Team:Goettingen/Experiments

• HOME
• TEAM
• PROJECT
  • Description
  • Experiments & Protocols
  • Results
  • Design
• PARTS
  • Team Parts
  • Basic Parts
  • Composite Parts
• NOTEBOOK
• ATTRIBUTIONS
• COLLABORATIONS
• HUMAN PRACTICES
• SAFETY
• MODELING

LB Medium

-       Add the following components

NaCl	10 g
Yeast extract	5 g
Tryptone	10 g
H2O	Add to 1 L

• To obtain solid media add 15g/L agar.

-       Autoclave at 121 ^oC for 20 min.

-       The preferred antibiotic is added with the proper concentration (e.g Ampicilin is added to a final concentration of 100 µg/ml)

• To the liquid medium antibiotic is added upon usage.
• For the preparation of agar plates antibiotic is added after autoclaving the media and cooling it to 60 ^oC. 

Plasmid Extraction - using peqGOLD Plasmid Miniprep Kit I (PEQLAB Technologies)

Select few TOP10/BL21 E.coli transformed colonies from the LB Amp plates containing the propagated transformed colonies and inoculate them into liquid LB medium (5 ml) containing preferred antibiotic of desired concentration in each tube.

Incubate the LB tubes with the transformed colonies at 37°C in a shaker for about 12 – 15 hours (overnight) with agitation (150 rpm).

Extract the plasmids from the incubated LB cultures using the peqGOLD Plasmid Miniprep Kit I.

Centrifuge the culture at 10000 x g for 2 min to obtain the pellet and repeat the process until the culture is completely centrifuged. Store the pellet of 1 ml of the culture at -20°C for future use.

Resuspend the pellet in 250 µl of Solution I of the Kit (which is normally kept at 4°C because of the RNase) and vortex until the pellet is resuspended.

Add 250 µl of Solution II to the resuspended mixture and gently mix by inverting and rotating the tubes 6 -10 times to obtain a cleared lysate. Incubate the mixture for 2 min to obtain optimum results.

Add 350 µl of Solution III to the cleared lysate and gently mix by inverting the tubes 6 -10 times until a flocculent white precipitate is formed. Centrifuge at 10000 x g for 10 min at room temperature.

Transfer the clear supernatant to a fresh PerfectBind DNA Column in a 2 ml Collection Tube. Centrifuge the Column with the Collection Tube for 1 min at 10000 x g at room temperature. Discard the flow-through liquid.

Add 500 µl of PW Plasmid buffer to the PerfectBind DNA Column in the Collection Tube and centrifuge for 1 min at 10000 x g. Discard the flow-through.

Add 750 µl of DNA Wash buffer to the PerfectBind DNA Column in the Collection tube and centrifuge for 1 min at 10000 x g. Discard the flow-through. Repeat this step to obtain optimum results.

Place the PerfectBind DNA Column in the Collection tube and centrifuge for 2 min at 10000 x g to dry the column matrix. This step is essential to remove ethanol from the column.

Place the PerfectBind DNA Column into a fresh 1.5 ml Eppendorf tube. Add 50 µl of pre-warmed sterile deionized water directly to the binding matrix in the PerfectBind DNA Column and centrifuge for 1 min at 5000 x g to elute the DNA.

Discard the PerfectBind DNA Column and store the eluted plasmid DNA at -20°C.

Check the concentration of the plasmids by using a NanoDrop and note down the values for future experiments.

Plasmid Extraction - using QIAprep Spin Miniprep Kit (QIAGEN)

This protocol describes the purification of plasmid DNA from 5 ml overnight cultures of E. coli grown in LB medium using the QIAprep Spin Miniprep Kit (QIAGEN)

• Add the provided RNase A solution to buffer P1, mix, and store at 4 ^oC.
• Add ethanol (96–100%) to Buffer PE before use.
• All centrifugation steps are carried out at 17,900 x g (13,000 rpm) in a conventional table-top microcentrifuge at room temperature.

