Team:XMU-China/Experiments
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Editing Team:XMU-China/Experiments
● Ni-bead with EpCAM coated
● 5% PBS-BSA Buffer (see Appendices)
● Antibody of EpCAM (PE labeled)
● Flow Cytometer (BD FACSVerseTM)
Prepare 5% PBS-BSA: Weigh 0.5 g BSA, then add 1×PBS to the volume being 10 mL, then mix it evenly to make sure the solid dissolved.
1. Make distributions:
Add reagent to 3 1.5 mL tubes respectively according to the following instructions. Add PBS-BSA first then the antibody.
1) Sample Group: 5 μL EpCAM-Ni bead + 185 μL PBS-BSA + 10 μL antibody of EpCAM.
2) Positive Control: 5 μL EpCAM-Ni bead + 185 μL PBS-BSA + 10 μL antibody of EpCAM.
3) Negative Control: 5 μL EpCAM-Ni bead + 195 μL PBS-BSA.
2. Wash the free antibody:
Take out the filter of a 10 μL filter tip and insert it into a 200 μL tip to make a 200 μL filter tip.
The above three tubes are respectively subjected to the following operations:
1) Transfer the 200 μL of solution to the 200 μL filter tip, then pipette it up and down to mix evenly.
2) Use a syringe to squeeze out the solution in the 200 μL filter tip.
3) Remove the filter tip and place it in the previous tube.
4) Rinse the tip with 450 μL of 1×PBS Buffer.
5) Take out the tip, then transfer 150μL of Buffer from 4) to the filter tip and pipette up and down to mix evenly.
6) Use a syringe to squeeze out the solution in the 200 μL filter tip.
7) Repeat 5) to 6) three times, at which time 450 μL of the solution from 4) was filtered.
8) Use a pair of scissors to cut the thin end of the filter's head and loosen the filter.
9) Transfer 200 μL of 1×PBS Buffer to a new 1.5 ml tube.
10) Use a pipette to insert the cut filter tip into the tube from 9) and pipette it up and down for several times.
3. Flow Cytometer test:
Precautions:
1) Turn on the regulator first, then turn on the computer, and finally turn on the instrument 30 minutes before measuring.
2) Check if the sheath tank has a solution, if the waste container is full, and if the dehumidifier is turned on.
3) Remember to perform a two-step self-test.
4) Please use daily clean after measuring.
5) Shutdown sequence: Click shut down on the software, turn off the instrument, then turn off the computer, and finally turn off the regulator.
● SYL3C-FAM (Sangon Biotech®, see Appendices)
● EpCAM (ACROBiosystems®)
● Binding Buffer (see Appendices)
● Fluorescence Spectrometer (Shimadzu® RF-6000)
● Polarizer (from a pair of 3D glasses)
1. Make distributions in 1.5 mL centrifuge tubes:
1) Tube 1 (Aptamer Group): 1 μL 100 μM (100 pmol) SYL3C-FAM + 179 μL binding Buffer.
2) Tube 2 (Aptamer-EpCAM Group): 1 μL 100 μM (100 pmol) SYL3C-FAM + 179 μL binding Buffer.
2. Sample processing:
The above 2 tubes are simultaneously subjected to the following steps:
1) Denature at 95℃ for 10 minutes.
2) Remove the tubes, then put them at room temperature for about 20 minutes.
3) Add 20 μL of 100 μg/mL EpCAM protein to Tube 2.
4) Add 20 μL of binding Buffer to Tube 1.
5) Incubate all tubes in a shaker for 40 minutes (37℃, 200 rpm).
Note: Avoiding light in whole process is necessary.
3. Measure fluorescence intensity from vertical/parallel direction:
1) Turn on the instrument for 30 minutes before measuring.
2) Choose "Emission Mode". The excitation wave length is 495 nm, and the range of emission wave length is from 500 nm to 600 nm.
3) Before measuring, dilute the solution from step 2 to about 3 mL with binding Buffer in the fluorescence cuvette.
4) Attach a polarizer to the exit of the excitation light, and attach another polarizer to the receiving inlet of the emission light to make sure the polarization directions of the two polarizers are vertical/parallel.
5) Start measuring to obtain I∥, max (Aptamer), I⊥, max (Aptamer), I∥, max (Aptamer + EpCAM), I⊥, max (Aptamer + EpCAM).
● Sequence of SYL3C-FAM:
5'-CACTACAGAGGTTGCGTCTGTCCCACGTTGTCATGGGGGGTTGGCCTG-FAM-3'
● Binding Buffer (pH 7.3~7.5) contains:
1×PBS Buffer with 5 mM MgCl2
● SYL3C-TEG-biotin (BoruiTM, see Appendices)
● C3-FITC (BoruiTM, see Appendices)
● C4-FITC (BoruiTM, see Appendices)
● Binding Buffer (see Appendices)
● 50×TAE concentrate solution (Solarbio®)
● Agarose (Biowest®)
● DNA dye (TransGen® GelStain)
● Distilled water
● Microwave oven
● 10×Loading Buffer (Takara®)
● Electrophoresis instrument
Dilute 50×TAE concentrate solution to 1×TAE Buffer with distilled water.
