Team:Stockholm/7 October 2010

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{{Stockholm/Top2}}
{{Stockholm/Top2}}
==Andreas==
==Andreas==
 +
 +
===Transfer of nCPP⋅SOD⋅His.RBS.yCCS operons to pEX===
 +
====Sequencing====
 +
15 μl plasmid DNA, 1.5 μl primer
 +
 +
*'''pEX.nTra10⋅SH.Ry_pEXf:''' ASB0045 768
 +
*'''pEX.nTra10⋅SH.Ry_pEXr:''' ASB0045 769
 +
*'''pEX.nTAT⋅SH.Ry_pEXf:''' ASB0045 770
 +
*'''pEX.nTAT⋅SH.Ry_pEXf:''' ASB0045 771
 +
*'''pEX.nLMWP⋅SH.Ry_pEXf:''' ASB0045 772
 +
*'''pEX.nLMWP⋅SH.Ry_pEXf:''' ASB0045 773
 +
 +
===Removal of insertion in BioBrick suffixes===
 +
An insertion between SpeI and PstI present in IgGp, bFGF, ProtA, yCCS and SOD needs to be removed before submission to the Registry. This will be done by digestion with SpeI (inside insertion) and moving digested gene into a new vector.
 +
 +
====Digestions====
 +
No sample of SOD available for the moment, so this will be digested after plasmid prep.
 +
 +
{|border="1" cellpadding="1" cellspacing="0"
 +
| 
 +
!width="50"|pC.IgGp<br />(A)
 +
!width="50"|pC.bFGF<br />(B)
 +
!width="50"|pC.ProtA<br />(C)
 +
!width="50"|pC.yCCS<br />(D)
 +
!width="50"|pC.RFP<br />(E)
 +
|-
 +
|10X FastDigest buffer
 +
|align="center"|2
 +
|align="center"|2
 +
|align="center"|2
 +
|align="center"|2
 +
|align="center"|2
 +
|-
 +
|DNA
 +
|align="center"|6
 +
|align="center"|10
 +
|align="center"|16
 +
|align="center"|14
 +
|align="center"|11
 +
|-
 +
|dH<sub>2</sub>O
 +
|align="center"|10
 +
|align="center"|5
 +
|align="center"|0
 +
|align="center"|2
 +
|align="center"|5
 +
|-
 +
|FD SpeI
 +
|align="center"|1
 +
|align="center"|1
 +
|align="center"|1
 +
|align="center"|1
 +
|align="center"|1
 +
|-
 +
|FD EcoRI
 +
|align="center"|1
 +
|align="center"|1
 +
|align="center"|1
 +
|align="center"|1
 +
|align="center"|1
 +
|-
 +
|&nbsp;
 +
!20 &mu;l
 +
!20 &mu;l
 +
!20 &mu;l
 +
!20 &mu;l
 +
!20 &mu;l
 +
|}
 +
*Incubation: 37 &deg;C, 30 min
 +
 +
====Gel verification====
 +
[[image:Dig_insertion_7oct.png|200px|thumb|right|'''Gel verification of digested genes for removal of insertion between SpeI and PstI.'''<br />3 &mu;l &lambda;; 3 &mu;l sample.<br />&lambda; = O'GeneRuler 1 kb DNA ladder.]]
 +
1 % agarose, 130 V
 +
 +
IgGp
 +
bFGF
 +
ProtA
 +
yCCS
 +
RFP
 +
 +
'''Expected bands'''
 +
*'''pSB1C3.IgGp (A)'''
 +
**Vector: 2050 bp
 +
**Insert: 990 bp
 +
*'''pSB1C3.bFGF (B)'''
 +
**Vector: 2050 bp
 +
**Insert: 520 bp
 +
*'''pSB1C3.ProtA (C)'''
 +
**Vector: 2050 bp
 +
**Insert: 230 bp
 +
*'''pSB1C3.yCCS (D)'''
 +
**Vector: 2050 bp
 +
**Insert: 800 bp
 +
*'''pSB1C3.RFP (E)'''
 +
**Vector: 2050 bp
 +
**Insert: 1120 bp
 +
 +
'''Results'''<br />
 +
Relevant-sized for all samples showing successful (but incomplete) digestion. Proceeded to gel extraction.
 +
 +
====Gel extraction====
 +
Loaded remaining 17 &mu;l of each sample on a new 1 % agarose gel. Relevant bands excised by gel extraction and saved in -20 &deg; for later purification.
 +
 +
===Colony PCR of nCPP&sdot;SOD&sdot;His.RBS.yCCS operons in BL21===
 +
#BL21 pEX.nTra10&sdot;SOD&sdot;His.RBS.yCCS (A & B)
 +
#BL21 pEX.nTAT&sdot;SOD&sdot;His.RBS.yCCS (A & B)
 +
#BL21 pEX.nLMWP&sdot;SOD&sdot;His.RBS.yCCS (A & B)
 +
 +
*Standard colony PCR settings.
 +
*Elongation: 1:30 (too short?)
 +
 +
====Gel verification====
 +
[[image:ColPCR_BL21_operons_7oct.png|200px|thumb|right|'''Colony PCR gel verification of BL21 with pEX carrying the nCPP&sdot;SOD/yCCS operons.'''<br />&3 &mu;l &lambda;; 5 &mu;l sample.<br />&lambda; = O'GeneRuler 1 kb DNA ladder.]]
 +
1 % agarose, 130 V
 +
 +
'''Expected bands'''<br />
 +
#1553 bp
 +
#1523 bp
 +
#1532 bp
 +
 +
'''Results'''<br />
 +
Bands with relevant sizes for all clones.