 

- Add the proper antibiotic with the proper concentration to 5 ml LB medium (e.g Ampicilin is added to a final concentration of 100 µg/ml).

- Inoculate the medium with the desired E.coli strain and incubate overnight at 37 ^oC with agitation (150 rpm).

- Pellet the overnight culture by centrifugation at 8000 rpm (6800xg) for 3 min at room temperature.

- Resuspend pelleted bacterial cells in 250 μl Buffer P1 and transfer it to a microcentrifuge tube.

- Add 250 μl Buffer P2 and mix thoroughly by inverting the tube 4–6 times. Do not allow the lysis reaction to proceed for more than 5 min.

- Add 350 μl Buffer N3 and mix immediately and thoroughly by inverting the tube 4–6 times.

- Centrifuge for 10 min at 13,000 rpm (~17,900 x g) in a table-top microcentrifuge.

- Apply the supernatant to the QIAprep spin column by decanting. Centrifuge 60 s. Discard the flow-through.

- Wash the QIAprep spin column by adding 500 μl Buffer PB and centrifuging for 60 s. Discard the flow-through.

- Wash QIAprep spin column by adding 750 μl Buffer PE and centrifuging for 30–60 s.

- Discard the flow-through, and centrifuge for an additional 1 min to remove residual wash buffer.

- Place each QIAquick column in a clean 1.5 ml microcentrifuge tube.

- To elute DNA, add 50 μl water (40 – 60 ^oC) to the center of the QIAquick membrane, let the column stand for 1 min, and then centrifuge for 1 min.

Blunt End Ligation in pJET1.2 vector –Clone JET PCR Cloning Kit–Thermo Scientific

 

-       Set up the following componentson ice for the ligation reaction.

Components	Volume
2x Reaction buffer	10µl
Blunt end PCR product	125ng
pJET 1.2 Plasmids	50ng (1µl)
T4 DNA Ligase	1µl
Water(RNase free)	xµl
Total Volume	20µl

-       Vortex briefly and centrifuge for 3-5 sec at 5000 rpm.

-       Carry out the ligation at 20°C for 20 min at room temperature (22-25°C) and then place in ice for 5 min and use for transformation immediately or store at -20°C.

Cloning principle:

• pJET1.2 is a linearized cloning vector which accepts inserts from 6 bp to 10 kb. Since the 5’-ends of the vector contain phosporyl groups, therefore phosphorylation of the PCR products is not required.

• Optimal insert/vector ratio is 3:1. (0.15 pmol ends of insert and 0.05 pmol ends of vector)

• Optimal PCR product quantity for ligation reaction is to be calculated from the Kit protocol, For the length of 2500 bp of PCR product, to have 0.15 pmol ends of the PCR product in the ligation reaction 125 ng of the PCR product should be used.

• For PCR products more than 3 kb, ligation can be prolonged to 30 min.

TOPO® Cloning protocol usingChampion™ pET Directional TOPO® Expression Kits. Thermo Fisher Scientific

• You will perform TOPO® Cloning in a reaction buffer containing salt. Note that the amount of salt added to the TOPO® Cloning reaction varies depending on whether you plan to transform chemically competent cells or electrocompetent cells.

 -    Set up the TOPO® Cloning reaction depending on the transformation method.

Reagents	Chemically Competent E. coli	Electrocompetent E. coli
Fresh PCR product	0.5 to 4 μl (15 – 40 ng)	0.5 to 4 μl (15 – 40 ng)
Salt Solution	1 μl	---
Dilute Salt Solution (1:4)	---	1 μl
Sterile Water	add to a final volume of 5 μl	add to a final volume of 5 μl
TOPO® vector 1	1 μl (15 – 20 ng)	1 μl (15 – 20 ng)
Total Volume	6 μl	6 μl

 -    Mix reaction gently and incubate for 15 - 30 minutes at room temperature (22-23°C).

 -    Place the reaction on ice and proceed with the transformation or store at - 20 °C.

