Team:Heidelberg/Templates/Del week13 FG

From 2013.igem.org

(Difference between revisions)
(Created page with "==22-07-2013== ===Amplification from FS_20/FS_21 to FS_09; 8.5 kb=== [[File:Heidelberg_20130722 log2 OP22to13long FG20to9 FG21to9besch.png |150px|thumb| Re-PCR of DelOP (22-13...")
(→Restriction digest of fragment from FS_20 to FS_07; 5.2 kb; 23-07-2013 and 23-07-2013) with ClaI)
 
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==22-07-2013==
==22-07-2013==
===Amplification from FS_20/FS_21 to FS_09; 8.5 kb===
===Amplification from FS_20/FS_21 to FS_09; 8.5 kb===
Line 299: Line 300:
* The amplification of FS_06 to FS_07 did not work. No bands were visible
* The amplification of FS_06 to FS_07 did not work. No bands were visible
* The amplification of FS_21 to FS_07 led to several bands, but none of these was the intended product
* The amplification of FS_21 to FS_07 led to several bands, but none of these was the intended product
-
* The amplfication of FS_20 to FS_07 also led to several bands, one band at the right height was observed. Consequently the specificity of the PCR weill be increased by a higher annealing temperature
+
* The amplfication of FS_20 to FS_07 also led to several bands, one band at the right height was observed. Consequently the specificity of the PCR will be increased by a higher annealing temperature
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<div style="clear:both"></div>
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==25-07-2013==
==25-07-2013==
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===Restriction digest of DelFG (FS_20 to FS_07; 5.2 kb;  [[DelF-G#23-07-2013|23-07-2013]] and  [[DelF-G#24-07-2013|24-07-2013]]) with XmaI===
+
===Restriction digest of fragment from FS_20 to FS_07; 5.2 kb;  23-07-2013 and  24-07-2013 with XmaI===
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[[File:Heidelberg_20130725 FS20toFS07 test restrictionbesch.png|150px|thumb|Restriction digest of Fragment FS_20 to FS_07 (23.07 and 24.07) with XmaI <span style="color:red"> The second lane is also a digest </span>; Expected size of digested fragments: 0.9kbp and 4.3kbp; run at 100 V, 0.8 % gel (TAE)]]
+
[[File:Heidelberg_20130725 FS20toFS07 test restrictionbesch.png|150px|thumb|Restriction digest of Fragment FS_20 to FS_07 (23.07 and 24.07) with XmaI ; Expected size of digested fragments: 0.9kbp and 4.3kbp; run at 100 V, 0.8 % gel (TAE)]]
Incubation at 37°C for 45 min
Incubation at 37°C for 45 min
{| class="wikitable"
{| class="wikitable"
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! what !! µl   
! what !! µl   
|-
|-
-
| FS_20 to FS_07 ([[DelF-G#23-07-2013|23-07-2013]] and  [[DelF-G#24-07-2013|24-07-2013]]) || 15
+
| FS_20 to FS_07 (23-07-2013 and  24-07-2013) || 15
|-
|-
| XmaI || 0.8
| XmaI || 0.8
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|-
|-
| dd H<sub>2</sub>O || 2.2
| dd H<sub>2</sub>O || 2.2
 +
|-
 +
| Expected fragment lengths [bp]|| 4307, 879
|}
|}
<div style="clear:both"></div>
<div style="clear:both"></div>
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* Annealing temperature will be increased further, to optimize primer specifity
* Annealing temperature will be increased further, to optimize primer specifity
-
===Restriction digest of fragment from FS_20 to FS_07; 5.2 kb;  [[DelF-G#23-07-2013|23-07-2013]] and [[DelF-G#24-07-2013|23-07-2013]]) with ClaI===
+
===Restriction digest of fragment from FS_20 to FS_07; 5.2 kb;  23-07-2013 and 23-07-2013) with ClaI===
[[File:Heidelberg_20130726 restrictdigest OP 4µL2log tyr3-8cut.png|100px|thumb|restriction digest of FS_20 to FS_07 (26.07.13) with ClaI and concentration measurement of DelOP (25.07.13); run at 100 V, 0.8 % gel (TAE)]]
[[File:Heidelberg_20130726 restrictdigest OP 4µL2log tyr3-8cut.png|100px|thumb|restriction digest of FS_20 to FS_07 (26.07.13) with ClaI and concentration measurement of DelOP (25.07.13); run at 100 V, 0.8 % gel (TAE)]]
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! what !! µl   
! what !! µl   
|-
|-
-
| FS_20 to FS_07 ([[DelF-G#23-07-2013|23-07-2013]] and [[DelF-G#24-07-2013|23-07-2013]]) || 25
+
| FS_20 to FS_07 (23-07-2013 and 23-07-2013) || 25
|-
|-
| ClaI || 1
| ClaI || 1
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|-
|-
| dd H<sub>2</sub>O || 1
| dd H<sub>2</sub>O || 1
 +
|-
 +
| Expected fragment lengths [bp]|| 2743, 1519, 1208
|}
|}

