Team:Stockholm/28 August 2010

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{{Stockholm/Top2}}
{{Stockholm/Top2}}
==Andreas==
==Andreas==
 +
===Gel extraction===
 +
{|border="1" cellpadding="1" cellspacing="0" align="right"
 +
|+ align="bottom"|''No measurable DNA conc. for "Extr. Dig SOD E+A"''
 +
!colspan="3"|DNA concentrations
 +
|-
 +
!Sample
 +
!Conc [ng/μl]
 +
!A<sub>260</sub>/A<sub>280</sub>
 +
|-
 +
|Extr. N-CPP
 +
|align="center"|40.91
 +
|align="center"|1.69
 +
|-
 +
|Extr. Dig SOD E+A
 +
|align="center"|&ndash;
 +
|align="center"|&ndash;
 +
|-
 +
|Pur. Dig pMA.His E+N
 +
|align="center"|36.02
 +
|align="center"|1.80
 +
|}
 +
 +
''From 27/8''<br />
 +
Purified DNA from excised samples "Extr. Dig. SOD E+A" and "Extr. N-CPP cluster" using the E.Z.N.A. Gel extraction kit; procedures according to provided protocol.
 +
 +
Elution volume: 30 &mu;l (eluted twice to increase DNA yield)
 +
*Extr. N-CPP
 +
*Extr. Dig SOD E+A
 +
 +
===DNA purification of "Dig. pMA.His (E+N)"===
 +
''From 27/8''<br />
 +
DNA clean-up using the E.Z.N.A. Gel Extraction kit, following procedures for DNA purification.
 +
 +
Elution volume: 30 &mu;l (eluted twice to increase DNA yield)
 +
*Pur. Dig. pMA His E+N
 +
 +
===Gel verification===
 +
[[image:Gelver_DNAextr_28aug.png|200px|right|thumb|'''Gel verification of gel extracted and purified DNA samples.'''<br />3 &mu;l &lambda;; 2 &mu;l sample.<br />1 kb &lambda;=O'GeneRuler 1 kb DNA ladder. 50 bp &lambda;=GeneRuler 50 bp DNA ladder.]]
 +
Since no DNA content was measurable for "Extr. Dig SOD E+A", a gel was run to verify DNA content in the three purified samples.
 +
 +
1 % agarose, 110 V
 +
 +
Samples:
 +
*SOD: Extr. Dig SOD E+A
 +
*pMA: Pur. Dig pMA.His E+N
 +
*CPP: Extr. N-CPP cluster
 +
 +
Expected bands:
 +
*SOD: 492 bp
 +
*pMA: 2427 bp
 +
*CPP: 379 bp
 +
 +
====Results====
 +
*CPP resulted in a clear band of correct size.
 +
*A very weak band at &asymp;500 bp is visible for SOD, which might be traces of DNA.
 +
*No band visible for pMA.
 +
 +
Nevertheless, proceeded to ligation and cloning, hoping that the DNA is there.
 +
 +
===Cloning of SOD into pMA.His===
 +
 +
====Ligation====
 +
{|border="1" cellpadding="1" cellspacing="0"
 +
|&nbsp;
 +
![&mu;l]
 +
|-
 +
|Extr. Dig SOD E+A
 +
|align="center"|12
 +
|-
 +
|Pur. Dig pMA.His E+N
 +
|align="center"|3
 +
|-
 +
|5X Rapid Ligation buffer
 +
|align="center"|4
