Team:DTU-Denmark/Notebook/6 August 2013

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6 August 2013

Contents

lab 208


Main purpose


Who was in the lab


Kristian, Gosia, Natalia, Henrike

Procedure


PCR for AMO

Made four reactions using 1 uL respectively 10 uL of culture from the -20 or from the glycerol stock (-80) as template and adjusted volume of water accordingly.

Primers 10a, 10b.

PCR for SPL (synthtic promoter library)

template: pZa21 with RFP, primers: 52a, 52b1, temperature: 50C, time: 2:30

PCR for reference promoter

template: pZa21 with RFP, primers: 52a, 52b2, temperature: 50C, time: 2:30

PCR for araBAD K808000

template: K808000, primers: 12a, 12bn, temperature: 50C, time: 2:30

PCR to extract Nir2 from P. aeruginosa

PCR for araBAD and SPL with DMSO

Template and primers as previous.

PCR on Nir1 with MgCl2 gradient

Used previous isolation from a gel purification to make PCR for amplification of the strand. Used 5% DMSO as additive. The PCR was done with primer pair 41 and with x7 polymerase at 55C annealing and 5:00 min extension. Also we used 20 sec as denaturing time instead of the normal 10. The magnesium gradient was as follow:

  • 0
  • 1uL MgCl2 2mM per 50uL reaction
  • 5uL MgCl2 2mM per 50uL reaction
  • 20uL MgCl2 2mM per 50uL reaction

Gel purification

of the Nir1 fragment extraced from P. aeruginosa. Nanodrop: 8ng/uL

Plasmid miniprep

HAO in pZA21 from USER cloning was purified for restriction analysis. Nanodrop measurement: 180ng/uL

Results


Gel 1

1% agarose gel

  • 1 kb ladder
  • Nir1 col. Taq
  • Nir1 col. Taq
  • Nir2 col. Taq
  • Nir2 col. Taq
  • Nir1 frag. Taq
  • Nir1 frag. Taq
  • Nir1 col. x7
  • Nir1 col. x7
  • neg
  • Hi spec. buffer
  • Hi spec. buffer
  • DMSO
  • DMSO
  • Nir1
  • Nir1
  • Nir2
  • Nir2
  • 1 kb ladder

2013-08-06 nir.jpg

Nir1 was purified.

Gel 2

1% agarose gel

  • 1 kb ladder
  • NirW
  • NirW
  • araBAD biobrick K808000
  • araBAD biobrick K808000
  • SPL in pZA21 containing RFP
  • SPL in pZA21 containing RFP
  • reference promoter in pZA21 containing RFP
  • reference promoter in pZA21 containing RFP
  • neg
  • neg
  • 1 kb ladder

2013-08-06 small gel.jpg

Gel 3

1% agarose gel

  • 1 kb ladder
  • AMO, 1uL of -20 culture as template
  • AMO, 10uL of -20 culture as template
  • AMO, 1uL of glycerol stock as template
  • AMO, 10uL of glycerol stock as template
  • neg from AMO PCR
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 1 kb ladder

2013-08-06 AMO and spl.jpg

Gel result:

  • 1 - ladder
  • 2 - sample nr 1 - SPL, primers 52a, 52b1, template pZA21 with RFP, 50C, 2:30 min extension
  • 3 - sample nr 2 - SPL, primers 52a, 52b1, template pZA21 with RFP, 50C, 2:30 min extension
  • 4 - sample nr 3 - ref, primers 52a, 52b2, template pZA21 with RFP, 50C, 2:30 min extension
  • 5 - sample nr 4 - ref, primers 52a, 52b2, template pZA21 with RFP, 50C, 2:30 min extension
  • 6 - sample nr 5 - araBAD, primers 12a, 12bn, template K80800, 50C, 2:30 min extension
  • 7 - sample nr 6 - araBAD, primers 12a, 12bn, template K80800, 50C, 2:30 min extension
  • 8 - sample nr 7 - Nir2, extraction PCR, primers 42a, 42b, cells in water, Phusion polymerase
  • 9 - sample nr 8 - Nir2, extraction PCR, primers 42a, 42b, cells in water, Phusion polymerase
  • 10 - sample nr 9 - Nir2, extraction PCR, primers 42a, 42b, cells in water, x7 polymerase
  • 11 - sample nr 10 - Nir2, extraction PCR, primers 42a, 42b, cells in water, x7 polymerase
  • 12 - sample nr 11 - Nir2, extraction PCR, primers 42a, 42b, cells in water, plus MgCl2 additive, Phusion polymerase
  • 13 - sample nr 12 - - Nir2, extraction PCR, primers 42a, 42b, cells in water, plus MgCl2 additive, x7 polymerase
  • 14 - sample nr 13 - Nir1 with USER primers, primers 39a, 39b, x7, template - Nir purified from gel
  • 15 - sample nr 14 - Nir1 with USER primers, primers 39a, 39b, x7, template - Nir purified from gel
  • 16 - sample nr 15 - check Nir1 with primers for NirM+S, primers 11a, 44, template - Nir purified from gel, Phusion polymerase
  • 17 - sample nr 16 - check Nir1 with primers for NirM+S, primers 11a, 44, template - Nir purified from gel, Phusion polymerase
  • 18 - ladder

Conclusion


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