1. Make distributions in 1.5 mL centrifuge tubes according to the following:
1) Tube 1 (Aptamer Group): 1 μL 100 μM (100 pmol) SYL3C-TEG-biotin + 19 μL binding Buffer.
2) Tube 2 (C4 Group): 1 μL 100 μM (100 pmol) C4-FITC + 19 μL binding Buffer.
3) Tube 3 (C3 Group): 1 μL 100 μM (100 pmol) C3-FITC + 19 μL binding Buffer.
4) Tube 4 (C4&Aptamer Group): 1 μL 100 μM (100 pmol) SYL3C-TEG-biotin +1 μL 100 μM (100 pmol) C4-FITC + 18 μL binding Buffer.
5) Tube 5 (C3&Aptamer Group): 1 μL 100 μM (100 pmol) SYL3C-TEG-biotin +1 μL 100 μM (100 pmol) C3-FITC + 18 μL binding Buffer.
Note: The Tube 2, 3, 4 and 5 should be coated by tin foil properly after distributing.
2. Sample processing:
The above 5 tubes are simultaneously subjected to the following steps:
1) Denature at 95℃ for 10 minutes.
2) Anneal to room temperature for 20 minutes.
3. Prepare 3% agarose gel:
1) Weigh 0.9 g of agarose in a 100 mL Erlenmeyer flask.
2) Add 30 mL of 1×TAE Buffer into the flask from 1).
3) Make agarose melt by microwave oven (medium-high heat, about 3 minutes).
4) Add 3 μL of GelStain, mix by shocking.
5) Assemble gel pouring apparatus by inserting gate into slots.
6) Pour agarose gel into the gel tray.
7) Cool for 40 minutes to solidify the DNA agarose gel.
8) Remove the pouring apparatus, put the gel into an electrophoresis instrument.
4. Electrophoresis:
1) Add 2 μL of 10×Loading Buffer to each tube, then pipette up and down to evenly mix.
2) Pipette all samples which have been mixed with loading Buffer into the slots.
3) Turn on the electrophoresis instrument, set the working electric current at 150 mA and the working electric voltage at 110 V.
4) Electrophoresis for 50 minutes.
5. Gel imaging:
Turn off the instrument, take the gel into the gel formatter to take and save photos.
● Sequence of SYL3C-TEG-biotin:
5'-CACTACAGAGGTTGCGTCTGTCCCACGTTGTCATGGGGGGTTGGCCTG-TEG-Biotin-3'
● Sequence of C3-FITC:
5'-CTCTGTAGTGTTTTTTTTTTTTTT-FITC-3'
● Sequence of C4-FITC:
5'-TCTGTAGTGTTTTTTTTTTTTTTT-FITC-3'
● Binding Buffer (pH 7.3~7.5)contains:
1×PBS Buffer with 5 mM MgCl2
● SYL3C-TEG-biotin (BoruiTM, see Appendices)
● C3-FITC (BoruiTM, see Appendices)
● EpCAM (ACROBiosystems®)
● Magnetic Beads (InvitrogenTM)
● Binding & Washing Buffer (see Appendices)
● Incubation Buffer (see Appendices)
● Vortex (IKA® lab dancer)
● Fluorescence Spectrometer (Shimadzu® RF-6000)
1.8 μL of 100 μM SYL3C-TEG-biotin is diluted by 1×B&W Buffer up to 75 μL, and 1.2 μL of C3-FITC is also diluted by 1×B&W up to 50 μL.
The tube of 100 μg/mL C3-FITC should be coated properly by tin foil in order to avoid being quenched.
1. Make distributions in 1.5 mL centrifuge tubes according to the following:
Tube 1 (Blank Control): 100 μL incubation Buffer.
Tube 2 (Negative Control): 25 μL diluted SYL3C-TEG-biotin + 25 μL 1×B&W Buffer.
Tube 3 (Competition Group): 25 μL diluted SYL3C-TEG-biotin + 25 μL diluted C3-FITC.
Tube 4 (Competition Group without EpCAM): 25 μL diluted SYL3C-TEG-biotin + 25 μL diluted C3-FITC.
Tube 5 (Positive Control): 0.6 μL 100 μM C3-FITC + 100 μL incubation Buffer.
Note: The Tube 3, 4 and 5 should be coated by tin foil properly after distributing.
