Experiments
1. Polymerase Chain Reaction (PCR)
1.1 Preparing Fanta solution
• Combine all components:
Reagent volume Concentration
DNA sequence (template) 1μl
primer-f 1μl 10μmol/ml
primer-r 1μl 10μmol/ml
DNA Polymerase 25μl
double distilled water(ddwater) 22μl
Total 50ml
1.2 Starting the PCR reaction
• Place the solution into PCR machine
• Start machine with following settings:
Step # Temperature (°C) Time Purpose
1 95 3min Break hydrogen bonds between nucleotides
2 95 30s Activate DNA polymerase
3 55 30s Primers attach to sense & antisense strands
4 72 3min DNA polymerase builds a complimentary strand
5 Repeat steps 2-4 25 times
6 72 5min Stabilize DNA
7 12 - Storage
2. Plasmid Construction
2.1 Preparing solutions for restriction enzymes.
• For pMD19-xynA (xynA) plasmid:
For pMD19-xynA (xynA) plasmid For pUC57-PKC-OP (PKC) plasmid
Reagent Volume (μl) Reagent Volume (μl)
Pet28 a plasmid 5 Pet28 a plasmid 5
pMD19-xynA plasmid 5 PKC plasmid 5
Nhe I 1 Xba I 1
Hind III 1 BamH I 1
ddwater 42 ddwater 42
Cut smart 6 Cut smart 6
Total 60 Total 60
2.2 Preparing agarose regular gel for gel electrophoresis
• Add 0.4g Agarose Regular to 40ml TAE Buffer
• Mix together and bring to a boil in a microwave (stop immediately once boiling)
• When the solution is cool enough to touch, remove from microwave and add 5μl GelRed
• Cool the solution away from light.
• Pour into gel electrophoresis mold with the comb inserted.
• Remove when solidified and place in gel electrophoresis machine. The end with indents left by the comb should be facing the cathode.
2.3 Screening of target genes (gel electrophoresis and retrieving genes)
• Add 20μl PCR products, enzymatic plasmid cutting products, and marker (control group) into individual indents in the agarose gel.
• Conduct electrophoresis at 140V for 30 minutes.
• Observe the gel under blue light. Bands of DNA show up as brightly lit.
• Slice the desired DNA fragment from the gel.
• Place the gel in a labeled microfuge tube.
• Add 650μl gel dissolving buffer (adjust amounts according to instructions on the kit) to the tube and immerse in 56˚C water bath.
• Transfer solution to adsorption columns and centrifuge at 5100g for 5 minutes, 4 times (add 650μl Wash Buffer in 2-3 times)
2.4 Enzymatic plasmid connecting
• Mix the solution and let it sit for 1 hour in 16°C.
Reagent Volume (μl)
Pet28 a plasmid 11.4
enzymatic plasmid cutting products (xynA) 0.6
T4 ligase 1
T4 ligase buffer 2
ddH2O 5
Total 20
2.5 Homologous recombination
• For Xyloglucosidase (Xyl3A) and Acetylxylan esterase gene (CcXynA)
• Mix the solution and wait 30min in 37°C
Reagent Volume (μl)
Mix Buffer (5x) 2
Homologous recombinase 1
Pet28 a plasmid 0.5
Xyl3A or CcXynA 1.5
ddwater 5
Total 10
3. Amplification of Target Plasmids
3.1 Preparing LB culture media
• Prepare liquid and solid culture media in separate flasks
Liquid Solid
Reagent Amount Reagent Amount
ddwater 294ml ddwater 200ml
NaCl 3.3g NaCl 2g
Yeast 2g Yeast 2g
Tryptone 3.3g Tryptone 2g
Total 300ml Agar 3g
Total 200ml
3.2 Transformation of TOP10 competent cells
• Add 100μl pET28A-xynA, pET28-PKC, pET28a-ccXynA, and pET28a-xyI3A into separate test tubes each containing 100μl TOP10 competent cells and place on ice for 30 minutes.
• Immerse in 42°C water bath for 60 seconds.
• Place on ice for 2 minutes.
• Add 1ml LB culture media (liquid) to each tube and let sit for 1 hour.
• Inoculate the TOP10 competent cells onto solid LB culture media for 12 hours.
• Pick single colonies and inoculate into 5ml liquid LB culture media that contain 250μg Kanamycin and allow bacteria to grow for 12 hours.
3.3 Plasmid extraction from TOP10 cells
• Add 250μl Buffer S into an absorption column, then centrifuge at 12000g for 1 minute. • Centrifuge the 5ml liquid culture medium at 8000g for 2 minutes and discard the resulting liquid (keep the sediment).
• Add 250μl of SP1 Buffer into the tube and mix well.
• Add 250μl of SP2 Buffer into the liquid and mix gently until it becomes clear.