Latest revision as of 18:37, 3 October 2013

Contents

22-07-2013

Amplification from FS_20/FS_21 to FS_09; 8.5 kb

Re-PCR of DelOP (22-13long), Amplification of DelFG (20-9 and 21-9) (22.07); run at 100 V, 0.8 % gel (TAE)
Re-PCR of DelOP (22-13long), Amplification of DelFG (20-9 and 21-9) (22.07) cut; run at 100 V, 0.8 % gel (TAE)
Reaction
what µl
D. acidovorans DSM-39 1
FS_20/FS_21: (1/10) 2
FS_09: (1/10) 2
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad MyCycler*
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
65 ↓ 0.5 5
72 2:20
18 98 1
63 5
72 2:20
1 72 10 min
1 12 inf

Results:

  • Amplification of DelFG did not work
  • other primers/combinations of primers will be used
  • somehow getting annoyed by this part of D. Acidovorans

Amplification from FS_20/FS_21 to FS_11_short; 11.6 kb

Amplification of DelFG (22.07); run at 100 V, 0.8 % gel (TAE)

4x 20µl (70 touchdown, 65 touchdown)

Reaction
what µl
D. acidovorans DSM-39 1
FS_20 or FS_21: (1/10) 2
FS_11_short: (1/10) 2
Phusion flash Master Mix 10
DMSO 1
dd H2O 4


Conditions I
Biorad MyCycler*
Cycles temperature [°C] Time [s]
1 98 5
12 98 1
70 ↓ 0.5 5
72 3:40
18 98 1
68 5
72 3:40
1 72 13min
1 12 inf
Conditions II of Del FG
Biorad T100
Cycles temperature [°C] Time [s]
1 98 5
12 98 1
65 ↓ 0.5 5
72 3:40
18 98 1
63 5
72 3:40
1 72 13min
1 12 inf

Results:

  • Amplification of DelFG did not work neither with a touchdown PCR starting at an annealing temperature of 65°C nor 70°C

Amplification from FS_20/FS_21 to FS_23; 11.6 kb

Amplification of DelFG (22.07); run at 100 V, 0.8 % gel (TAE)

4x 20µl (70 touchdown, 65 touchdown)

Reaction
what µl
D. acidovorans DSM-39 1
FS_20 or FS_21: (1/10) 2
FS_23: (1/10) 2
Phusion flash Master Mix 10
DMSO 1
dd H2O 4


Conditions I
Biorad MyCycler*
Cycles temperature [°C] Time [s]
1 98 5
12 98 1
70 ↓ 0.5 5
72 3:40
18 98 1
68 5
72 3:40
1 72 13min
1 12 inf
Conditions II
Biorad T100
Cycles temperature [°C] Time [s]
1 98 5
12 98 1
65 ↓ 0.5 5
72 3:40
18 98 1
63 5
72 3:40
1 72 13min
1 12 inf

Results:

  • Neither the amplification with the primers FS_20 to FS_23 or FS_21 to FS_23 did work. Another primer combination has to be tried.