2. Denature, anneal and renature:
The Tube 2, 3, and 4 are denatured at 95°C for 5 minutes, then anneal to room temperature.
3. Wash magnetic beads:
1) Resuspend the beads and vortex for 10 seconds to make them even.
2) Transfer 75 μL of 10 mg / mL beads to 3 200 μL centrifuge tubes (ie 25 μL per tube).
3) Add 25 μL of 2×B&W Buffer to each tube.
4) Vortex for 5 seconds to resuspend.
5) Place the tubes in a magnetic field for 1 minute, then aspirate the supernatant.
6) Remove the tubes from the magnetic field and add 50 μL of 1×B&W Buffer to each tube.
7) Repeat steps 4) to 5).
8) Add 50 μL of 1×B&W Buffer to each tube.
4. Bind to magnetic beads:
1) Add 50 μL of solution of Tube 2,3 and 4 from step 2 to 50 μL of washed beads, respectively.
2) Vortex for 5 seconds to resuspend.
3) Incubate at room temperature for 30 minutes in the dark.
4) Vortex for 5 seconds to resuspend.
5) Place the tubes in a magnetic field for 2 minute, then aspirate the supernatant.
6) Remove the tubes from the magnetic field and add 100 μL of 1×B&W Buffer to each tube.
7) Repeat steps 4) to 5).
8) Add 100 μL of incubation Buffer to Tube2, 3 and 4, respectively.
5. Compete:
1) Add 17 μL of diluted EpCAM to Tube 2 and 3. And add 17 μL of incubation Buffer to the last each tube.
2) Incubate at room temperature for 40 minutes in the dark.
3) Place the tubes in a magnetic field for 2~3 minutes, then pipette 100 μL of the supernatant into a new 200 μL centrifuge tube and mark it.
4) Measure the fluorescence intensity of Tube 1, 5 and the supernatant from 3).
Note: Before measuring, the solution of each tube will be further diluted by adding 3, 000 μL of incubation Buffer into it. The excitation wave length is 495 nm, and the range of emission wave length is from 500 nm to 600 nm.
● Sequence of SYL3C-TEG-biotin:
5'-CACTACAGAGGTTGCGTCTGTCCCACGTTGTCATGGGGGGTTGGCCTG-TEG-Biotin-3'
● Sequence of C3-FITC:
5'-CTCTGTAGTGTTTTTTTTTTTTTT-FITC-3'
● 2×Binding & Washing Buffer (pH 7.5) contains:
10 mM Tris 1 mM EDTA 2 M NaCl
● Incubation Buffer (pH 7.5) contains:
20 mM Tris 140 mM NaCl 5 mM KCl 1 mM MgCl2
● Cas12a (Alt-R® CRISPR-Cas12a (Cpf1) System)
● crRNA (IDT®)
● TE Buffer (Sangon Biotech®)
● DNaseAlertTM Substrate Nuclease Detection System[1](IDT®, see Appendices)
● 21nt ssDNA (BoruiTM, see Appendices)
● Black 96-well plate (Corning®)
● Microplate reader (Tecan Infinite® M200 Pro)
● Add 26.7 μL of filtered TE Buffer into the tube of crRNA to make a 75 μM stock.
● Add 88.6 μL of filtered TE Buffer into the tube of ssDNA to make a 100 μM stock.
1. Form the RNP complex:
1) Prepare 3 200 μL tubes. Add 1 μL of Cas12a and 1 μL of diluted crRNA into each nuclease-free 200 μL tube.
2) Incubate Cas12a with crRNA at 37℃ for 30 minutes to form the RNP complex.
2. Pretreatment of substrate:
1) Prepare 3 DNaseAlertTM Substrate single-use tubes. Add 5 μL of Nuclease-Free Water to each tube.
2) Add 5 μL of 10×DNaseAlertTM Buffer to each tube.
3. Make distributions:
1) Cas12a Group: DNaseAlertTM Substrate (from step 2) + 2 μL RNP complex (from step 1) + 1 μL diluted ssDNA + 37 μL filtered TE Buffer + 40 μL Nuclease-Free Water.
2) Negative Control: DNaseAlertTM Substrate (from step 2) + 40 μL Nuclease-Free Water + 40 μL Nuclease-Free Water.
3) Positive Control: DNaseAlertTM Substrate (from step 2) + 1 μL DNase I + 39 μL filtered TE Buffer + 40 μL Nuclease-Free Water.
4. Measure fluorescence intensity by microplate reader:
1) Incubate the reaction system at 37℃ for 30 minutes, then transform the reaction system into the black 96-well plate.
2) Before measure, add 12 μL of TE Buffer into each tube.
3) Set temperature: 37℃, choose plate type: Black. Set excitation wavelength: 536 nm and emission wavelength: 556 nm. Choose mode: Optimal.
