Team:Illinois/Antibody GPCR Fusion Notebook

From 2008.igem.org

(Difference between revisions)
(23rd October)
Line 24: Line 24:
** 1ml 1M Tris-Cl pH 8.0 (10mM)
** 1ml 1M Tris-Cl pH 8.0 (10mM)
** 200uL 0.5M EDTA (1mM)
** 200uL 0.5M EDTA (1mM)
 +
 +
 +
==Primers==
 +
 +
PGK promoter
 +
5'TTTT GAATTC AAAGATGCCGATTTGGGCGC    5'TTTT GAGCTC GTTTTATATTTGTTGTAAAA
 +
 +
PGK terminator
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5'TTAT GGGCCC GAAATAAATTGAATTGAATT    5'TTTTG AAGCTT CAGCTTTAACGAACGCAGA
 +
 +
Ste2
 +
5'GCCC TCTAGA ATGTCTGATGCGGCTCCTTC      5'TTAT GGGCCC TCATAAATTATTATTATCTT
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Fus1 upstream
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5'GTGG GAATTC TAATAATCAGAACTCCAACA      5'GGCG TCTAGA TTTGATTTTCAGAAACTTGA
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 +
Fus1 downstream:
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5'GCGA GGTACC  TGAAAATAATATTGACGTTC  5'TTAT GCGGCCGC TATTCACCAGACCCGCTCCT
 +

Revision as of 02:55, 30 October 2008

GPCRnotebookpic.png


Contents

Recipes

  • Tris-Cl, 1M
    • Dissolve 121g Tris base in 800ml H2O
    • Adjust to desired pH with concentrated HCl
    • Mix and add H2O to 1 liter
    • (Approximately, 20ml HCl for pH 7.4 and 42ml for pH 8.0)


  • EDTA, 0.5M (pH 8.0)
    • Dissolve 186.1g Na2 EDTA-2H2O in 700ml H20
    • Adjust pH to 8.0 with 10M NaOH(~50ml)
    • Add H2O to 1 liter


  • Breaking buffer - 100ml
    • 2ml Triton X-100
    • 1ml Sodium dodecyl sulfate (SDS)
    • 0.5844g NaCl (100mM)
    • 1ml 1M Tris-Cl pH 8.0 (10mM)
    • 200uL 0.5M EDTA (1mM)


Primers

PGK promoter 5'TTTT GAATTC AAAGATGCCGATTTGGGCGC 5'TTTT GAGCTC GTTTTATATTTGTTGTAAAA

PGK terminator 5'TTAT GGGCCC GAAATAAATTGAATTGAATT 5'TTTTG AAGCTT CAGCTTTAACGAACGCAGA

Ste2 5'GCCC TCTAGA ATGTCTGATGCGGCTCCTTC 5'TTAT GGGCCC TCATAAATTATTATTATCTT

Fus1 upstream 5'GTGG GAATTC TAATAATCAGAACTCCAACA 5'GGCG TCTAGA TTTGATTTTCAGAAACTTGA

Fus1 downstream: 5'GCGA GGTACC TGAAAATAATATTGACGTTC 5'TTAT GCGGCCGC TATTCACCAGACCCGCTCCT


22nd July

  • Yeast obtained from Dr. Zhao
    • W303a S. Cerevisiae

24th July

  • Prepared liquid culture for DNA extraction
  • Made 1M Tris. Cl pH 8.0
  • Made 4M ammonium acetate


22nd August

  • Attempted DNA extraction of W303a genomic DNA
    • Protocol from Wiley's Current Protocols in Molecular Biology
    • Result: Failed to finish protocol
  • Obtained more yeast from Dr. Zhao
    • W303a S. cerevisiae

25th August

  • Prepared overnight culture for DNA extraction (3:27pm)


26th August

  • Attempted DNA extraction
  • Prepped overnight culture


27th August

  • Performed PCR: PGK Terminator
Buffer G 12.5uL x4 50uL
Forward Primer 0.5uL x4 2uL
Reverse Primer 0.5uL x4 2uL
H2O 10.8uL x4 43.2uL
Taq 0.2uL x4 0.8uL
template 0.5ul
Negative control 3 H2O


