Team:Freiburg/Labjournals/Cloning/August

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Cloning

2015/08/01

Mini-Prep of the ligations for untagged antigens, pET_804 (3) and pIG15_804 (3) (RE)

  • Qiagen-kit
  • eluted in 30 µl dH2O
  • NanoDrop:
plasmid concentration [ng/µl]
pET_802 - 1 234.4
pET_802 - 2 204.0
pET_1002 - 1 223.2
pET_1002 - 2 214.6
pET_1102 - 1 220.3
pET_1102 - 2 236.4
pET_1502 - 1 199.0
pET_1502 - 2 250.0
pET_1702 - 1 238.9
pET_1702 - 2 213.7
pET_804 - 3 254.4
pET_804 - 3 257.7
pIG15_804 - 3 241.2
pIG15_804 - 3 322.3

Digest of the ILS plasmids (RE)

  • Bba_K823013 with SpeI and PstI-HF
  • Bba_K823008 with SpeI and PstI-HF
  • Bba_K823005 with SpeI and PstI-HF
  • Bba_I13504 with XbaI and PstI-HF
  • 1 µl of each restr. enzyme
  • 5 µl CutSmart
  • 10 µl DNA
  • 33 µl dH2O
  • incubated for 1 h at 37°C

analysis on 1 % agarose gel:

Digest of pET_804 and pIG15_804 (RE)

Both plasmids were digested with BamHI and HindIII (to insert other antigens) as well as HindIII and AflII (to insert the Halo-tag instead of Spy)

  • 1 µl of each restr. enzyme
  • 5 µl FD Green Buffer
  • 14 µl DNA
  • 33 µl dH2O
  • incubated for 5 min at 37°C

analysis on 1 % agarose gel: DNA is totally destructed by the enzymes

Repetition of the digest with NEB enzymes (RE)

  • incubated for 1 h at 37°C

analysis on 1 % agarose gel: digest worked and the backbones were extracted from the gel (TAE buffer was exchanged before running the gel, maybe it caused the problems with DNA destruction instead of the restriction enzymes)

Test digest of pET_SpyC_GST (RE)

  • 1 µl HindIII
  • 1 µl PstI-HF
  • 2 µl CutSmart
  • 5 µl DNA
  • 11 µl dH2O
  • incubated for 1 h at 37°C
  • expected fragment sizes: ~1700 and ~4100 bp

Test digest of pET_x02 (untagged antigens) (RE)

  • 1 µl BamHI
  • 1 µl PstI-HF
  • 2 µl CutSmart
  • 5 µl DNA
  • 11 µl dH2O
  • incubated for 1 h at 37°C
  • expected fragment sizes:
Plasmid Backbone Antigen-containing fragment
pET_802 ~4100 bp ~1700 bp
pET_1002 ~4100 bp ~1900 bp
pET_1102 ~4100 bp ~3000 bp
pET_1502 ~4100 bp ~3400 bp
pET_1702 ~4100 bp ~1800 bp

analysis of both test digests on 1 % agarose gel: DNA is destructed by the enzymes (TAE buffer was exchanged afterwards); only for pET_1502 and pET_1702, correct fragments are visible among the smeer

Ligations (RE)

  • InterLab study:
Backbone Bba_K823013 Bba_K823008 Bba_K82_3005
Backbone amount [µl] 2.17 1 2.08
GFP (Bba_I13504) amount [µl] 3.09 3.09 3.09
  • Halo-tag:
Backbone pIG15_804
Backbone amount [µl] 0.93
Halo-tag amount [µl] 4.5
  • Antigens:
Backbone pET_804 pIG15_804
Backbone amount [µl] 0.83 0.43
10 (HCV) amount [µl] 2.12 1.18
11 (Tetanus) amount [µl] 1.12 0.62
15 (Salmonella) amount [µl] 1.21 0.67
17 (HIV) amount [µl] 2.27 1.26
  • 1 µl T4 ligase
  • 2 µl T4 ligase buffer
  • up to 20 µl dH20
  • incubated for 1 h at RT

Transformation of the ligation products (5 µl) into E.coli TOP10 (RE)

  • pILS1-3, pIG15_805 and pIG15_1004-1704 were plated on LB-cml
  • pET_1004-1704 were plated on LB_amp

2015/08/03

Sequencing results (LS)

  • pET_804 (3): correct
  • pET_804 (4): correct
  • pIG15_804 (3): correct
  • pIG15_804 (4): correct

Test digest: pEtX04, pIG15_X04, pILS1-3 and pIG15_805 (LS)

  • Interlab Study: pILS1, 2 and 3–>EcoRI HF and SpeI HF
6xMasterMix
6µlEcoRI HF
6µlSpeI Hf
12µlCut smart
66µldH2O
  • pETX04, pIG15_X04, pIG15_805–>BamHI HF and PstI HF
18xMasterMix
18µlBamHI HF
18µlPstI HF
36µlCut smart
198µldH2O
  • addition of 5µl plasmid each
  • incubation at 37°C, 1h
  • analysis on 1% agarose gel:
Upper part: First six rows are the digested plasmids for the interlab study. pILS1 is pSB1C3 with Anderson Promoter 17 (J23117) followed by GFP (~ 940bp). pILS2 contains the Anderson Promoter 06 (J23106), and pILS3 the Anderson Promoter 01 (J23101). Test digest of the plasmids for protein expression (pETX04)in E.coli with His_tag-antigen-Spy_tag insert. Expected band length for the different constructs: pET_1004:~1900bp pET_1104:~2700bp pET_1504:~3100bp pET_1704:~1900bp Lower part: Test digest for the Cellfree Expression Constructs, containing a His_tag-antigen-Spy_tag insert. Expected band lenght for the different constructs: pIG15_1004:~800bp pIG15_1104:~1500bp pIG15_1504:~1900bp pIG15_1704:~800bp Test digest of pIG15_805 for cellfree expression containing His_tag-antigen 8-Halo_tag. Expected band lenght of insert: ~1500bp.

PCR for biobricks + PCR for GFP insert (LS)

Antigens 6, 8, 10, 11, 17 and 18 will be amplified using primers with matching overlap for pSB1C3 for Gibson cloning. The plasmids pIG15_X01 containg antigen fragments will be used as template. For GFP amplification pQE-60 GFP will be used as template.

MasterMix
high GC buffer60µl
dNTPs6µl
DMSO9µl
Polymerase3µl
dH2O190,5µl

+0,1µ template (~100ng/µl) +1µl of each primer

Cycling
98°C3min
98°C30s
60°C30s
72°C40s
72°C10 min
4°C–
  • analysis on 1% agarose gel:
Upper part:Fragment 6,10,11 and 17. Expected band lengths: fragment 6:312bp fragment 10:657bp fragment 11:1440bp fragment 17:624bp Lower part: Fragment 18 and GFP. Expected band lengths: fragment 18:615bp GFP:~800bp Antigen 6 could not be amplified and antigen 11 shows only a very slight band a the correct size. The other fragments were amplified correctly.

Gel-ex: PCR products (LS)

  • qiagen kit
concentrations [ng/µl]
GFP37,8
frg. 830,9
frg. 1041,1
frg. 1111,6
frg. 1742,5
frg. 1839,0

2015/08/04

Digest: pIG15_104 with EcoRI HF and SpeI HF (LS)

For Gibson assembly of the biobricks containing the antigens, digested backbone is needed. pIG15_104 is the cellfree expression vector inside the pSB1C3 standard and can thus be used for digestion.

