Difference between revisions of "Team:NTNU Trondheim/Experiments"

1. Separate the PCR product from circular DNA
2. Isolate the linear DNA (pgRNA with anti-luxS from the gel
3. Transform the linear DNA into competent cells
4. InterLab study - transformation of plasmids to competent cells

1. Thaw the competent cells on ice (10 min), and pre-chill the eppendorf tubes.
2. Resuspend the DNA in the wells (provided by iGEM HQ) with dH₂O (10 μL).
3. Add competent cells (50 μL) to the eppendorf tubes.
4. Add resuspended DNA (1 μL) to the Eppendorf tubes.
5. Incubate on ice for 25 min
6. Heat shock the cells for 45 s at 42℃ in water bath
7. Incubate on ice for 5 min.
8. Add LB-medium (950μL) to the tubes
9. Incubate for 1h at 37℃ with shacker
10. Pipette each sample (100 μL) to agar plate with CM
11. Centrifuge the samples for 3 min at 6800g, discard supernatant (800 μL) and resuspend the pellet with the remaining supernatant
12. Pipette each sample (100 μL) to agar plate with CM
13. Incubate overnight at 37℃.

1. Inoculate colonies of successful transformed competent cells
2. InterLab study - transformation of plasmids to competent cells

1. InterLab - transformation of plasmids into competent cells
2. Verification of succsesful insertion of anti-luxS in pgRNA(2)

1. Transform both pdCas9 and pgRNA with anti-luxS into competent cells
2. InterLab study - inoculate colonies in LB-medium

1. Inoculate successful double transformed cells (probably carrying pdCas9 and pgRNA with anti-luxS)
2. InterLab study - measure absorbance and the fluorescence of each cell cultures

1. A colony from each agar plates with AMP and CM (made from day 13 – 05. July 2018) was picked and inoculated in LB medium (20 mL) with AMP (25 μL) and CM (25 μL).
2. The cell cultures were incubated at 37℃ with shaker.

Goal:

Procedure:

• 7.1 μL Plasmids
• 0.5 μL PstI
• 0.5 μL BamHI-HF
• 2 μL NEBuffer 1.1
• 10.4 μL ddH2O

Results:

Goal : InterLab Study: Revive bacteria glycerol stock

• Temperature: 37,0°C, varying from 36,5°C to 37,5°C
• Kinetic cycles: 750
• Gain: 40
• Z position: 18055 µM
• Shaking: 300 s
• Orbital shaking amplitude: 3 mm

1. Measure biofilm after 48 hrs.
2. Prepare RRVT-Biobrick and biobrick backbone
3. Ligate and transform RRvT- biobrick and biobrick backbone into DH5alpha cells.

1. Ligate plasmid backbone and RRvT-plasmid and transform into cells.
2. Due to the lack of colonies from yesterdays transformation the ligation of plasmid backbone and RRvT-plasmid and transformation into E.Coli Dh5α cells was redone.

Preparations of plasmid backbone and RRvT-biobrick:


Made enzyme master mix for plasmid backbone by adding 5μL NEB buffer 2, 0.5 μL EcoRI-HF, 0.5 μL PstI, 0.5 μL BSA and 18.5 μL dH₂O to an Eppendorf tube.

Made enzyme master mix for RRvT-biobrick by adding 5μL NEB buffer 2, 0.5μL EcoRI-HF, 0.5 μL PstI and 19 μL dH₂O to an Eppendorf tube. Incubated mix for 20 min at 50℃.

Digested Plasmid backbone by adding 4 μL linearized backbone (25 ng/μL for 100 ng) and 4 μL of enzyme master mix for plasmid backbone.

Digested RRvT-biobrick by adding 4 μL of the biobrick and 4 μL of the enzyme master mix for RRvT-biobrick. Digested both reactions at 37℃ for 90 min and did heat kill at 80℃ for 20 min.



Ligation:


Added 2 μL of digested plasmid backbone.

Added 2 μL of digested RRvT-biobrick.

Added 1 μL T4 DNA ligase buffer.

Added 0.5 μL of T4 DNA ligase.

Added water to 10 μL.

Ligated at 16℃ for30min. Did heat kill at 80℃ for 20 min.




Transformed E.Coli Dh5α cells with 1-2 μL of product following the protocol for transformation.

Inoculated .. plates and let them incubate at 37℃ to the next day.

1. Inoculate successful transformed cells into LB medium with CM.
2. Revive TG1 and DH5α cells in LB medium with AMP, CM and 0% glucose.

Preparation for biobrick (RRvT) measurement:

Successful transformed cell colonies from yesterday's incubation were inoculated into LB - medium with CM and incubated at 37°C with shaking.

Preparation for cell cultures for biofilm assay:

TG1 and DH5α cells with pgRNA and pdCas9 were revived in LB medium with AMP, CM and 0% glucose. The cell cultures were incubated at 37°C with shaking.

• Dilute the overnight cultures for biofilm assay.
• Do Crystal Violet assay after 3 h, 5 h and 8 h of incubation of a 96-well plate.

The media for biofilm assay were made by adding the following ingredients:

• LB 0.4% glucose, TET: 10 mL LB, 10µL AMP, 10µL CM, 0.2 mL 20% Glucose, 19.7µL 0.5mg/mL TET
• LB 0.8% glucose, TET: 10 mL LB, 10µL AMP, 10µL CM, 0.4 mL 20% Glucose, 20µL 0.5mg/mL TET
• LB 0.4% glucose: 10 mL LB, 10µL AMP, 10µL CM, 0.2 mL 20% Glucose
• LB 0.8% glucose: 10 mL LB, 10µL AMP, 10µL CM, 0.4 mL 20% Glucose
• M63B1 0.4% glucose, TET: 10 mL M63B1, 10µL AMP, 10µL CM, 10 µL 1M MgSO₄*7H₂O, 0.2 mL 20% Glucose, 19.7 µL TET
• M63B1 0.8% glucose, TET: 10 mL M63B1, 10µL AMP, 10µL CM, 10 µL 1M MgSO₄*7H₂O, 0.4 mL 20% Glucose, 20 µL TET
• M63B1 0.4% glucose: 10 mL M63B1, 10µL AMP, 10µL CM, 10 µL 1M MgSO₄*7H₂O, 0.2 mL 20% Glucose
• M63B1 0.8% glucose: 10 mL M63B1, 10µL AMP, 10µL CM, 10 µL 1M MgSO₄*7H₂O, 0.4 mL 20% Glucose

Biofilm assay:

• Pipette 3-4 mL overnight cultures to sterile tubes (total 16 tubes).
• Centrifuge the cultures for 10 min at 2000 rpm at 9°C.
• Remove the supernatant.
• Add 3-4 mL media (LB/ M63B1, with 0.4%/ 0.8% glucose, with/ without TET) to 2 tubes each.
• Resuspend/ vortex the cultures, and measure OD 600.
• Dilute the cultures until target OD 600 = 0.1 and store the cells on ice until they are added to the wells.
• Resuspend/ vortex the cultures, add 100 µL culture to each well on the plate.
• Seal the top of the plate with parafilm, and incubate the plate at 37°C.
• Do CV assay after 3 h, 5 h, 8 h, 24 h and 48 h incubation.

