Team:Potsdam Bioware/Labjournal/July

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28th Labday 2011-07-01

Agarose gel electrophoresis of PCR (mdnA for phage display, strategy 1)

Investigators: Sabine, Sandrina


Aim: Verification of mdnA for phage display (strategy 1)


Time: 2011-06-30,14:00-15:30

Materials:

  • Agarose broad range (Roth)
  • 1x TAE buffer
  • Gel Red
  • PCR products: mdnA for phage display (strategy 1) from 2011-06-30
  • DNA Ladder Gene Ruler, 100bp plus (Fermentas)
  • 6x Loading Dye (Fermentas)


Method:

1. Production of a 1 % agarose gel

  • mAgarose = 0.5 g in 50 ml 1x TAE
  • adding 2 µl gel red

2. Loading samples

  • 5 µl PCR product and 6x loading dye
  • 2 µl DNA ladder gene ruler (1:10)

3. Run

  • 100 V
  • time: 00:45 h


Results:

lane Sample Volume in µl Expected size in bp
M marker 2
1 mdnA with SfiI 6 224

125 px


further tasks:

purification of PCR product

purification of PCR product mdnA SfiI for phage display

Investigators: Sabine, Sandrina


Aim:

  • purification of PCR product mdnA with SfiI restriction sites for phage display (strategy 1)


Time: 2011-06-24, 15:30-16:00


Materials/Methods:

  • QIAquick Gel Extraction Kit (250)


Further tasks:

  • digestion of the fragments with SfiI

Agarose gel electrophoresis of myc-tagged mdnA

Investigators: Jessica


Aim: Verification of myc-tagged mdnA


Time: 2011-07-01,13:00-15:30

Materials:

  • Agarose broad range (Roth)
  • 1x TAE buffer
  • Gel Red
  • PCR product: myc-tagged mdnA from 2011-06-29
  • DNA Ladder Gene Ruler, 100bp plus (Fermentas)
  • 6x Loading Dye (Fermentas)


Method:

1. Production of a 1 % agarose gel

  • mAgarose = 0.5 g in 50 ml 1x TAE
  • adding 2 µl gel red

2. Loading samples

  • 45 µl PCR product and 9 µl 6x loading dye
  • 6 µl DNA Ladder Gene Ruler (1:10)

3. Run

  • 100 V
  • time: 1 h


Results:

lane Sample Volume in µl Expected size in bp
M marker 6
1 myc-tagged mdnA 27 233
2 myc-tagged mdnA 27 233


UP AG PCR mdnAmycC 2011-07-01 JE.jpg

  • Gel excision of bands, stored at -20 °C (PCR box, blue)


Further tasks:

  • Gel extraction
  • Restriction digest


29th Labday 2011-07-04

digestion of PCR product mdnA with restriction enzyme SfiI (strategy 1)

Investigators: Sandrina, Sabine


Aim: digestion of mdnA with SfiI for cloning into pak100


Time: 2011-07-04,14:00-16:30

Materials:

Digestion with SfiI

  • 50 µl sample
  • NEB 10x buffer 4
  • 100x BSA
  • 3 µl restriction enzyme SfiI
  • PCR product (mdnA with SfiI restriction sites)

Further tasks:
ligation with pak100bla-KDIR

ligation of mdnA into pak100(strategy 1)

Investigators: Sandrina, Sabine


Aim: ligation of mdnA into pak100 for phage display


Time: 2011-07-04,16:00-16:30

Materials:

Ligation: 2 µl vector (pak100 bla KDIR, digested with SfiI), 2 µl insert (mdnA, digested with SfiI), 1 µl quick ligase, 5 µl 2x quick ligase NEB, 10 min, room temperature

Further tasks:
purification


Realization:
amplified mdnA does not contain a myc-tag --> further task: order a new reversed primer for mdnA (strategy 1) containing a myc-tag

Amplification of mdnA for phage display (strategy 2)

Investigators: Sandrina, Sabine


Aim: amplificate mdnA of pARW089 with primers pf_mdnA_sfi_1 and pr_mdnA_sfi_1


Time: 2011-06-10,14:00-16:30


Materials/Methods:

PCR

  • 5 µl Vector pARW089
  • Eppendorf Mastercycler Gradient (program sabrina)
  • 0,25 µl OneTaq DNA Polymerase (NEB)
  • 1 µl dNTPs
  • 1 µl per primer
  • 31,75 µl DNase free water
  • 10 µl 5xOneTaq Standard Reaction Buffer

Gel electrophoresis PCR product mdnA (strategy 2)

Investigators: Sandrina, Sabine


Aim:verification of mdnA (strategy 2)


Time: 2011-07-04,17:00-19:00


Materials/Methods:

  • Agarose broad range (Roth)
  • 1x TAE buffer
  • Gel Red
  • PCR products: mdnA for phage display (strategy 1
  • DNA Ladder Gene Ruler, 100bp plus (Fermentas)
  • 6x Loading Dye (Fermentas)


Method:

1. Production of a 1 % agarose gel

  • mAgarose = 0.5 g in 50 ml 1x TAE
  • adding 2 µl gel red

2. Loading samples

  • 5 µl PCR product and 6x loading dye
  • 2 µl DNA ladder gene ruler (1:10)

3. Run

  • 100 V
  • time: 01:15 h



Results:

lane Sample Volume in µl Expected size in bp
1 marker
2 PCR product mdnA 5 ca. 230


150px

30th Labday 2011-07-06

digestion of PCR products mdnA, geneIII and vector pARW089 (strategy 2)

Investigators: Sandrina, Sabine


Aim: digestion of mdnA, gene III and pARW089 for getting an mdnA-geneIII fusion gene with rfc25 restrition sites in pARW089 by ligation of the three fragments


Time: 2011-07-06,14:00-16:00

Materials:

Digestion of mdnA with NarI (EheI isoschizomere) and AgeI

  • 40 µl sample
  • NEB 10x buffer (4 µl)
  • 1 µl restriction enzyme NarI
  • 1 µ restriction enzyme AgeI
  • 30 µl PCR product (mdnA with rcf 25 and EheI/NarI restriction sites)
  • 4 µl H²O


Digestion of geneIII with NgoMIV and AatII

  • 40 µl sample
  • NEB 10x buffer (4 µl)
  • 1 µl restriction enzyme NgoMIV
  • 1 µ restriction enzyme AatII
  • 30 µl PCR product (geneIII with rcf 25 and AatII restriction sites)
  • 4 µl H²O