Digest
10µlpIG15_104
1µlSpeI HF
1µlEcoRI HF
5µlCut Smart
33µldH2O
  • 1h, 37°C
  • analysis on 1% agarose gel
  • gel-ex: 45,0ng/µl

Inoculation of Gly-Stocks in liquid LB-Amp (LS)

To build biobricks with all antigens some of the Gly-stocks have to be inoculated again, followed by miniprep of the respective plasmids. The following E.coli Gly-stocks were inoculated:

  • pIG15_301
  • PIG15_401
  • pIG15_501
  • pIG15_701
  • pIG15_901
  • incubation at 37°C, shaking

Gibson-Assembly (RE)

  • inserts: PCR products of the antigens 8, 10, 11, 17 and 18
  • backbone: pSB1C3, EcoRI and SpeI digested
  • DNA-Mix:
Antigen Backbone [µl] Antigen [µl]
8 0.53 1.24
10 0.53 1.4
11 0.24 4.76
17 0.53 1.14
18 0.53 1.23
  • 5 µl were directly transformed into E. coli TOP10

Transformation (RE)

  • pET_804
  • pIG15_804
  • pET_SpyC_GST
  • pIG15_1104
  • pILS_1
  • pILS_2
  • pILS_3
  • pET_804 and pET_SpyC_GST were plated on LB_amp
  • all the others were plated on LB_cml

2015/08/05

Inocculation of 5 ml liquid culture (RE)

  • pET_804 (LB_amp, 2x)
  • pIG15_804 (LB_cml, 2x)
  • pET_SpyC_GST (LB_amp)
  • pIG15_1104 (LB_cml)
  • pILS_1 (LB_cml)
  • pILS_2 (LB_cml)
  • pILS_3 (LB_cml)

Preparation of Gibson MasterMix (RE)

  • according to the protocol of AG Weber
  • 100 µl 5X ISO Buffer
  • 50 µl Taq ligase
  • 6.25 µl Phusion polymerase
  • 0.2 µl T5 Exonuclease
  • 218.55 µl ddH2O
  • –> 15 µl aliquots stored at -20°C

Mini-Prep (LS)

  • qiagen kit
concentrations
pIG15_401715,8
pIG15_301243,1
pIG15_501437,3
pIG15_701329,3
pIG15_901606,5

PCR for amplification of the antigens (LS)

  • amplification of the following antigens: 3,4,5,6,7,9
  • 2×20µl each (antigen 6: 4×20µl)
  • PCR mix and cycling protocol same way as last time (3.8.2015)

Inoculation (LS)

  • 3 colonies from Gibson-Assembly plates each
  • 5ml LB-Amp
  • incubation at 37°C o/n

Mini-Prep (RE)

  • Qiagen-Kit
  • eluted in 30 µl dH2O
  • pET_804
  • pIG15_804
  • pET_SpyC_GST
  • pIG15_1104

2015/08/06

Digest of pET_804 and pIG15_804 (RE)

  • ~2 µg per construct were digested with BamHI and HindIII for insertion of antigens
  • ~1 µg per construct was digested with HindIII and AflII for insertion of the Halo-tag
  • 1 µl of each restriction enzyme (Fermentas)
  • 5 µl FD Green Buffer
  • ad 50 µl dH2O

Analysis of PCR (from yesterday) on 1% agarose gel (LS)

Antigen fragments 3,4 and 6 were amplified correctly. 5,7 and 9 did not work well. Expected band lengths: antigen 3: ~1100bp antigen 4: ~1100bp antigen 5: ~1100bp antigen 6: ~260bp antigen 7: ~1600bp antigen 9: ~1300bp

Gel-ex: PCR products for biobricks (LS)

  • qiagen kit
concentrations [ng/µl]
antigen 659,1
antigen 454,1
antigen 56,9
antigen 3109,9

Digest: pET804 with BamHI+HindIII and HindIII+AflII (LS)

Digest
1µlFD BamHI/AflII
1µlFD HindIII
5µl FD buffer
5/3µlDNA
  • incubation at 37°C, 30 min

Mini-Prep of Gibson products for standardized plasmids (LS)

  • Zymo Research kit
concentrations
pRIG15_81429,5
2180,2
3190,9
pRIG15_101176,4
2352,5
3184,5
pRIG15_181231,0
2199,4
3189,1

Test digest of standardized plasmids (LS)

  • digest with: EcoRI HF and PstI HF
Master Mix
5,5µlEcoRI HF
5,5µlPstI HF
22µlbuffer
132µldH2O
+5µl plasmid DNA
  • incubation at 37°, 1h
  • analysis on 1% agarose gel
Expected band lenghts for digested fragments: antigen 8:~430bp antigen 10:~600bp antigen 17:~580bp antigen 18:~570bp. For pRIG15_8, clone 3 shows correct bands, for pIRG15_10 clone 3, pRIG15_17 clone 1 and pRIG15_18 clone 2 and 3 are correct. Correct clones were sent for sequencing.

PCR for amplification of antigens 5, 7, 9 and 11 (RE)

  • gradient for annealing temp., because the PCR did not work for those antigens the last time
  • 5X Master-Mix per antigen
  • 20 µl Phusion High GC Buffer
  • 5 µl of each primer
  • 2 µl dNTPs
  • 3 µl DMSO
  • 1 µl Phusion polymerase
  • 0.5 µl Template (100 ng/µl)
  • 63.5 µl dH2O

cycling:

  • the same cycling conditions as before were used, except the gradient for the annealing temperature (55°C-65°C)

analysis on 1% agarose gel:

  • amplification of 5, 7 and 9 was successful for every annealing temperature
  • amplification of 11 did not work again

Gel-Ex of the PCR products (RE)

  • Qiagen-Kit
  • eluted in 20 µl dH2O
  • 5: 72.4 ng/µl
  • 7: 98.3 ng/µl
  • 9: 76.7 ng/µl

Ligations (RE)

  • 1 µl T4 ligase
  • 2 µl T4 ligase buffer
  • ad 20 µl dH2O
  • incubation 1 h at RT
  • transformation of 5 µl ligation product into E. coli TOP10
Backbone Backbone amount [µl] Insert Insert amount [µl]
pET_804 (BamHI and HindIII digested ) 6 10 10.77
pET_804 (BamHI and HindIII digested ) 6 11 10.84
pET_804 (BamHI and HindIII digested ) 6 15 10.84
pET_804 (BamHI and HindIII digested ) 6 17 10.66
pIG15_804 (BamHI and HindIII digested ) 5.43 10 1.55
pIG15_804 (BamHI and HindIII digested ) 5.43 15 1.06
pIG15_804 (BamHI and HindIII digested ) 5.43 17 2.31
pET_804 (HindIII and AflII digested ) 10.42 Halo 0.66
pIG15_804 (HindIII and AflII digested ) 3.09 Halo 1.2

Gibson-Assembly (JN)

  • assembly of pSB1C3 backbone with different antigens for standardization
Backbone amount [µl] Insert Insert amount [µl] H2O [µl]
0.53 3 0.88 3.59
0.53 4 1.75 2.69
0.53 5 1.33 3.13
0.53 6 0.41 4.06
0.53 7 1.47 3.00
0.53 9 1.52 2.95

2015/08/07

Inoculation of ligation/gibson clones (LS)

  • 2x each
  • 5ml LB-Amp/Cml
  • 37°C, shaking

Repetition of PCR for biobrick fragments: 10, 11, and 18 (LS)

  • 4×20µl, gradient PCR
Master Mix
high GC buffer16µl
primer 14µl
primer 34µl
dNTPs1,6µl
DMSO2,4µl
Phusion Polymerase0,8µl
template0,4µl
dH2O50,8µl
cycling
98°C3min
98°C30s
55°C-65°C30s
72°C1min
72°C10min
4°C–
  • analysis on 1% agarose gel
  • 11 did not work…

Mini-Prep (JN)