24-07-2013

Amplification of DelFG (FS_06 to FS_07; 5.2 kb)

PCR of FG (FS_06 to FS_07) or (FS_20 to FS_07) or (FS_21 to FS_07) as indicated; run at 100 V, 0.8 % gel (TAE)
Reaction I
what µl
D. acidovorans DSM-39 1
FS_06: (1/10) 4
FS_07: (1/10) 4
Phusion flash Master Mix 10
DMSO 1

Amplification from FS_20 to FS_07; 5.2 kb

PCR of FG (FS_06 to FS_07) or (FS_20 to FS_07) or (FS_21 to FS_07) as indicated; run at 100 V, 0.8 % gel (TAE)
Reaction II
what µl
D. acidovorans DSM-39 1
FS_20: (1/10) 4
FS_07: (1/10) 4
Phusion flash Master Mix 10
DMSO 1

Amplification from FS_21 to FS_07; 5.2kb

PCR of FG (FS_06 to FS_07) or (FS_20 to FS_07) or (FS_21 to FS_07) as indicated; run at 100 V, 0.8 % gel (TAE)
Reaction III
what µl
D. acidovorans DSM-39 1
FS_21: (1/10) 4
FS_07: (1/10) 4
Phusion flash Master Mix 10
DMSO 1
Conditions for reactions I - III
Biometra TProfessional Basic
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
68 ↓ 0.5 5
72 2:10
18 98 1
64 5
72 2:10
1 72 10min
1 12 inf

Results:

  • The amplification of FS_06 to FS_07 did not work. No bands were visible
  • The amplification of FS_21 to FS_07 led to several bands, but none of these was the intended product
  • The amplfication of FS_20 to FS_07 also led to several bands, one band at the right height was observed. Consequently the specificity of the PCR will be increased by a higher annealing temperature

Amplification from FS_20 to FS_07; 5.2 kb

2x20µl (one with conditions I, other one with conditions II)

Reaction
what µl
D. acidovorans DSM-39 1
FS_20: (1/10) 4
FS_07: (1/10) 4
Phusion flash Master Mix 10
DMSO 1
Conditions I
Biorad MyCycler*
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
70 ↓ 0.5 5
72 2:10
18 98 1
68 5
72 2:10
1 72 10min
1 12 inf
Conditions II
Biometra TProfessional Basic
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
68 ↓ 0.5 5
72 2:10
18 98 1
66 5
72 2:10
1 72 10min
1 12 inf

Results:

  • Amplification of DelFG did not work, several bands occured, one of these had the size of the intended product but purity of the PCR was not sufficient for Gibson Assembly
  • nethertheless bands were cut out and DNA purified using QIAquick Gel Extraction Kit for restriction digest

Amplification from FS_20 to FS_07; 5.2 kb

Amplification of DelFG II (FS20 to FS07; 24.07),; run at 100 V, 0.8 % gel (TAE)
Amplification of DelFG II (FS20 to FS07; 24.07), ; run at 100 V, 0.8 % gel (TAE)

4x20µl

Reaction
what µl
D. acidovorans DSM-39 1
FS_20: (1/10) 4
FS_07: (1/10) 4
Phusion flash Master Mix 10
DMSO 1
Conditions
Biometra TProfessional Basic
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
70 ↓ 0.5 5
72 2:10
18 98 1
68 5
72 2:10
1 72 10min
1 12 inf

Results:

  • Amplification of DelFG did not work, several bands occured, one of these had the size of the intended product but purity of the PCR was not sufficient for Gibson Assembly
  • nethertheless bands were cut out and DNA purified using QIAquick Gel Extraction Kit for restriction digest

25-07-2013

Restriction digest of fragment from FS_20 to FS_07; 5.2 kb; 23-07-2013 and 24-07-2013 with XmaI

Restriction digest of Fragment FS_20 to FS_07 (23.07 and 24.07) with XmaI ; Expected size of digested fragments: 0.9kbp and 4.3kbp; run at 100 V, 0.8 % gel (TAE)

Incubation at 37°C for 45 min

what µl
FS_20 to FS_07 (23-07-2013 and 24-07-2013) 15
XmaI 0.8
Buffer CutSmart 2
dd H2O 2.2
Expected fragment lengths [bp] 4307, 879

Results:

  • restriction digest of DelFG did not work, only very slight bands were visible
  • digest will be repeated with higher amount of DNA and enzyme to improve analysis on the gel

