Team:TPHS San Diego/Notebook
Day 1
Miniprep bacteria with pBAD-D4 (name of the plasmid in which we will be inserting the Chitinase genes, tags, etc.) to isolate the pBAD backbone
Final DNA concentration: 123.7 ng/μL
Day 2
Restriction digest using BamHI and EcoRI to check for bacterial transformation to check to make sure that the plasmid is the expected length (will also send samples for sequencing)
Wells: 1. DNA Ladder. 2. Just EcoRI 3. Just BamHI. 4. No enzyme. 5. Both enzymes
Day 3
Made KPi Buffer… (used in Chitinase Assay)
- Prepare 800 mL of dH2O in a suitable container.
- Add 2.405 g of K2HPO4 to the solution.
- Add 11.73 g of KH2PO4 to the solution.
- Add distilled water until volume is 1 L.
Day 4
Started Cloning of pBAD-GST-ChiA-FLAG construct.
(Function of GST and FLAG: these are protein tags (onto chitinase) to purify and detect chitinase respectively)
Did the restriction digest portion, will do gel purification, ligation, and plating tomorrow
For protocol click here
Day 5
Ran gel of restriction digest of pBAD only and did Gel Purification (very straightforward after PCR, you want only the copied DNA) of restriction digest of GST/gBlock as we want to preserve the amount of DNA gBlock that we have and will lose less sample via PCR purification.
Final concentrations:
pBAD: 22 ng/μL
gBlock: 10.6 ng/μL
Did DNA ligation and plated BL21 competent cells cloned with GST-ChiA full construct (complete protocol is linked in yesterday’s log)
Day 6
Selected 10 colonies from Vector+Insert plate and put in 4 mL of LB+Ampicillin (LB is nutrients for bacterial growth, Ampicillin assists selection of transformed bacteria) media. Incubate in 37 ºC shaker for 24 hrs. Also, did restriction digest and gel on pBAD-D4 vector using MluI and HindIII to check and make sure the enzymes are cutting properly. (If DNA length match expected length, then enzymes are working properly) There is a chance we will have to do ligation and stuff again because there aren’t that many colonies. We will most likely use primers to enhance the gBlock/insert DNA and then try again. Depending on how these colonies turn out after we sequence them.
Vector+Insert colony
Day 7
Did Miniprep of the 10 bacteria colonies that we selected from Wednesday. Used NanoDrop machine to find DNA concentrations of all 10 samples.
| Sample 1: 97.1 ng/μL | Sample 2: 39.6 ng/μL | Sample 3: 47.3 ng/μL |
| Sample 4: 47.0 ng/μL | Sample 5: 41.8 ng/μL | Sample 6: 57.8 ng/μL |
| Sample 7: 33.6 ng/μL | Sample 8: 51.7 ng/μL | Sample 9: 41.5 ng/μL |
| Sample 10: 23.0 ng/μL | Sample pBAD-D4: 123.7 ng/μL |
Then we chose a specific restriction enzyme to cut both the original pBAD-D4 plasmid and our constructed plasmid such that we can distinguish between the two based on the length of their base pairs and the number of cuts that are made. We chose EcoRI-HF. This is in order to check that the plasmids that we are using are what we think they actually are.
We want to have 250 ng per restriction digest reaction. Add 2 μL of buffer, 1 μL of enzyme, and fill to 20 μL with water. (Always add enzyme last). Then incubate at 37 ºC for 30 mins-1hr.
| Sample | Amount of DNA | Amount of Cut Smart Buffer | Amount of Water | Amount of Enzyme (EcoRI) |
|---|---|---|---|---|
| pBAD-D4 | 2.02 μL | 2 μL | 14.98 μL | 1 μL |
| Sample 1: | 2.57 μL | 2 μL | 14.43 μL | 1 μL |
| Sample 2: | 6.31 μL | 2 μL | 10.69 μL | 1 μL |
| Sample 3: | 5.29 μL | 2 μL | 11.71 μL | 1 μL |
| Sample 4: | 5.32 μL | 2 μL | 11.68 μL | 1 μL |
| Sample 5: | 5.98 μL | 2 μL | 11.02 μL | 1 μL |
| Sample 6: | 4.33 μL | 2 μL | 12.7 μL | 1 μL |
| Sample 7: | 7.44 μL | 2 μL | 9.56 μL | 1 μL |
| Sample 8: | 4.84 μL | 2 μL | 12.16 μL | 1 μL |
| Sample 9: | 6.02 μL | 2 μL | 10.98 μL | 1 μL |
| Sample 10: | 10.87 μL | 2 μL | 6.13 μL | 1 μL |
Make a 1.0% agarose gel with 150 mL 1x TAE buffer and 15 μL of Ethidium Bromide in a medium sized gel frame. Load 10 μL of DNA Ladder and put 4 μL of 6x loading dye into each sample.Run the gel at 175 V for 45 mins-1 hr.
Here is a picture of the gel simulated on a computer
program called SnapGene.
Here is a picture of the actual gel.