  • pRIG15_06/07, pIG15_1004/1504/1704, pET_1004/1104
  • Qiagen kit
  • eluted in 30µl dH2O
plasmid concentration [ng/µl]
pRIG15_06 - 1 72.5
pRIG15_06 - 2 82.8
pRIG15_07 - 1 92.1
pRIG15_07 - 2 111.4
pIG15_1004 - 1 144.5
pIG15_1004 - 2 147.9
pIG_1504 - 1 130.4
pIG_1504 - 2 151.2
pIG_1704 - 1 74.1
pIG_1704 - 2 69.3
pET_1004 - 1 78.0
pET_1004 - 2 57.0
pET_1104 - 1 100.8
pET_1104 - 2 125.0

2015/08/08

Mini-Prep (RE)

  • Biozym-kit (Solution 2 from Peqlab-kit was used, because it was empty in the Biozym-kit)
  • eluted in 30 µl dH2O
  • pET_1504 - 1: 156.4 ng/µl
  • pET_1505 - 2: 84.2 ng/µl
  • pET_1704 - 1: 104.8 ng/µl
  • pET_1704 - 2: 144.7 ng/µl
  • pIG15_805 - 1: 189.1 ng/µl

Test Digests (RE)

  • pRIG15_06 and pRIG15_07 with EcoRI-HF and PstI-HF (NEB –> 1 h incubation at 37°C)
  • pET_1001, pET_1104, pET_1504, pET_1704, pIG15_1004, pIG15_1504, pIG15_1704 with BamHI and HindIII (Fermentas FD –> 30 min incubation at 37°C)
  • pIG15_805 with HindIII and AflII (Fermentas FD –> 30 in incubation at 37°C)
Result of the test digests

Repetition of Test Digests (JN)

  • pET_1001, pET_1104, pET_1504, pET_1704, pIG15_1004, pIG15_1504, pIG15_1704 with BamHI and HindIII (Fermentas FD –> 15 min incubation at 37°C)

Gel-ex: PCR product for biobricks 10 and 18 (LS)

  • qiagen kit
  • eluted in 20µl
concentrations [ng/µl]
fragment 1050,9
fragment 1855,3

Repetition of PCR for biobrick 11 (LS)

Q5 Master Mix
Q5 2x Master Mix50µl
oIG15_b11015µl
oIG15_b11025µl
dH2O19,6µl
pIG15_11010,4µl
  • 4×25µl
cycling
98°C3min
98°C30s
55°C-65°C30s
72°C1min
72°C10min
4°C–
  • analysis on 1% agarose gel

Transformation (LS)

blunt-end ligation: GFP ind pJet
0,3µlGFP (PCR product
1µlT4 DNA Ligase
10µl2x buffer
1µlpJet
up to 20µl dH2O
  • 5min, RT
Gibson
1.15µl
0.53µlpSB1C3
+Gibson mix
  • transformation of blunt-end ligation/ gibson (7µl) in E.coli T10
  • transformation of pIG15_105 (1µl) in E.coli T10
  • transformation according to protocol

PCR for fragment 17 with HA-tag (LS)

Primer combination
resulting plasmidprimer 1primer2
pET_1703-HAoIG15_17_HA002oIG15_17_HA004
pET_1704-HAoIG15_17_HA001oIG15_17_HA005
pET_1705-HAoIG15_17_HA001oIG15_17_HA006
pIG15_1704-HAoIG15_17_HA003oIG15_17_HA005
pIG15_1705-HAoIG15_17_HA003oIG15_17_HA006
Q5 PCR (x25µl)
25µlQ5 MM
2.5µlprimer 1
2.5µlprimer 2
0.4µlpIG15_1701
9.6µldH2O
cycling
98°C3min
98°C30s
55°C-65°C30s
72°C1min
72°C10min
4°C–
  • analysis on 1% agarose gel
  • gel-ex:qiagen kit

Inoculation: pIG15_105 and pIG15_805 (LS)

  • 5ml LB-ml
  • 37°C, shaking o/n

2015/08/09

Inoculation: pRIG15_10, pRIG15_18, ligation of pJet_GFP (JN)

  • 3 clones for each
  • 5ml LB-medium (pRIG with Cml, pJet with Amp)
  • 37°C, shaking, until evening

Gibson Assembly (JN)

  • antigen 11 with pSB1C3 backbone to send it in
  • pET_803 backbone with 1703-HA
  • pET_804 backbone with 1704-HA
ingredient pRIG15_11 pET_1703-HA pET_1704-HA
backbone 0.53µl 0.94µl 1.47µl
insert 1.21µl 2.32µl 0.75µl
H2O 3.26µl 1.73µl 2.78µl
  • transformation into E.coli Top10 and plating (pRIG on Cml, pET on Amp)

Mini-Prep of pIG15_105 and pIG15_805 (JN)

  • Zymo Research kit
  • eluted in 30 µl dH2O
  • NanoDrop:
plasmid concentration [ng/µl]
pIG15_105 23.2
pIG15_805 28.8

Digest: pIg15_105, pIG15_804 and pIG15_805 (LS)

  • pIG15_105: HindIII + AflII
  • pIG15_804:BamHI + HindIII
  • pIg15_805: BamHI + HindIII
  • 5µl FD green buffer
  • 1µl of Enzyme 1 and 2 each
  • up to 50µl dH2O
  • incubation at 37°C for approx. 45min
  • analysis on 1% agarose gel: no results for pIG15_105 and pIG15_805
  • gel-ex (qiagen kit): pIg15_804 backbone. 65,8ng/µl

Blunt-end ligation: Antigen 15 (Salmonella) in pJET + Transformation (LS)

Ligation
volume [µl]component
0,6PCR product antigen 15
1µllinearized pJET
10µl2x reaction buffer
1µlT4 DNA ligase
up to 20µldH2O
  • 5min, RT
  • transformation in E.coli T10 (transformation according to protocol)

Mini-prep of pJet_GFP and pRIG15_10 (RE)

  • Zymo-kit
  • pelleted cells were resuspended in LB medium
  • elution in 30 µl dH2O
  • NanoDrop:
plasmid concentration [ng/µl]
pJet_GFP - 1 233.9
pJet_GFP - 2 154.9
pJet_GFP - 3 195.6
pRIG15_10 - 1 39.6
pRIG15_10 - 2 141.5
pRIG15_10 - 3 46.1

Test digest of pJet_GFP and pRIG15_10 (RE)

  • pJet_GFP was digested with BamHI and HindIII (FastDigest; 30 min incubation)
  • pRIG15_10 was digested with EcoRI-HF and PstI-HF (NEB; 1 h incubation)
  • 1 µl of each restriction enzyme
  • 2 µl of the respective buffer
  • 5 µl DNA
  • 11 µl dH2O
  • incubation at 37°C

Inocculation of liquid cultures (RE)

  • pRIG15_11 (LB_cml)
  • pET_1703_HA (LB_amp)
  • pET_1704_HA (LB_amp)
  • 3 clones each

2015/08/10

Mini-Prep of pRIG15_11 (antigen 11 for iGEM Registry), pET_1703-HA and pET_1704-HA (JN)

  • Zymo Research kit
  • eluted in 30 µl dH2O
  • NanoDrop:
plasmid concentration [ng/µl]
pRIG15_11 - 1 132.6
pRIG15_11 - 2 350.3 (strange curve)
pRIG15_11 - 3 93.4
pET_1703-HA - 1 92.7
pET_1703-HA - 2 119.0
pET_1703-HA - 3 89.4
pET_1704-HA - 1 121.3
pET_1704-HA - 2 102.1
pET_1704-HA - 3 122.4

Test digest of all clones above (LS)

  • pRIG15_11. EcoRI + PstI (1h incubation at 37°C)
  • pET1703/4-_HA: BamHI + AflII (30 min incubation at 37°C)
  • 5µl plasmid
  • 1µl of each restriction enzyme
  • 2µl 10x buffer
  • up to 20µl dH2O
  • analysis on 1% agarose gel