Revision as of 13:15, 13 October 2010

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Contents

Andreas

Transfer of nCPP⋅SOD⋅His.RBS.yCCS operons to pEX

Sequencing

15 μl plasmid DNA, 1.5 μl primer

  • pEX.nTra10⋅SH.Ry_pEXf: ASB0045 768
  • pEX.nTra10⋅SH.Ry_pEXr: ASB0045 769
  • pEX.nTAT⋅SH.Ry_pEXf: ASB0045 770
  • pEX.nTAT⋅SH.Ry_pEXf: ASB0045 771
  • pEX.nLMWP⋅SH.Ry_pEXf: ASB0045 772
  • pEX.nLMWP⋅SH.Ry_pEXf: ASB0045 773

Removal of insertion in BioBrick suffixes

An insertion between SpeI and PstI present in IgGp, bFGF, ProtA, yCCS and SOD needs to be removed before submission to the Registry. This will be done by digestion with SpeI (inside insertion) and moving digested gene into a new vector.

Digestions

No sample of SOD available for the moment, so this will be digested after plasmid prep.

  pC.IgGp
(A) 		pC.bFGF
(B) 		pC.ProtA
(C) 		pC.yCCS
(D) 		pC.RFP
(E)
10X FastDigest buffer 2 2 2 2 2
DNA 6 10 16 14 11
dH2O 10 5 0 2 5
FD SpeI 1 1 1 1 1
FD EcoRI 1 1 1 1 1
  20 μl 20 μl 20 μl 20 μl 20 μl
  • Incubation: 37 °C, 30 min

Gel verification

Gel verification of digested genes for removal of insertion between SpeI and PstI.
3 μl λ; 3 μl sample.
λ = O'GeneRuler 1 kb DNA ladder.

1 % agarose, 130 V

IgGp bFGF ProtA yCCS RFP

Expected bands

  • pSB1C3.IgGp (A)
    • Vector: 2050 bp
    • Insert: 990 bp
  • pSB1C3.bFGF (B)
    • Vector: 2050 bp
    • Insert: 520 bp
  • pSB1C3.ProtA (C)
    • Vector: 2050 bp
    • Insert: 230 bp
  • pSB1C3.yCCS (D)
    • Vector: 2050 bp
    • Insert: 800 bp
  • pSB1C3.RFP (E)
    • Vector: 2050 bp
    • Insert: 1120 bp

Results
Relevant-sized for all samples showing successful (but incomplete) digestion. Proceeded to gel extraction.

Gel extraction

Loaded remaining 17 μl of each sample on a new 1 % agarose gel. Relevant bands excised by gel extraction and saved in -20 ° for later purification.

Colony PCR of nCPP⋅SOD⋅His.RBS.yCCS operons in BL21

  1. BL21 pEX.nTra10⋅SOD⋅His.RBS.yCCS (A & B)
  2. BL21 pEX.nTAT⋅SOD⋅His.RBS.yCCS (A & B)
  3. BL21 pEX.nLMWP⋅SOD⋅His.RBS.yCCS (A & B)
  • Standard colony PCR settings.
  • Elongation: 1:30 (too short?)

Gel verification

Colony PCR gel verification of BL21 with pEX carrying the nCPP⋅SOD/yCCS operons.
&3 μl λ; 5 μl sample.
λ = O'GeneRuler 1 kb DNA ladder.

1 % agarose, 130 V

Expected bands

  1. 1553 bp
  2. 1523 bp
  3. 1532 bp

Results
Bands with relevant sizes for all clones.

Retrieved from "http://2010.igem.org/Team:Stockholm/7_October_2010"