4) Measure fluorescence intensity at 30 min, 40 min, 50 min, 60 min, 70 min, 90 min, 110 min (Timing is from the beginning of incubation).
● DNaseAlertTM Substrate Nuclease Detection System contains:
1) DNaseAlertTM Substrate (25 single-use tubes (50 pmol per tube) or 2 tubes bulk substrate (2 nmol per tube))
2) DNaseAlertTM Buffer (250 μL)
3) Nuclease-Free Water (2 mL)
4) DNase I Enzyme (25 μL)
5) Nuclease Decontamination Solution (50 mL)
● Sequence of 21nt ssDNA:
5'-CAGGCCAACCCCCCATGACAA-3'
● TE Buffer (Sangon Biotech®)
● DNaseAlertTM Substrate Nuclease Detection System[1] (IDT®, see Appendices)
● Fluorescence spectrometer (Shimadzu® RF-6000)
1. Make distributions:
Add reagent into 2 DNaseAlertTM Substrate single-use tubes according to following instruction. Avoiding light is necessary during the whole process.
1) Negative Control: 5 μL Nuclease-Free Water + 5 μL 10×DNaseAlert Buffer + 40 μL Nuclease-Free Water + 40 μL Nuclease-Free Water.
2) Enzyme Group: 5 μL Nuclease-Free Water + 5 μL 10×DNaseAlert Buffer + 39 μL Nuclease-Free Water + 40 μL Nuclease-Free Water.
Place the two tubes at room temperature for 30 minutes to enough dissolve fluorescent substance.
2. Make distributions further according to the time gradient:
1) Prepare 6 200μL-PCR tubes in advance, then divide into 2 groups (3 tubes per group). Mark "W" and "I" on the tubes of two groups, respectively. Further mark the tubes according to the time gradient of 3 min, 15 min and 30 min (e.g. "W 3", "I 15").
2) Add 1 μL of DNase I into the DNaseAlertTM Substrate single-use tube of Enzyme Group.
3) Mix immediately, then transfer 30 μL of reaction liquid from each single-use tube to each PCR tube marked before. Place all PCR tubes in 37℃ water bath. Then start timing.
4) Each tube: React for corresponding time, then measure florescence intensity immediately.
3. Measure fluorescence intensity:
1) Turn on the instrument for 30 minutes before measuring.
2) Choose "Emission Mode". The excitation wave length is 536 nm, and the range of emission wave length is from 540 nm to 580 nm.
3) Before measuring, dilute the reaction liquid to about 3 mL with TE Buffer in the fluorescence cuvette.
● DNaseAlertTM Substrate Nuclease Detection System contains:
1) DNaseAlertTM Substrate (25 single-use tubes (50 pmol per tube) or 2 tubes bulk substrate (2 nmol per tube))
2) DNaseAlertTM Buffer (250 μL)
3) Nuclease-Free Water (2 mL)
4) DNase I Enzyme (25 μL)
5) Nuclease Decontamination Solution (50 mL)
● SYL3C-TEG-biotin (BoruiTM, see Appendices)
● C3 (BoruiTM, see Appendices)
● EpCAM (ACROBiosystems®)
● Magnetic Beads (InvitrogenTM)
● Binding & Washing Buffer (see Appendices)
● Incubation Buffer (see Appendices)
● Cas12a (Alt-R® CRISPR-Cas12a (Cpf1) System)
● crRNA (BoruiTM, see Appendices)
● TE Buffer (Sangon Biotech®)
● DNaseAlertTM Substrate Nuclease Detection System[1] (IDT®, see Appendices)
● Vortex (IKA® lab dancer)
● Fluorescence Spectrometer (Shimadzu® RF-6000)
0.6 μL of 100 μM SYL3C-TEG-biotin is diluted by 1×B&W buffer up to 25 μL, and 0.6 μL of C3 is also diluted by 1×B&W up to 25 μL.
1. Make distributions in a 1.5 mL centrifuge tube according to the following:
25 μL diluted SYL3C-TEG-biotin + 25 μL diluted C3.
2. Denature, anneal and renature:
The tube are denatured at 95°C for 10 minutes, then anneal to room temperature.
3. Wash magnetic beads:
1) Resuspend the beads and vortex for 10 seconds to make them even.
2) Transfer 25 μL of 10 mg / mL beads to a 200 μL centrifuge tube.
3) Add 25 μL of 2×B&W buffer to the tube.
4) Vortex for 5 seconds to resuspend.
5) Place the tube in a magnetic field for 1 minute, then aspirate the supernatant.
6) Remove the tube from the magnetic field and add 50 μL of 1×B&W buffer to the tube.
7) Repeat steps 4) to 5).
8) Add 50 μL of 1×B&W buffer to the tube.
