Team:DTU-Denmark/Notebook/19 August 2013

From 2013.igem.org

(Difference between revisions)
(→PCR on NIR1 and NIR2 via. colony PCR for template to Morten Nørholm)
Line 117: Line 117:
|-
|-
| sample N1 or N2# || HF || HF 2% DMSO 1mL MgCl2 50mM ||HF 5% DMSO || HF 1M Betaine || GC || GC 2% DMSO || GC 5% DMSO || GC 5% DMSO 1mL MgCl2 50mM || GC 5% DMSO 2mL MgCl2 50mM || GC 1M Betaine  
| sample N1 or N2# || HF || HF 2% DMSO 1mL MgCl2 50mM ||HF 5% DMSO || HF 1M Betaine || GC || GC 2% DMSO || GC 5% DMSO || GC 5% DMSO 1mL MgCl2 50mM || GC 5% DMSO 2mL MgCl2 50mM || GC 1M Betaine  
-
|-
 
-
| temperature || 48.3 || 48.7 || 50.0 || 51.8 || 53.3 || 54.7 || 56.3 || 57.5 || 59.1 || 60.8 || 62.5 || 63
 
|}
|}
Line 144: Line 142:
|-
|-
|}
|}
-
 
==Results==
==Results==

Revision as of 14:04, 20 August 2013

19 August 2013

Navigate to the Previous or the Next Entry

Contents

lab 208

Main purpose

Who was in the lab

Kristian, Henrike, Julia

Procedure

Preparation of constructs to send for sequencing

Sec2, TAT3-2, TAT3-1a, CycAX and HAO constructs were prepared for sequencing. Sample preparation was performed following the indications given by the EZ-Seq service by Macrogen:

5uL of 100~150ng/ul plasmid + 5uL of 5uM primers.

An overview of the sample composition can be found in the following link: File:Construct for sequencing - Sheet1.pdf

The samples were sent to Macrogen for sequencing.

Gradient PCR for creation of Biobricks

Made a screening to find good conditions for the extraction of our constructs for subsequent ligation into BioBricks.

conditions:

A:

  • HF buffer
  • 2% DMSO
  • 1uL 50mM MgCl2

B:

  • HF buffer
  • 3% DMSO
  • 2uL 50mM MgCl2

C:

  • HF buffer
  • 5% DMSO
  • 1uL 50mM MgCl2

D:

  • HF buffer
  • 3% DMSO
  • 1uL 50mM MgCl2

The annealing temperature was a gradient from 48C to 63C in 12 steps.

sample # 1 2 3 4 5 6 7 8 9 10 11 12
temperature 48.3 48.7 50.0 51.8 53.3 54.7 56.3 57.5 59.1 60.8 62.5 63

PCR to linearize pZA21::RFP::araBAD

Used GC buffer and 5% DMSO. Made three samples with varying concentrations of 50mM MgCl2: 0,5 uL, 1uL and 2 uL.

template: pZA21::RFP::araBAD

primers: 55a, 55b

program:

temperature time cycles
98C 2:00 -
98C 0:10 36
65C 1:00 36
72C 3:00 36
72C 5:00 -
10C hold -

colony PCR on one of the Hello Wolrd constructs to confirm it's intact

Performed colony PCR on the construct containing Sec2 to check the template is correct because our PCRs on it are not working.

template: Sec2 construct

primers: sequencing primers 4_FW_pZA21 and 5_RV_pZA21

temperature time cycles
98C 10:00 -
98C 0:10 36
61C 0:20 36
72C 2:00 36
72C 5:00 -
10C hold -


PCR on NIR1 and NIR2 via. colony PCR for template to Morten Nørholm

sample N1 or N2# HF HF 2% DMSO 1mL MgCl2 50mM HF 5% DMSO HF 1M Betaine GC GC 2% DMSO GC 5% DMSO GC 5% DMSO 1mL MgCl2 50mM GC 5% DMSO 2mL MgCl2 50mM GC 1M Betaine


temperature time cycles
98C 10:00 -
98C 0:20 14
71C -0.5C increment 0:30 14
72C 2:30 14
98C 0:20 20
64C 0:30 20
72C 2:30 20
72C 5:00 -
10C hold -

Results

gels

  • 1: 1 kb ladder
  • 2: N1 HF
  • 3: N1 HF 2% DMSO 1 mL MgCl2
  • 4: N1 HF 5% DMSO
  • 5: N1 HF 1M Betaine
  • 6: N1 GC
  • 7: N1 GC 2% DMSO
  • 8: N1 GC 5% DMSO
  • 9: N1 GC 5% DMSO 1 mL MgCL2
  • 10: N1 GC 5% DMSO 2 mL MgCl2
  • 11: N1 GC 1M Betaine
  • 12: N2 HF
  • 13: N2 HF 2% DMSO 1 mL MgCl2
  • 14: N2 HF 5% DMSO
  • 15: N2 HF 1M Betaine
  • 16: N2 GC
  • 17: N2 GC 2% DMSO
  • 18: N2 GC 5% DMSO
  • 19: 1 kb ladder

(picture big gel)

  • 1 kb ladder
  • N2 GC 5% DMSO 1 mL MgCl2
  • N2 GC 5% DMSO 2 mL MgCl2
  • N2 GC 1M Betaine
  • pZA21::RFP::araBAD 0,5 uL MgCl2
  • pZA21::RFP::araBAD 1 uL MgCl2
  • pZA21::RFP::araBAD 2 uL MgCl2
  • negative pZA21::RFP::araBAD
  • col Sec2
  • col Sec2 (duplicate)
  • negative col Sec2
  • screening A1
  • screening A2
  • screening A3

(pic small gel)

Conclusion

Navigate to the Previous or the Next Entry

Retrieved from "http://2013.igem.org/Team:DTU-Denmark/Notebook/19_August_2013"