 

• Before transformation into electrocompetent E.coli the salt is removed via microdialysis.  For more information refer to transformation in electrocompetent BL21 E.coli. 

PCR product purification using QIAquick® PCR Purification Kit (QIAGEN)

• Add ethanol (96–100%) to Buffer PE before use.
• All centrifugation steps are carried out at 17,900 x g (13,000 rpm) in a conventional table-top microcentrifuge at room temperature.

 

-       Add 5 volumes Buffer PB to 1 volume of the PCR reaction and mix.

-       Place a QIAquick column in a provided 2 ml collection tube.

-       To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s. Discard flow-through and place the QIAquick    column back in the same tube.

-       To wash, add 0.75 ml Buffer PE to the QIAquick column, centrifuge for 30–60 s. Discard flow-through and place the QIAquick      column back in the same tube.

-       Centrifuge the QIAquick column once more in the provided 2 ml collection tube for 1 min to remove residual wash buffer.

-       Place each QIAquick column in a clean 1.5 ml microcentrifuge tube.

-       To elute DNA, add 50 μl water (40 – 60 ^oC) to the center of the QIAquick membrane, let the column stand for 1 min, and then    centrifuge for 1 min.

Plasmid transformation into chemically competent E. coli

 

-          Thaw chemically competent E.coli cells (BL21 or TOP10) on ice.

-          Add 100 – 250 ng of ligation product. Mix gently, do not pipette up and down.

    (add 30 – 60 ng pET 101 construct depending on the cloning protocol).

-          Place on ice for 5 – 15 min.

-          Heat shock 45-50 seconds at 42 °C. 

-          Incubate 2-5 min on ice.

-          Add 300 - 500 μl of LB medium.

-          Incubate at 37°C for 1 hour with shaking.

-          Plate 100 – 150 μl on prewarmed LB plate containing the proper antibiotic. Centrifuge the rest for 2 min at 5000 xg. Decant the supernatant and move the tube against hard surface to suspend the pellets in the residual medium. Plate the cells on another LB plate containing the proper antibiotic. 

-          Incubate LB plates at 37°C overnight.

-          Check plates for colonies growth.

 

• For positive control set up another transformation using an equal amount of a circular plasmid possessing the proper antibiotic resistance.

 

 

Preparation of competent E.coli cells

• Method 1: Low amount of competent cells

Materials:

Buffer RF1 (150 ml): 1.44 g RbCl

1.16 g MnCl₂.4H₂O

3.6 ml Potassium acetate (1M)

                                  pH 7.5 with acetic acid

Buffer RF2 (80 ml):  1.6 ml MOPS (0.5 M) stock solution

  PH 6.8 with NaOH

                                  0.096 g RbCl

                                  0.88 g CaCl₂.2H₂O

Procedure

-          Inoculate a 4 ml culture either with a single colony or with a cryoculture of the desired E.coli strainand incubate the culture with agitation overnight at 37°C

_-                     Inoculate a 300 ml shake flask containing 100 ml LB medium with the overnight culture to an OD₆₀₀  of 0.05 and grow the culture at 37°C until the OD₆₀₀is about 0.3

-          Transfer the cells into two 50 ml falcon tubes, incubate the cultures for 15 minues on ice and harvest the cells by centrifugation for 15 min at 5000 rpm and 4°C. Discard the supernatants.

-          Resuspend the cells in 1/3 of the original volume (~16 ml/50 ml) of buffer RF1, incubate the cells again on ice and harvest the cells by centrifugation for 15 min at 5000 rpm and 4°C. Discard the supernatants.

-          Resuspend the cells in 4 ml of buffer RF2 and incubate the suspensions for 15 min on ice. Prepare the Eppendorf tubes and liquid nitrogen.