Redo CV assay from 17th August to check the validity of previous results.

Perform Bactiter-Glo Assay parallell to CV Assay (3h, 5h, 8h, 24h, 30h) to examine the amount of living cells in biofilm.

Crystal Violet Assay: Same procedure as from 17.08.2018.

Bactiter-Glo Assay

The results and measurement settings can be found in the attached files.

Make LB medium and 10x v2 salts for Vibrio natrigens

Amplify and introduce site directed mutagenesis in pdCas9

LB - medium

10x v2 salts:

• 11.935 g NaCl (204 mM)
• 0.3134 g KCl (4.2 mM)
• 4.710 g MgCl2*6H2O (23.14 mM)
• 1 L ddH2O

Site directed mutagenesis:

Goal: Introduce site directed mutagenesis in pdCas9 Amplify RRvT and pSB1C3 via PCR

Procedure: Site directed mutagenesis in dCas9: pdCas9 was amplified via gradient PCR, where the annealing temperatures were 57.3 ℃, 59.3 ℃, 61.1 ℃ and 64.1℃ with an elongation time for 5 min. The samples were stored in the fridge after the PCR was finished. Amplification of RRvT and pSB1C3: RRvT and pSB1C3 fragments were amplified by running the samples (6 µL FW primer, 6 µL REV primer, 1 µL template, 12.5 µL Takara Hi-Fi PCR premix) on PCR with the following settings: annealing temperature 37 ℃ for 10 s, elongation temperature 72 ℃ for 1 min. The samples were stored in the fridge after the PCR was finished.

Separate the PCR products of RRvT and pSB1C3 on gel, and miniprep the desired fragments on the gel. Incubate Vibrio natreigens (V. natriegens). Do another round of site directed mutagenesis on pdCas9 via PCR.

5 μL loading dye was added to the PCR products (25.5 μL). The PCR products were separated on Gel green (90 V, 40 min). The desired fragments were cut out from the gel and collected in eppendorf tubes Gel digestion and DNA isolation of RRvT and fragment of pSB1C3: The PCR products with the desired length on the gel was isolated by following after the same protocol from 02.07.2018.

Sample of V. natriegens sent by the iGEM team from Marburg, was inoculated and incubated by following after the protocol provided by the team.

PCR mix with pdCas9 was prepared after following the same protocol from 29.06.2018. Two samples were set on two different programs: 3 step PCR: DNA denaturation temperature at 98℃, primer annealing temperature at 55 ℃ for 10 s, elongation temperature at 72 ℃ for 7 min. 2 step PCR: same conditions as 3 step PCR without the primer annealing step.

• Measure the growth curve of V. natrigens
• Gel purification of RRvT
• Separte the PCR products of pdCas9 on gel

Growth curve of V. natrigens:

The experiment failed due to dilution in the flasks and not in the cuvettes

Gel purification of RRvT:

The PCR product of RRvT was purified on gel, and the DNA was isolated after following the same protocol from 02.07.2018.

Gel separation of pdCas9 PCR product:

The PCR products of pdCas9 were separated on both gel red and gel green for imaging and for isolation of the desired fragments by following the same protocol from 02.07.2018.

See results page for results

Goal:

Amplify RRvT and introduce SDM in pdCas9 via PCR

Procedure:

RRvT and introduction of pdCas9 was necessary since the concentration of the products isolated from gel on 08.09.2018 were too low.

Amplification of RRvT:

RRvT was amplified via PCR with an annealing temperature 55 ℃ for 10 s and elongation temperature at 72 ℃ for 1 min.

Introduce SDM in pdCas9:

Site directed mutagenesis was introduced via PCR with an annealing temperature at 55 ℃ for 10 s and elongation temperature 72 ℃ for 7 min.

The products were stored in the fridge.

Goal:

Gel purification of PCR products Gel digestion and isolation of desired DNA fragments Assemble RRvT and pSB1C3 via Gibson assembly Transform pdCas9 and the assembled RRvT into competent cells

Gel purification: The PCR products were separated on gel green RRvT: 25.5 µL DNA, 5.05 µL loading dye pdCas9: 25 µL DNA, 5 µL loading dye

Gel digestion and DNA isolation:

The desired fragments (RRvT: approx. 2000 bp, pdCas9: approx. 6000 – 7000 bp) were cut out from the gel. The gel was digested by following after the protocol from 02.07.18.

Transformation of SDM pdCas9 into competent cells:

6 µL DNA was transformed into competent cells by following after the protocol from 25.06.18.

Gibson assembly of RRvT and pSB1C3:

The fragments were assembled together by following the protocol provided from the kit 2 µL RRvT, 8 µL pSB1C3 (0.03 – 0.2 pmol fragments), 10 µL assembly master mix was incubated in a thermocycler at 50C for 15 min. The sample was stored on ice for transformation.

Transformation of assembled RRvT and pSB1C3 into competent cells:

2 µL Gibson assembly product was transformed into competent cells by following after the protocol from 25.06.2018.

Goal:

• PCR colony screening of RRvT gene
• Isolate pdCas9 from cell cultures
• Verify successful SDM on pdCas9 by restriction digest the plasmid

Procedure:

PCR colony screening:

None of the colonies were red/ pink coloured like the colonies with RFP.

PCR colony screening was done to test whether assembly of RRvT and pSB1C3 fragments was successful

PCR mix was prepared after the following protocol: 5 µL Takara Hi-Fi PCR premix, 1 µL ddH2O, 6 µL RRvT FWD primer, 6 µL RRvT REV primer 8 different colonies were chosen and transferred to a new agar plate with CM, before the colony was transferred to a PCR tube with PCR mix. The samples ran on a PCR machine with the same settings from day 28 – 06. 09. 2018.

Plasmid isolation:

pdCas9 with SDM was isolated from three cell replicates by following the protocol from day 3 – 22. 06. 2018.

Restriction digest:

Introduction of SDM in pdCas9 was verified by adding restriction enzyme which originally recognize and cut at a specific site in the plasmid. EcoRI has two restriction sites in pdCas9 before any mutations.

Mix 2 µL DNA (pdCas9 SDM), 2 µL Cut smart buffer, 15.5 µL ddH2O, 0.5 µL EcoRI Hi-Fi Spin down the solutions Incubate overnight at 37 ℃

Goal:

• Separate the DNA fragments of pdCas9 SDM after restriction digest
• Visualize the products from PCR colony screening on gel
• Amplify the different fragments of pdCas9 for Gibson assembly
• Inoculate colonies with RRvT in LB medium with CM

Procedure:

Gel electrophoresis:

Both pdCas9 fragments obtained from restriction digest, and the products from PCR colony screening of RRvT were separated and visualized on gel by mixing the DNA with loading dye

RRvT: 3 µL DNA, 2 µL dye, 7 µL ddH2O

pdCas9: add 4 µL loading dye to each samples

The DNA fragments were separated on gel red.