Digestion of vector pARW089 with NarI (EheI isoschizomere) and AatII

  • 20 µl sample
  • NEB 10x buffer (2 µl)
  • 1 µl restriction enzyme NarI
  • 1 µ restriction enzyme AatII
  • 12 µl vector DNA
  • 4 µl H²O


  • 1 h at 37°C

Further Tasks:

  • gel electrophoresis and purification of the three digested fragments

Gel extraction from agarose gel of digested fragments mdnA, geneIII and pARW089 (strategy 2)

Investigators: Stefan


Aim: Purification of mdnA, geneIII and pARW089 (strategy 2) to obtain an mdnA-geneIII fusion gene which can be cloned into pARW089


Time: 2011-07-06,17:00-19:00


Materials/Methods:

  • PCR Clean-up Kit NucleoSpin ExtractII (Machery-Nagel)


Method:


1. Cut out visible DNA bands of the digestion product of a 0.8% and 1% agarose gel, respectivly

2. Use protocol of PCR clean-up

3. Two bands were cut out for the vector and genIII. Just use the lower two bands for first ligation.


Results:

  • DNA concentration geneIII: 5,4 ng/µl
  • DNA concentration mdnA: 8,2 ng/µl
  • DNA concentration pARW089: 3,8 ng/µl
  • measured by NanoDrop

Further Tasks:

  • Repeat digestion of pARW089 (because of low concentration)and ligation of the three fragments

31th Labday 2011-07-07

repeated digestion of pARW089 with NarI and AatII (strategy 2)

Investigators: Sabine, Sandrina


Aim: Digestion of pARW089 (strategy 2) so that an mdnA-geneIII fusion gene can be cloned into pARW089


Time: 2011-07-07,10:00-12:00


Materials/Methods:

Digestion of vector pARW089 with NarI (EheI isoschizomere) and AatII

  • 20 µl sample
  • NEB 10x buffer (2 µl)
  • 1 µl restriction enzyme NarI
  • 1 µ restriction enzyme AatII
  • 3 µl vector DNA (ca. 800 ng/ µl)
  • 13 µl H²O


  • 2 1/2 h at 37°C
  • afterwards: inactivation of restriction enzymes: 20 min, 65°C


Further tasks:

gel electrophoresis of digested vector

Gel electrophoresis of digested pARW089 vector(strategy 2)

Investigators: Sandrina, Sabine


Aim:Purification of pARW089 (strategy 2) so that an mdnA-geneIII fusion gene can be cloned into pARW089


Time: 2011-07-07,14:30-15:30


Materials/Methods:

  • Agarose broad range (Roth)
  • 1x TAE buffer
  • Gel Red
  • digested vector pARW089
  • DNA Ladder Gene Ruler 1kb plus(Fermentas)
  • 6x Loading Dye (Fermentas)


Method:

1. Production of a 0,5 % agarose gel

  • mAgarose = 0.25 g in 50 ml 1x TAE
  • adding 2 µl gel red

2. Loading samples

  • digestion product and 6x loading dye
  • pARW089 digestion product (first try, conc: 3,8 ng/µl) to verify measured concentrations

3. Run

  • 100 V
  • time: 00:45 h



Results:

lane Sample Volume in µl Expected size in bp
1 marker
2 purificated, digested vetor try 1 30 ca. 10 000
3 digested pARW089 vector 30 ca. 10.000


File:UP versuch2 pARW Verdau.7.7.png

one band was cutted out of the gel for purifacation


Further tasks:

ligation of mdnA, geneIII and pARW089

ligation of mdnA and geneIII into pARW089(strategy 2)

Investigators: Sabine


Aim: ligation of mdnA, geneIII, and pARW089 to get an mdnA-geneIII fusion gene in pARW089for phage display


Time: 2011-07-07,15:30-17:30

Materials:

Ligation: 2 µl vector (pARW089 digested with NarI and AatII), 3 µl insert (mdnA digested with NarI and AgeI, and geneIII digested with AatII and NgoMIV), 1 µl T4 ligase, 1 µl T4 ligase NEB-buffer,over night, 16°C

Further tasks:
transformation of E. coli cells(XL1-blue)

32th Labday 2011-07-12

Transformation of ligation mdnA, geneIII, and pARW089 (2011-07-07) for phage display (strategy 2)

Investigators: Sandrina, Sabine


Aim:amplification of previous ligation


Time: 9:00-11:30


Method:

  • ligation-samples from 2011-07-07;

(ligation of mdnA, geneIII and pARW089)


protocol:

addition of 10 µl ligation reaction to cells (XL1-blue, tet-resistance) in 1.5 ml Eppi,

incubation 25 min on ice,

heat shock 45 sec at 42°C,

incubation 2 min on ice,

addition of 750 µl LB medium,

incubation at 37 °C for 60 min in Eppendorf thermomixer at 750 rpm,

plating on LB medium with 1,5 % agar, 100 µg/ml ampicillin, 100 µg/µl tetracyclin

storage over night at 37°C


Further tasks:
control cell clones

33th Labday 2011-07-13

Error prone PCR (varied MnCl2 concentration) of mdnA

Investigators: Steffi, Jessica, Katharina


Time: 2011-06-29,14:00-16:00


Aim: Random mutation of mdnA gene based on increased MnCl2 concentration


Materials and Methods: see 26th Labday

34th Labday 2011-07-14

Agarose gel electrophoresis of error prone PCR of mdnA from 2011-07-13 and gel extraction

Investigators: Katharina


Time: 2011-06-29,8:00-11:00


Materials:

  • Agarose broad range (Roth)
  • 1x TAE buffer Gel Red
  • 10 PCR products of mutated mdnA
  • DNA Ladder GeneRuler, 100bp plus (1:10) (Fermentas)
  • 6x Loading Dye (Fermentas)

Method:

1. Production of two 1 % agarose gel

For each gel: mAgarose = 0.5 g in 50 ml 1x TAE adding 2 µl gel red

2. Loading samples

50 µl PCR product and 6x loading dye

6 µl DNA Ladder GeneRuler (1:10) (Fermentas)

3. Run

  • 110 V time: 1 h

Results:

gel 1 gel 2
lane Sample Volume in µl Expected size in bp Sample Volume in µl Expected size in bp
1 marker 6 marker 6
2 PCR sample 1a 50 276 PCR sample 1b 50 276
3 PCR sample 2a 50 276 PCR sample 2b 50 276
4 PCR sample 3a 50 276 PCR sample 3b 50 276
5 PCR sample 4a 50 276 PCR sample 4b 36 276
6 PCR sample 5a 50 276 PCR sample 5b 50 276


300px 300px

The bands were excised and purified using the NucleoSpin Extract II (Macherey-Nagel) extraction Kit.