-          Put 0.4 ml of the cell suspension into the Eppendorf reaction tubes and freeze the cells by transferring them immediately to the liquid nitrogen. Store the competent cells at -80°C

 

• Method 2 (High amount of competent cells, time consuming)

Materials

TB                       3.46 g Piperazine-N,N'-bis(2-ethanesulfonic Acid) Pipes, 11 mM

2.2 g CaCl₂.2H₂O (15 mM)

18.64 g KCl (250 mM)

                            PH 6.7, autoclave, add 55 ml MnCl₂ (1M, sterile) to a final volume of 1 l

SOB-Mg              20 g/l tryptone (2%)

                             5 g/l Yeast extract (0.5%)

                             0.58 g/l NaCl (10 mM)

                            0.186 g/l KCl (2.5 mM)

 

SOB                    SOB-Mg

                           10 mM MgCl₂

10 mM MgSO₄

LB liquid medium

DMSO (Dimethyl sulfoxide)

 

Procedure:

-          Inoculate a 20 ml culture either with a single colony or with the cryoculture of the desired E.coli strainand incubate the culture with agitation for 20 h at 28°C

-          Inoculate a 250 ml SOB medium supplemented in a 2 l shake flask and grow the cells to an OD₆₀₀  of 0.5- 0.9 (20-20 h) at 18°C and 200-250 rpm

-          Incubate the whole flask for 10 min on ice. Collect the cells by centrifugation for 10 min at 4°C and 5000 rpm. Resuspend the cells in 80 ml of ice-cold TB and incubate them for 10 min on ice. Collect the cells by centrifugation for 5 min at 5000 rpm.

-          Resuspend the cells in a 20 ml of ice-cold TB. Add DMSO to a final concentration of 7% (1.4 ml) and gently shake the falcon tube.

-          Transfer 0.2 ml aliquots into labelled eppendorf reaction tubes and freeze the cells in liquid nitrogen. Store the cells at –80°C.

 

 

Esterase activity test

Materials:

Substrate- 1mM 4-nitrophenyl butyrate prepared in Na-Phosphate buffer (pH8.0)

Protein sample

Procedure:

-          Add 2 µl of the protein sample to 2ml of the substrate and incubate for 5 minutes

-          The colour change from white/transparent to yellow is observed which indicates the presence of the enzyme

 

 

PCR Gel extraction, peqGOLD Gel Extraction Kit

 

-          Fractionate DNA fragments by running a agarose gel (Do not stain the gel with Ethidium bromide or expose the DNA to UV for too long).

-          Add equal volume of Binding Buffer to the gel slice and incubate at 65ᵒC for 8 min. Vortex or mix every 2 to 3 min until the agarose dissolves completely. (0.2 g of gel equivalent to 0.2 ml)

-          Pour the mixture into PerfectBind DNA column (which is placed in a 2 ml collection tube) and centrifuge for 1 min at 10,000 x g.(max. 750 µl) Discard the flow-through and place the PerfectBind DNA column in the same tube. Repeat the steps if required.

-          Add 300 µl of binding Buffer to the PerfectBind DNA column for the washing the contaminants and centrifuge for 1 min at 10,000 x g. Discard the flow-through and place the column in the same tube

-          Add 750 µl of CG Wash Buffer to the PerfectBind DNA column for the wash, incubate for 2 to 3 min and centrifuge for 1 min at 10,000 x g. Discard the flow-through and place the column in the same tube. Repeat this step once more.

-          Centrifuge the PerfectBind DNA column once more in the 2 ml collection tube for 1 min at 10,000 x g to remove the residual wash buffer.

-          Place the PerfectBind DNA column in a clean 1.5 ml eppendorf tube.

-          Add 50 µl of pre-warmed sterile water to the PerfectBind DNA column and incubate for 2 to 3 min (normally in a 2 step process of 30 µl in first elution step and 20 µl in second elution step) and centrifuge at 5,000 x g for 1 min.

-          Store the purified DNA at -20ᵒC.

 

Electroporation of BL21 cells with pJET_RFP

 

-          Apply microdialysis for 30 -45 min by applying the transformation mixture (plasmid+buffer) on (Millipore® MF-Millipore™ DNA Fillter Paper for Dialysis of DNA and Proteins – capitol scientific) after placing the membrane on sterile water.

