Team:Marburg/Notebook:September

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Revision as of 23:00, 1 October 2013

Notebook: September

06.09.2013

PCR
Investigator: Franzi
Aim: Construction of iBB14 → Adding of pre- and suffix via PCR.

Dissolved BioBrick BBa_E1010 (RFP) from spring distribution Kit 2013 with 10 µl H2O (P3, 12N). Used as template for PCR.

Volume Reagent   Temp (°C) Time
1 µl Phusion-Polymerase   95 3 min
1 µl Primer 50 fw (10pmol/µl)   95 30 sec
1 µl Primer 51 rv (10pmol/µl)   60 1 min x35
1 µl Template   72 1 min
1 µl dNTPs   72 5 min
10 µl 5xGC buffer  
34 µl ddH20  

Gel electrophoresis (done 09.09.13)
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe in 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

The relevant fragments were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf). Elution into 30 µl elution buffer.

09.09.2013

Transformation
Investigator: Franzi
Aim: Construction of iBB14 → Retransformation of BBa_E1010.

Retransformation of 1 µl pSB1C3 BBa_E1010 into E. coli DH5α (30 min ice, 60 sec 42°C, 90 min 37°C + 900 µl LB), plated on LBCM, oN 37°C.

PCR
Investigator: Franzi
Aim: Construction of iBB15 (MTS) → Adding pre- and suffix via PCR.
Volume Reagent   Temp (°C) Time
1 µl Phusion-Polymerase   95 3 min
1 µl Primer 52 fw (10pmol/µl)   95 30 sec
1 µl Primer 53 rv (10pmol/µl)   65 30 sec x32
1 µl Template (provided by AG Bange)   72 45 sec
1 µl dNTPs   72 7 min
10 µl 5xGC buffer  
35 µl ddH20  

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 2% Agarose gel
  • 10 µl RedSafe in 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

Expectations

  • 1 band at 107 bp

The relevant fragments were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf). Elution into 30 µl elution buffer.

10.09.2013

Digest
Investigator: Franzi
Aim: Construction of iBB14-15 → Digestion of single parts.
  • 10 µl DNA template
  • 1 µl enzyme 1
  • 1 µl enzyme 2
  • 2 µl Cut Smart buffer
  • 6 µl H2O

Samples:

Digestion of iBB15 with XbaI and PstI-HF

Digestion of iBB14 with EcoRI-HF and SpeI-HF.

The samples were incubated for 1,5 h at 37° C.

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe per 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

The relevant fragments were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf). Elution into 20 µl elution buffer.
Ligation
Investigator: Franzi
Aim: Construction of iBB14-15 → Ligation of two single parts into pSB1C3.
  • 23 ng vector DNA (pSB1C3; EcoRI/PstI-cut)
  • 44 ng iBB14 (EcoRI/PstI-cut)
  • 41 ng iBB15 (EcoRI/PstI-cut)
  • 2 µl 10x T4 DNA ligase buffer
  • 1 µl T4 DNA ligase
  • ad 20 µl H2O

The samples were incubated for 2 h at RT.

Transformation
Investigator: Franzi
Aim: Construction of iBB14-15 → Transformation of combined BioBrick in pSB1C3 into E. coli DH5α.

Complete ligation samples were transformed into E. coli DH5α (30 min ice, 60 sec 42°C, 60 min 37°C + 900 µl LB), plated on LBCM, oN 37°C.

Digest
Investigator: Franzi
Aim: Construction of iBB15 → Digestion with EcoRI and PstI.
  • 10 µl DNA template (iBB15 from PCR)
  • 1 µl EcoRI-HF
  • 1 µl PstI-HF
  • 2 µl Cut Smart buffer
  • 6 µl H2O

The samples were incubated for 30 min at 37° C.

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe per 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

The relevant fragments were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf). Elution into 20 µl elution buffer.
Ligation
Investigator: Franzi
Aim: Construction of iBB15 → Ligation of iBB15 into pSB1C3.
  • 23 ng vector DNA (pSB1C3; EcoRI/PstI-cut)
  • 40 ng iBB15 (EcoRI/PstI-cut)
  • 2 µl 10x T4 DNA ligase buffer
  • 1 µl T4 DNA ligase
  • ad 20 µl H2O

The samples were incubated for 30 min at RT.

Transformation
Investigator: Franzi
Aim: Construction of iBB15 → Transformation of iBB15 in pSB1C3 into E. coli DH5α.

Complete ligation samples were transformed into E. coli DH5α (30 min ice, 60 sec 42°C, 60 min 37°C + 900 µl LB), plated on LBCM, oN 37°C.

11.09.2013

Ligation
Investigator: Franzi
Aim: Construction of iBB15 → Repeat of ligation of iBB15 into pSB1C3.