2015/08/11

Digest of pJet_GFP 1-3, pET_1703_HA and pET_1704_HA (RE)

  • 1 µl BamHI
  • 1 µl HindIII
  • 5 µl FD Green Buffer
  • 10 µl DNA
  • 33 µl dH2O
  • incubation for 30 min at 37°C

Ligation (LS)

Backbone Insert
concentration [ng/µl]volume [µl] concentration [ng/µl]volume [µl]
pET_1703-HA (BamHI+HindIII)21,72,3Tetanus (antigen 11)58,90,25
GFP17,71,19
pET_1704-HA (BamHI+HindIII)16,03,31Tetanus (antigen 11)58,90,36
GFP17,71,19
pET_804 (HindIII+AflII)4,810,34Halo-tag37,60,56
pIG15_804 (HindIII+AflII16,23,09Halo-tag37,60,93
pET_804 (BamHI+HindIII116,40,43HIV(antigen 1710,81,39
Salmonella (antigen 1570,70,72
Tetanus (antigen 11)58,90,25
HCV (antigen 1012,91,37
GFP17,71,19
pIG15_804 (BamHI and HindIII)65,90,76HIV (antigen 17)10,82,31
Salmonella (antigen 1570,71,2
HCV (antigen 1012,91,94
GFP17,71,98
  • added 2µl T4 DNa Ligase buffer
  • 1µl T4 DNA Ligase
  • up to 20µl dH2O
  • incubation at Rt for 1h
  • Transformation into E.coli T10 (according to protocol)

Retrafo: pET_1703-HA in E.coli T10 (LS)

  • 1µl plasmid
  • transformation according to protocol

Inoculation of pSB1C3_SpyC (JN)

  • 3 colonies were picked and inoculated in 5ml each of LB-medium with Cml

Mini-prep of pJet_15 (JN)

  • ZymoResearch kit
  • eluted in 30µl dH2O
  • concentrations
plasmid concentration [ng/µl]
pJet_15-1 240.9
pJet_15-2 259.2

Digest with BamHI and HindIII of pJet_15 (JN)

ingredient amount [µl]
DNA 5
buffer 5
BamHI 1
HindIII 1
H2O 38
  • 37°C for 30min
  • analysis on 1% agarose gel
Expected fragment sizes: pJet backbone ~3000bp, fragment 15 ~1700bp. The bands were visible at the expected heights and the bands for fragment 15 were cut out

Gel-ex of fragment 15 (JN)

  • fragment 15, digested with BamHI and HindIII, was extracted out of the gel
  • Qiagen gel extraction kit
  • concentrations
fragment 15 -1 16.7 ng/µl
fragment 15 -2 16.6 ng/µl

2015/08/12

Inoculation of many colonies (RE/JN)

  • Gibson and ligation
  • in 5ml LB medium
  • 2 colonies each

Mini-prep of pSB1C3_SpyC_correct (JN)

  • ZymoResearch kit
  • eluted in 30µl dH2O
  • concentrations
plasmid concentration [ng/µl]
pSB1C3_SpyC_correct-1 76.3
pSB1C3_SpyC_correct-2 263.5
pSB1C3_SpyC_correct-2 89.4

Test-digest of pSB1C3_SpyC_correct (JN)

ingredient amount [µl]
DNA 5
EcoRI 0.5
PstI 0.5
buffer 2
dH2O 12
  • 37°C for 1 hour
  • analysis on 1% agarose gel

Mini-prep (JN)

  • Qiagen kit
  • eluted in 30dH2O
  • concentrations
plasmid concentration [ng/µl]
pET_1704-1 129.0
pET_1704-2 94.2
pET_805-1 84.6
pET_805-2 119.7
pET_203-HA-1 68.6
pET_203-HA-2 77.6
pET_1504-1 50.1
pET_1504-2 47.5
pET_1103-HA-2 48.8
pET_1104-HA-1 39.4
pET_1104-HA-2 56.8
pRIG15_10-1 106.8
pRIG15_10-2 145.6

Test digests (RE)

  • pRIG15_10

–> EcoRI + PstI

  • pET_805
  • pIG15_805

–> HindIII + AflII

  • pET_1704
  • pET_203_HA
  • pET_1103_HA
  • pET_1104_HA
  • pET_1504
  • pET_1004
  • pET_1104
  • pET_204
  • pET_204_HA
  • pIG15_1504
  • pIG15_1704
  • pIG15_204

–> BamHI + HindIII

Mini-Prep (LS)

  • qiagen kit
plasmidconcentration [ng/µl]
pET_1104 (1)172,8
pET_1104 (2)116,2
pET_204(1)160,6
pET_204 (2)172,2
pET_204-HA (1)228,6
pET_204-HA (2)146,5
pIG15_805 (1)394,0
pIG15_805 (2)463,2

Sequencing (RE)

  • pET_203_HA - 1
  • pET_204 - 1
  • pET_204_HA - 1
  • pET_1104 - 1
  • pET_1104_HA - 1
  • pET_1704 - 1
  • pIG15_204_HA - 1
  • pIG15_1704 - 1
  • pIG15_805 - 1
  • pRIG15_10 - 2

edit 08/13: all results are positive, except pRIG15_10. pIG15_805 should be sequenced with a reverse primer again to verfiy the whole Halo-tag sequence.

Ligations (RE)

Backbone Insert
new plasmid name c [ng/µl] V [µl] name c [ng/µl] V [µl] dH2O [µl]
pET_1504 pET_804 (BamHI+HindIII) 127.6 0.39 fragment 15 (from pJet) 16.7 2.45 14.16
pET_1004 pET_804 (BamHI+HindIII) 127.6 0.39 fragment 10 26.7 0.59 16.02
pIG15_1504 pIG15_804 (BamHI+HindIII) 65.9 0.76 fragment 15 (from pJet) 16.7 2.45 11.83
pIG15_1004 pIG15_804 (BamHI+HindIII) 65.9 0.76 fragment 10 26.7 1.06 15.18
pET_805 pET_804 (HindIII+AflII) 57.5 0.88 Halo tag 37.6 0.66 15.46
  • 1 µl T4 ligase
  • 2 µl T4 ligase buffer
  • incubated for 1h at RT
  • directly transformed into E. coli TOP10 (pET constructs plated on LB_amp; pIG15 constructs plated on LB_cml)

2015/08/13

Inocculation of liquid cultures (RE)

  • yesterday's ligations
  • 2 single colonies per construct

Test digest: pIG15_1704 (LS)

  • 5µl plasmid
  • 1µl BamHI + HindIII
  • 2µl buffer
  • up to 20µl dH2O
  • analysis on 1% agarose gel

2015/08/14

Inoculation of pIG15_1504/10004, pET_1004/805/1504 (JN)

  • 5ml LB-medium each

Mini-Prep of pIG15_1704-HA (JN/LS)

  • Zymo Research kit
  • eluted in 30µl H2O
  • concentrations
plasmid concentration [ng/µl]
pIG15_1704-HA-1
pIG15_1704-HA-2

Test-Digest pIG15_1704-HA (LS)

Mini-Prep of pIG15_1504/10004, pET_1004/805/1504 (JN)

  • Zymo Research kit
  • eluted in 30µl H2O
  • concentrations
plasmid concentration [ng/µl]
pIG15_1504-1 71.6
pIG15_1504-2 34.8
pIG15_1004-1 79.9
pIG15_1004-2 80.2
pET_1004-1 68.9
pET_1004-2 54.8
pET_805-1 53.0
pET_805-2 58.1
pET_1504-1 63.4
pET_1504-2 60.3

Digest of pIG15_805 (RE)

  • 1 µl BamHI
  • 1 µl HindIII
  • 5 µl FD Green Buffer
  • 5 µl DNA
  • 38 µl dH2O
  • incubation for 30 min at 37°C