-          Defreeze 40 µl aliquots of chemically competent cells on ice

-          Mix 50-200 ng DNA with the cells. (desalted)

-          Transfer the culture without any air bubbles into pre-cooled electroporation cuvettes (40 µl maximum) and incubate on ice for 10 minutes.

-          Electroporate using the electroporator with 1.25 mV, 5 decharge time.

-          Immediately after electroporation, transfer 300 µl room temperature LB medium on top of the cells  and transfer it into an 1.5ml fresh E-cup

-          Incubate the culture for 1 hour at 37°C and 150 rpm

^-                     Spread a 100 µl from the dilution series (10^-3 to 10^-6) on a pre-warmed LB plate containing ampicillin

^-                     Incubate the plates overnight at 37°C 

 

Media preparation for cellulase activity screening

A: LB_ agar base

• Add the following components 

 

Yeast extract	5 g
Tryptone	10 g
NaCl	10 g
H2O	Add to 1 L
Agar	15 g

 

• Make sure to put a stirrer in the bottle.
• Sterilize the culture medium by autoclaving at 121 ^oC for 20 min.  

 

B: Substrate for cellulase screening

In 15 ml falcon tube, the substrate with final concentration 1% (w/v) is prepared in 96% (v/v) ethanol. For-example, to prepare 10 ml stock solution, weight 0.1 g of AZCL-HE-Cellulose and transfer it to 15 ml falcon tube, then add 96% (v/v) ethanol until the volume reached 10 ml.

The stock solution will be stored at +4 °C.

C: Prepare the agar plates

When the medium cools down to around 60°C, put the bottle containing LB-agar base on a magnetic mixer. At the same time, disperse the substrate by flip the falcon tube several times. Then, pour the substrate into the LB-agar base gently until the substrate suspend evenly in the agar medium (For how much substrate should be poured, ask the supervisor). Other reagents like antibiotic can also be added. Ca. 3-5 ml substrate per Liter medium.

D: Preparation of agar plates contacting cellulose substrate

After dispersing substrate and adding antibiotic to LB-agar , pour the medium quickly with continuous stirring onto the plates and make sure to make a thin layer of medium. Let the plates to dry and store them at 4 °C.

 

E: Another method of pouring Substrate for cellulase screening on to the agar plates

Rather than using normal pouring method one can first prepare regular LB plates having  just a thin layer of LB. After preparation of substrate for cellulase screening add the proper antibiotic to it and then pour this mixture on top of this thin LB layer with constant stirring. Let the plates to dry and then store at 4 °C.

 

 

 

 

 

Cellulase activity screening

 

• Streak Competent Top10 E. coli cells or Competent BL21 cells transformed with appropriate vector containing cellulase construct onto agar plates containing cellulose substrate.
• Incubate plates at 37^oC for minimum 3-4 days (timing can be extended depending on bacterial strain).
• After 3-4 days look for plates having clear zone of activity around cellulose substrate.

Esterase Activity plates, with 1% Tributyrin

 

To 500ml of LB Media add 7,5g of Agar and 5ml of Tributyrin and homogenize with a mixer.

This culture medium must be directly sterilized by autoclaving at 121˚C for 20 min.

If you wait too long it will be inhomogeneous again!

When the medium cools down enough, the antibiotic can be added.

 

Result: Halo formation is visible around the positive clones.