Preparation for Gibson assembly of pdCas9:

Segments for Gibson assembly were obtained by amplify the desired fragments with designed primer pairs via PCR.

Primers for Gibson assembly (ordered from Sigma Aldrich), were resuspended with ddH2O and diluted to 1 µ Dilute pdCas9 SDM – 2 µL DNA (PC1), 8 µL ddH2O (to obtain <26 ng/µL) PCR samples (1 µL diluted template (pdCas9 SDM, <26 ng/μL), 6 µL FWD primer, 6 µL REV primer, 12.5 µL Takara HI-FI PCR premix) were incubated in PCR machine with the same settings from day 29 – 07. 09. 2018.

Inoculate cell colonies with RRvT:

Colonies with RRvT was inoculated in LB medium with CM from the agar plate, and the cell cultures were incubated overnight at 37 ℃ with shaking.

Cells were inoculated from the following agar plate. Cells with RFP were revived in LB medium with CM.

Goal:

• Gel purification of the PCR product of pdCas9 fragments
• Gel digestion and isolation of the pdCas9 fragments
• Gibson assemble the pdCas9 fragments
• Transformation of Gibson assembled product into competent cells
• Test round of RRvT by measuring the fluorescence

Procedure:

Gel purification of pdCas9 fragments:

25.5 µL PCR products were mixed with 5.05 µL loading dye, and separated on gel by following after the same procedure from 22.06.2018.

Gel digest and DNA isolation:

After gel electrophoresis, the desired pdCas9 fragments were cut out from the gel. The gel was digested and the DNA fragments were isolated by conducting the same protocol from 02.07.2018.

Gibson assembly of the pdCas9 fragments:

The pdCas9 fragments, isolated from the gel, were assembled after the following protocol

Mix 0.60 µL G1 fragment, 3.49 µL G2 fragment, 3.67 µL G3 fragment, 2.24 µL G4 fragment (the volumes were calculated by our instructor) with 10 µL NEBuilder HiFi DNA Assembly Master mix, and the sample was incubated at 50 ℃ for 1 hour.

The thermocycler was switched off without notice, so the samples stayed at room temperature for an hour before the thermocycler was turned on again…

Transformation of Gibson assembly product:

2 µL Gibson assembly product was transformed into DH5α cells by following after the procedure from 25. 06. 2018

Measure the fluorescence of RRvT:

The overnight cultures with RRvT, RFP and a negative control was diluted until target absorbance Abs600 = 0.1 Four replicates of each culture (100 µL) were added to a 96 well microtiter plate. The Absorbance and the fluorescence were measured with the following settings: 150 cycles with 5 min interval Emission wavelength: 607 nm Exitation wavelength: 584 nm Temperature: 37 ℃ Gain: 22

Results:

Gel purification of pdCas9 fragments for Gibson assembly:

The order of the different fragments from left to right: ladder, G1, G2, G3 and G4. The fragments for Gibson assembly should have the length of 641 bp, 481 bp, 2917 bp and 1468 bp, respectively.

Fluorescence of RRvT:

The values of the fluorescence were too low when the samples were measured with a gain of 22. The liquid in the wells has been evaporated during the measurement.

Goal:

• Inoculate successful transformed cells
• Restreak V. natriegens on agar plates
• Amplify gRNA and dCas9 (without mutation) sequence for insertion into LITMUS28i vector

Procedure:

Colony picking:

Successful transformed cells (probably with correct Gibson Assembly product of pdCas9) were inoculated to LB medium with CM. The cell cultures were incubated at 37 ℃ overnight with shaking.

Re-streak Vibrio natriegens on agar plates:

Vibrio natriegens was inoculated and was stoke on LA with v2 salt aseptically. The agar plates were incubated at room temperature.

Amplification of gRNA and dCas9:

The primer pairs of gRNA and dCas9 (ordered from Sigma Aldrich) were diluted with ddH2O, so the concentration of the primers was 100 µM The primers were further diluted until target concentration = 1 µM PCR mix were prepared after the following recipe: pgRNA (0.5 µL, 37.2 ng/ µL), 6 µL FWD primer, 6 µL REV primer, 12.5 µL Takara HiFi PCR premix. pdCas9 (0.5 µL, 53.4 ng/ µL), 6 µL FWD primer, 6 µL REV primer, 12.5 µL Takara HiFi PCR premix. The gRNA sequence was amplified by running the sample with a PCR machine with an annealing temperature 55 ℃ for 10 s, and an elongation temperature 72 ℃ for 1 min. The dCas9 sequence was amplified with an annealing temperature 55 ℃ for 10 s, and an elongation temperature 72 ℃ for 7 min.

Goal:

• Isolate Gibson assembled pdCas9 from overnight cultures
• Test digest the Gibson assembled pdCas9
• Make glycerol stock of cells with Gibson assembled pdCas9 (pdCas9 mutated)
• Gel separate the PCR products of gRNA and dCas9 (for insertion into LITMUS28i vector)
• Gel digest and isolate the gRNA and dCas9 fragments (for insertion into LITMUS28i vector)
• Inoculate natriegens in LB medium with v2 salts

Procedure:

Isolation of Gibson assembled pdCas9:

Overnight cultures were diluted until OD600 ≈9 pdCas9 was isolated from the cells by following after the miniprep protocol from 22.06.2018.

Test digest Gibson assembled pdCas9:

The enzymes EcoRI and XbaI were selected to verify whether the Gibson assembly of pdCas9 was successful or not. For 0.5 µL enzyme, 250 ng DNA is required. The different replicates were prepared by following recipe:

PC1: 5 µL DNA, 2 µL Buffer, 0.5 µL EcoRI, 0.5 µL XbaI, 12 µL ddH2O

PC2: 7 µL DNA, 2 µL Buffer, 0.5 µL EcoRI, 0.5 µL XbaI, 10 µL ddH2O

PC3: 12 µL DNA, 2 µL Buffer, 0.5 µL EcoRI, 0.5 µL XbaI, 5 µL ddH2O

The samples were incubated at 37 ℃ for 3h, before gel separation.

Glycerol stock of Gibson assembled pdCas9 (pdCas9 mutated):

DH5α cells with the Gibson assembled pdCas9 were stored in glycerol stock at -80 ℃ by following after the procedure from day 28.06.2018.

Gel separation of gRNA and dCas9 (not mutated) fragments (for insertion into LITMUS28i vector):

5 µL loading dye was added to each sample. The samples ran on gel green at 90 V for 50 min.

Gel digest and DNA isolation:

The gRNA and dCas9 fragments were isolated from the gel by conducting the same protocol from 02.07.2018.