 +
|-
 +
|T4 DNA ligase
 +
|align="center"|1
 +
|}
 +
 +
Incubation: 22 &deg;C, 10 min
 +
 +
====Transformation====
 +
*3 &mu;l ligation mix. 30 min on ice.
 +
*30 sec heat shock in 42 &deg;C
 +
*Cells grown on Amp 100 LB agar, 37 &deg;C
 +
 +
===Amplification of N-CPPs from N-CPP cluster===
 +
Ran PCRs from the gel extracted N-CPP cluster with the following primers:
 +
*'''Tra10:''' pSB-VF2 & pSB-VR
 +
*'''TAT:''' pEXf & pEXr
 +
*'''LMWP:''' pGexf & pGexr
 +
 +
Also ran 4 colony PCRs for Mimmi from cells transformed with pSB1C3.MITF plasmids (MITF 1-4); positive control (PC) pSB1C3.RFP; negative control (NC) blank; primers pSB-VF2 & pSB-VR.
 +
 +
'''PCR tubes'''<br />
 +
*illustra Ready-to-Go PCR beads
 +
*22.5 &mu;l dH<sub>2</sub>O
 +
*1 &mu;l forward primer
 +
*1 &mu;l reverse primer
 +
*0.5 &mu;l template DNA
 +
 +
Standard colony PCR settings; 1:45 elongation time.
 +
 +
====Gel verification====
 +
[[image:Gelver_CPP_MITF_PCR_28aug.png|200px|right|thumb|'''Gel verification of PCR amplified pSB1C3.MITF and N-CPPs.'''<br />3 &mu;l &lambda;; 4 &mu;l sample.<br />1 kb &lambda;=O'GeneRuler 1 kb DNA ladder. 50 bp &lambda; GeneRuler 50 bp DNA ladder.]]
 +
1 % agarose, 100 V
 +
 +
'''Expected bands:'''
 +
*'''MITF:''' 1586 bp
 +
*'''PC:''' 1385 bp
 +
*'''Tra10:''' 182 bp
 +
*'''TAT:''' 91 bp
 +
*'''LMWP:''' 94 bp
 +
 +
=====Results=====
 +
No relevant bands for MITF samples. Ran the gel too far for the CPP bands. Tra10 is still visible and seems correct. There might also be two bands at the very edge of the gel, supporting the 91 bp and 94 bp for TAT and LMWP, respectively.<br />
 +
Decided to go on with gel extraction of CPPs anyway.
 +
 +
====Gel extraction====
 +
1 % agarose, 110 V. 22 &mu;l sample (Tra10/TAT/LMWP)
 +
 +
Bands on UV table seemed correct relative to each other. Bands excised and gel excisions saved in -20 &deg;C for later.
 +
 +
===N-CPP===
 +
====Plasmid prep====
 +
Prepared plasmid from Mimmi's 5 ml ON culture. 50 &mu;l elution volume.
 +
 +
{|border="1" cellpadding="1" cellspacing="0"
 +
|&nbsp;
 +
|[ng/&mu;l]
 +
!A<sub>260</sub>/A<sub>280</sub>
 +
|-
 +
|N-CPP plasmid
 +
|align="center"|671.9
 +
|align="center"|1.94
 +
|}
 +
 +
====Glycerol stock====
 +
Inoculated 3 ml LB + Amp 100 with 10 &mu;l from Mimmi's ON culture. Incubated 6 h 37 &deg;C, 225 rpm.<br />
 +
Prepared glycerol stock:
 +
*N-CPP 28/8
 +
 +
{{Stockholm/Footer}}