4. Bind to magnetic beads:
1) Add 50 μL of solution of the tube from step 2 to 50 μL of washed beads, respectively.
2) Vortex for 5 seconds to resuspend.
3) Incubate at room temperature for 30 minutes.
4) Vortex for 5 seconds to resuspend.
5) Place the tube in a magnetic field for 2 minute, then aspirate the supernatant.
6) Remove the tube from the magnetic field and add 100 μL of 1×B&W buffer to the tube.
7) Repeat steps 4) to 5).
8) Add 20 μL of incubation buffer to the tube.
5. Compete:
1) Add 30 μL of 100 μg/mL EpCAM to the tube.
2) Incubate at room temperature for 40 minutes.
3) Place the tube in a magnetic field for 2~3 minutes, then pipette 38 μL of the supernatant into a new 200 μL centrifuge tube and mark it.
6. Form the RNP complex:
1) Prepare a 200 μL tube. Add 1 μL of 63 μM Cas12a and 1 μL of diluted crRNA (75 μM) into the tube.
2) Incubate Cas12a with crRNA at room temperature for 30 minutes to form the RNP complex.
7. Detect using DNaseAlertTM:
1) Add reagent into a DNaseAlertTM Substrate single-use tube according to the following instruction. Avoiding light is necessary during the whole process.
5 μL Nuclease-Free Water + 5 μL 10×DNaseAlert Buffer + 40 μL supernatant （from the tube in step 5 & the RNP complex） + 40 μL Nuclease-Free Water.
2) Incubate the reaction system at 37℃ for 30 minutes in the dark.
3) Measure fluorescence intensity:
① Turn on the instrument for 30 minutes before measuring.
② Choose “Emission Mode”. The excitation wave length is 536 nm, and the range of emission wave length is from 540 nm to 580 nm.
③ Before measuring, dilute the reaction liquid to about 3 mL with TE buffer in the fluorescence cuvette.
● Sequence of SYL3C-TEG-biotin:
5'-CACTACAGAGGTTGCGTCTGTCCCACGTTGTCATGGGGGGTTGGCCTG-TEG-Biotin-3'
● Sequence of C3:
5'-CTCTGTAGTGTTTTTTTTTTTTTT-3'
● Sequence of crRNA:
5'-UAAUUUCUACUCUUGUAGAUAAAAAAAAAAACACUACAGAG-3’
● 2×Binding & Washing Buffer (pH 7.5) contains:
10 mM Tris 1 mM EDTA 2 M NaCl
● Incubation Buffer (pH 7.5) contains:
20 mM Tris 140 mM NaCl 5 mM KCl 1 mM MgCl2
● 0.45 μm syringe filters
● LB broth culture
● OptimaTM XE-90 Ultracentrifuge (Beckman Coulter)
● SW41 Ti Swinging-Bucket Rotor
1) Prepare 100 mL 10×LB broth medium.
2) Pass the culture through a 0.45 μm syringe filter.
3) Ultracentrifuge each tube for 18 hours at 100,000 g in a Swinging-Bucket rotor to precipitate the biomass.
4) Recover the supernatant of each tube and dilute them to 1×LB broth culture.
5) Sterilize the 1×LB broth culture.
● PBS
● 0.45 μm syringe filters
● OMVs-free LB broth culture
● OptimaTM MAX-XP Ultracentrifuge (Beckman Coulter)
● TLA120.2 Rotor
1. Bacteria Growth:
1) Inoculate each strain for analysis to 10 mL OMVs-free culture with appropriate antibiotic, and place them on a shaking incubator at 37°C, 200 rpm.
2) After about 5 hours of incubation (when the OD600 of each culture is 0.6-0.8), add any necessary inducing agents (IPTG at 0.5 mM or Arabinose at a 0.2% final concentration) into the cultures, and then leave them on the shaking incubator at 37°C, 200 rpm overnight.
2. Cell Extraction:
1) Measure the OD600 of each culture before OMVs harvest.
2) Centrifuge each culture for 10 min at 1,000 g and then 10 min at 2,000 g in a fixed angle rotor to pellet the biomass.
3) Recover the supernatants and then pass them through a 0.45 μm syringe filter.
3. OMVs Purification:
1) Load 10 mL syringe-filtered supernatant into ultracentrifugal tubes, and then ultracentrifuge them at 100,000 g in a TLA120.2 rotor for 17 min at 4°C。
2) Discard the supernatant, add enough PBS Buffer and repeat the step 1 above, and then discard the supernatant again.
3) Add 100 μL PBS into the tubes and then pipet up and down for about 200 times.
4) OMVs are stored at 4°C until analysis.
