Team:Heidelberg/Templates/DelH week25

From 2013.igem.org

(Difference between revisions)
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== 14-10 - 20-10-13 ==
== 14-10 - 20-10-13 ==
===Generation of DelH plasmids pFS02, pFS03, pFS04 and pFS05===
===Generation of DelH plasmids pFS02, pFS03, pFS04 and pFS05===
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====Amplification of pFS_03 Backbone (HM_17 to FS_78; 4.1 kbp)====
 
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:'''Reaction'''
 
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{| class="wikitable"
 
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|-
 
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! Reagent !! Amount [µl] 
 
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|-
 
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| pSB6A1 || 1
 
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|-
 
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| HM_17:  (1/10) || 1
 
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|-
 
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| FS_78:  (1/10) || 1
 
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|-
 
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| Phusion flash Master Mix || 10
 
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|-
 
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| DMSO || 1
 
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|-
 
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| dd H<sub>2</sub>O || 4
 
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|}
 
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:'''Conditions '''
 
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{| class="wikitable"
 
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|-
 
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! colspan="3" | Biorad T100
 
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|-
 
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! Cycles !! temperature [°C] !! Time [s]
 
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|-
 
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| 1 || 98 || 10
 
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|-
 
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| rowspan="3"| 35 || 98 || 1
 
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|-
 
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| 58  || 5
 
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|-
 
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| 72  || 1:25
 
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|-
 
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| 1 || 72 || 10min
 
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|-
 
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| 1  || 12 || inf
 
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|}
 
====Amplification of ccdB fragment for pFS_04 (FS_90 to FS_93; 700 bp)====
====Amplification of ccdB fragment for pFS_04 (FS_90 to FS_93; 700 bp)====
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====Amplification of Backbone fragment for pFS_02 (HM_17 to FS_87; 4.2 kbp)====
 
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4 reactions with 20µl each, followed by DpnI digest
 
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:'''Reaction'''
 
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{| class="wikitable"
 
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|-
 
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! Reagent !! Amount [µl] 
 
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|-
 
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| pSB6A1 || 0.2
 
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|-
 
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| HM_17:  (1/10) || 1
 
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|-
 
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| FS_87:  (1/10) || 1
 
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|-
 
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| Phusion flash Master Mix || 10
 
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|-
 
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| DMSO || 1
 
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|-
 
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| dd H<sub>2</sub>O || 4.8
 
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|}
 
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:'''Conditions'''
 
-
 
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{| class="wikitable"
 
-
|-
 
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! colspan="3" | Biorad T100
 
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|-
 
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! Cycles !! temperature [°C] !! Time [s]
 
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|-
 
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| 1 || 98 || 10
 
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|-
 
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| rowspan="3"| 12 || 98 || 1
 
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|-
 
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| 68 ↓ 0.5  || 5
 
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|-
 
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| 72  || 1:25
 
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|-
 
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| rowspan="3"| 18 || 98 || 1
 
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|-
 
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| 66  || 5
 
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|-
 
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| 72  || 1:25
 
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|-
 
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| 1 || 72 || 10min
 
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|-
 
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| 1  || 12 || inf
 
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|}
 
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-
 
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==Gibson assembly of pFS_02==
 
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{|class="wikitable"
 
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|-
 
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! Reagent !! Volume added (µl)
 
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|-
 
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| BB (HM_17-FS_78) || 0.24
 
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|-
 
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| DN11-FS66 || 2.13
 
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|-
 
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| FS_67-FS_68 || 2.89
 
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|-
 
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| FS_69-FS_70 || 2.38
 
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|-
 
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| FS_71-HM08 || 2.36
 
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|-
 
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| Gibson Master Mix 2x || 10
 
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|}
 
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====Colony-PCR, screening for pFS_02====
 
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{| class="wikitable" style="float:left; margin-right:1em"
 
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|-
 
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| Template || 96x 1 picked colony
 
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|-
 
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| Expected length [bp] ||  521
 
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|-
 
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| Named || 1A - 12H, DelH_pSB6A1_weak_promotor
 
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|-
 
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| Primer fw 10 µM ||96x 1 µl FS_73 
 
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|-
 
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| Primer rev 10 µM ||96x 1 µl FS_95
 
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|-
 
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| One-Taq Polymerase (2x) ||96x 5 µl
 
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|-
 
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| ddH<sub>2</sub>O || 96x 4 µl 
 
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|}
 
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{| class="wikitable" style="float:left; margin-right:1em"
 
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|-
 
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! Cycles !! Temperature [°C] !! Time [s]
 
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|-
 
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| 1 || 95 || 120
 
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|-
 
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| rowspan="3" | 12 || 95 || 30
 
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|-
 
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| 68 (touchdown -0.5°C) || 30
 
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|-
 
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| 72 || 45 s
 
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|-
 
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| rowspan="3" | 18 ||  95 || 30
 
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|-
 
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| 65  || 30
 
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|-
 
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| 72 || 45
 
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|-
 
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| 1  || 12 || inf
 
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|}
 
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<div style="clear:both"></div>
 
==Gibson assembly of pFS_03==
==Gibson assembly of pFS_03==

Revision as of 11:09, 26 October 2013

Contents

14-10 - 20-10-13

Generation of DelH plasmids pFS02, pFS03, pFS04 and pFS05

Amplification of pFS_04 Backbone (FS_85 to FS_94; 4.1 kbp)

