were replated on kanamycin plates produced colonies, indicating that hypothesis II was invalid. To test whether these colonies did contain the proper insert however, a colony PCR was performed:

1% agarose of colony PCR. Gel runned at 100V for 1 hour. Of all samples 5 µL was loaded with 1 µL loadingbuffer. 5 µL was loaded of marker

Lane description:

# Description Expected Length (bp) Primers Status Remarks
1 SmartLadder n/a n/a ✓
2 transformant #1 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
3 transformant #2 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
4 transformant #3 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
5 transformant #4 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
6 transformant #5 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
7 transformant #6 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
8 transformant #7 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
9 transformant #8 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
10 transformant #9 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
11 transformant #10 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
12 transformant #11 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
13 transformant #12 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
14 transformant #13 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
15 transformant #14 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
16 transformant #15 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
17 transformant #16 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
18 transformant #17 of ligation mix: E-K081005-S + E-pSB1AK2-I13401-X 1239 G00101 + G00101 ✗
19 BioRad EZ Load N/A N/A ✓
Method 4

The obtained colonies on ampicillin plates were screened for GFP fluorescence, those that fluoresced were inoculated in 5 mL of LB medium for over night growth.

Solvent Tolerance and Hydrocarbon Sensing

Characteristic digestion of isolated plasmids

To determine whether the plasmids are correct. Characteristic cuts were made using the restriction enzyme PvuI.

# Sample Enzyme 1 Buffer Needed fragments
1 1450 μg K398328T PvuII Buffer II 252, 1647, 69, 36, 3246
2 378 μg K398407T PvuII Buffer II 2552
3 716.5 μg Control (pSB1T3, B0015: this does not ligate) PvuII (this enzyme does not work here) Buffer II 172, 2463
4 245.4 μg K398300C PvuII Buffer II 654, 252, 1647, 69, 36, 2004
5 1481.4 μg K398000C PvuII Buffer II 495, 2901
6 1198.5 μg K398002C PvuII Buffer II 2243
7 42.3 μg K398002C PvuII Buffer II 3120
8 1612.8 μg K398200C PvuII Buffer II 558, 135, 177, 1887
9 1633.3 μg K398201C PvuII Buffer II 2529
10 938.6 μg K398400C PvuII Buffer II


Results of the digestion on 1% agarose gel

1% agarose of plasmid check using digestion reaction. Gel runned at 100V for 1 hour. Of all samples 10 μL was loaded with 2 μL loadingbuffer. 5 μL was loaded of marker

Lane description:

# Description Expected Length (bp) Status Remarks
1 marker n/a n/a n/a
2 Digested K398328T 252, 1647, 69, 36, 3246 ✗
3 Digested K398407T 2552 ✗
4 pSB1T3 with B0015 (control) 172, 2463 ✗ The upper band is most likely circular pSB1T3. There's a strange band around 600 bp.
5 Digested K398000C 654, 252, 1647, 69, 36, 2004 ✗
6 Digested K398000C 495, 2901 ? There's no band of 495 bp
7 Digested K398002C 2243 ✓
8 Digested K398200C 3120 ✗
9 Digested K398201C 558, 135, 177, 1887 ✓
10 Digested K398400C 2529 ✗
11 pSB1T3 (control) 2463 ? A bright band around 2500 bp was shown. There are also a lot of unexplainable bands visible.

Unfortunately most of the lanes showed incorrect bands. So from this gel we conclude that the ligation has failed.

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