Reason: No colonies of pSB1C3 iBB15 on transformation plates.

  • 46 ng vector DNA (pSB1C3; EcoRI/PstI-cut)
  • 40 ng iBB15 (EcoRI/PstI-cut)
  • 3 µl 10x T4 DNA ligase buffer
  • 1 µl T4 DNA ligase
  • ad 30 µl H2O

The samples were incubated for 30 min at RT.

Transformation
Investigator: Franzi
Aim: Construction of iBB15 → Repeat of transformation of iBB15 in pSB1C3 into E. coli DH5α.

Complete ligation samples were transformed into E. coli DH5α (30 min ice, 60 sec 42°C, 60 min 37°C + 1 ml LB), plated on LBamp, oN 37°C.

Inoculation
Investigator: Franzi
Aim: Construction of iBB14-15 and iBB14, inoculation of pSB1C3 iBB14-15 and pSB1C3 BBa_E1010 for miniprep.

5 colonies of pSB1C3 iBB14-15 and 2 colonies of pSB1C3 BBa_E1010 inoculated in 5 ml LBCM, oN 37°C.

12.09.2013

Miniprep
Investigator: Franzi
Aim: Construction of iBB14-15 and iBB14 → Miniprep of pSB1C3 iBB14-15 and pSB1C3 BBa_E1010.

Miniprep of the liquid cultures (“QIAprep Spin Miniprep Kit” (Qiagen, Düsseldorf)), eluted in 50 µl elution buffer.

Digest
Investigator: Franzi
Aim: Construction of iBB14-15 → Control digestion of pSB1C3 iBB14-15.
  • 2 µl DNA template
  • 0,5 µl EcoRI-HF
  • 5 µl PstI-HF
  • 1 µl Cut Smart buffer
  • 6 µl H2O

The samples were incubated for 1 h at 37° C.

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe per 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

Expectations

  • pSB1C3: 2 kb
  • iBB14-15: 850 bp
  • iBB14 E/S: 750 bp

All positive.
Sequencing
Investigator: Franzi
Aim: Construction of iBB14-15 → K4 and K5 sent for sequencing.

IBB14-15 K4 and K5 sequenced with primers VF2_fw and VR_rv (AGBOOOK565-568).

Digest
Investigator: Franzi
Aim: Construction of iBB15 → Repeat of digestion with EcoRI and PstI.

Reason: Transformations of 11.09.13 unsuccessful.

  • 9 µl DNA template (iBB15 from PCR)
  • 1 µl EcoRI-HF
  • 1 µl PstI-HF
  • 2 µl Cut Smart buffer
  • 7 µl H2O

The samples were incubated for 2 h at 37° C.

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe per 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

The relevant fragments were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf). Elution into 20 µl elution buffer.
Ligation
Investigator: Franzi
Aim: Construction of iBB15 → Repeat of ligation of iBB15 into pSB1C3.
  • 20 ng vector DNA (pSB1C3; EcoRI/PstI-cut)
  • 40 ng iBB15 (EcoRI/PstI-cut)
  • 2 µl 10x T4 DNA ligase buffer
  • 1 µl T4 DNA ligase
  • ad 20 µl H2O

The samples were incubated for 2,5 h at RT.

Transformation
Investigator: Franzi
Aim: Construction of iBB15 → Repeat of transformation of iBB15 in pSB1C3 into E. coli DH5α.

Complete ligation samples were transformed into E. coli DH5α (30 min ice, 60 sec 42°C, 60 min 37°C + 900 µl LB), plated on LBCM, oN 37°C.

Transformation
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Retransformation of BBa_R0010 and BBa_B0034.

Retransformation of BBa_R0010 (PlacI, pSB1C3), BBa_B0034 (RBS, pSB1A2) into E.coli DH5α (30 min ice, 60 sec 42°C, 60 min (PlacI)/30 min (RBS) 37°C + 900 µl LB), plated on LBCM (PlacI)/LBamp, oN 37°C.

13.09.2013

Sequencing
Investigator: Franzi
Aim: Construction of iBB14-15 → Sequencing results.

Sequencing of pSB1C3 iBB14-15 negative (wrong restriction enzymes used, constructed with BamHI, not standard 23)

PCR
Investigator: Franzi
Aim: Construction of iBB14315 → Adding of pre- and suffix via PCR.

PCR of iBB15 repeated like 09.09.13.

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe in 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

The relevant fragments were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf). Elution into 30 µl elution buffer.
Transformation
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Retransformation of BBa_R0010 and BBa_B0034.

Reason: All transformations (12.09.13) unsuccessful.