Phosphatase Activity plates, Sperber media

 

A: Stock reagents

1M IPTG (4,76 g in 20ml Millipore-H2O) filter with blue 0,22 um sterile filter and freeze at -20˚C

50mg/ml Kanamycin in Millipore H2O, filter with blue 0,22 um sterile filter and freeze at -20˚C

100mg/ml Ampicillin in 50% ethanol, filter with blue 0,22 um sterile filter and freeze at -20˚C

25mg/ml BCIP (in DMF) filter with blue 0,22 um sterile filter and keep in a falcon tube wrapped with aluminum foil at 4˚C. BCIP: Biomol Nr. 2291 (MG 433,64)

Glycerol (99%), autoclaved and kept at room temperature

 

B: Sperber medium

1g Yeast extract

3,5 ml 50% w/w Phytic acid

0,2g CaCl2

0,5g MgSO4

Adjust the pH to 7,2 with NaOH

Ad 2L of Millipore H2O

32g agar

Autoclave

 

After autoclaving the medium must cool down to ca. 50˚C. Now glycerol, IPTG, BCIP and the respective antiobiotic can be added.

 

For 2 L medium:

2ml BCIP

2ml 1M IPTG

2ml Ampicllin or Kanamycin

40mL Glycerol

The media is now ready for plating

Result: On Sperber medium phosphatase-recombinant colonies should develop a distinct color blue after 2 days.

 

Competent Cell Test Kit, RFP construct (iGEM)

Before using our competent E. coli TOP10 cells in the important experiments, we used the Competent Cell Test Kit to test the efficiency of our competent cells!

The kit includes five vials of each different DNA concentration: 50pg/μl, 20pg/μl, 10pg/μl, 5pg/μl, 0.5pg/μl of purified DNA from BBa_J04450 (RFP construct) in plasmid backbone pSB1C3.

 

Protocol as distributed by iGEM (modified)

Spin down the DNA tubes from the Competent Cell Test Kit to collect all of the DNA into the bottom of each tube prior to use. A quick spin of 20-30 seconds at 8,000-10,000 rpm will be sufficient. Note: There should be 50 µL of DNA in each tube sent in the Kit.

Thaw competent cells on ice. Label one 2.0 ml microcentrifuge tube for each concentration and then pre-chill by placing the tubes on ice.

Pipet 1 µL of DNA into each microcentrifuge tube. For each concentration, use a separate tube.

Pipet 50 µL of competent cells into each tube. Flick the tube gently with your finger to mix. Incubate on ice for 30 minutes. Pre-heat heating block now to 42°C.

Heat-shock the cells by placing onto the heating block for 1 minute.

Immediately transfer the tubes back to ice, and incubate on ice for 5 minutes. This helps the cells recover.

Add 200 µL of LB media per tube, and incubate at 37°C for 1 hours. Prepare the LB-Cam (Chloramphenicol) agar plates during this time: label them.

Pipet 20 µL from each tube onto the appropriate plate, and spread the mixture evenly across the plate. Do triplicates (3 each) of each tube if possible, so you can calculate an average colony yield. Incubate at 37°C overnight. Position the plates so the agar side is facing up, and the lid is facing down.

Count the number of colonies on a light field or a dark background, such as a lab bench. Use the following equation to calculate your competent cell efficiency. If you've done triplicates of each sample, use the average cell colony count in the calculation.

(colonies on plate) / ng of DNA plated x 1000ng/µg

Note: The measurement "ng of DNA plated" refers to how much DNA was plated onto each agar plate, not the total amount of DNA used per transformation. You can calculate this number using the following equation:

1 µL x concentration of DNA (refer to vial) x (volume plated / total reaction volume)

NOTE: Since this protocol led to a very low transformation efficiency we repeated the experiment with 5 µL RFP construct each instead of 1 µL and plated 100 µL instead of 20 µL.

 

Results

Competent cells should have an efficiency of 1.5x10⁸ to 6x10⁸ cfu/µg DNA, where "cfu" means "colony-forming unit" and is a measurement of cells.

Here are some sample results:

DNA concentration	0.5pg/μl	5pg/μl	10pg/μl	20pg/μl	50pg/μl
# of colonies	10 - 20	120 - 170	280 - 360	480 - 802	500 - 1000+

 

Experiments & Protocols

Describe the experiments, research and protocols you used in your iGEM project.

What should this page contain?

• Protocols
• Experiments
• Documentation of the development of your project

Inspiration

• 2014 Colombia
• 2014 Imperial
• 2014 Caltech