Latest revision as of 11:03, 26 October 2010

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Contents

Andreas

Gel extraction

No measurable DNA conc. for "Extr. Dig SOD E+A"
DNA concentrations
Sample Conc [ng/μl] A260/A280
Extr. N-CPP 40.91 1.69
Extr. Dig SOD E+A – –
Pur. Dig pMA.His E+N 36.02 1.80

From 27/8
Purified DNA from excised samples "Extr. Dig. SOD E+A" and "Extr. N-CPP cluster" using the E.Z.N.A. Gel extraction kit; procedures according to provided protocol.

Elution volume: 30 μl (eluted twice to increase DNA yield)

  • Extr. N-CPP
  • Extr. Dig SOD E+A

DNA purification of "Dig. pMA.His (E+N)"

From 27/8
DNA clean-up using the E.Z.N.A. Gel Extraction kit, following procedures for DNA purification.

Elution volume: 30 μl (eluted twice to increase DNA yield)

  • Pur. Dig. pMA His E+N

Gel verification

Gel verification of gel extracted and purified DNA samples.
3 μl λ; 2 μl sample.
1 kb λ=O'GeneRuler 1 kb DNA ladder. 50 bp λ=GeneRuler 50 bp DNA ladder.

Since no DNA content was measurable for "Extr. Dig SOD E+A", a gel was run to verify DNA content in the three purified samples.

1 % agarose, 110 V

Samples:

  • SOD: Extr. Dig SOD E+A
  • pMA: Pur. Dig pMA.His E+N
  • CPP: Extr. N-CPP cluster

Expected bands:

  • SOD: 492 bp
  • pMA: 2427 bp
  • CPP: 379 bp

Results

  • CPP resulted in a clear band of correct size.
  • A very weak band at ≈500 bp is visible for SOD, which might be traces of DNA.
  • No band visible for pMA.

Nevertheless, proceeded to ligation and cloning, hoping that the DNA is there.

Cloning of SOD into pMA.His

Ligation

  [μl]
Extr. Dig SOD E+A 12
Pur. Dig pMA.His E+N 3
5X Rapid Ligation buffer 4
T4 DNA ligase 1

Incubation: 22 °C, 10 min

Transformation

  • 3 μl ligation mix. 30 min on ice.
  • 30 sec heat shock in 42 °C
  • Cells grown on Amp 100 LB agar, 37 °C

Amplification of N-CPPs from N-CPP cluster

Ran PCRs from the gel extracted N-CPP cluster with the following primers:

  • Tra10: pSB-VF2 & pSB-VR
  • TAT: pEXf & pEXr
  • LMWP: pGexf & pGexr

Also ran 4 colony PCRs for Mimmi from cells transformed with pSB1C3.MITF plasmids (MITF 1-4); positive control (PC) pSB1C3.RFP; negative control (NC) blank; primers pSB-VF2 & pSB-VR.

PCR tubes

  • illustra Ready-to-Go PCR beads
  • 22.5 μl dH2O
  • 1 μl forward primer
  • 1 μl reverse primer
  • 0.5 μl template DNA

Standard colony PCR settings; 1:45 elongation time.

Gel verification

Gel verification of PCR amplified pSB1C3.MITF and N-CPPs.
3 μl λ; 4 μl sample.
1 kb λ=O'GeneRuler 1 kb DNA ladder. 50 bp λ GeneRuler 50 bp DNA ladder.

1 % agarose, 100 V

Expected bands:

  • MITF: 1586 bp
  • PC: 1385 bp
  • Tra10: 182 bp
  • TAT: 91 bp
  • LMWP: 94 bp
Results

No relevant bands for MITF samples. Ran the gel too far for the CPP bands. Tra10 is still visible and seems correct. There might also be two bands at the very edge of the gel, supporting the 91 bp and 94 bp for TAT and LMWP, respectively.
Decided to go on with gel extraction of CPPs anyway.

Gel extraction

1 % agarose, 110 V. 22 μl sample (Tra10/TAT/LMWP)

Bands on UV table seemed correct relative to each other. Bands excised and gel excisions saved in -20 °C for later.

N-CPP

Plasmid prep

Prepared plasmid from Mimmi's 5 ml ON culture. 50 μl elution volume.

  [ng/μl] A260/A280
N-CPP plasmid 671.9 1.94

Glycerol stock

Inoculated 3 ml LB + Amp 100 with 10 μl from Mimmi's ON culture. Incubated 6 h 37 °C, 225 rpm.
Prepared glycerol stock:

  • N-CPP 28/8





The Faculty of Science at Stockholm University Swedish Vitiligo association (Svenska Vitiligoförbundet) Geneious Fermentas/ Sigma-Aldrich/

Retrieved from "http://2010.igem.org/Team:Stockholm/28_August_2010"