Incoulation of V. natriegens:

Coloies of V. natriegens were inoculated into LB medium with v2 salt. The cell cultures were incubated at 37 ℃ overnight with shaking.

Goal:

• Transform the part BBa_R0040 (plasmid with TetR) into competent cells
• Make glycerol stocks of natriegens

Procedure:

Transformation of BBa_R004:

The plasmid was resuspended with 10 µL ddH2O in the well of the plate (provided by iGEM).

10 µL DNA was transformed into DH5α by following after the protocol from 25.06.2018.

Glycerol stock of Vibrio natriegens:

Overnight cultures of V. natriegens was stored in glyrecol stock at -80 ℃.

Goal:

• Amplification of LITMUS28i sequence
• Inoculate successful transformed cells with part BBa_R0040 (plasmid with TetR)
• Revive cells with RRvT and RFP

Procedure:

Amplification of LITMUS28i sequence:

• Designed primers (bought from Sigma Aldrich) were resuspended and diluted to 1 μM.
• The LITMUS28i vector (sponsored by NEB) was diluted to 25 ng/μ
• The diluted primer pair (6 μL of each primer) for LITMUS28i was mixed with the diluted LITMUS28i vector (1 μL) and Takara HiFi PCR premix (12.5 μL).
• The LITMUS 28i sequence was amplified after running in a PCR machine with an annealing temperature of 55 ℃ for 10 s and elongation temperature 72 ℃ for 2 min.

Inoculation of successful transformed cells:

Successful transformed cells with TetR was inoculated into LB medium with CM. The cell culture was incubated overnight at 37 ℃ with shaking.

Revive cells with RRvT and RFP:

Cells stored at -80 ℃ were revived by inoculation into LB medium with CM and incubated overnight at 37 ℃ with shaker.

Goal:

• Measure the fluorescence of RRvT, RFP and TetR
• Separate LITMUS28i sequence on gel
• Gel digest and isolate LITMUS28i segment
• Gibson assemble LITMUS28i sequence, dCas9 and gRNA with anti-luxS

Procedure:

Fluorescence measurement:

• The overnight cell cultures with RRvT, RFP and TetR were diluted to target Abs600 = 0,2.
• 100 μL of each cell cultures were pipetted to a 96 well plate with 4 replicates. The cellcultres were surrounded with LB medium with CM to reduce evaporation of the cell cultures in the wells. The plate was covered with a lid and the plate was sealed with parafilm.
• The absorbance and the fluorescence were measured with a five-minute interval for 150 cycles with a target temperature 37 ℃. The gain was set to 40, wave length of absorbance was set to 588 nm, while the excitation and the emission wavelength were set to 584 nm and 607 nm, respectively.

Gel electrophoresis:

05 μL loading dye was added to the PCR product of LITMUS28i vector (25 μL). The PCR product was separated on gel green, and the desired sequence was cut out from the gel.

Gel digest and DNA isolation:

The desired DNA sequence was isolated by digesting the gel by conducting the same procedure from 02.07.2018.

Gibson assembly:

LITMUS28i, dCas9 and gRNA with anti-luxS were assembled via Gibson assembly. The amount (pmol) required of the different fragments were calculated by the calculator provided by the homepage of NEB, and by following after the protocol of NEBuilder HiFi DNA Assembly

LITMUS28i sequence (2295 bp, 68 ng/μL): 0.8 μL gRNA (538 bp, 43 ng/μL): 0.59 μL dCas9 (5025 bp, 52 ng/ μL): 4.92 μL NEBuilder HiFi DNA assembly master mix: 10 μL ddH2O: 3.69 μL

The sample was incubated at 50 ℃ for an hour. The sample was stored in the fridge

Results:

Fluorescence measurement of RRvT:

The fluorescence of RRvT and RFP was constant over time, and the value of the fluorescence of RRvT and RFP was lower than the fluorescence measured from the medium...

Goal:

• Measure the growth curve of V. natriegens
• Transform Gibson assembled LITMUS28i (with unmutated dcas9 and gRNA with anti-luxS) into DH5α cells
• Test digest the mutated pdCas9 with EcoRI and SpeI

Procedure:

Growth curve of V. natriegens:

Overnight cultures were diluted to a target OD600 = 0.05 in 250 mL baffled flasks with a final volume 40 mL. The cell cultures were incubated at 37 ℃ with shaking. The OD600 of each replicate was measured after 10 min incubation for 5 hours.

Transformation of Gibson assembled LITMUS28i vector:

2 μL Gibson assembled LITMUS28i vector that consists unmutated dCas9 and gRNA with anti-luxS was transformed into competent cells after following the same procedure from 25.06.2018.

Restriction digest the mutated pdCas9:

The mutated pdCas9 was cut with EcoRI and SpeI by mixing 5 μL DNA (PC1), 2 μL cut smart buffer, 0.5 μL EcoRI, 0.5 μL SpeI and 12 μL dH2O. The reagent was incubated overnight at 37 ℃.

Goal:

Gel separation of the product from the enzyme digestion of mutated pdCas9

Digestion of mutated pdCas9 and pSB1C3 (preparation for ligation of dCas9 and pSB1C3).

Procedure:

Gel electrophoresis:

The products of enzyme digestion of mutated pdCas9 that has been incubated overnight, were mixed with 3.34 μL loading dye. The DNA segments were separated after running them on gel red at 90 V for 45 min.

Digestion of mutated pdCas9 and pSB1C3:

The DNA were digested after the following recipe

pdCas9: 5 μL DNA (PC1, 50.8 ng/μL), 2 μL 2.1 buffer, 0.5 μL EcoRI, 0.5 μL PstI, 12 μL ddH2O. Linear pSB1C3: 10 μL DNA (linear pSB1C3, 25 ng/μL), 2 μL 2.1 buffer, 0.5 μL EcoRI, 0.5 μL PstI, 7 μL ddH2O.

The samples were incubated at 37 ℃ overnight.

Goal:

• Gel separate the overnight product of enzymatic digested mutated pdCas9 and linear pSB1C3.
• Gel digestion and isolate the desired DNA fragments of mutated and enzymatic digested pdCas9 and pSB1C3.
• Isolate Gibson assembled LITMUS28i vector (with unmutated dCas9 and gRNA) from overnight cultures
• Test digest the Gibson assembled LITMUS28i vector, and separate on gel

Procedure:

Gel separation of fragments of mutated pdCas9 and linear pSB1C3:

3.34 μL loading dye was added to each sample, and the fragment were separated on gel green at 90 V for 45 min.

The fragments with the desired length (dCas9: approx. 5000bp, backbone: approx. 2000bp) were cut out from the gel and collect in separate tubes.

Gel digestion and DNA isolation:

The DNA fragments of mutated pdCas9 and pSB1C3 were isolated from the gel by following after the protocol form 02.07.2018.