Gel-Ex of pIG15_805 backbone (RE)

  • Qiagen-kit
  • eluted in 20 µl dH2O
  • NanoDrop: 39.6 ng/µl

2015/08/15

Ligations (RE)

- Backbone: pIG15_805 (BamHI and HindIII digested; 39.6 ng/µl) 1.25 µl
- Inserts:

  • fragment 10: 0.87 µl
  • fragment 11: 0.9 µl
  • fragment 15: 3.78 µl
  • fragment 17: 2.14 µl
  • GFP: 1.67 µl
  • + ligation control

- Backbone: pET_804 (HindIII and AflII digested) 0.86 µl
- Insert: Halo-tag 0.66 µl

  • incubation for 1 h at RT
  • 5 µl ligation product were directly transformed into E. coli TOP10

Transformation for ProtPur (RE)

  • pET_203_HA into E. coli BL21 pLys
  • pET_1104_HA into E. coli C43
  • pET_1704_HA into E. coli BL21 pLys

Mini-Prep of Retrafo pET_1703-HA (JN)

  • Zymo Research kit
  • eluted in 30µl dH2O
  • concentration: 57.1ng/µl

Test-Digest of pET_805/1004/1504, pIG15_1004/1504 (JN)

ingredient pET_805 all the others
DNA 5µl 5µl
BamHI - 1µl
HindIII 1µl 1µl
AflII 1µl -
buffer 2µl 2µl
DNA 11µl 11µl
  • 30min at 37°C
  • analysis on 1% agarose gel but with unknown ladder –> no reliable statement about digest possible
expected fragment sizes: pET_1004 ~570+5500bp, pET_1504 ~1700+5500bp, pET_805 ~940+5900bp
expected fragment sizes: pIG15_1004 ~570+2400bp, pIG15_1504 ~1700+2400bp

2015/08/16

Digest (RE)

  • analysis on 1% agarose gel
expected bands were visible and cut out pJet_15: ~1700+3000bp pET_1104: 1400+5500bp pET_1704-HA: 540+5500bp
expected bands were visible and cut out pIG15_804: ~400+2400bp pIG15_805: ~400+3300bp pIG15_1704-HA: ~540+2400bp

Gel-ex of fragment 15, backbones pET_1104/1704-HA, pIG15_804/805/1704-HA (JN)

  • Qiagen kit
  • eluted in 20µl dH2O
DNA concentration [ng/µl]
fragment 15 12.5
pET_1104 12.9
pET_1704-HA 9.3
pIG15_804 19.7
pIG15_805 7.2
pIG15_1704-HA 12.8

Ligation of fragment 15 into different backbones, GFP into pIG15_805, Halo into pET_804 (JN)

Backbone Insert
new plasmid name V [µl] name V [µl] dH2O [µl]
pET_1504 pET_1104 (BamHI+HindIII) 3.9 fragment 15 (from pJet) 3.7 9.4
pET_1504-HA pET_1704-HA (BamHI+HindIII) 5.4 fragment 15 (from pJet) 2.8 8.8
pIG15_1504 pIG15_804 (BamHI+HindIII) 2.5 fragment 15 (from pJet) 8.5 6
pIG15_1504-HA pIG15_1704-HA (BamHI+HindIII) 3.9 fragment 15 (from pJet) 8.5 4.6
pIG15_1505 pIG15_805 (BamHI+HindIII) 6.9 fragment 15 (from pJet) 6.9 3.7
pIG15_205 pIG15_805 (BamHI+HindIII) 6.9 GFP (PCR product) 6.9 8.1
pET_805 pET_804 (HindIII+AflII) 0.9 Halo tag 1.2 14.9
  • 1 µl T4 ligase
  • 2 µl T4 ligase buffer
  • incubated for 1h at RT

Transformation (RE)

  • 5 µl of the ligation products and the Gibson Mix into E. coli TOP10
  • pET constructs were plated on LB_amp
  • pIG15 constructs were plated on LB_cml

Mini-prep (RE)

  • Zymo-Kit; elution into 30 µl dH2O
  • pIG15_1005 - 1: 230.9 ng/µl
  • pIG15_1005 - 2: 162.1 ng/µl
  • pIG15_1105 - 1: 121.3 ng/µl
  • pIG15_1105 - 2: 117.8 ng/µl
  • pIG15_1505 - 1: 96.6 ng/µl
  • pIG15_1505 - 2: 139.1 ng/µl

2015/08/17

Test digests (RE)

  • pIG15_1005, pIG15_1105 and pIG15_1505 with BamHI and HindIII (FastDigest)
  • pRIG15_10 with EcoRI and SpeI (NEB)
  • 0.5 µg DNA
  • 1 µl of each RE
  • 2 µl of the respective buffer
  • ad 20 µl dH2O
  • incubation for 30 min (FastDigest) or 1 h (NEB) at 37°C

Seuencing (RE) The following constructs have been send in for sequencing:

  • pIG15_1005 - 2
  • pIG15_1105 - 1
  • pIG15_1505 - 1
  • pIG15_805 - 2 (again with the pET_RP to verfiy the sequence of the Halo-tag)

Re-trafo (RE)

  • of pIG15_1704_HA into E. coli TOP10

Inoculation of pET_1504/1504-HA, pIG15_1504/1504-HA/1505/1705-HA/205 (JN)

  • 2 single colonies were picked of each plate
  • in 5ml LB medium (pET with Amp, pIG15 with Cml)

Resuspension of IDT gBlocks (JN)

  • pOP fragment 1 was eluted in 50µl dH2O, pOP fragment 2/3/4/5 were eluted in 100µl dH2O after short centrifugation
  • according to the protocol delivered by IDT the fragments were incubated at 50°C for 20min and afterwards vortexed and centrifuged again

Ligation of pOP fragments into blunt end pJet (JN)

  • the delivered fragments were cloned into blunt end pJet according to protocol
ingredient amount [µl]
DNA 1
pJet 0.5
T4 buffer 2
T4 ligase 1
dH2O 5.5
  • incubation for 5min at RT
  • directly afterwards trafo with 5 µl according to protocol into E.coli TOP10

Gibson Assembly 1 of pOP (JN)

  • pOP fragments 2+3+4 were assembled via Gibson according to protocol
ingredient amount [µl]
fragment 2 2
fragment 3 2
fragment 4 1
  • trafo with 5µl according to protocol into E.coli TOP10 followed directly after short incubation

Mini-Prep (JN)

  • Zymo Research kit
  • eluted in 30µl dH2O
plasmid concentration [ng/µl]
pET_1504-1 54.8
pET_1504-2 63.3
pET_1504-HA-1 85.5
pET_1504-HA-2 59.3
pIG15_1705-HA-1 64.3
pIG15_1705-HA-2 114.8
pIG15_205-1 140.6
pIG15_205-2 66.9
pIG15_1504-1 77.5
pIG15_1504-2 77.2
pIG15_1504-HA-1 64.1
pIG15_1504-HA-2 92.5
pIG15_1505-1 80.4
pIG15_1505-2 119.2

2015/08/18

Inoculation (JN)

  • pJet_pOP fragments in 5ml LB-Amp
  • Re-trafo pIG15_1704-HA in LB Cml
  • Gibson 1 pOP in LB without antibiotics

Test-digest of pET_1504/1504-HA, pIG15_1504/1504-HA/1505/1705-HA/205 (JN)

  • all prepared the same way with BamHI and HindIII
ingredient amount [µl]
DNA 5
BamHI 1
HindIII 1
FD buffer 2
dH2O 11
  • incubation for 30min at 37°C
  • analysis on 1% agarose gel
expected fragment sizes: pET_1504 ~1700+5500bp pET_1504-HA ~1700+5500bp pIG15_1504 ~1700+2400bp pIG15_1504-HA ~1700+2400bp
expected fragment sizes: pIG15_1504-HA ~1700+2400bp pIG15_1505 ~1700+3200bp pIG15_1705-HA ~540+3200bp pIG15_205 ~740+3200bp