26-07-2013

Amplification from FS_20 to FS_07; 5.2 kb

Reaction I
what µl
D. acidovorans DSM-39 1
FS_20: (1/10) 4
FS_07: (1/10) 4
Phusion flash Master Mix 10
DMSO 1
Conditions
Biometra TProfessional Basic
Cycles temperature [°C] Time [s]
1 98 10
30 98 1
70 5
72 2:10
1 72 10min
1 12 inf

Results:

  • Amplification of DelFG did not work, several bands occured, one of these had the size of the intended product but purity of the PCR was not sufficient for Gibson Assembly
  • Annealing temperature will be increased further, to optimize primer specifity

Restriction digest of fragment from FS_20 to FS_07; 5.2 kb; 23-07-2013 and 23-07-2013) with ClaI

restriction digest of FS_20 to FS_07 (26.07.13) with ClaI and concentration measurement of DelOP (25.07.13); run at 100 V, 0.8 % gel (TAE)

Incubation at 37°C for 45 min

what µl
FS_20 to FS_07 (23-07-2013 and 23-07-2013) 25
ClaI 1
Buffer CutSmart 3
dd H2O 1
Expected fragment lengths [bp] 2743, 1519, 1208

Results:

  • restriction digest of Del FG did not lead to the expected results
  • as no DNA was visible in the restriction digest, experiment will be repeated with a higher amount of DNA

Amplification from FS_06 to FS_07; 5.2 kb

4 x Amplification of DelFG (FS20 to FS07; 26.07), 4 x Amplification of DelOP (FS_22 to FS13; 25.07); run at 100 V, 0.8 % gel (TAE)
4 x Amplification of DelFG (FS20 to FS07; 26.07), 4 x Amplification of DelOP (FS_22 to FS13; 25.07) after cutting; run at 100 V, 0.8 % gel (TAE)

4 x 20µL

Reaction I
what µl
D. acidovorans DSM-39 1
FS_20: (1/10) 4
FS_07: (1/10) 4
Phusion flash Master Mix 10
DMSO 1
Conditions
Biometra TProfessional Basic
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
72 ↓ 0.5 5
72 2:10
18 98 1
70 5
72 2:10
1 72 10min
1 12 inf

Results:

  • Amplification of DelFG did not work, several bands occured, one of these had the size of the intended product but purity of the PCR was not sufficient for Gibson Assembly
  • nethertheless bands were cut out and DNA purified using QIAquick Gel Extraction Kit for restriction digest
  • Does anyone know, why we are constantly repeating this totally deficient PCR?

Amplification from FS_6/FS_20/FS_21 to FS_24 (PRIMER FS_24 MIXED UP!)

run at 100 V, 0.8 % gel (TAE)
Reaction
what µl
D. acidovorans DSM-39 1
FS_06/FS_20/FS_21: (1/10) 2
FS_24: (1/10) 2
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad MyCycler*
Cycles temperature [°C] Time [s]
1 98 10
30 98 1
65 5
72 1:20
1 72 7 min
1 10 inf

Results:

  • no PCR product occured since the wrong primers were used

28-07-2013

Amplification from FS_21 to FS_24; (PRIMER 24 was MIXED UP!)

2log ladder / FS21-FS24 60const / FS07-FS26 65const / FS07-FS26 68const / FS24-FS26 65const / FS24-FS26 68const; run at 100 V, 0.8 % gel (TAE)
Reaction
what µl
D. acidovorans DSM-39 1
FS_21: (1/10) 2
FS_24: (1/10) 2
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad T100
Cycles temperature [°C] Time [s]
1 98 10
30 98 1
58 5
72 2:30
1 72 8 min
1 12 inf
Reaction
what µl
D. acidovorans DSM-39 1
FS_21: (1/10) 2
FS_24: (1/10) 2
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad MyCycler*
Cycles temperature [°C] Time [s]
1 98 10
30 98 1
60 5
72 2:30
1 72 8 min
1 12 inf

Results:

  • no PCR product occured since the wrong primers were used
Retrieved from "http://2013.igem.org/Team:Heidelberg/Templates/Del_week13_FG"