Retransformation of PlacI and RBS like 12.9.13, in addition into competent cells provided by AG Bange; RT over weekend.

All transformations will be unsuccessful (16.09.13).

16.09.2013

Digest
Investigator: Franzi
Aim: Construction of iBB14-15 → Digestion with EcoRI/PstI and BamHI.
  • 10 µl DNA template
  • 1 µl enzyme 1
  • 1 µl enzyme 2
  • 2 µl Cut Smart buffer
  • 6 µl H2O

Samples:

Digestion of PCR-products, iBB14 with EcoRI-HF and BamHI-HF, iBB15 with BamHI-HF and PstI-HF.

The samples were incubated for 1,5 h at 37° C.

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe per 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

The relevant fragments were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf). Elution into 30 µl elution buffer.
Ligation
Investigator: Franzi
Aim: Construction of iBB14-15 → Ligation of iBB14 and iBB15 into pSB1C3.
  • 20 ng vector DNA (pSB1C3; EcoRI/PstI-cut)
  • 40 ng iBB14 (EcoRI/PstI-cut)
  • 40 ng iBB15 (EcoRI/PstI-cut)
  • 2 µl 10x T4 DNA ligase buffer
  • 1 µl T4 DNA ligase
  • ad 20 µl H2O

The samples were incubated for 2 h at RT.

Transformation
Investigator: Franzi
Aim: Transformation-tests, Construction of iBB14-15 and RFP-MTS-test → Transformation into E. coli (AG Bölker).

IBB14-15: Complete ligation samples were transformed into E. coli (AG Bölker) (30 min ice, 60 sec 42°C, 60 min 37°C + 900 µl LB), plated on LBCM, oN 37°C.

Retransformation of PlacI and RBS like above, RBS 30 min 37°C, plated on LBamp.

Testtransformation of pSB1A3 J04450 into E. coli (own, AG Bange and AG Bölker), like above, plated on LBamp.

Testtransformation will be all positive (17.09.13).

17.09.2013

Inoculation
Investigator: Franzi
Aim: Construction of iBB14-15 and RFP-MTS-test → Inoculation of transformants.

2 colonies of pSB1A2 RBS inoculated in 5 ml LBamp, 2 colonies of pSB1C3 PlacI and 6 colonies of pSB1C3 iBB14-15 inoculated in 5 ml LBCM, oN 37°C.

18.09.2013

Miniprep
Investigator: Franzi
Aim: Construction of iBB14-15 and RFP-MTS-test → Miniprep of transformants.

Miniprep of the liquid cultures (“QIAprep Spin Miniprep Kit” (Qiagen, Düsseldorf)), eluted in 30 µl elution buffer.

Digest
Investigator: Franzi
Aim: Construction of iBB14-15 → Control digestion of pSB1C3 iBB14-15.
  • 2 µl DNA template (pSB1C3 iBB14-15)
  • 0,5 µl EcoRI-HF
  • 0,5 µl PstI-HF
  • 1 µl Cut Smart buffer
  • 6 µl H2O

The samples were incubated for 2 h at 37° C.

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe per 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

Expectations

  • iBB14-15: 850 bp
  • iBB14 crtl: 750 bp

All positive.
Sequencing
Investigator: Franzi
Aim: Construction of iBB14-15 → Sequencing.

Sequencing K1 + K4 with primers VF2_fw and VR_rv (AGBOOOK 569-572).

Digest
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Digestion of PlacI and RBS.
  • 10 µl pSB1C3 PlacI
  • 1 µl SpeI
  • 1 µl PstI-HF
  • 2 µl Cut Smart buffer
  • 6 µl H2O
  • 15 µl pSB1A3 RBS
  • 1 µl XbaI
  • 1 µl PstI
  • 2 µl buffer 3.1
  • 1 µl H2O

Both samples were incubated for 2 h at 37° C.

RBS was heat-inactivated (80°C, 30 min).

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe per 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

The relevant fragments of PlacI were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf). Elution into 20 µl elution buffer.
Ligation
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Ligation of PlacI and RBS into pSB1C3.
  • 67 ng pSB1C3 PlacI
  • 10 µl RBS
  • 2 µl 10x T4 DNA ligase buffer
  • 1 µl T4 DNA ligase
  • ad 20 µl H2O

The samples were incubated for 2 h at RT.

Transformation
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Transformation of pSB1C3 PlacI RBS into E. coli DH5α.

IBB14-15: Complete ligation samples were transformed into E. coli DH5α (30 min ice, 60 sec 42°C, 60 min 37°C + 900 µl LB), plated on LBCM, oN 37°C.

19.09.2013

Sequencing
Investigator: Franzi
Aim: Construction of iBB14-15 → Sequencing results.