  • PCR program:
    • 4 min 94 degrees
    • 25-30x 30s 94 degrees
    • 30s Tm primers
    • 1 min/KB 72 degrees
    • 7 min 72 degrees
  • For the gel: 5uL loading dye gel is in cold room
  • Prepped 3 overnight cultures

28th August

  • Extracted DNA from 4 cultures
  • Ran gel of PCR products (1.5% agarose, 200V)
    • Result: No bands present

GPCR8-28.jpg

2nd September

  • PCR: PGK Terminator
5 PRIME Mastermix 10uL x3 30uL
Forward Primer 0.5uL x3 1.5uL
Reverse Primer 0.5uL x3 1.5uL
Template 10uL x3 30uL
H2O 10.8uL x4 43.2uL
Negative control 25uL H2O

3rd September

  • Ran gel
    • Ladder lane 7
    • Sample 7 spilled
    • 1% agarose
    • 120V
      • Too low
    • 50 minutes
  • Poor results--no bands present

8th September

  • PCR: PGK Terminator
5PRIME Mastermix 10uL x3 30uL
Forward Primer 0.5uL x3 1.5uL
Reverse Primer 0.5uL x3 1.5uL
Template 14uL x3 42uL
  • Prepped 4 overnight cultures
    • Yeast dried out again

9th September

  • Signs of life in 3 of the cultures
    • Wait until tomorrow
  • Ran gel on PCR from 8th September--no bands present
    • 150V, 50 minutes
    • No sign of DNA
  • Ladder from Courtney

10th September

  • Split culture
  • Ran gel from 8th September again--no bands present
    • 150V, 50 minutes
    • 0.75% gel
    • Ladder from Courtney

11th September

  • PCR: PGK Terminator
5 PRIME Mastermix 10uL x3 30uL
Forward Primer 0.5uL x3 1.5uL
Reverse Primer 0.5uL x3 1.5uL
Template 14uL x3 42uL

12th September

  • Isolated genomic DNA from 8 cultures of W303a yeast cells
    • Protocol from Wiley's Current Protocols in Molecular Biology
    • Labeled templates 1,2,3,4 and 1a,2a,3a,4a


  • Ran gel of PCR from 11th September
    • 1% agarose
    • 150V
    • 38 mins
      • Poor results

15th September

  • PCR PGK Promotor
    • Finnzymes Phusion High Fidelity DNA Polymerase
      • F-530, 20V (2V/uL)
5x Phusion HF Buffer 10uL x3 30uL
10mM dNTPs 1uL x3 3uL
Primer A(Forward) 1uL x3 3uL
Primer B(Reverse) 1uL x3 3uL
Template 1 10uL x3 30uL
Phusions DNA polymerase 0.5uL x3 1.5uL
H2O 26.5uL x3 79.5uL

18th September

  • Ran reaction mentioned on 15th September
  • Extracted DNA from gel from 8th September (PGK Terminator)
Tube Gel(g)
1 0.332
2 0.278
3 0.307
4 0.349
5 0.385

19th September

  • Gel of PGK Promotor from 15th September has no DNA present

23rd September

  • PCR: Fus1 Downstream
  • EPICENTRE Bioetechnologies - MasterAmp(TM) Taq DNA Polymerase
  • Per 50uL of reaction,
MasterAmp Taq 10x PCR Buffer 5uL
1mM dNTPs 1uL
Primer 1 0.5uL
Primer 2 0.5uL
25mM MgCl2 2uL
Taq DNA Polymerase 0.25uL
Template 2 20uL
Water 20.75uL
  • PCR Settings:
    • 4mins, 94 degree celcius
    • 30s, 94 degree celcius
    • 30s, 5 degrees below primer melting temperature
    • 1 min, 72 degree celcius -- to step 2 -- 30x
    • 7 min, 72 degree celcius

24th September

  • Ran gel of Fus1 Downstream from 23rd September
    • Result: No DNA present on gel