Reaction
Reagent Amount [µl]
pSB6A1 1
FS_85: (1/10) 1
FS_94: (1/10) 1
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad T100
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
68 ↓ 0.5 5
72 1:25
18 98 1
66 5
72 1:25
1 72 10min
1 12 inf


Amplification of pFS_03 Backbone (FS_86 to FS_87; 4.1 kbp)

Reaction
Reagent Amount [µl]
pSB4K5 1
FS_86: (1/10) 1
FS_87: (1/10) 1
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad T100
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
68 ↓ 0.5 5
72 1:25
18 98 1
66 5
72 1:25
1 72 10min
1 12 inf

Amplification of pFS_04 Backbone (FS_85 to FS_94; 4.1 kbp)

Reaction
Reagent Amount [µl]
pSB6A1 1
FS_85: (1/10) 1
FS_94: (1/10) 1
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad T100
Cycles temperature [°C] Time [s]
1 98 10
35 98 1
58 5
72 1:25
1 72 10min
1 12 inf

Amplification of pFS_03 Backbone (FS_86 to FS_87; 4.1 kbp)

Reaction
Reagent Amount [µl]
pSB4K5 1
FS_86: (1/10) 1
FS_87: (1/10) 1
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad T100
Cycles temperature [°C] Time [s]
1 98 10
35 98 1
58 5
72 1:25
1 72 10min
1 12 inf


Amplification of ccdB fragment for pFS_04 (FS_90 to FS_93; 700 bp)

4 reactions with 20µl each, followed by DpnI digest

Reaction
Reagent Amount [µl]
pDonor-Plasmid 1
FS_90: (1/10) 1
FS_93: (1/10) 1
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad T100
Cycles temperature [°C] Time [s]
1 98 10
35 98 1
72 0:18
1 72 10min
1 12 inf

Amplification of pFS_04 Backbone (FS_85 to FS_94; 4.1 kbp)

4 reactions with 20µl each, followed by DpnI digest

Reaction
Reagent Amount [µl]
pSB6A1 1
FS_85: (1/10) 1
FS_94: (1/10) 1
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad T100
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
68 ↓ 0.5 5
72 1:25
18 98 1
66 5
72 1:25
1 72 10min
1 12 inf

Amplification of pFS_03 Backbone (FS_86 to FS_87; 4.1 kbp)

4 reactions with 20µl each, followed by DpnI digest

Reaction
Reagent Amount [µl]
pSB4K5 1
FS_86: (1/10) 1
FS_87: (1/10) 1
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad T100
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
68 ↓ 0.5 5
72 1:25
18 98 1
66 5
72 1:25
1 72 10min
1 12 inf

Amplification of DelH fragment (FS_69 to FS_70; 7.0 kbp)

7 reactions with 20µl each

Reaction
Reagent Amount [µl]
D. acidovorans SPH-1 1
FS_69: (1/10) 1
FS_70: (1/10) 1
Phusion flash Master Mix 10
DMSO 1
dd H2O 4
Conditions
Biorad T100
Cycles temperature [°C] Time [s]
1 98 10
12 98 1
68 ↓ 0.5 5
72 1:25
18 98 1
66 5
72 1:25
1 72 10min
1 12 inf



Gibson assembly of pFS_03

Reagent Volume added (µl)
BB (FS_86 - FS_87) 0.61
DN11-FS66 1.00
FS_67-FS_68 1.35
FS_69-FS_70 6.34
FS_71-HM08 0.70
Gibson Master Mix 2x 10

Colony-PCR, screening for pFS_03

Template 60x1 picked colony
Expected length [bp] 521
Named 1A - 12H, DelH_pSB6A1_weak_promotor
Primer fw 10 µM 60x 0.5 µl FS_73
Primer rev 10 µM 60x 0.5 µl FS_95
One-Taq Polymerase (2x) 60x 5 µl
ddH2O 60x 4 µl
Cycles Temperature [°C] Time [s]
1 95 120
12 95 30
68 (touchdown -0.5°C) 30
72 45 s
18 95 30
65 30
72 45
1 12 inf

Gibson assembly of pFS_04

Reagent Volume added (µl)
BB (FS_85-FS_94) 0.44
ccdB (FS_90-FS_93 0.15
ddH2O 9.41
Gibson Master Mix 2x 10


Colony-PCR, screening for pFS_04

Template 30x1 picked colony
Expected length [bp] ~800bp
Named 1A - 6C, pSB6A1_ccdB
Primer fw 10 µM 30x 0.5 µl KH_9
Primer rev 10 µM 30x 0.5 µl VF2
One-Taq Polymerase (2x) 30x 5 µl
ddH2O 30x 4 µl
Cycles Temperature [°C] Time [s]
1 95 120
35 95 30
57 30
72 45
1 12 inf

18.10

HM17-FS_78

Annealing temps: 62°C, 60°C, 57°C, 55°C
Elongation time: 2:10
--> Did not work


ccdB

Annealing temps: </br> 12 cycles 74, 68, 64 and 58°C
18 cycles 72, 66, 62 and 56°C

20-10-2013

Inocultation triple dummy clone

Screening triple clone

each with positive control IK25+VF2 -->54°C, 90s elongation
FS47+FS48 --> 66t,62 40s elongation
FS95+FS73 --> 66t,62 40s elongation

Retrieved from "http://2013.igem.org/Team:Heidelberg/Templates/DelH_week25"