Plasmid isolation of Gibson assembled LITMUS28i vector:

The Gibson assembled LITMUS28i vector was isolated from two overnight cultures (L1 and L2) by following after the same protocol from 22.07.2018.

Test digest the Gibson assembled LITMUS28i vector:

The vectors were digested with two different enzyme pairs.

The samples cut with AlwNI and EcoRI were incubated at 37 ℃ for 2 hours, while the samples cut with PstI and EcoRI were incubated for 1 hour.

Gel separation of enzymatic digested L1 and L2:

3.34 μL loading dye was added to each sample, the DNA fragments were visualized by running them on gel red at 90 V for 45 min.

Results:

Successfully transformed cells with LITMUS28i (probably with dCas9 and gRNA with anti-luxS) The concentrations of the fragments of mutated pdCas9 and pSB1C3 were too low (negative values)… L2 may be the correct Gibson assembled phagemid. However, there is an extra segment with a length approx. 6000 bp. Probably, the enzymatic activity of AlwNI is slower compared to EcoRI and PstI, hence some fragments were not cut by AlwNI. In order to verify this, another sample of L2 was cut with AlwNI and EcoRI and incubated overnight at 37℃.

Goal:

• Gel separation of fragments from enzymatic digested mutated pdCas9, linear pSB1C3 and Gibson assembled LITMUS28i vector.
• Gel digestion and isolation of the desired DNA fragments of pdCas9 and linear pSB1C3.
• Incubate new samples of mutated pdCas9 and linear pSB1C3 were incubate overnight with restriction enzymes.
• Revive competent cells with mutated pdCas9 (PC1)

Procedure:

Gel separation:

Fragments of mutated pdCas9 and pSB1C3 (digested with EcoRI and PstI overnight) were separated on gel green. The desired segments were cut out and isolated from the gel by following after the same procedures from 02.07.2018.

Fragments of L2 (incubated from yesterday – 21.09.2018) were digested with AlwNI and EcoRI, separated and visualized on gel red.

Revive competent cells with mutated pdCas9:

Cells with PC1 stored at -80 ℃ were inoculated in LB medium with CM and incubated overnight at 37 ℃ with shaking.

We were running out of plasmids with mutated pdCas9, so it’s necessary to isolate the them from the cells again…

Restriction digest mutated pdCas9 (PC2) and linear pSB1C3:

PC2: 10 μL DNA, 2 μL 2.1 buffer, 0.5 μL EcoRI, 0.5 μL PstI, 7 μL ddH2O

pSB1C3: 10 μL DNA, 2 μL 2.1 buffer, 0.5 μL EcoRI, 0.5 μL PstI, 7 μL ddH2O

The samples were incubated overnight at 37 ℃

Results:

The concentrations of the desired fragments of pdCas9 and pSB1C3 were too low to be detected. New samples of mutated pdCas9 and pSB1C3 were incubated with EcoRI and PstI overnight

Goal:

• Ligation of enzymatic digested pSB1C3 and mutated pdCas9
• Plasmid isolation from overnight cultures
• Digest the mutated pdCas9 and pSB1C3 with restriction enzymes

Procedure:

Ligation of DNA fragments:

According to the protocol for ligation of DNA fragments, the amount of the fragments was calculated by using the NEBiocalculator.

We assume that all of the DNA is completely cut by the enzymes, so we have 400 ng dCas9 and 250 ng digested backbone

The concentration of PC2 is 40 ng/μL and 10 μL pdCas9 was cut with enzymes, while the concentration of linear pSB1C3 was 25 ng/ μL and 10 μL was digested.

If we would like to have 25 ng backbone in the reaction solution, we should have approx. 181.3 ng dCas9 according to NEBiocalculator with the ratio of 3:1 for insert and backbone.

The theoretical concentration of the digested pdCas9 is 20 ng/ μL (total 400 ng plasmid was cut, and the final volume in the restriction digest tube was 20 μL), and 12.5 ng/ μL for the digested pSB1C3 (total 250 ng linear pSB1C3 was cut, and the final volume in the restriction digest tube was 20 μL).

Thus, the volume of the different compounds for ligation is

• 2 μL T4 DNA ligase buffer
• 1 μL T4 DNA ligase
• 2 μL Backbone
• 10 μL dCas9
• 5 μL ddH2O
• Total volume: 20 μL

The sample was incubated at 16 ℃ overnight

P.S. The fragments were not separated on gel before ligation (after so many times of failure to isolate DNA from gel…), wrong insert or re-ligation of pdCas9 fragments may occur…

Plasmid isolation from competent cells:

The plasmid with mutated pdCas9 was isolated from two cell cultures by following the same procedure from 02.07.2018.

Enzymatic digestion of mutated psCas9 and linear pSB1C3:

PCI: 17 μL DNA, 2 μL 2.1 buffer, 0.5 μL EcoRI, 0.5 μL PstI

Dried linearized pSB1C3 was resuspended with 10 μL ddH2O to obtain the final concentration 100 ng/ μL

pSB1C3: 9 μL DNA (100 ng/ μL), 2 μL 2.1 buffer, 0.5 μL EcoRI, 0.5 μL PstI, 8 μL ddH2O

The samples were incubated overnight at 37 ℃.

Goal:

• Separation of DNA fragments on gel
• Gel digestion and DNA isolation of dCas9 and pSB1C3
• Transformation of ligation product
• Amplify mutated dCas9 and linear pSB1C3

Procedure:

Gel electrophoresis:

Enzymatically digested pdCas9 and pSB1C3 (prepared from yesterday - 23.09.2018) were separated on gel green at 90 V for 45 min.

Gel digestion and DNA isolation:

The desired fragments of dCas9 and backbone were cut out from the gel. The DNA fragments were further isolated by following after the same procedure fromn02.07.2018.

Transformation of ligation product into competent cells:

Heat inactivate the ligase at 65 ℃ for 20 min Transform 5 μL of ligation product into competent cells by following the protocol from 25.06.2018 P.S. The fragments were not separated on gel before ligation (after so many times of failure to isolate DNA from gel…), wrong insert or re-ligation of pdCas9 fragments may occur… so inoculate more colonies and store one of the plates sealed with parafilm in the fridge.

Amplify mutated pdCas9 and pSB1C3:

PCR mix for amplification of pdCas9 and pSB1C3 were prepared by mixing:

pdCas9: 0.5 μL template (PCII, 65.8 ng/ μL), 6 μL FWD GA1 primer, 6 μL REV GA3 primer, 12.5 μL Takara HiFi PCR premix.

This sample was amplified in a PCR machine with an annealing temperature at 55 ℃ for 10 s, and an elongation temperature at 72 ℃ for 7 min.

pSB1C3: 1 μL template (linear pSB1C3, 25 ng/ μL), 6 μL FWD primer, 6 μL REV primer, 12.5 μL Takara HiFi PCR premix.

The sample of pSB1C3 ran in a PCR machine with an annealing temperature at 55 ℃ for 10s, and an elongation temperature 72 ℃ for 2 min.