• Add 350μl SP3 Buffer and mix gently until precipitates form, then centrifuge the tube at 12000g for 10 minutes
• Add resulting liquid to the absorption column, then centrifuge at 8000g for 1 minute and discard the liquid.
• Add 500μl of DW1 Buffer and centrifuge at 9000g for 1 minute and discard the liquid.
• Add 500μl Wash solution and centrifuge at 9000g for 1 minute and discard the liquid. Repeat this step again (total 2 times)
• Centrifuge the absorption column at 9000g for 2 minutes and discard any liquid.
• Add 50μl Elution Buffer and centrifuge at 9000g for 1 minute. Keep the resulting liquid.
• Use the resulting liquid to check for the density of plasmids
• Serialization and Identification of DNA sequences.
4. Protein Expression and Purification
4.1 Preparing Buffers
• Create the following solutions:
His Buffer A (500ml pH 7.4) His Buffer B (250ml pH 7.4)
Reagent Amount Reagent Amount
Na2HPO4·2H2O 1.78g Na2HPO4·2H2O 0.89g
NaCl 14.6g NaCl 7.3g
Imidazole 1.02g Imidazole 8.5g
ddwater 500ml ddwater 250ml
4.2 Transformation of Bacteria and Expression of Genes
• Mix 100 ng of pET28A-xynA, pET28-PKC, pET28a-ccXynA, and pET28a-xyI3A with 100μl of E.coli BL21(AI) Strain competent cells (BL21 competent cells) in separate tubes. Place on ice for 30 minutes.
• Immerse in 42°C water bath for 60 seconds.
• Place on ice for 2 minutes.
• Add 1ml liquid LB culture media and let the culture grow for 12 hours.
• Inoculate the BL21 competent cells onto solid LB culture medium for 12 hours.
• Pick single colonies and inoculate into 5ml liquid LB culture media containing 250μg Kanamycin for 12 hours
• Inoculate into 100ml liquid LB culture media at room temperature for 2-3 hours.
• When the detected OD is at 0.4-0.6, add 0.24mM IPTG and culture overnight.
4.3 Protein purification
• Centrifuge 100ml cultures at 1530g for 15min. Discard the liquid (keep sediment).
• Add 20ml of His Buffer A and mix well so that there is no more sediment at the bottom of the tubes.
• Pack ice in a container and place the tube containing the solution in it, then sonicate the solution for 5 minutes with settings for 3-second work and 2-second pause; collect the liquid.
• Centrifuge at 9000g or 20 minutes. Keep the liquid but discard of the sediment (keep 50μl samples of both)
• Add 500μl of Ni-NTA beads and let sit for 2 hours at 4˚C.
• Centrifuge at 500g for 5 minutes and collect the sediment (discard the liquid)
• Add 5ml of Buffer A and mix so that the sediment is suspended, then transfer to beads column.
• Add 1ml of His Buffer A 5 times, waiting for all the liquid to filter before each addition.
• Add 500μl of His Buffer B 6 times, waiting for all the liquid to filter before each addition. Collect the final liquid.
• Use His buffer B to elute protein 500μl (by 5 times) and collect the liquid.
• Measure the concentration of protein in the liquid.
4.4 Verification of Proteins.
4.4.1 SDS PAGE
• Mix protein gel solution (components shown below) and solidify to a thickness of 1.5mm
Protein gel solution Buffer Improved Coagulation Promotion Solution
Resolving layer 4ml 4ml 80μl
Stacking layer 1ml 1ml 20μl
• Mix 500ml of protein gel buffer
Reagent Volume
Tris-Glycine 50ml
ddwater 450ml
• Mix 100ml of coomassie brilliant blue decolorizing solution
Reagent Volume
ethanol 40ml
Acetic acid 10ml
ddwater 50ml
• Inject samples and a marker into the wells.
• Add 12.5μl of G250 Loading into target protein and inject into a well
• Electrophoresis at 180V for 1 hour.
• Use coomassie brilliant blue to dye the gel for 1 hour and decolorize for 1 hour.
• Imaging of gel
4.4.2 Enzyme activity measurement by DNS
• Prepare 50ml of MnCl2 solution at a concentration of 5mM
• Add 0.15g Xylan into 30ml of the MnCl2 solution.
• Prepare 1ml each of xynA, PKC, xyl3A, and cCxynA
• Divide the experiment into four groups
Group 1 350μl of xylan solution + 50μl of enzyme
Group 2 70μl of xylan solution + 280μl of MnCl2 solution + 50μl of enzyme
Group 3 14μl of xylan solution + 336μl of MnCl2 solution + 50μl of enzyme
Control group 350μl of xylan solution + 50μl of enzyme (denature)
• Immerse all groups in a 37˚C water bath 10 minutes.
• Add 800μl of DNS solution and boil for 5min to denature all enzymes.
• Calculate the enzyme activity.