Further Tasks:

  • digestion of the purified samples
  • ligation

Digestion of error prone PCR of mdnA from 2011-07-13 and pARW089 and agarose gel electrophoresis

Investigators: Jessica


Time: 2011-06-29,11:00-15:00


Materials:

  • Restriction enzymes: AatII, NarI
  • NEB Buffer 4
  • PCR products of random mutated mdnA(1a-5a), purified from gel
  • vector pARW089
  • Agarose broad range (Roth)
  • 1x TAE buffer
  • Gel Red
  • GeneRuler DNA Ladder Mix (1:10) (Fermentas)
  • GeneRuler 1kb DNA Ladder (Fermentas)
  • 6x Loading Dye (Fermentas)


Method:

1. Digestion:

components volume of PCR products /µlvolume of pARW089 /µl
DNA 30 10
NEB Buffer 4(10x) 4 4
Enzyme AatII 0.5 0.8
Enzyme NarI 2 2
H2O 3.5 23.2
Total volume 40 40
  • digestion at 37°C for 1 h

2. Production of agarose gel

  • 1.7% gel for PCR products: mAgarose = 0.85 g in 50 ml 1x TAE adding 2 µl gel red
  • 0.8% gel for vector: mAgarose = 0.4 g in 50 ml 1x TAE adding 2 µl gel red

3. Loading samples

  • 40 µl digest and 8 µl 6x loading dye

4. Run

  • 80 V, time: >1 h


Results:

Gel 1

lane Sample Volume in µl Expected size in bp
M GeneRuler DNA Ladder Mix (1:10) 6
1 digested mdnA 1a 48
2 digested mdnA 2a 48
3 digested mdnA 3a 48
4 digested mdnA 4a 48
5 digested mdnA 5a 48


Gel 2

lane Sample Volume in µl Expected size in bp
M GeneRuler 1kb DNA Ladder 2
1 digested pARW089 48


UP AG EPPCR digest1a-5a 2011-07-14 JE.jpg

UP AG digest pARW089 JE 2011-07-14 JE.jpg


  • Gel excision and storage at -20°C (DNA box, orange)

over night culture from PDV089


Investigators: Sandrina, Sabine


Aim:
control plasmid ligation (pARW089, mdnA, geneIII --> PDV089, strategy 2)


Time: 2011-07-13,12:00-13:00


Materials/Methods:

  • LB-medium with tet and amp
  • cell clones from over night plate
  • incubate over night at 37°C and 750 rpm


Further tasks:

  • plasmid preparation and analytic digestion

Repeated PCR of mdnA for phage display (strategy 1) repeated with new ordered reversed primer (with myc-tag) and geneIII

Investigators: Sandrina, Sabine


Time: 2011-06-30,13:00-16:00


Aim:

  • amplification of mdnA with SfiI restriction sites and myc (vector pARW089) to clone it into pAk100 bla KDIR
  • amplificate GeneIII of pak100 with primers pf_iGEM_GenIII_NgoMIV and pr_GenIII_iGEM_AatII (phage display strategy 2), because there were two bands after digestion with NgoMIV and AatII after gel electrophoresis


Materials/Methods:

see 2011-06-10

changes:

  • program: 123, Thermo Hybrid, PX2


further tasks:

gel electrophoresis with PCR product

35th Labday 2011-07-15

Ligation of mutated mdnA into pARW089

Investigators: Katharina


Aim: create pARW089 vector with inserted mutated mdnA


Time: 10:00-14:00


Materials:

Ligation: 2 µl vector (pARW089 digested with NarI and AatII), 3 µl insert (mdnA digested with NarI and AatII), 1 µl T4 ligase, 1 µl T4 ligase NEB-buffer, 4 h at room temperature

Further tasks:
transformation of E. coli cells(XL1-blue)

Transformation of competent E. coli cells with mutated mdnA in pARW089

Investigators: Katharina


Aim:Transformation of ligations


Time: 14:00-15:00


Method:

protocol:

addition of 2 µl ligation reaction to cells (XL1-blue) in 1.5 ml Eppi,

incubation 25 min on ice,

heat shock 45 sec at 42°C,

incubation 5 min on ice,

addition of 750 µl LB medium,

incubation at 37 °C for 60 min in Eppendorf thermomixer at 750 rpm,

plating on LB medium with 1,5 % agar, 100 µg/ml kanamycin

storage over night at 37°C


Further tasks:
control cell clones

ligation of mdnA into pak100(strategy 1)

Investigators: Sandrina, Sabine


Aim: ligation of mdnA into pak100 for phage display


Time: 2011-07-15,11:00-13:00

Materials:

Ligation: 2 µl vector (pak100 bla KDIR, digested with SfiI), 2 µl insert (mdnA, digested with SfiI), 1 µl T4 ligase, 5 µl 2x 10x T4 ligase buffer, 20 min, room temperature

Further tasks:
transformation into competent cells


Transformation of ligation mdnA into PAK100 bla KDIR for phage display (strategy 1)

Investigators: Sandrina, Sabine


Aim:amplification of previous ligation


Time: 13.00-15:00


Method:

  • ligation-samples

(ligation of mdnA into PAK100 bla KDIR)


protocol:

addition of 10 µl ligation reaction to cells (XL1-blue, tet-resistance) in 1.5 ml Eppi,

incubation 25 min on ice,

heat shock 45 sec at 42°C,

incubation 2 min on ice,

addition of 750 µl LB medium,

incubation at 37 °C for 60 min in Eppendorf thermomixer at 750 rpm,

plating on LB medium with 1,5 % agar, 100 µg/ml ampicillin, 100 µg/µl tetracyclin

storage over night at 37°C


Further tasks:
control cell clones

ligation of mdnA and geneIII for strategy 2

Investigators: Sabine, Sandrina


Aim:ligation of mdnA and geneIII to get an mdnA-geneIII fusion gene phage display


Time: 2011-07-15,15:00-16:00

Materials:

Ligation: 3 µl insert mdnA digested with NarI and AgeI and geneIII digested with AatII and NgoMIV), 1 µl T4 ligase, 1 µl T4 ligase NEB-buffer, 2 µl H2O , 20 min, room temperature


Results:

lane Sample Volume in µl Expected size in bp
M marker, DNA ladder mix ladder mix 10
1 mdnA ligated with geneIII ca. 600

500 px


Further tasks:
ligation with pARW089

ligation of the fusion gene mdnA-geneIII into pARW089(strategy 2)

Investigators: Sabine, Sandrina


Aim:ligation of mdnA-geneIII in pARW089 to get an mdnA-geneIII fusion gene in pARW089for phage display


Time: 2011-07-07,17:00-19:00

Materials:

  • Ligation: 2 µl vector (pARW089 digested with NarI and AatII), 3 µl insert, 1 µl T4 ligase, 1 µl T4 ligase NEB-buffer,over night, 16°C
  • two bands were observed after mdnA-geneIII ligation (red boxes)--> ligation with pARW089 was tried with both bands

Further tasks:
transformation of E. coli cells(XL1-blue)

36th Labday 2011-07-16

Transformation of ligated pARW089 with mdnA-geneIII

Investigators: Stefan


Aim:Transformation of phage display ligations (pARW089 with mdnA-geneIII) using heat shock


Time: 12:00-20:00


Method/Materials:


1) Take chemically competent E. coli XL1 blu cells from –80°C freezer.