25th September

  • PCR: Fus1 Upstream
Mastermix 8.25uL x3 24.75uL
Forward Primer 0.5uL x3 1.5uL
Reverse Primer 0.5uL x3 1.5uL
Template 3 20uL x3 60uL
Water 20.75uL x3 62.25uL
    • same protocol as 23rd September
    • The master mix contains the buffer, dNTPs, MgCl, and Taq
    • Template 3 (3 reactions run)

30th September

  • PCR: Fus1 Upstream
Mastermix 8.25uL x3 24.75uL
Forward Primer 0.5uL x3 1.5uL
Reverse Primer 0.5uL x3 1.5uL
Template 3 20uL x3 60uL
Water 20.75uL x3 62.25uL
    • same protocol as 23rd September
    • Template 4 and 1a (3 reactions each)
    • Gel: 1% agarose, 150V, 35 minutes -> poor results
    • lanes 2,3 -> faint smear

GPCR FUS1 upstream 9-30.jpg

1st October

  • PCR: Ste2
Mastermix 8.25uL x3 24.75uL
Forward Primer 0.5uL x3 1.5uL
Reverse Primer 0.5uL x3 1.5uL
Template 3 20uL x3 60uL
Water 20.75uL x3 62.25uL
    • same protocol as 23rd September
    • Templates 2a, 3a, 4a used (3 reactions each)

3rd October

  • Ran Ste2 gel from 1st October

GPCR10-3.jpg

8th October

  • PCR: PGK Terminator
PCR Buffer 5uL
10mM dNTPs 1uL
Forward Primer 1uL
Reverse Primer 1uL
MgCl2 5uL
Taq DNA Polymerase 0.25uL
Template 25uL
Water 11.75uL
    • same protocol as 23rd September
    • Use DNA extracted from gel on 18th September (5 reactions)
  • Also extracted DNA from gel from 30th September (Fus1 Upstream)

9th October

  • PCR: Ste2
    • Protocol is the same as 23rd September
    • Template used is product from 1st October (9 reactions total)
  • PCR: Fus1 Upstream
    • Protocal matches 23rd September
    • Template used was DNA extracted from the gel from the 8th October, which came from the PCR run on 30th September (5 reactions total)


  • Ran Ste2 gel from today

GPCR10-09Ste2.jpg

  • Ran PGK terminator gel from yesterday

GPCR10-09PGKp.jpg

12th October

  • PCR: Fus1 (3 reactions each)
    • Template is products from 9th October

13th October

  • Ran gel of PCR with Fus1
  • Used 25uL or product, 5uL of loading dye

GPCR10-13.jpg

14th October

  • Fus1 PCR
MasterAmp Taq 10x PCR Buffer 5uL
1mM dNTPs 1uL
Primer 1 0.5uL
Primer 2 0.5uL
25mM MgCl2 5uL
Taq DNA Polymerase 0.25uL
Template 25uL
Water 11.75uL
  • Template is reaction from 12th October

15th October

  • PCR PGK Terminator
5 PRIME MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 25uL
Water 4uL
  • Ran gel of Ste2 from 10/14

GPCR10-15Ste2.jpg

  • Ran gel of Fus1 upstream from 10/14 (no ladder, oops)

GPCR10-15.jpg

16th October

  • PCR: Fus1 Downstream, PGK Promoter
MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 20uL
Water 9uL
    • Tube 1: Template 4 - Fus1
    • Tube 2: Template 4a - Fus1
    • Tube 3: Template 4 - PGK Promoter
    • Tube 4: Template 4a - PGK Promoter
  • ran Gel of above

GPCR10-16Fusd.jpg

  • ran Gel of PGK terminator from 10/15

GPCR10-16.jpg


  • Extracted Ste2 from 10/15 and re-amplified:
MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 20uL
Water 9uL

17th October

  • Ran gel of Ste2 from 10/16
    • Tube 1 - lane 2,3
    • Tube 2 - lane 5,6

GPCR10-17.jpg

  • PCR: Fus1 upstream
MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 20uL
Water 9uL
    • template is products from 10/14
  • PCR: PGK Terminator
MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 20uL
Water 9uL
    • Template is products from 10/15
  • Extracted Ste2(Gel from today)