Mini-Prep of pOP Gibson 1 (JN)

  • Qiagen kit
  • eluted in 30µl dH2O
plasmid concentration [ng/µl]
pOP Gibson 1 (1) 61.8
pOP Gibson 1 (2) 41.3
pOP Gibson 1 (3) 40.7
pOP Gibson 1 (4) 20.4
pOP Gibson 1 (5) 6.1
pOP Gibson 1 (6) 20.4
pOP Gibson 1 (7) 46.2
pOP Gibson 1 (8) 68.0
pOP Gibson 1 (9) 61.6
pOP Gibson 1 (10) 63.6
pOP Gibson 1 (11) 61.0

Digest of pOP Gibson 1 (8) and (10) (JN)

ingredient amount (8) [µl] amount (10) [µl]
DNA 14.7 15.7
BamHI 1 1
HindIII 1 1
FD buffer 5 5
dH2O 28.3 27.3
  • 30min at 37°C
  • analysis on 1% agarose gel
expected fragment size: ~3400 bp. Nothing was visible at all –> no positive clones were picked

Digest of fragment 2 + 4 of pOP for 5-fragment Gibson (JN)

ingredient amount [µl]
fragment 44
enzyme 1
FD buffer 5
  • fragment 2 digested with HindIII
  • fragment 4 digested with BamHI
  • 30min at 37°C
  • analysis on 1% agarose gel
expected fragment sizes: ~1300bp for fragment 2, ~800bp for fragment 4. In both cases, strangely two bands were visible. Anyways, the upper bands were considered correct and extracted from the gel.

Gel-ex fragment 2+4 digest (RE)

  • Qiagen-Kit
  • eluted in 15 µl dH2O
  • fragment 2: 6.7 ng/µl
  • fragment 4: 8.1 ng/µl

Gibson assembly for pOP (JN)

  • fragment 1, digested fragment 2, fragment 3, digested fragment 4, fragment 5
fragment amount [µl]
1 0.5
2 2
3 1
4 0.5
5 1
  • DNA added to Gibson Master Mix
  • after 5min of incubation at RT, 5µl were used for a transformation into E.coli TOP10 according to protocol
  • the rest was incubated for 1h at 50°C, 3min at RT, 3min on ice
  • then another transformation was performed
  • both were plated on Amp plates

Mini-Prep of pJet_pOP fragments and pIG15_1704-HA (JN)

  • Zymo Research kit
  • eluted in 30µl dH2O
plasmid concentration [ng/µl]
pJet_pOP1 (1) 132.9
pJet_pOP1 (2) 194.9
pJet_pOP2 (1) 189.0
pJet_pOP2 (2) 193.3
pJet_pOP3 (1) 130.6
pJet_pOP3 (2) 183.9
pJet_pOP4 (1) 205.9
pJet_pOP4 (2) 116.4
pJet_pOP5 (1) 213.8
pJet_pOP5 (2) 91.3
pIG15_1704-HA (1) 83.0
pIG15_1704-HA (2) 138.6

2015/08/19

PCR for pOP Gibson (JN)

As the fragments for the pOP vector were wrongly cloned, there is a antibiotic resistance missing after the first Gibson Assembly. Therefore, colonies cannot be selected for taking up the plasmid. Yesterday we tried an approach with a 5 fragment Gibson Assembly but no colonies were growing on the plate overnight. The next approach is to assemble two and accordingly 3 fragments via PCR. We decided to use fragments 5, 1 and 2 for one reaction, where the antibiotic resistance would be restored. The other reaction should assemble fragments 3 and 4. The PCR reaction mixes were prepared as follows. For the first reactions, the primers pOOP_5fw and pOOP_2rv were used, for the second pOOP_3fw and pOOP_4rv. As template a 1:10 dilution of the prepped pJet constructs (1) from yesterday was prepared. From this dilution 1µl per fragment was used.

ingredient fr. 5,1,2 fr. 3,4
template 3µl 2µl
Phusion 0.5µl 0.5µl
dNTP 1µl 1µl
primer fw 2.5µl 2.5µl
primer rv 2.5µl 2.5µl
DMSO 1.5µl 1.5µl
buffer 10µl 10µl
dH2O 29µl 30µl
Cycling
98°C3min
98°C30s
60°C20s
72°C1min
72°C10 min
4°C–
  • analysis on 1% agarose gel
expected fragment sizes: pOP_521 ~3000bp –> the bright band was excised pOP_34 ~2100bp –> the faint lower band was excised

Gel-ex of pOP_512 and pOP_34 (JN)

  • Qiagen kit
  • eluted in 20µl dH2O
plasmidconcentration [ng/µl]
pOP_5126.3
pOP_344.3

Gibson Assembly of PCR products pOP_512 and pOP_34 for pOP (JN)

  • 1.5µl of pOP_512 and 3.5µl of pOP_34 were added to Gibson Master Mix
  • after 5min of incubation at RT, 5µl were used for a transformation into E.coli TOP10 according to protocol
  • the rest was incubated for 1h at 50°C, 3min at RT, 3min on ice
  • then another transformation was performed
  • both were plated on Amp plates

PCR for SpyCatcher amplification (RE)

  • The SpyCatcher was amplified with two different reverse primers. oIG15_SpyC_02 a HindIII restrcition site, oIG15_SpyC_03 a BamHI site. PCR fragments obtained by 02 are named 1-2, the others 1-3.
Ingredient Volume [µl]
Template (pSB1C3 with SpyC (Munich)) 0.25
Fwd primer (oIG15_SpyC_01) 2.5
Rev primer (oIG15_SpyC_02 or _03) 2.5
dNTPs 1
DMSO 1.5
High GC Buffer 1
Phusion polymerase 0.5
dH2O 31.75

Cycling (25 cycles):

98°C 180 s
98°C 30 s
60°C 20 s
72°C 25 s
72°C 600 s
4°C infinite

Digest of pET_SpyC and pET_SpyC_GST (RE)

  • digests to open the backbone for insertion of the real SpyC sequence (wrong sequence is excised)
  • pET_SpyC was digested with BamHI and HindIII
  • pET_SpyC_GST was digested with BamHI
  • 1 µl of each RE
  • 5 µl FD Green Buffer
  • 1 µg DNA
  • 1 µl Antarctic phosphatase
  • ad 50 µl dH2O

Analysis of the SpyC PCR products and the backbone digests (RE)

  • 1 % agarose gel
  • both amplifications were successful
  • both digests were successful
  • all fragments were extracted from the gel
  • Qiagen-kit
  • elution in 30 µl dH2O
  • NanoDrop:
Fragment Concentration [ng/µl]
SpyC PCR product 1-2 30
SpyC PCR product 1-3 30
pET_SpyC backbone 31
pET_SpyC_GST backbone 14

Digest of the purified SpyCatcher PCR products (RE)

  • 1-2 was digested with BamHI and HindIII
  • 1-3 was digested with BamHI
  • 1 µl of each RE
  • 5 µl FD Green Buffer
  • 17 µl DNA
  • 26 µl dH2O
  • incubated for 30 min at 37°C

Gel-Ex (RE)

  • of the digested SpyC PCR products
  • Qiagen-kit
  • eluted in 20 µl dH2O

Blunt end ligation of the SpyCatcher PCR products (undigested!) into pJET (RE)

  • 1 µl pJet
  • 10 µl reaction buffer
  • 1.5 µl PCR product
  • 1 µl T4 ligase
  • 6.5 µl dH2O
  • incubated for 5 min at RT and subsequently transformed into E. coli TOP10 (plated on LB_amp)

Transformation (RE)