Nanodrop - mutated dCas9 and backbone:

The concentrations of enzymatically digested pdCas9 and pSB1C3 were too low to be detected (negative values).

Therefore, the mutated pdCas9 and pSB1C3 were amplified via PCR to increase the amount. Further we plan on cutting the PCR product with restriction enzymes over two nights, before separation on gel and isolate the desired fragments. This may increase the concentration of the products after gel digestion. Probably, heat inactivation of the restriction enzymes after gel digestion and DNA isolation may be a good idea (most of the enzymes are separated from the DNA fragments on gel), before the ligation step.

Goal:

• Restriction digest of PCR-amplified mutated dCas9 and pSB1C3
• Make LB and M63B1 medium
• Make 0.8% agarose GelRed and GelGreen
• Inoculation of LB medium with transformed bacteria

Procedure:

Restriction digest of mutated dCas9 and pSB1C3:

PCR-amplified dCas9 and pSB1C3 were digested in separate tubes. The restriction mixtures were made by combining:

• 17 µL PCR-amplification product (mutated dCas9 or pSB1C3)
• 2 µL NEB 2.1 buffer
• 0.5 µL EcoRI-HF
• 0.5 µL PstI
• The restriction mixtures were incubated at 37 °C for two days.

Media preparation

Both, LB and M63B1 medium were prepared as described previously (____). The pH was adjusted to 7.1-7.2 by adding NaOH. The media were autoclaved and stored for later use.

Agarose gel preparation

For preparation of 200 mL of both GelGreen and GelRed 0.8% agarose gel, 1.6 g agarose was added to 200 mL 1xTAE. The solution was heated in a microwave until the agarose was completely dissolved (approximately 3 min at maximum heat). The gel was cooled down before 10 µL of dye (GelGreen or GelRed) was added.

Colony picking and inoculation

Four colonies from agar plates with bacteria transformed with possibly ligated dCas9 and pSB1C3 were picked and inoculated in 25 mL LB medium containing 25 µL chloramphenicol. The cultures were incubated at 37 °C with shaking (225 rpm) until the next day.

Goal:

Miniprep yesterday’s bacterial cultures

Measure quantity and quality of miniprep product (Nanodrop)

Procedure:

The OD600 value of the bacterial cultures from yesterday were measured. The cultures were diluted to a final OD600 value of about 1, and miniprepped following the ZR Plasmid Miniprep protocol. The isolated plasmids were nanodropped and stored at 4 °C till next day.

Goal:

• Gel separation and purification of digested PCR-amplified dCas9 and pSB1C3
• Measure the quality and quantity of the purified product (Nanodrop)
• Restriction digest of yesterday’s miniprep product

Procedure:

Gel separation and purification of digested PCR-amplified dCas9 and pSB1C3

4 μL loading dye was added to the digested PCR-amplified dCas9 and pSB1C3 backbone and the total volume of the samples (24 μL) were run on a 0.8% agarose gel containing GelGreen. The bands at approximately 5000 bp and 2000 bp for dCas9 and pSB1C3, respectively, were excised from the gel. The plasmid fragments were further purified following the ZymocleanTM Gel DNA Recovery protocol, using 480 μL and 210 μL ADB buffer for dCas9 and pSB1C3 backbone, respectively. The concentration and quality of the products were measured using the Nanodrop.

Restriction digest of plamids isolated from colonies

Yesterday’s miniprepped plasmids from the bacterial cultures with potentially correctly ligated dCas9 into the pSB1C3 backbone were nanodropped and digested with EcoRI-HF and PstI at 37 °C for about 2 hours. The products was ran on a 0.8% agarose gel containing GelRed.

• 7.5 μL dH2O
• 0.5 μL EcoRI-HF
• 0.5 μL PstI
• 2.0 μL NEB 2.1 buffer
• 10 μL miniprepped plasmids

Goal:

Analyze ligated mutdCas9 and backbone

Procedure:

Gel electrophoresis of enzyme digested mutated dCas9:

Ran tube 1, 2, 3 and 4 on gel electrophoresis.

Ligation of mutated dCas9 and iGEM-backbone:

Started ligation process of mutated dCas9 and iGEM-backbone from samples collected in the freezer.

How we did it:

• Added (in order) 2uL T4 DNA ligase buffer, 3uL backbone, 9,5 uL mutated dCas9, 4,5 uL ddH2O and 1uL T4 DNA ligase (thawed in room temperature, no contact with hands)
• mixed gently by pipetting up and down
• microfuged tubes at 16^C, 10 rpm in one minute.
• incubated at 16*C over night

Watered out DNA fragments from idt:

- Both DNA fragments from idt were watered out with 40 uL ddH2O till a concentration of 25ng/uL. stored in fridge.

Next step will be: PCR amplification->run gel and isolate -> nanodrop to find concentration -> Gibson assembly with primers (same primers as with RRvT biobrick)

Results:

Gel electrophoresis:

Had only two bands on gel, which meant that the backbone and the mutated dCas9 was not ligated correctly.

Goal:

Ligation of PCR-amplified dCas9 and pSB1C3

Restriction digest and ligation of dCas9 ordered from IDT in two separate parts

Procedure:

Ligation of PCR-amplified dCas9 and pSB1C3

The gel purified dCas9 and pSB1C3 backbone were heated at 80 °C for 20 min in order to heat kill any restriction enzymes still present in the samples. The ligation mixture was prepared as follows:

• 2 μL T4 DNA ligase buffer
• 1 μL T4 DNA ligase
• 3 μL backbone
• 9 μL dCas9 (Note! Not fully 9 μL was added)
• 5 μL ddH2O
• The fragments were incubated overnight at 16 ºC

Restriction cutting and ligation of dCas9 ordered from IDT in two separate parts

The two dCas9 fragments were restriction digested in separate tubes with BtgI. The recipe for the restriction mixtures is given below. Each fragment was handled similarly.

• 20 μL dCas9 (diluted yesterday)
• 1 μL BtgI
• 5 μL cutsmart buffer
• 24 μL dH2O

The fragments were digested at 37 ºC for about 2 hours and the restriction enzymes were then heat killed at 80 ºC for 20 min. Finally, the separate dCas9 fragments were combined in ligation mixtures with varying concentrations of dCas9 and T4 DNA ligase buffer:

• 2 μL | 2 μL | 2.5 μL T4 DNA ligase buffer
• 1 μL T4 DNA ligase (same for all)
• 5 μL | 10 μL | 15 μL dCas9 fragment 1
• 5 μL | 10 μL | 15 μL dCas9 fragment 2

The ligation reaction was run overnight at 16 ºC.

Goal:

Transformation of PCR-amplified dCas9 and pSB1C3 into competent DH5α cells.