18th October

Ran gel of Fus1 upstream and PGK terminator from yesterday GPCR10-18.jpg

20th October

  • Extracting chromosomal DNA from yeast cells
    • W303A - Yellow
    • YPD DL
    • YHP1 YPD HD - One is orange (YHP1)(Cap was removed in incubator), Other is Yellow
    • Orange - YHP1 YPD HD
    • Green - YHP2 YPD HD
    • Pink - W303A YPA DL
    • Yellow - WD303A YPD DL

21st October

  • PCR: Ste2
MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 20uL
Water 9uL
  • 2 tubes
  • Block B of black machine
  • Annealing temperature: 31 degrees celcius
  • Ran gel on Ste2 from today

GPCR10-21.jpg

22nd October

  • New primers for biobricks are here
    • Brought to standard concentration, 30uM
    • Added 33.3uL of water per nmol primer
  • PCR: Fus1 and PGK Terminator
MasterMix 20uL
Primer Fwd 0.75uL
Primer Rev 0.75uL
Template 25uL
Water 3.5uL
    • Forward and Reverse primers are new biobrick primers that arrived today
    • Template is PCR product from 17th October
    • A,B,C -> Fus1 Upstream -> 1,2,3
    • 1,2 -> PGK Terminator -> 4,5
    • Annealing temperature: 38 degrees celcius
    • In freezer in yellow case
  • PCR: Ste2
MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 25uL
Water 4uL
    • Forward primer, Reverse Primer are new primers that arrived today
    • Template is PCR product from 21st October
    • Two tubes in block B
  • The 3 gels in the cold room do not have EtBr

23rd October

  • Ran gel of Fus1 Upstream, PGK Terminator, Ste2 from yesterday
    • 1% Agarose

GPCR10-23.jpg

  • PCR: Fus1 Downstream, PGK Promoter
MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 20uL
Water 9uL
    • 4 reactions each of Fus1 Upstream(1,2,3,4) and PGK Promoter(A,B,C,D)
  • Gel shows no bands.


  • PCR: Fus1 Downstream, Fus1 Upstream, PGK Promoter, PGK Terminator, Ste2
    • Template genomic DNA from 20th October (x4 different reactions)
    • Used all Template
MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 20uL
Water 9uL
  • Gel shows no bands

24th October

  • Ran gel of Fus1 upstream(lanes 3,4,5), PGK terminator(lanes6,7), and Ste2(lanes 8,9) from 10/22
    • ladder is lane 2; 1 and 10 are nothing

GPCR10-22.jpg

  • PCR of Fus1 downstream, Fus1 upstream, PGK promoter, PGK terminator, Ste2
MasterMix 20uL
Primer Fwd 0.5uL
Primer Rev 0.5uL
Template 29uL
    • The templates were the rest of the genomic DNA extracts from 9/12
    • Three reactions of each gene were run
  • Gel from above:

GPCR10-24.jpgGPCR10-24(cont.).jpg

  • (on left)Fus1 downstream lanes 2,3,4; Fus1 upstream lanes 5,6,7; PGK promoter lanes 8,9,10;
  • (on right)PGK terminator lanes2,3,10; Ste2 lanes 4,5,6; Fus1 downstream lanes 7,8,9;

25th October

  • Extracted DNA from the gel from 10/24
    • FUS1 upstream from the higher bands of lanes 3 and 4
    • PGK terminator from the lower bands of lanes 6 and 7
  • DNA ligation
DNA 5uL
buffer 5uL
Re1 (Pst1) 1uL
Re2 (EcoR1) 1uL
Water 37.5uL

26th October

  • Incubate for 20mins at 80 degrees celcius
Ligation Buffer 4uL
DNA Ligase 1uL
DNA 3uL
Plasmid 9uL
Water 3uL
  • Let sit for 5 min.
  • 5uL of above mixture to competent cells
    • 30 min. on ice
  • Heat shock 30s (42 degrees)
  • Add SOC Media (200uL)
    • Incubate 60 min.(37 degrees)
  • Plate 200uL
    • Incubate 37 degrees celcius overnight

27th October

The transformation failed; try again with the same protocol:

  • Using extracts 3 and 7 (+Ligation buffers, Ligase, Plasmid, and Water)
  • Failed again.