  • pOP 2-fragment Gibson (50°C incubation) after fusion PCR (JN)
  • E. coli TOP10; plated on LB_amp

Ligations (SpyCatcher) (RE)

1.:

  • pET_SpyC (BamHI / HindIII digested): 1.61 µl
  • PCR product 1-2 (same digest): 0.52 µl
  • dH2O: 14.87 µl
  • T4 ligase: 1 µl
  • T4 ligase buffer: 2 µl


2.:

  • pET_SpyC_GST (BamHI digested): 3.33 µl
  • PCR product 1-2 (same digest): 0.42 µl
  • dH2O: 13.25 µl
  • T4 ligase: 1 µl
  • T4 ligase buffer: 2 µl

Incubated at 16°C over night

2015/08/20

Transformation: Ligation pET_Spy-C (LS)

  • 7µl of ligation mix
  • transformation according to protocol
  • incubation on LB-Amp plates at 37°C

Miniprep: pOP and pIG15_1504-HA (LS)

  • qiagen kit
concentrations
pIG15_1504-HA (1)89,1
pIG15_1504-HA (2)159,0
pOP after F-PCR (5min) (1)161,8
pOP after F-PCR (5min) (2)100,8
pOP after F-PCR (5min) (3)216,9

Picked clones from ligation plate (LS)

  • 3x pET_SpyC
  • 3x pET_SpyC-GST
  • incubation in 5ml LB-Amp at 37°C o/n

Pelleting of liquid culure (LS)

  • 5ml liquid culture
  • pJET-Spy-C
  • frozen at -20°C

2015/08/21

Mini-Prep (RE)

  • 6 cultures pelleted yesterday by LS (pJet_SpyC 1-2; pJet_SpyC 1-3)
  • 3 cultures of pET_SpyC (ligation after PCR product digest)
  • 3 cultures of pET_SpyC_GST (ligation after PCR product digest)

(Test)Digest (RE)

  • pET_SpyC_GST and pJet_SpyC 1-3 with BamHI
  • pET_SpyC and pJet_SpyC 1-2 with BamHI and HindIII
  • pOP with PstI and MluI
  • DNA: 1 µg for pJets; 0.5 µg for pET and pOP
  • Buffer: 5 µl CutSmart for pOP; FD Green for the others
  • 1 µl of each RE
  • ad 50 µl dH2O
  • incubation for 1 h (pOP) or 30 min at 37°C

Dilution of primers (LS)

  • biobrick SpyC (GST)
  • Salmonella mutagenesis

PCR: Salmonella mutagenesis (LS)

2x MM
25µlQ5 MM
2,5µlprimer 1
2,5µlprimer2
3µlpIG15_1501
18µldH2O
  • first part: oIG15_1503f + oIG15_1504r
  • second part: oIG15_1505f + oIG15_1506r
  • third part: oIG15_1507f + oIG15_1508r
cycling
98°C5min
98°C10s
60°C30s
72°C40s
72°C10min
4°C–

Gel-ex: Spy-Catcher (LS)

1. Spy-C: BamHI digested 2. Spy-C: BamHI and HindIII digested

  • qiagen kit:
concentration [ng/µl]
1.5,5
2.25,6

Fusions PCR for pOOP fragments (RE)
Fragment 5-1:

Ingredient Volume [µl]
Template (pJet_pOOP_5) 1
Template (pJet_pOOP_1) 1
Fwd primer (oIG15_pOOP5_fw) 2.5
Rev primer (oIG15_pOOP1_rv) 2.5
dNTPs 1
DMSO 1.5
High GC Buffer 10
Phusion polymerase 0.5
dH2O 30

Fragment 2-3-4:

Ingredient Volume [µl]
Template (pJet_pOOP_2) 1
Template (pJet_pOOP_3) 1
Template (pJet_pOOP_4) 1
Fwd primer (oIG15_pOOP2_fw) 2.5
Rev primer (oIG15_pOOP4_rv) 2.5
dNTPs 1
DMSO 1.5
High GC Buffer 10
Phusion polymerase 0.5
dH2O 29

Cycling (25 cycles):

98°C 180 s
98°C 30 s
60°C 20 s
72°C 90 s
72°C 600 s
4°C infinite

Gel-ex: PCR product for Salmonella mutagenesis (LS)

  • qiagen kit
  • eluted in 20µl
concentration [ng/µl
1.part65,6
2.part132,3
3.part115,3

Digest of pIG15_104 to get pSB1C3 backbone (RE)

  • 10 µl DNA
  • 5 µl CutSmart
  • 1 µl XbaI
  • 1 µl PstI-HF
  • 33 µl dH2O
  • incubation for 1 h at 37°C

Ligation: Spy-Catcher (LS)

  • backbone: pET_SpyC(old) BamHI or BamHI+HindIII digested
  • insert: gel-ex of SpyC (GST) fragment
Ligation mix
pET_SpyC pET_SpyC-GST
backbone3,471,58
insert1,640,35
buffer22
T4 Ligase0,50,5
dH2O1215
  • 1h, RT

Transformation: Ligation of pET_SpyC (-GST) into E.coli T10 (LS)

  • 10µl of ligation mix
  • transformation according to protocol
  • plated on LB-Amp
  • incubation at 37°C o/n

2015/08/22

Picking colonies from pET_SpyC (-GST) Ligation (LS)

  • 3x 5ml LB-Amp each
  • incubation at37°C

Gel-ex: pSB1C3 XbaI and PstI digested (LS)

  • qiagen kit
  • concentration (20µl): 14,3ng/µl

Fusion-PCR: pOOP (LS)

1.PCR frg.1 + frg.5 frg.2 + frg.3
frg.13µlfrg.23µl
frg.53µlfrg.33µl
Phusion Polymerase0,5
high GC buffer10µl
dNTPS2µl
DMSO2µl
dH2O30µl
cycling
frg. 1+ frg.5 frg.2 + frg.3
98°C5min98°C5min
98°C1min98°C1min
72°C30s78°C30s
72°C45s72°C1min 15s
72°C5min72°C5min
4°C –
addition of frg. 4
– 98°C5min
– 98°C1min
– 78°C30s
– 72°C2min
– 72°C5min
– 4°C –
addition of primers
primer 1 rev2,5mlprimer 4 rev2,5µl
primer 5 fw2,5µlprimer 2fw2,5µl
98°C 5min
98°C 1min
60°C 30s
72°C 1/2min
72°C 5min
4°C –
  • analysis on 1%agarose gel
  • fusion of frg. 1+5 worked, fusion of frg. 2+3+4 did not work

Gibson: Salmonella mutagenesis (LS)

fragmentconcentration [ng/µl]volume [µl]
pSB1C3 (XbaI+PstI14,32,52
fragment 165,50,22
fragment 2132,30,44
fragment 3115,30,83
  • added 15µl Gibson mix
  • incubation at RT, 5 min
  • transformation in E.coli T10
  • plated on LB-Cml

Gel-ex of fusion PCR product 5-1 (RE)

  • qiagen kit
  • eluted in 20µl dH2O
  • NanoDrop: 11.8ng/µl

2015/08/23

Repetition of Fusion PCR (RE)

  • assembly of pOP fragments 2 and 3
Ingredient Volume [µl]
Fragment 2 2
Fragment 3 2
dNTPs 2
DMSO 3
High GC Buffer 10
Phusion polymerase 0.5
dH2O 30.5

Cycling (4 cycles):

98°C 180 s
98°C 30 s
75°C 20 s
72°C 120 s
72°C 300 s
4°C infinite

Addition of Primers oIG15_pOOP2_fw and oIG15_pOOP3_rv (2.5 µl each)

Cycling (20 cycles):

98°C 180 s
98°C 30 s
60°C 20 s
72°C 120 s
72°C 300 s
4°C infinite

PCR clean-up of fragment 2-3 (RE)