Point mutation at position 743 (G→A, silent) in both clones.

Shipping of the BioBricks
Investigator: Franzi
Aim: Finally sending the BioBricks to the registry. "☺"

Prepared all completed BioBricks for shipping: 250 ng Brick in 10 µl H2O.

PCR
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Control colony-PCR.

Colony-PCR of 7 colonies of pSB1C3 PlacI RBS.

Volume Reagent   Temp (°C) Time
0,5 µl Q5 HF polymerase   95 3 min
0,5 µl Primer fw (54, RBS fw)   95 30 sec
0,5 µl Primer rv (38, VR_rv)   65 30 sec x33
0,5 µl dNTPs   72 45 sec
1 µl Q5 buffer   72 7 min
18 µl H2O  

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe in 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

Expectations

  • positive: 180 bp
  • negative: none
Inoculation
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Inoculation of pSB1C3 PlacI RBS for miniprep.

K3, 4 and 7 inoculated in 5 ml LBCM, oN 37°C.

20.09.2013

Miniprep
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Miniprep of pSB1C3 PlacI RBS.

Miniprep of the liquid cultures (“QIAprep Spin Miniprep Kit” (Qiagen, Düsseldorf)), eluted in 30 µl elution buffer.

Digest
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Digestion of pSB1C3 PlacI RBS and iBB14-15.
  • 10 µl DNA template
  • 1 µl enzyme 1
  • 1 µl enzyme 2
  • 2 µl Cut Smart buffer
  • 6 µl H2O

Samples:

Digestion of pSB1C3 iBB14-15 with XbaI and PstI-HF

Digestion of pSB1C3 PlacI RBS K3,4,7 with EcoRI-HF and SpeI-HF.

The samples were incubated for 1,5 h at 37° C.

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe per 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

The relevant fragments were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf). Elution into 20 µl elution buffer.
Ligation
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Ligation of PlacI RBS and iBB14-15 into pSB1A3.
  • 40 ng pSB1C3
  • 150 ng iBB14-15
  • 160 ng PlacI RBS K3,4 or 7
  • 2 µl 10x T4 DNA ligase buffer
  • 1 µl T4 DNA ligase
  • ad 20 µl H2O

The samples were incubated for 1,5 h at RT.

Transformation
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Transformation of pSB1A3 PlacI RBS iBB14-15 into E. coli DH5α.

IBB14-15: Complete ligation samples were transformed into E. coli DH5α (30 min ice, 60 sec 42°C, 30 min 37°C + 900 µl LB), plated on LBamp, oN 37°C.

22.09.2013

Inoculation
Investigator: Franzi
Aim: Construction of RFP-MTS-test, inoculation of transformants for miniprep.

4 colonies of pSB1A3 PlacI RBS K4 iBB14-15 inoculated in 5 ml LBamp and spread onto new LBamp-plates, oN 37°C.

No colonies for K3 and K7.

23.09.2013

Miniprep
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Miniprep of pSB1A3 PlacI RBS iBB14-15.

Miniprep of the liquid cultures (“QIAprep Spin Miniprep Kit” (Qiagen, Düsseldorf)), eluted in 30 µl elution buffer.

Digest
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Control digestion of pSB1A3 PlacI RBS iBB14-15.
  • 2 µl DNA template
  • 0,5 µl EcoRI-HF
  • 5 µl PstI-HF
  • 1 µl Cut Smart buffer
  • 6 µl H2O

The samples were incubated for 1 h at 37° C.

Gel electrophoresis
gel-electrophoresis-image

Gel substances

  • 1% Agarose gel
  • 10 µl RedSafe per 50 ml gel
  • 6 µl GeneRuler™ 1kb plus DNA Ladder (Thermo Scientific)
  • 6x loading buffer (for samples)

Expectations

  • pSB1A3: 2150 bp
  • Insert: 1020 bp

All positive.
Sequencing
Investigator: Franzi
Aim: Construction of RFP-MTS-test → Sequencing.

Sequencing K1 and K3 with primer VF2_fw and VR_rv (AGBOOOK573-576)

25.09.2013

Microscopy
Investigator: Franzi
Aim: Microscopy of RFP-MTS-test → Inoculation of pre-culture.

PSB1A3 PlacI RBS iBB14-15 K1 inoculated in 5 ml LBamp, oN 37°C.

26.09.2013

Microscopy
Investigator: Franzi
Aim: Microscopy of RFP-MTS-test → Preparation of cultures for microscopy.

125 µl culture transferred into 5 ml LBamp, 5 ml LBamp + 0,5 % Glucose and 5 ml LBamp + 1 mM IPTG

Incubation for 3 h at 37°C for investigations at a microscope.

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