● PBS
● 0.45 μm syringe filters
● OMVs-free LB broth culture
● OptimaTM XE-90 Ultracentrifuge (Beckman Coulter)
● SW41 Ti Swinging-Bucket Rotor
1. Bacterial Growth:
1) Inoculate each strain for analysis into 100 mL OMVs-free culture with appropriate antibiotic, and then place them on a shaking incubator at 37°C, 200 rpm.
2) After about 5 hours of incubation (when the OD600 of each culture is 0.6-0.8), add any necessary inducing agents (IPTG at 0.5 mM or Arabinose at a 0.2% final concentration) into the cultures, and leave them on the shaking incubator at 37°C overnight.
2. Cell Extraction:
1) Measure the OD600 of each culture before OMVs harvest.
2) Centrifuge each culture for 10 min at 1,000 g and then 10 min at 2,000 g in a fixed angle rotor to pellet the biomass.
3) Recover the supernatants and then pass them through a 0.45 μm syringe filter.
3. OMVs Purification:
1) Load 100 mL syringe-filtered supernatant into ultracentrifugal tubes, and then ultracentrifuge them at 100,000 g in a Swinging-Bucket rotor for 2 hours at 4°C。
2) Recover the supernatant, repeat the step 1 above, and then discard the supernatant.
3) Add 100 μL PBS into the tube and then pipet up and down for about 200 times.
4) OMVs are stored at 4°C until analysis.
4. SDS-PAGE:
1) Prepare the 1×Tris-Glycine electrophoresis Buffer (2 L)
2) Add 5×Protein loading Buffer (V/V) to the OMVs pellet, and then pipet up and down to mix the sample.
3) Put the tube in 100°C water bath for 10 min.
4) Make the gel for SDS-PAGE according to the manufacture's instructions.
5) Add 10 μL protein marker to the first well and add about 25 μL samples to other wells.
Note: You must keep enough sample loaded in every well. You can add 25 μL firstly and after the sample pass through the stacking gel, stop the instrument immediately and add 25 μL sample again.
6) Start the electrophoresis apparatus, the parameters are showed below:
7) Turn off the instrument, take the gel into a clean plate with deionized water, ish it gently and then discard the water.
8) Add the Coomassie blue stain into the plate and then heat it to about 50°C.
9) Incubate for 30 min on a shaking bed.
10) Discard the stain and add the destaining solution (acetic acid: ethyl alcohol: deionized water=10: 50: 40, V/V/V), then heat it to about 50°C.
11) Incubate for 30 min on a shaking bed.
12) Repeat step10-11 for 3 times.
13) Take the gel into the gel formatter to take and save photos.
● PBS
● 0.45 μm syringe filters
● LB broth culture
● OptimaTM MAX-XP Ultracentrifuge (Beckman Coulter)
● TLA120.2 Rotor
1. Bacterial Growth:
1) Inoculate each strain for analysis into 100 mL OMVs-free culture with appropriate antibiotic, and then place them on a shaking incubator at 37°C, 200 rpm.
2) After about 5 hours of incubation (when the OD600 of each culture is 0.6-0.8), add arabinose at a 0.2% final concentration to initiate the production of siRNA-C/Dbox.
After an additional 3 h incubation period, add IPTG to a final concentration of 0.5 mM to initiate the production of L7Ae-SpyCatcher. Incubate the culture at 37°C and 200 rpm for an additional 18 h.
2. Cell Extraction:
1) Measure the OD600 of each culture before OMVs harvest.
2) Centrifuge each culture for 10 min at 1,000 g and then 10 min at 2,000 g in a fixed angle rotor to pellet the biomass.
3) Recover the supernatants and then pass them through a 0.45 μm syringe filter.
3. OMVs Purification:
1) Load 100 mL syringe-filtered supernatant into ultracentrifugal tubes, and then ultracentrifuge them at 100,000 g in a Swinging-Bucket rotor for 2 hours at 4°C.
2) Discard the supernatant, add enough PBS Buffer and repeat the step one above, then discard the supernatant again.
3) Add 100 μL PBS into the tube and then pipet up and down for about 200 times.
4) OMVs are stored at 4°C until analysis.
4. RNASelect dye:
The experiment below is designed according to the manufacture' s instruction.[2]
1) Prepare a 1 mM DMSO stock solution of the SYTOTM RNASelectTM.
2) Add 1 μL of the dye stock solution to the 100 μL OMVs sample and mix them to obtain a final dye concentration of 10 μM. Incubate it at 37°C for 20 min (protect from light).
3) Analyze the efficiency of OMVs labeling using HSFCM.
● PBS solution with protein EpCAM (imitative plasma)
● Microfluidic chips
1) Pipette appropriate imitative plasma solution into the sample chamber.
2) Gradually increase the motor speed by software and find the critical speed for the second chamber in which the competition reaction happens.
3) Find a second critical speed for the third chamber-incubation chamber.