  • Qiagen-kit
  • elution in 20 µl dH2O
  • NanoDrop: 7.2 µl

Fusion PCR of frg. 2-3 and 4 (RE)

^ Ingredient ^ Volume [µl] ^

Fragment 2-3 2
Fragment 4 2
dNTPs 2
DMSO 3
High GC Buffer 10
Phusion polymerase 0.5
dH2O 30.5

Cycling (4 cycles):

98°C 180 s
98°C 30 s
75°C 20 s
72°C 120 s
72°C 300 s
4°C infinite

Addition of Primers oIG15_pOOP2_fw and oIG15_pOOP4_rv (2.5 µl each)

Cycling (20 cycles):

98°C 180 s
98°C 30 s
60°C 20 s
72°C 120 s
72°C 300 s
4°C infinite

Mini-Prep (RE)

  • pET_SpyC (3x; ligation with pJet digest product)
  • pET_SpyC_GST (3x; ligation with pJet digest product)
  • Zymo-kit
  • elution in 30 µl dH2O
Construct Concentration [ng/µl]
pET_SpyC-1 33.1
pET_SpyC-2 28.3
pET_SpyC-3 23.0
pET_SpyC_GST-1 30.1
pET_SpyC_GST-2 24.6
pET_SpyC_GST-3 29.8

Test-Digest of pET_SpyC and pET_SpyC-GST (RE)

  • 8 µl DNA
  • 2 µl FD Green Buffer
  • 1 µl BamHI
  • (1 µl HindIII - only for pET_SpyC)
  • ad 20 µl dH2O
  • incubation for 30 min at 37°C

Repetition of Fusion PCR (LS)

  • same components/cycling as last time
  • 2×25µl
Ingredient Volume [µl]
Fragment 2 2
Fragment 3 2
dNTPs 2
DMSO 2
High GC Buffer 10
Phusion polymerase 0.5
dH2O 30

Cycling (4 cycles):

98°C 180 s
98°C 30 s
75°C 20 s
72°C 120 s
72°C 300 s
4°C infinite

Addition of Primers oIG15_pOOP2_fw and oIG15_pOOP3_rv (1µl each)

Cycling (20 cycles):

98°C 180 s
98°C 30 s
60°C 20 s
72°C 120 s
72°C 300 s
4°C infinite
  • analysis on 1% agarose gel
  • correct band at ~2700bp visible
  • gel-ex (qiagen kit): 20µl –>18.5ng/µl
  • second PCR: fusion of frg. 4 to frg.2-3 (2×25µl)
Ingredient Volume [µl]
Fragment 2-3 2
Fragment 4 2
dNTPs 2
DMSO 3
High GC Buffer 10
Phusion polymerase 0.5
dH2O 30.5

Cycling (4 cycles):

98°C 180 s
98°C 30 s
75°C 20 s
72°C 120 s
72°C 300 s
4°C infinite

Addition of Primers oIG15_pOOP2_fw and oIG15_pOOP4_rv (1µl µl each)

Cycling (20 cycles):

98°C 180 s
98°C 30 s
60°C 20 s
72°C 120 s
72°C 300 s
4°C infinite
  • analysis on 1% agarose gel
  • correct band at ~3400bp visible
  • excision/ frozen at -20°C

Picking clones from Gibson: Salmonella mutagenesis (LS)

2015/08/24

Mini-prep of pRIG15_15 (RE)

  • Zymo-Kit
  • eluted in 30 µl dH2O
  • pRIG15_15 - 1: 54.9 ng/µl
  • pRIG15_15 - 2: 47.2 ng/µl
  • pRIG15_15 - 3: 37.8 ng/µl

Gel-Ex of Fusion PCR product 2-3-4 (RE)

  • Qiagen-Kit
  • eluted in 20 µl dH2O
  • NanoDrop: 7.4 ng/µl

Test digest of pRIG15_15 (RE)

  • 7 µl DNA
  • 1 µl EcoRI-HF
  • 1 µl SpeI
  • 2 µl CutSmart
  • 9 µl dH2O
  • incubation for 1 h at 37°C

2015/08/25

Mini-Prep of pOOP (3x) (RE)

2015/08/26

Colony PCR (LS)

  • 12 colonies from ligation plate + control (pSB1C3 with Spy-Catcher from munich)
  • dipped sterile filter tip in colony, put some of the colony in PCR tube, streaked the rest of th colony on new LB-Amp plate
PCR Master Mix
32,5µlDream Taq buffer
32,5µldNTPs
13µloIG15_SpyC-01
13µloIG15_SpyC-02
4µl Dream Taq
162,5µldH2O
cycle (20x)
95°C10min
95°C30s
60°C30s
72°C40s
72°C5min
4°C–
  • analysis on 1%agarose gel

PCR for Salmonella antibody (JN)

Q5 2x Master Mix25µl
oIG15_b11012,5µl
oIG15_b11022,5µl
dH2O19.8µl
pIG15_13020.2µl
  • 2×25µl
cycling (20x)
98°C5min
98°C30s
60°C30s
72°C30s
72°C10min
4°C–
  • analysis on 1% agarose gel
  • no bands were visible at all

Repetition: PCR for Salmonella antibody (LS)

Q5 Master Mix
Q5 2x Master Mix25µl
oIG15_1303f2,5µl
oIG15_1304r2,5µl
dH2O18µl
pIG15_13012µl
  • 2×25µl
cycling (20x)
98°C3min
98°C10s
60°C30s
72°C40s
72°C10min
4°C–
  • analysis on 1% agarose gel
  • correct bands visible: gel-ex (qiagen kit)

Gibson assembly for pRIG15_13 (LS)

  • 2,13 µl pSB1C3 (PstI+XbaI)
  • 0,74µl frg. 13
  • added to Gibson mix
  • 5 min, RT
  • transformation into E.coli Top 10

2015/08/27

Repetition of transformation of E.coli Top 10 with Gibson mix for pRIG15_13 (LS)

2015/08/28

Miniprep of pET_SpyC 8-12 (RE)

2015/08/29

Picked one clone from Gibson plate for pRIG15_13 (LS)

Repetition of PCR for frg. 13 (LS)

  • same as last tim
  • analysis on 1% agarose gel: correct
  • gel-ex (qiagen): 138,3ng/µl

Miniprep: pRIG15_13 (1) (LS)

  • 5ml
  • Zymo kit: 216,5 ng/µl

Test Digest: pRIG15_13(1) with EcoRI HF and SpeI HF (LS)

5µlpRIG15_13 (1)
0,5µlEcoRI HF
0,5µlSpeI HF
14µldH2O
  • 37°C, 1h
  • analysis on 1% agarose gel: not convincing

Repetition of Gibson assembly for pRIG15_13 (LS)

  • 2,03µl pSB1C3 (XbaI + PstI)
  • 0,60µl frg. 13
  • added Gibson MasterMix
  • 5min, RT
  • transformation into E.coli Top 10

Transformation: pOP (2) + (LS)

  • 2µl plasmid
  • transformation according to protocol

2015/08/30

Digest of pOP, BBa_I712669 and BBa_K592009 (JN)

DNA5µl
EcoRI1µl
Spe1µl
CutSmart5µl
dH2O38µl
  • analysis on 1% agarose gel, correct fragments for pOP and BBa_I712669 were cut out of the gel

Gel-ex of pOP and BBa_I712669 (JN)

  • Qiagen kit
  • eluted in 20µl dH2O
pOP20.3ng/µl
BBa_I7126692.6ng/µl

Ligation of pOP and BBa_I712669 (JN)

pOP backbone2.46µl
BBa_I712669 insert16.15µl
T4 buffer2µl
T4 ligase1µl
  • 1h at RT

Trafo of ligation product (10µl) into E.coli TOP10 (JN)

  • plated on LB-Amp plates