2) Turn on heat block to 42°C.

3) use 60 µL of competent cells for each approach

4) Keep tubes on ice.

5) Add 2 µL DNA solution into the E. coli cell suspension, mix by flicking the tube. Incubate on ice for 15-30 min.

6) Put tubes into heat block at 42°C for 45 seconds.

7) Put tubes back on ice for 2 minutes to reduce damage to the E. coli cells.

8) Add 750 µL of LB with no antibiotic. Incubate tubes for 1 hour at 37°C and 750 rpm.

9) spin down the cell suspension for 3 min at 6000 rcf at 4 °C , discard most of the supernatant, resuspend the bacterial pellet by pipetting and use this for spreading.

10) Spread 100 ul of the resulting culture on LB agar plates with Tet/CM.

11) Grow overnight at 37 °C.

12) Pick colonies about 12-16 hours later.


Further tasks:
picking clones and plasmid preparation

Overnight culture of XL1 blue with mdnA in PAK100blaKDIR

Investigators: Stefan


Aim: Picking clone 1 from plate and do an overnight culture


Time: 12:00-20:00


Method/Materials:


*Clone ID_1: Strain:XL1 blue, Plasmid:mdnA in PAR100bla KDIR, Clone number:1

15 mL of LB media were supplied with 15 µL of Tet and CM and cells were incubated at 37 °C overnight.


Further tasks:
plasmid preparation

37th Labday 2011-07-17

Miniprep of E. coli overnight culture containing PAK100blaKDIR

Investigators: Stefan


Aim: isolate the plasmid


Time: 12:00-20:00


Method/Materials:


protocol 5.1 of the NucleoSpin Plasmid Kit was used


Further tasks:
sequence the plasmid

E. coli XL1 blue stock culture containing PAK100blaKDIR with mdnA (Phage Display-strategy 1)

Investigators: Stefan


Aim: set up a stock culture


Time: 12:00-20:00


Method/Materials:


2 x 700 µL culture were mixed with 300 µL of glycerol and stored in -80 °C freezer


Further tasks:

overnight culture of E. coli Xl blue m. Ligation089jessi, u.Ligationvector089jessi,u.Ligationu.BandemdnAgeneIIIpARW089, mLigatiojnm.BandemdnAgeneIIIpARW089

Investigators: Stefan


Aim: pick two clones each and inoculate them overnight in 15 mL LB supplied with 15 µL Tet and Amp


Time: 12:00-20:00


Method/Materials:




Further tasks:
plasmid preparation

38th Labday 2011-07-18

overnight culture of E. coli XL-1 blue containing mutated mndA in parW089

Investigators: Katharina


Aim: Picking 5 clones from each plate and do an overnight culture


Time: 14:00-15:00


Method/Materials:


E. coli Strain:XL1 blue, Plasmid:mdnA in parW089

5 mL of LB media were supplied with 5 µL of Kan and cells were incubated at 37 °C overnight.


Further tasks:
plasmid preparation

Dual-Tranformation of XL1-blu (E. coli) with pTEV-SCS1 and pJC354_ssTorA_NheI_CS-TEV_XhoI_bla

Investigators: Sascha


Aim:

  • Dual-Transformation of XL1-blue to test the in-vivo selection system (pTEV-SCS1 + pJC354_ssTorA_NheI_CS-TEV_XhoI_bla)


Materials:

  • Plasmids:
    • pTEV-SCS1 (TEV protease, res. against kanamycin)
    • pJC354_ssTorA_NheI_CS-TEV_XhoI_bla (res. against chloramphenicol)
  • competent cells XL1-blue
  • LB media and diffenet antibiotics

Used method:

  • standard protocol for heat shock transformation

Output: transformed cultures with plasmids

  • XL1-blue without plasmid (negativ control - no growth over night)
  • XL1-blue transformed with pTEV-SCS1 - growth with kanamycin in LB media
  • XL1-blue transformed with pJC354_ssTorA_NheI_CS-TEV_XhoI_bla - growth with chloramphenicol in LB media
  • XL1-blue transformed with pTEV-SCS1 and pJC354_ssTorA_NheI_CS-TEV_XhoI_bla - growth with kanamycin and chloramphenicol in LB media

Further tasks:

  • reinfect media with cultures for new growth period and distribution to LB Agar with different antibiotic concentrations

Test digestion of ligations for strategies 1 and 2

Investigators: Sandrina


Aim:control if liagation of geneIII and mdnA into pARW089 (strategy 2) and ligation of mdnA into PAK100 bla KDIR worked


Time: 15:30-19:00


Materials/Methods:

Strategy 1:

  • 0,5 µl SfiI
  • 2 µl 10x buffer 4 (NEB)
  • 0,2 µl BSA
  • 10 µl vector DNA
  • 13,3 µl H2O

incubate for 1 h at 50°C

Strategy 2:

  • 0,5 µl XbaI
  • 0,5 µl SpeI
  • 2 µl 10x buffer 4 (NEB)
  • 0,2 µl BSA
  • 10 µl vector DNA
  • 12,8 µl H2O

incubate for 1 h at 37°C


Results:

  • expected bands: strategy 1: ca. 5000 bp and 200bp
  • expected bands: strategy 2: ca. 5000 bp, 4000 bp, 600 bp and 200

observed bands:

  • srtategy 1: ca. 5000 and 800 bp
  • strategy 2: ca. 5000 and 200 bp

Further tasks:

  • repeat ligations

39th Labday 2011-07-19

Resistance test of the Dual-Transformation of XL1-blue (E. coli) with pTEV-SCS1 and pJC354_ssTorA_NheI_CS-TEV_XhoI_bla

Investigators: Stefan and Sebastian


Aim:

  • Dual-Transformation of XL1-blue to test the in-vivo selection system (pTEV-SCS1 + pJC354_ssTorA_NheI_CS-TEV_XhoI_bla)


Materials:

  • Overnight cultures
    • XL1-blue transformed with pTEV-SCS1 - growth with kanamycin in LB media
    • XL1-blue transformed with pJC354_ssTorA_NheI_CS-TEV_XhoI_bla - growth with chloramphenicol in LB media
    • XL1-blue transformed with pTEV-SCS1 and pJC354_ssTorA_NheI_CS-TEV_XhoI_bla - growth with kanamycin and chloramphenicol in LB media
  • LB media and different antibiotics

Used method:

  • growth over night
  • set OD (600 nm) after measurement cells were dilutes to OD 0,1, transformed XL1-blue grow again to OD 0,5. Out of this approach a dilution to OD= 0.002 was done and platted to LB agar with kanamycin, IPTG and different concentrations of ampicillin (range form 0-800 ng/ml ampicillin)

Output:

  • survival of dual transformed cells...

UP resistance test agar plattes with TEV and TorAbla 11-7-20 STW picture1.jpg

UP resistance test agar plattes with TEV 11-7-20 STW picture1.jpg

Further tasks:

There was no growth on the TorAbla plates due to the choice of the wrong antibiotic. This was set up again as well as well as the double transformed cells.

Stock cultures of XL1-blue(E. coli)with pTEV-SCS1 and pJC354_ssTorA_NheI_CS-TEV_XhoI_bla and of XL1-blue(E. coli)with pTEV-SCS1 and of XL1-blue(E. coli)pJC354_ssTorA_NheI_CS-TEV_XhoI_bla

Investigators: Stefan


Aim:

  • make stock cultures


Materials:

  • Overnight cultures were used. 700 µL culture were spun down to remove antibiotics. The pellets is resuspended in 700 µL LB media and 300 µL glycerol.

Used method:

Further tasks:

Design of Primers for BioBrick mdnA and mdn-Cluster

Investigators: Nicole, Nadine


Aim: Design primers for mdnA and mdn-Cluster(from pARW089) for BioBricks pBAD_mdn_Cluster, pSB_mdn_Cluster and pSB_mdnA


Time: 2011-07-19,14:00-17:00


Materials:

  • Geneious Pro 5.1.7


Method:

  • Primer design
    • melting temperature based on 4+2 method (for mdnA-overlapping part)
    • adding sequences for restriction sites (considering reading frame)
    • Check self-complementarity and melting temperature using Oligo Calc

Plan:

  • mdn-Cluster BioBricks

UP BioBrick plan mdn cluster 2011 07 19.png

  • mdnA BioBrick

UP BioBrick plan mdnA 2011 07 19.png


Results:

Primer sequences

600px


Further tasks:

  • do PCR of mdnA


Miniprep of E. coli Xl blue containing mutated mndA in parW089

Investigators: Niels


Aim: 25x overnight cultures :

- miniprep

Time: 2011-07-19,12:00-16:00


Materials:

  • E. coli Xl blue


Kit:

  • Nucleic Acid and Protein Purification
    • Support protocol for NucleoSpin Plasmid


Results:

Nanodrop:

UP Nanodrop 2011-07-19 NW.png


Further task:

  • sequencing
  • digest

40th Labday 2011-07-20

Resistance test of the Dual-Transformation of XL1-blue (E. coli) with pTEV-SCS1 and pJC354_ssTorA_NheI_CS-TEV_XhoI_bla

Investigators: Stefan


Aim:

  • overnight cultures for resistance test


Materials:

  • Overnight cultures of
    • XL1-blue transformed with pJC354_ssTorA_NheI_CS-TEV_XhoI_bla - growth with chloramphenicol in LB media
    • XL1-blue transformed with pTEV-SCS1 and pJC354_ssTorA_NheI_CS-TEV_XhoI_bla - growth with kanamycin and chloramphenicol in LB media

Used method:

Restriction enzyme digestion pARW089 and pARW071

Investigators: Katharina, Nadine


Time: 2011-07-21,11:00-12:00


Aim: Restriction enzyme digestion of pARW089 and pARW071


Materials:

  • Restriction enzymes: AatII, EheI (both from Elke)
  • NEB Buffer 4
  • Plasmids: pARW089, pARW071

Problem:

  • AatII was empty (ordered new batch for tomorrow)

overnight culture of E. coli Xl blue m. ligation mdnA and geneIII into pARW089

Investigators: Sandrina


Aim: repeated test digestion of ligation mdnA and geneIII into pARW089 from 2011-07-12/13


Time: 16:30-18:00


Method/Materials:

  • LB medium




Further tasks:
plasmid preparation and test digestion

Repeated PCR of mdnA and gene III for phage display (strategy 1+2)

Investigator: Sandrina


Time: 2011-07-26,9:00-11:00


Aim:

  • amplification of mdnA with SfiI restriction sites (strategy 1)
  • amplification of mdnA with NarI and AgeI and rfc 25 restriction sites (strategy 2)
  • amplificate GeneIII with NgoMIV and AatII and rfc 25 restriction sites (strategy 2)


Primer:

  • primer: pf_sfi-mdnA_2 and pr_sfi_mdnA_myc (mdnA, strategy 1)
  • primer: pf_mdnA_iGEM_EheI and pr_mdnA_iGEM_AatII (mdnaA, strategy 2)
  • primer: pf_geneIII_NgoMIV and pr_geneIII_iGEM_AatII (geneIII, strategy 2)


Reaction Components:

  • 5 µl Vector pARW089
  • 0,25 µl OneTaq Polymerase
  • 1 µl dNTPs
  • 1 µl per primer
  • 5 µl 5x PCR Buffer
  • 37,75 µl DNase free water


  • purification of PCR fragments with QIAquick Gel Extraction Kit (250)


Further tasks:

  • digestion of PCR products

digestion of PCR products and vectors (strategy 1+2)

Investigator: Sandrina


Time: 2011-07-26,11:00-13:00


Aim:

  • digestion of mdnA and gene III for getting an mdnA-geneIII fusion gene with rfc25 restrition sites after ligation
  • digestion of pARW089 for ligation of mdnA/geneIII fusion gene into it (strategy 2)
  • digestion of pak100blaKDIR and and mdnA to enable ligation


Time: 2011-07-26,14:00-17:30

digestion enzymes:

  • digestion of mdnA (strategy 2) with NarI and AgeI
  • digestion of geneIII (strategy 2) with NgoMIV and AatII
  • digestion of pARW089 (strategy 2) with NarI and AatII
  • digestion of pak100blaKDIR (strategy 1) with SfiI
  • digestion of mdnA (strategy 1) with SfiI

reaction components:

  • 4 µl NEB 10x buffer
  • 1 µl per restriction enzyme
  • 30 µl PCR product / 5 µl vector
  • 4 µl H²O
  • BSA (only Sfi digestion)

reaction conditions:

  • 1 h for PCR fragments
  • 3 h for plasmids
  • 50°C (SfiI digestion)
  • 37°C NarI, AgeI, NgoMIV and AatII digestion


ligation of mdnA and geneIII into digested pARW089(strategy 2)

Investigators: Sandrina


Aim: get phage display vector pPDV089


Time: 2011-07-20,14:00-16:00

Materials:

  • 6 µl digested vector pARW089 (NarI, AatII)
  • 1 µl geneIII
  • 1 µl mdnA

vector and insert should be added in ratio 1:3

  • 2 µl 10x T4 Ligase Buffer
  • 1 µl T4 Ligase
  • 9 µl water
  • incubation over night at 16°C


Further Tasks: transormation of competent cells

ligation of mdnA into pak100blaKDIR (stategy 1)

Investigator: Sandrina


Aim: generate phage display vector pPDV100 (strategy 1)


Time: 2011-07-20,14:00-16:00

Method/Materials:

  • 3 µl (ca 90 ng) Sfi-digested vector pak100
  • 1 µl (ca 20 ng) Sfi-digested PCR fragment mdnA
  • 2 µl 10x T4 Ligase Buffer
  • 1 µl T4 Ligase
  • 13 µl water
  • incubate over night at 16°C


Further Tasks: transformation of competent cells

41th Labday 2011-07-21

Test digestion of ligation for strategy 2

Investigators: Sandrina


Aim:repeated test digestion of ligation mdnA and geneIII into pARW089 from 2011-07-12/13


Time: 15:30-19:00


Materials/Methods:

Strategy 2:

  • 0,5 µl XbaI
  • 0,5 µl SpeI
  • 2 µl 10x buffer 4 (NEB)
  • 0,2 µl BSA
  • 10 µl vector DNA
  • 12,8 µl H2O

incubate for 1 h at 37°C


Results:

lane Sample Volume in µl Expected size in bp
M marker, DNA ladder mix, fermentas 2
1-20 digested ligations 6 ca. 5000 bp, 4000 bp, 600 bp and 200

400 px

400 px

Further tasks:

sequencing of clone 6

Transformation of ligated pARW089 with mdnA-geneIII and ligated PAK100 bla KDIR with mdna

Investigators: Sandrina


Aim:Transformation of phage display ligations (strategy 1 and2) (2011-7-20) using heat shock


Time: 10:00-12:00


Method/Materials:


1) Take chemically competent E. coli XL1 blu cells from –80°C freezer.

2) Turn on heat block to 42°C.

3) use 60 µL of competent cells for each approach

4) Keep tubes on ice.

5) Add 2 µL DNA solution into the E. coli cell suspension, mix by flicking the tube. Incubate on ice for 15-30 min.

6) Put tubes into heat block at 42°C for 45 seconds.

7) Put tubes back on ice for 2 minutes to reduce damage to the E. coli cells.

8) Add 750 µL of LB with no antibiotic. Incubate tubes for 1 hour at 37°C and 750 rpm.

9) spin down the cell suspension for 3 min at 6000 rcf at 4 °C , discard most of the supernatant, resuspend the bacterial pellet by pipetting and use this for spreading.

10) Spread 100 ul of the resulting culture on LB agar plates with Tet/CM.

11) Grow overnight at 37 °C.

12) Pick colonies about 12-16 hours later.


Further tasks:
picking clones and plasmid preparation

42th Labday 2011-07-22

Restriction enzyme digestion pARW089 and pARW071 AND trouble-shouting

Investigators: Katharina, Nadine


Time: 2011-07-22,10:00-15:00


Aim: Restriction enzyme digestion of pARW089 and pARW071


Materials:

  • Restriction enzymes: AatII, NarI
  • NEB Buffer 4
  • Plasmids: pARW089, pARW071

43th Labday 2011-07-23

Restriction enzyme digestion pARW089 (different incubation times), plasmid purification and ligation with EP-PCR mdnA

Investigators: Nadine


Time: 2011-07-22,14:30-20:30


Aim: Restriction enzyme digestion of pARW089 with different incubation times to test best digestion conditions, problems with the digestion of pARW089 in the last trials (-->gel excision and ligation if it worked out


Materials:

  • Restriction enzymes: AatII, NarI, control: XmaI
  • NEB Buffer 4
  • PCR products of random mutated mdnA(1a-5a), purified from gel
  • vector pARW089
  • Agarose broad range (Roth)
  • 1x TAE buffer
  • Gel Red
  • GeneRuler 1kb DNA Ladder (Fermentas)
  • 6x Loading Dye (Fermentas)


Method:

1. Digestion:

components volume of pARW089 /µl
DNA 5
NEB Buffer 4(10x) 4
Enzyme AatII 0.8
Enzyme NarI 2
H2O 28.2
Total volume 40

2. Digestion: control

components volume of pARW089 /µl
DNA 5
NEB Buffer 4(10x) 4
Enzyme XmaI 1
BSA 0.2
H2O 29.2
Total volume 40
  • digestion at 37°C for 1 h

3. Production of agarose gel

  • 0.8% gel for vector: mAgarose = 0.4 g in 50 ml 1x TAE adding 4 µl gel red

4. Loading samples

  • 40 µl digest and 8 µl 6x loading dye

5. Run

  • 110 V, time: >40 min


Results:

Gel

lane Sample Volume in µl Expected size in bp
M GeneRuler 1kb DNA Ladder 2 10296, 116
1 digested pARW089 1 hr 48 10296, 116
2 digested pARW089 2 hrs 48 10296, 116
3 digested pARW089 2.5 hrs 48 10296, 116
4 digested pARW089 XmaI 3 hrs 48 3270, 7142
5 digested pARW089 3 hrs 48 10296, 116
6 digested pARW089 undigested 48


250px


6. Gel excision

  • lane 4 and 6, band: 10296, respectively

7. Ligation

Ligation: 3 µl vector (pARW089 digested with NarI and AatII, incubation 2.5 hrs and 3 hrs), 3 µl insert (mdnA digested with NarI and AatII from 2011-07-29), 1 µl T4 ligase, 1 µl T4 ligase NEB-buffer, overnight at 16°C

samples:

  • pARW089 (dig. 2.5 hrs) + mdnA 1A
  • pARW089 (dig. 2.5 hrs) + mdnA 2A
  • pARW089 (dig. 2.5 hrs) + mdnA 3A
  • pARW089 (dig. 2.5 hrs) + mdnA 4A
  • pARW089 (dig. 2.5 hrs) + mdnA 5A
  • pARW089 (dig. 3 hrs) + mdnA 1A
  • pARW089 (dig. 3 hrs) + mdnA 2A
  • pARW089 (dig. 3 hrs) + mdnA 3A
  • pARW089 (dig. 3 hrs) + mdnA 4A
  • pARW089 (dig. 3 hrs) + mdnA 5A

Further tasks:
transformation of E. coli cells(XL1-blue)

creation of pPDV089 in Genious

Investigators: Sandrina, Sabine


Aim: getting a model of pPDV089 for sequence alignment with purified pPDV089 plasmids from clones


Time: 09.00-11.00


Method/Materials:


software Genious


Further tasks:

perform alignment

sending pPDV089 from positive clone to GATC for sequencing

Investigators: Sabine


Aim: get sequence of generated phage display vector pPDV089 (strategy 2) to control the ligation of digested pARW089 with digested mdnA and gene III


Method/Materials:


10 µl of purified pPDV089 and 20 µl primer sf_mdna_1 were sent to GATC


Further tasks:

perform alignment

44th Labday 2011-07-24

Transform ligation from 42th Labday into E. coli XL blue 1 cells

Investigators: Stefan


Time: 2011-07-22,11:00-15:00


Aim: cells containing the desired vectors


Materials/Methods:1)


1)Take chemically competent E. coli XL1 blu cells from –80°C freezer.

2) Turn on heat block to 42°C.

3) use 60 µL of competent cells for each approach

4) Keep tubes on ice.

5) Add 2 µL DNA solution into the E. coli cell suspension, mix by flicking the tube. Incubate on ice for 15-30 min.

6) Put tubes into heat block at 42°C for 45 seconds.

7) Put tubes back on ice for 2 minutes to reduce damage to the E. coli cells.

8) Add 750 µL of LB with no antibiotic. Incubate tubes for 1 hour at 37°C and 750 rpm.

9) spin down the cell suspension for 3 min at 6000 rcf at 4 °C , discard most of the supernatant, resuspend the bacterial pellet by pipetting and use this for spreading.

10) Spread 100 ul of the resulting culture on LB agar plates with Tet/CM. 11) Grow overnight at 37 °C. 12) Pick colonies about 12-16 hours later.

45th Labday 2011-07-25

overnight culture of E. coli XL-1 blue containing mutated mndA in parW089

Investigators: Steffi


Aim: Picking 1 clone from each plate (Ligation pARW089 mdnA 2hrs 1A-5A, Ligation pARW089 mdnA 3hrs 1A-5A) and do an overnight culture


Time: 16:00-17:00


Method/Materials:


E. coli Strain: XL1 blue, Plasmid:mdnA in parW089

5 mL of LB media were supplied with 5 µL of Kan and cells were incubated at 37 °C overnight.


Further tasks:
plasmid preparation

46th Labday 2011-07-26

Miniprep of E. coli Xl blue containing mutated mndA in parW089

Investigators: Steffi


Aim: 10x overnight cultures :

- miniprep

Time: 2011-07-26,09:00-16:00


Materials:

  • E. coli Xl blue


Kit:

  • Nucleic Acid and Protein Purification
    • Support protocol for NucleoSpin Plasmid

Further task:

  • sequencing


Alignment of sequenced pPDV089 and model of pPDV089

Investigator: Sabine


Time: 2011-07-26,10:30-11:30


Aim: control of generated phage display vector pPDV089


Materials/Methods:

  • file sent from GATC
  • software Genious

Results:

  • 2 mutations in geneIII
  • the last 2 aminoacids of myc are absent

Further task:

  • repeat PCR of all fragments using polymerase S (not OneTaq as before)

Repeated PCR of mdnA and gene III for phage display (strategy 1+2)

Investigator: Sabine


Time: 2011-07-26,11:30-13:30


Aim:

  • amplification of mdnA with SfiI restriction sites (strategy 1)
  • amplification of mdnA with NarI and AgeI restriction sites (strategy 2)
  • amplificate GeneIII with NgoMIV and AatII restriction sites (strategy 2)


Primer:

  • primer: pf_sfi-mdnA_2 and pr_sfi_mdnA_myc (mdnA, strategy 1)
  • primer: pf_mdnA_iGEM_EheI and pr_mdnA_iGEM_AatII (mdnaA, strategy 2)
  • primer: pf_geneIII_NgoMIV and pr_geneIII_iGEM_AatII (geneIII, strategy 2)


Reaction Components:

  • 5 µl Vector pARW089
  • 0,25 µl Taq Polymerase S (BioScience)
  • 1 µl dNTPs
  • 1 µl per primer
  • 5 µl 10x PCR Buffer S
  • 37,75 µl DNase free water


  • purification of PCR fragments with QIAquick Gel Extraction Kit (250)


Further tasks:

  • digestion

digestion of PCR products and vectors (strategy 1+2)

Investigator: Sabine


Aim:

  • digestion of mdnA and gene III for getting an mdnA-geneIII fusion gene with rfc25 restrition sites after ligation
  • digestion of pARW089 for ligation of mdnA/geneIII fusion gene into it (strategy 2)
  • digestion of pak100blaKDIR and and mdnA to enable ligation


Time: 2011-07-26,14:00-17:30

digestion enzymes:

  • digestion of mdnA (strategy 2) with NarI and AgeI
  • digestion of geneIII (strategy 2) with NgoMIV and AatII
  • digestion of pARW089 (strategy 2) with NarI and AatII
  • digestion of pak100blaKDIR (strategy 1) with SfiI
  • digestion of mdnA (strategy 1) with SfiI

reaction components:

  • 4 µl NEB 10x buffer
  • 1 µl per restriction enzyme
  • 30 µl PCR product / 5 µl vector
  • 4 µl H²O
  • BSA (only Sfi digestion)

reaction conditions:

  • 1 h for PCR fragments
  • 3 h for plasmids
  • 50°C (SfiI digestion)
  • 37°C NarI, AgeI, NgoMIV and AatII digestion


Further Tasks:

  • gel electrophoresis for purification of the digested fragments and vectors

gel electrophoresis of digested fragments and vectors

Investigator: Sabine


Aim: control PCR and digestion


Time: 2011-07-06,18:00-19:00

Results:

sizes of bands

  • pak100blaKDIR (SfiI, strategy 1): ca 4,5 kp
  • pARW089 (NarI and AatII, strategy 2): ca 10,5 kb
  • mdnA (SfiI, strategy 1): ca 250 bp
  • mdnA (NarI and AgeI, stategy 2): ca 200 bp
  • geneIII (NgoMIV and AatII): no band


  • purification with QIAquick Gel Extraction Kit (250)


Further Tasks:

  • repeat PCR of geneIII
  • ligation

Repeated PCR gene III for phage display (strategy 2)

Investigator: Sabine


Time: 2011-07-26,19:00-19:30


Aim:

  • amplificate GeneIII with NgoMIV and AatII restriction sites (strategy 2)


Primer:

  • primer: pf_geneIII_NgoMIV and pr_geneIII_iGEM_AatII (geneIII, strategy 2)


Reaction Components:

  • 5 µl pak100blaKDIR
  • 0,25 µl Taq Polymerase S (BioScience)
  • 1 µl dNTPs
  • 1 µl per primer
  • 5 µl 10x PCR Buffer S
  • 37,75 µl DNase free water


Further tasks:

  • purification
  • digestion

47th Labday 2011-07-27

digestion of PCR product geneIII (strategy 2)

Investigator: Sabine


Aim: digestion of gene III for getting an mdnA-geneIII fusion gene with rfc25 restrition sites after ligation


Time: 2011-07-26,09:30-10:30

reaction components:

  • 4 µl NEB 10x buffer
  • 1 µl per restriction enzyme (NgoMIV and AatII
  • 30 µl PCR product
  • 4 µl H²O


reaction conditions:

  • 1 h, 37°C


Further Tasks:

  • gel electrophoresis for purification of the digested geneIII

gel electrophoresis of digested geneIII

Investigator: Sabine


Aim: control PCR and digestion


Time: 2011-07-27,10:30-11:30

Method/Materials:

  • 1% agarose gel
  • GeneRuler DNA Ladder Mix (SM0331)
  • 5x loading dye
  • purification with QIAquick Gel Extraction Kit (250)


Results: size of band: ca 550 bp


Further Tasks: ligation

ligation of mdnA into pak100blaKDIR (stategy 1)

Investigator: Sabine


Aim: generate phage display vector pPDV100 (strategy 1)


Time: 2011-07-27,11:30-12:30

Method/Materials:

  • 3 µl (ca 90 ng) Sfi-digested vector pak100
  • 1 µl (ca 20 ng) Sfi-digested PCR fragment mdnA
  • 2 µl 10x T4 Ligase Buffer
  • 1 µl T4 Ligase
  • 13 µl water
  • 1 h, room temperature


Further Tasks: transormation

Transformation of generated pPDV100 (strategy 1)

Investigators: Sabine


Aim:amplification of pPDV100


Time: 12:30-14:00


Method:

  • addition of 10 µl ligation reaction to XL1-blue cells
  • incubation 25 min on ice,
  • heat shock 45 sec at 42°C,
  • incubation 2 min on ice,
  • addition of 750 µl LB medium,
  • incubation 60 min at 37 °C and 750 rpm
  • plating on agar plates containing 100 µg/ml chloramphenicol
  • storage over night at 37°C


Further tasks:
control cell clones

48th Labday 2011-07-28

overnight culture of 10 picked clones of XL blue cells transformed with pPDV100

Investigators: Sabine


Aim: amplification and purification of generated phage display vector pPDV100 for test digestion and sequencing


Time: 10:00-10:30


Method/Materials:

5 ml LB medium per clone containining 100 µg/ml chloramphenicol

storage over night at 37°C and 800 rpm


Further tasks:

plasmid preparation, test digestion and sequencing

ligation of mdnA and geneIII (strategy 2)

Investigators: Sabine


Aim: get mdnA/geneIII fusion gene for cloning into pARW089


Time: 2011-07-28,11:00-12:30

Materials:

  • 5 µl (ca 25 ng) digested geneIII (NgoMIV, AatII)
  • 3 µl (ca 30 ng) digested mdnA (NarI, AgeI)
  • 2 µl 10x T4 Ligase Buffer
  • 1 µl T4 Ligase
  • 9 µl water
  • 1 h, room temperature


Further Tasks: ligation of mdnA/geneIII into digested pARW089

ligation of mdnA/geneIII into digested pARW089(strategy 2)

Investigators: Sabine


Aim: get phage display vector pPDV089


Time: 2011-07-28,12:30-13:00

Materials:

  • 6 µl (ca 70 ng) digested vector pARW089 (NarI, AatII)
  • 1 µl (ca 5 ng) fusion gene mdnA/geneIII
  • 2 µl 10x T4 Ligase Buffer
  • 1 µl T4 Ligase
  • 10 µl water
  • 1 h, room temperature


Further Tasks: transormation

Transformation of generated pPDV089 (strategy 2)

Investigators: Sabine


Aim: amplification of pPDV089


Time: 13:30-15:00


Method:

  • addition of 10 µl ligation reaction to XL1-blue cells
  • incubation 25 min on ice,
  • heat shock 45 sec at 42°C,
  • incubation 2 min on ice,
  • addition of 750 µl LB medium,
  • incubation 60 min at 37 °C and 750 rpm
  • plating on agar plates containing 100 µg/ml tetracyclin and 100 µg/µl ampicillin
  • storage over night at 37°C


Further tasks:
control cell clones

49th Labday 2011-07-29

Miniprep of E. coli overnight culture containing pPDV100

Investigators: Sabine


Aim: purification of pPDV100 for test digestion and sequencing


Time: 10:00-11:00


Method/Materials: see protocol 5.1 of the NucleoSpin Plasmid Kit


Further tasks: test digestion

gel electrophoresis of digested pPDV100

Investigator: Sabine


Aim: control ligated pPDV100


Time: 2011-07-29,11:30-12:30

Method/Materials:

1% agarose gel, GeneRuler DNA Ladder Mix (SM0331), 5x loading dye


Results: ligation of mdnA into pak100 has not worked


Further Tasks: control all working steps, repeat cloning

creation of pPDV100 in Genious

Investigators: Sandrina, Sabine


Aim: getting a model of pPDV100 for sequence alignment with purified pPDV089 plasmids from clones


Time: 14.00-16.00


Method/Materials: software Genious


Results: subsequent insertion of myc into reverse PCR primer (mdnA) caused frameshift, new primer ordered

Retrieved from "http://2011.igem.org/Team:Potsdam_Bioware/Labjournal/July"