● ssDNA (10 nt)
● Biotinylated aptamers
● PBS contained Mg2+ (5.0 mmol)
● 100× SYBR Green Ⅰ (exited by 488 nm)
● Microplate Reader(Tecan Infinite® M200 Pro)
1) Mix equivalent aptamer and ssDNA(dissolved in the PBS with Mg2+).
2) Keep the solution away from light at room temperature/ 37℃ water bath / PCR 95 ℃ for 10 min.
3) Mix 100×SYBR Green Ⅰ with the mixed solution for 20 min at room temperature.
4) Use Microplate Reader to detect the fluorescence of the solution(using the solution contained only aptamer or ssDNA as blank control).
● Biotinylated BSA
● NeutrAvidin
● Combined aptamer-ssDNA(with the fluorophore)
● PBS-0.1% Tween 20
1) Pour and coat Biotinylated BSA on our device for 10 min.
2) ish the remaining Biotinylated BSA with PBS-Tween for 5 min.
3) Pour and coat Neutravidin on our device for 10 min.
4) ish the remaining Neutravidin with PBS-Tween for 5 min.
5) Pour and coat Combined aptamers-ssDNA on our device for 10 min.
6) ish the remaining Neutravidin with PBS-Tween for 5 min.
7) Detect the fluorescence of ishing solution from step 6 to find whether ssDNA is tightly bonded to aptamer.
[1] Piraino, Francescoet, et al. ACS nano. 2016, 10: 1699-1710.
● Coated microfuidic chips
● EpCAM
● PBS-0.1% Tween 20
● Cas12a & crDNA systems
1) Pipette appropriate imitative plasma solution into the sample chamber.
2) Control the motor speed and make the solution flow into the competitive chamber, and then remain for 20 min at room temperature.
3) Increase the motor speed and make the solution flow into the detection chamber, and then remain for 10 min at room temperature.
4) Collect the solution from the last chamber and detect whether there is any fluorescence.
5) Use the camera of the hardware to find out whether there is any fluorescence and compare the data.
1) Prepare polyacrylamide gel according to standard protocol. The parameters are showed below:
2) At this point, the gel can either be transferred to a membrane or stained with Coomassie blue (see below).
3) Place gel in a plastic container, cover over with isopropanol fixing solution and shake at room temperature (RT). For 0.75 mm-thick gels, shake for 10 to 15 min; for 1.5 mm thick gels, shake for 30 to 60 min.
4) Pour off fixing solution, cover over with Coomassie blue staining solution and shake at RT for 2 h.
5) Pour off staining solution, ish the gel with 10% acetic acid to destain and shaking at RT overnight.
1. Transformation:
1) Transform E. coli BL21star (DE3) with pET28a + SAHS plasmids.
2) Inoculate each single colon with 10 mL of LB broth culture with kanamycin at 60 mg/mL.
3) Shake each culture at 200 rpm, 37 ˚C overnight.
2. Induced expression:
1) After about 3 hours of incubation (when the OD600 reaches to 0.5), add IPTG at a final concentration for 1 mM to induce expression.
2) Incubate the cultures for 8 h and pellet the cells at 7,000g, 25 ˚C for 10 min.
3. Centrifugation and lysis:
1) Store the cells pellet at -20 ˚C until use.
2) Resuspend the pellets in 12.5 mL PBS.
3) Lyse the cells by Ultrasonic Cell Disruptor.
4) Cool the lysates at 4 ˚C for 30 min.
5) Remove insoluble components by centrifugation at 25,000g, 4 ˚C for 20 min.
6) Harvest the supernatants to purify the SAHS protein.
4. Chromatography:
1) Equilibrate the Ni-NTA Agarose with PBS and then adjust the A280 value to the neutral line.
2) Load appropriate amount of supernatant into the Ni-NTA Agarose column and ish with lysis Buffer until the A280 value is below 0.01.
3) Clean the column with PBS until the A280 value is below 0.01.
4) Elute the SAHS protein with Elution Buffer and collect all eluates according to its A280.
5) Heat treatment: Collect all equates and place them in water bath at 85 ˚C for 15min. Remove insoluble components by centrifugation at 13,000g for 20 min.
1) Preferably, select single colony of E. coli from fresh LB plate for inoculating a 10 mL 2XYT overnight (O/N) starter culture. Alternatively, streak out frozen glycerol stock of bacterial cells onto LB plate, grow plate O/N, and then select single colony for starter culture. Grow 10 mL starter culture O/N in 37°C shaker (250 rpm).
2) Inoculate 1L of 2XYT media and place culture in 37°C shaker. Grow cells and measure OD600 every 45 min. When the OD600 equals 0.6-0.9 (log phase growth), remove the cells from the shaker and place on ice.