Verification of ligated dCas9 fragments from IDT

Procedure:

Transformation of PCR-amplified dCas9 and pSB1C3 into competent DH5a cells

Prior to the transformation, the T4 DNA ligase was heat killed at 80 ºC for 20 min. 5 μL of the ligation mixtures prepared September 28th and 29th was added to separate tubes of thawed competent DH5α cells. The cells were incubated on ice for 20 min, heat shocked at 42 ºC for 45 sek, 950 μL LB was added and the cells were further incubated for 1.5 hour at 37 ºC with shaking (225 rpm). 100 μL of the cell suspensions were added to agar plates containing chloramphenicol. The suspensions were then centrifuged at 6800 g for 4 min, and about 800 μL of supernatants were discharged. The cell pellets were resuspended in the remaining medium and plated.

Verification of ligated dCas9 fragments

The overnight ligation mixtures with the dCas9 fragments from IDT were heated at 80 ºC for 20 min. The total volume for each of the samples were run at 85 V for 45 min on an 0.8% agarose gel containing GelGreen. Fragments at 2000 bp and 3000 bp was excised from the gel and purified following the ZymocleanTM Gel DNA Recovery protocol. The recovered fragments were stored -20 ºC in case of further usage.

Goal:

Check colony formation on yesterday’s prepared agar plates

If colonies, pick a few single colonies and make pure bacterial cultures

Procedure:

Colonies were visible on all 7 agar plates. 7 colonies were picked and inoculated in 25 mL LB with 25 μL chloramphenicol. The cultures were incubated overnight at 37 °C with shaking (225 rpm).

Goal:

Verify successful ligation of mutated dCas9 and iGEM-backbone by:

• Isolating plasmids from overnight cultures
• Digest the plasmids containing mutated pdCas9 ligated with pSB1C3.
• Verify with gel electrophoresis

Procedure:

Yesterday 7 colonies were picked and incubated in culture medium overnight. Today, plasmids from each culture were isolated using the miniprep protocol.

The concentrations in each parallel were found using Nanodrop. After the plasmids were isolated they were digested using the BamH1 and Pst1 restriction enzymes (we used 3.5uL plasmids). If we have the correct plasmids, then there will be two fragments, one at 6181bp and one at 893bp.

Gel electrophoresis is performed using GelRed and standard protocol.

The remaining plasmids from the plasmid isolation (not enzyme digested) are stored in the freezer in the phage-lab. They are in the brown case and are marked "dCas9 +bb 02.10.18".

Results:

Gel electrophoresis showed only one band at about 1000bp. Cannot explain why (only backbone should be at 2000bp)

Goal:

Transform biobrick BBa_K592009 (plate 1, well 19E) and BBa_K592010 (plate 6, well 17G) into competent DH5α cells

Make bacterial cultures of mutated dCas9 (with Addgene backbone), RRvT and mRFP1

Procedure:

Transformation

10 μL ddH2O was used to resuspend the biobricks. For the transformation, 1.5 μL of the biobrick resuspensions were added to competent DH5α cells. The transformation was performed as described in our protocol section with slight modification: 1.5 μL of the biobrick resuspensions were added to competent DH5α cells, and 950 μL LB added prior to a 1.5 hour incubation time. The cells were plated on agar plates with chloramphenicol as the selective marker.

Make bacterial cultures

Bacterial cultures with mutated dCas9 (with Addgene backbone), RRvT and mRFP1 was made by inoculating previously transformed stored bacterial stocks in 25 mL LB medium containing 25 μL chloramphenicol. The cultures were incubated at 37 °C with shaking.

Goal:

- To get enough DNA for the backbone (blue) and dcas seperately to be ready for ligation.

Procedure:

1. 2 colonies of blue biobrick were picked and inoculated in LB+CM for 6h until OD-0.3. Checked the OD of dCas culture and diluted to approximately 1,4.

2. Did a miniprep from the inoculated culture of blue biobrick(3 paralelles) + dcas(2 paralelles per culture)

3. Test digest with restriction enzymes Pst1 (0.5 ul) and EcoR1-HF (0,5 ul), with NEBuffer 2.1 (2 ul) and water (see table) overnight at 37 degrees.

Goal:

• Gel elecrohoresis of yesterday’s digested mutated dCas9 and biobricks
• If visible, gel purification of bands at appr. 2000 for the biobricks (= pSB1C3 backbone) and 5000 bp for dCas9
• Measure quantity and quality of purified product (Nanodrop)

Procedure:

Gel electrophoresis, purification and nanodrop

The restriction enzymes in each sample was heat killed at 80 °C for 20 min. 4 μL loading dye was added to the samples and the total volumes of each sample (24 μL) were run at 80 V for 45 min on a 0.8% agarose gel containing GelGreen. Since neither of the biobrick replicates (B1 and B2) gave any visible bands, only the 5000 bp bands for two of the mutated dCas9 replicates (1.1 and 1.2) was excised from the gel.

The gel purification was conducted following the ZymocleanTM Gel DNA Recovery protocol, using 216 μL and 252 μL ADB buffer for dCas9 sample 1.1 and 1.2, respectively. The quantity and quality of purified product using Nanodrop.

Addition to the planned goal: Miniprep of BBa_K592009 and BBa_K592010 transformed bacterial cultures

Since the biobricks did not give any visible bands on the gel, bacterial cultures with cells transformed with BBa_K592009 and BBa_K592010 were miniprepped again. The cultures were diluted to a final OD600 value of about 1, and then two of the cultures containing BBa_K592009 and one culture containing BBa_K592010 was miniprepped following the ZR Plasmid MiniprepTM protocol. The quantity and quality of the miniprep products were measured using the Nanodrop. The isolated biobricks were then digested by combining:

• 15 μL sample (appr. 1500 ng, for all three samples)
• 0.5 μL EcoRI-HF
• 0.5 μL PstI
• 2 μL NEB 2.1 buffer
• 2 μL ddH2O

The restriction mixtures were incubated overnight at 37 °C with shaking (225 rpm).

Goal:

• Gel purification of overnight digested biobricks
• Measure quantity and quality of the purified digested biobricks
• Ligation of mutated dCas9 and digested biobricks
• Transformation of ligation mixture into competent DH5α cells

Procedure:

Gel purification of overnight digested biobricks

The overnight digested biobricks were heated at 80 °C for 20 min. Loading dye was added and the samples were run on a 0.8% agarose gel containing GelGreen. The bands at approximately 2000 bp was excised from the gel, and the fragments was recovered following the ZymocleanTM Gel DNA Recovery protocol. The quantity and quality of the purified digested biobricks were measured using the Nanodrop.

Ligation of mutated dCas9 and digested biobricks

The mutated dCas9 samples, which were gel purified yesterday, were ligated with the isolated pSB1C3 backbone of the biobricks. Two ligation mixtures was prepared using dCas9 1.1 and the backbone from BBa_K592009 (sample B2) and dCas9 1.2 and the backbone from BBa_K592010 (sample G2):

• 2 μL T4 DNA ligase buffer
• 5 μL T4 DNA ligase
• 16 μL dCas9 1.1 (40.0 ng) | 16 μL dCas9 1.2 (33.6 ng)
• 1 μL pSB1C3 from BBa_ (40.1 ng) | 1 μL pSB1C3 from BBa_ (32.5 ng)
• 5 μL ddH2O
• The ligation mixtures were incubated at 37 C for 2 hours.

Transformation of ligation mixture

10 μL of each ligation mixture was used in the transformation of competent DH5α cells. Also, 950 μL of LB was added prior to a 1.5 hours incubation period. Otherwise, the transformation was conducted as described in our protocol section.

Goal:

Dilute bacterial cultures with correctly inserted dCas9 into pSB1C3 and cultures containing RRvT

Miniprep plasmids from bacterial cultures

Measure quantify and quality of miniprep product (Nanodrop)

Plate and air dry plasmids

Procedure:

The bacterial culture with correctly inserted dCas9 (verified yesterday by colony PCR) and a culture containg RRvT were diluted to an OD600 of about 0.2. The cultures were incubated at 37 °C with shaking (225 rpm) until the OD600 reached a value of approximately 1. The plasmids were isolated following the ZR Plasmid MiniprepTM protocol and the quantity and quality of the products were measured by the Nanodrop. The miniprepped products were then diluted to a final concentration of 50 ng/μL for each of the samples. 10 μL diluted mutated dCas9-pSB1C3 plasmid and 10 μL diluted RRvT-pSB1C3 plasmid was plated on the 96-well plate to be shipped to iGEM Headquarters. The samples were left to air dry in the fume hood until the next day.

Goal:

1. Transformation of pgRNA and pdCas9 into DH5a and TG1-cells.

Procedure:

Both pdCas9(2) and pgRNA(2) with anti-luxS were simultaneously transformed into competent cells (DH5α) after the following protocol:

• Thaw competent cells on ice.
• Add pdCas9(2) (5μL) and pgRNA(2) with anti-luxS (5μL) to the same tube containing competent cells.
• Incubate the cells on ice for 20min.
• Heat shock the cells for 45s at 42℃.
• Incubate the cells on ice for 2min.
• Add LB- medium (900μL).
• Incubate the cells for 1.5h (max. 2h) at 37℃ with shaker.
• Plate the cells (100μL) on agar with AMP and CM
• Centrifuge the cell culture for 3min at 6800g.
• Discard the supernatant (200μL)
• Resuspend the pellet with the remining supernatant in the tube
• Plate the cells (100μL) on agar with AMP and CM.

Results:

Colonies on the plates with DH5a. No colonies on the plates with TG1.

Goal:

1. Transform pgRNA and new pdCas9 into TG1-cells.

Procedure:

Both pdCas9(2) and pgRNA(2) with anti-luxS were simultaneously transformed into competent cells (TG1) after the following protocol:

• Thaw competent cells on ice.
• Add pdCas9(2) (5μL) and pgRNA(2) with anti-luxS (5μL) to the same tube containing competent cells.
• Incubate the cells on ice for 20min.
• Heat shock the cells for 45s at 42℃.
• Incubate the cells on ice for 2min.
• Add LB- medium (900μL).
• Incubate the cells for 1.5h (max. 2h) at 37℃ with shaker.
• Plate the cells (100μL) on agar with AMP and CM (make minimum 5 plates)
• Centrifuge the cell culture for 3min at 6800g.
• Discard the supernatant (200μL)
• Resuspend the pellet with the remining supernatant in the tube
• Plate the cells (100μL) on agar with AMP and CM.

Results:

Bacteria colonies did not appear on agar plates the following day.

Goal:

1. Transform pgRNA and new pdCas9 into TG1-cells.

Procedure:

Both pdCas9(2) and pgRNA(2) with anti-luxS were simultaneously transformed into competent cells (TG1) after the following protocol:

• Thaw competent cells on ice.
• Add pdCas9(2) (5μL) and pgRNA(2) with anti-luxS (5μL) to the same tube containing competent cells.
• Incubate the cells on ice for 20min.
• Heat shock the cells for 45s at 42℃.
• Incubate the cells on ice for 2min.
• Add LB- medium (900μL).
• Incubate the cells for 1.5h (max. 2h) at 37℃ with shaker.
• Plate the cells (100μL) on agar with AMP and CM (make minimum 5 plates)
• Centrifuge the cell culture for 3min at 6800g.
• Discard the supernatant (200μL)
• Resuspend the pellet with the remining supernatant in the tube
• Plate the cells (100μL) on agar with AMP and CM.

Results:

Bacteria colonies did not appear on agar plates the following day.

Goal:

- Transformation of TG1 cells with the new dCas sequence (with iGEM backbone) and pgRNA

Procedure:

1. Eluted DNA from DH5a-cells with only pgRNA by following the protocol for ZR miniprep. 4 tubes of miniprepped pgRNA was made and stored in the fridge.

2. Did a double transformation of TG1-cells with both pgRNA and dCas by following the same protocol as the day befor, but changing the volume of DNA added and the growing time before plating. Two paralelles of our supercompetent TG1-cells and two paralelles of TG1 (felles) were made. 10 uL of pgRNA and 10 uL of dCas was added to each of them, and they were growing for 3 hours before plating on LA-petri dishes with CM and AMP.

Results

Transformation was successfull.

Nanodrop results from the miniprep of cells with pgRNA:

Succesful transformation, all the plates from the samples containing our supercompetent cells had colonies.

Procedure

Colonies of successfully transformed TGI and DH5a were picked and thrown in beakers with LB + CM + AMP, and incubated at 37 degrees celsius and 220 RPM shaking.

Cells containing the RRvT and mRFP biobrick were incubated in their respectful beakers with LB + CM at 37 degrees celsius and 220 RPM shaking

Goal:

• Measure biofilm formation after 0, 3, 5, 8, 24 and 30 hours.
• Measure metabolic activity after 0, 8 and 24 hours.

Procedure:

See Protocols and Measurement pages for details about the procedure.

Vitamine B was added to the M63B1 medium before inoculation to the 96 well plate in the following way: 0.9 ul of stock solution (90 ml, 0.9108 grams) was mixed in a bottle of M63B1 (900 ml).

0.9 mL MgSO4 and 18 mL glucose were also added to the M63B1 medium.

The media were mixed according to the table beneath.

Either TG1 or DH5a were added to the media in the table over, and diluted to 0.1 OD600, before biofilm measurements were conducted.

Goal:

• Measure biofilm formation after 0, 3, 5, 8, 24 and 30 hours.
• Measure metabolic activity after 0, 8 and 24 hours.

Procedure:

See Protocols and Measurement pages for details about the procedure.

Measurements of OD600 were taken and results presented in the table below.

Same procedure as the 16th of october was done, however; with different volumes, a new medium was made, and 1mL MgSO4 (1M) was added. The media were mixed accordingly to the table underneath.