Note: It is very important to keep the cells at 4°C (or on ice) for the remainder of the procedure.
3) Split the 1 L culture into four equal parts by pouring ~250 mL of culture into each chilled 250mL Corning pointed bottle.
4) Spin (#1) in GPR centrifuge at 4000 rpm, 25 min at 4°C.
(if you chose to use the J6/ JS-4.2 rotor (E. Davidson Lab), use 1L bottles , fill half full, spin 4000rpm, 20min, at 4°C.)
5) Place bottles on ice. Remove supernatant immediately as cell pellet begins to lift off quickly. Gently resuspend each pellet in 200 mL ice-cold dH20.
6) Spin (#2) in GPR centrifuge at 4000 rpm, 25 min at 4°C.
7) Place bottles on ice. Remove supernate. Gently resuspend each pellet in 100ml of ice-cold dH20.
8) Spin (#3) in GPR centrifuge at 4000rpm, 25min at 4°C.
9) Place bottles on ice. Remove supernatant. Gently resuspend each pellet in 20mL ice-cold 10% glycerol. For each pair of 250 mL Corning bottles, transfer both 20 mL cell suspension into one chilled 50 mL conical tube- therefore you should end up with two 50 mL conical tubes on ice where each tube contains ~40 mL of cells in 10% glycerol.
10) Spin (#4) in GPR centrifuge at 4000 rpm, 10 min at 4°C.
11) Place tubes on ice. Remove supernatant. Gently resuspend each cell pellet in 1 mL of ice-cold 10% glycerol. Final OD600 of resuspended cells » 200-250.
12) With cell suspensions on ice, prepared 70l aliquots of cells in pre-chilled 1.5 mL eppendorf tubes. Snap freeze tubes containing cells in liquid N2. Store frozen cells at -80°C.
Note: liquid N2 very hazardous- use carefully and don't contact N2 directly!
1) Thaw electrocompetent cells on ice.
2) Transfer 50 mL of electrocompetent cells to a pre-chilled electroporation cuvette with 1 mm gap.
3) Add 1 mL of the assembly product to electrocompetent cells.
4) Mix gently by pipetting up and down.
5) Once DNA is added to the cells, electroporation can be carried out immediately. It is not necessary to incubate DNA with cells.
6) Add 950 mL of room-temperature SOC media to the cuvette immediately after electroporation.
7) Place the tube at 37°C for 60 minutes. Shake vigorously (250 rpm) or rotate.
8) Warm selection plates to 37°C.
9) Spread 100 mL of the cells onto the plates.
10) Incubate overnight at 37°C.
1) Transfer the plasmid pKD46 into E.coli DH5α, and Incubate at 30° for 12h.
2) Make electro-competent cell with E.coli DH5α contains pKD46.
3) PCR amplification of CAHS fragments, and add two segments homologous arm.
4) DNA gel electrophoresis and gel extraction and purification.
5) Transfer the fragments into the electro-competent cell.
6) Add 100 mM L-Arabinose, then induced for 90min at 37°.
7) Activate for 2h in 37° shaking incubator.
8) Add 1 M IPTG to make the final concentration to be 1 mM.
9) Add 250 μL of the bacteria solution to plate.
10) Incubate at 37°C.
11) That the colony’s color turning to be red is regarded as success.
1) Set up the following reaction on ice: 
* Optimized cloning efficiency is 50–100 ng of vectors with 2–3 fold of excess inserts. Use 5 times more of inserts if size is less than 200 bps. Total volume of unpurified PCR fragments in Gibson Assembly reaction should not exceed 20%.
** Control reagents are provided for 5 experiments.
*** If greater numbers of fragments are assembled, additional Gibson Assembly Master Mix may be required.
2) Incubate samples in a thermocycler at 50°C for 15 minutes when 2 or 3 fragments are being assembled or 60 minutes when 4-6 fragments are being assembled. Following incubation, store samples on ice or at –20°C for subsequent transformation.
Note: Extended incubation up to 60 minutes may help to improve assembly efficiency in some cases (for further details see FAQ section).
3) Transform NEB 5-alpha Competent E. coli cells (provided with the kit) with 2 μL of the assembly reaction, following the transformation protocol.
1) Add a total of 100 μL of protein sample into centrifuge tubes.
2) Pre-freezing: put the centrifuge tubes into the refrigerator to freeze at -80 ℃ for 12h.
3) Operate the lyophilizer: start the lyophilizer to allow the chamber temperature to drop to -50℃.
4) Freeze-drying: after pre-freezing of the sample, put it into the lyophilizer. Then sublimation for 24 hours under vacuum condition which called Primary drying; Lastly, increase shelf temperature to about 30 ℃ to desorbe the residual water under vacuum condition.
5) Store the lyophilized sample under low temperature and dry conditions.