Wells 3-12 were extracted from bacterial colonies that all have the same DNA inserted. BUT! When we run a gel or a restriction digest in which all the samples were cut with ECORI the results are not the same. For some samples it is probably due to the enzyme not cutting the DNA, but for the rest it is unknown. We will have to do further testing to figure out what the issue is.
Resolved: The issue was likely caused by the incompatibility of the enzymes in the buffer and poor primer design. When performing PCR, it is important to add restriction sites to the primers so that the product would include the restriction site: this was not done originally. Also, the enzymes used to perform the restriction digest, HindIII-HF and MluI, were not compatible in the same buffer. The HF stands for High Fidelity, indicating that the enzyme has reduced star activity, or reduced tendency to lose specificity, and can be used in a wider range of buffers.
Day 8
Did restriction digest on pBAD-D4 vector using HindIII-HF and MluI-HF. Let incubate overnight.
Day 9
Did PCR on GST-ChiA with MluI forward primers and HindIII reverse primers. (these primers attach restriction sites onto the insert along with a buffer region in case of exonuclease action)
PCR cycle: 66ºC 10 seconds (phusion) 72ºC 1.5 mins
20 cycles
Then did PCR clean up using Qiagen kit (eluted with 50 μL H2O)
Performed restriction digest on PCR product
50 μL DNA+6 μL CutSmart Buffer+2 μL HindIII-HF+ 2 μL MluI-HF
Incubate at 37ºC ~3-4hrs
Made 1% gel and ran pBAD digest and GST-ChiA digest (from above)
GST-ChiA: 60 μL = 12 μL 6x loading dye (36 μL into each well)
pBAD: 50.4 μL = 10 μL 6x loading dye (30 μL into each well)
Used QiaGen gel purification kit to isolate pBAD
1. pBAD extract from 3,772 bp
GST-ChiA extract from ~2.7 kb
Day 10
Also made 5 g of colloidal chitin.
Redid PCR reaction for GST-ChiA. Ran Gel. Cut and purified ~2.7 kb
Used Qubits to find DNA concentrations.
pBAD 23.0 ng/μL GST-ChiA 39.2 ng/μL
Ligate the two pieces together.
Transform the bacteria. (repeated protocol from 7/30 except added primers before)
Plate 50 μL of cells on Amp-LB agar plate.
Incubate at 37C O/N
Day 11
Transformation attempt 2
| Results with Chitinase+Chitin incubation period of 2.5 hrs | 
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We made colloids (a type of mixture between a solution and suspension, meaning that particles are small but larger than those in a solution) of chitin, which we used in a Chitinase Assay to test the viability of using the assay for the experiment. For the assay, the Chitinase concentration was diluted in a series while the amount of chitin colloid was kept constant.
This is how the assay works:vv
- When chitinase digests chitin, chito-oligosaccharides are generated as a product.
- This is digested using ChitO, generating hydrogen peroxide.
- HRP uses the hydrogen peroxide to convert AAP and DCHBS into a pink compound, which allows us to visually detect the presence of chitinase.
- To quantify the amount of chitinase present, a spectrophotometer will be used to detect the absorbance: higher means more concentrated. (absorbance = extinction coefficient * cuvette length * concentration) (chem stuff).
Day 12
Mini-prep colonies that we picked yesterday. Ran a gel and sent the purified DNA for sequencing. Selected 9 colonies:
| Sample | DNA | Buffer | Enzyme | Water |
|---|---|---|---|---|
| General | 250 ng | 2 μL | 1 μL | To 20 μL |
| 1 | 132.1 ng/μL | 2 μL | 1 μL | 15.11 μL |
| 2 | 95.8 ng/μL | 2 μL | 1 μL | 14.39 μL |
| 3 | 70.4 ng/μL | 2 μL | 1 μL | 13.45 μL |
| 4 | 111.4 ng/μL | 2 μL | 1 μL | 14.76 μL |
| 5 | 76.9 ng/μL | 2 μL | 1 μL | 13.75 μL |
| 6 | 105.5 ng/μL | 2 μL | 1 μL | 14.63 μL |
| 7 | 83.6 ng/μL | 2 μL | 1 μL | 14.01 μL |
| 8 | 120.4 ng/μL | 2 μL | 1 μL | 14.92 μL |
| 8 | 132.9 ng/μL | 2 μL | 1 μL | 15.12 μL |
Ran gel using EcoRI, the expected results are the same as above. The first well is 1kb DNA ladder, wells 2-10 are GST-ChiA, and the last well is pBAD-D4 vector cut with EcoRI as a control.vv
This gel is just to check that he plasmid was transformed correctly as we know the restriction sites for the cloned construct. Based on this gel, 7/9 of the clones successfully received the plasmid and we can use all of those clones (except clone 3 and 7) in experimentation.
| Assay (take.1) | Assay (supernatant only) | Results (take.1) | Results (supernatant only) |
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Based on these results, it shows that the assay protocol that we chose is sensitive enough. We performed this assay with commercially purchased chitinase in order to test the sensitivity of the assay protocol that we chose. Based on these results it seems that our protocol could be usable, however we would need to filter the colloidal chitin somehow so that there is less chunks floating around in the solution. Considering, that we now have a potent strain of GST-ChiA, we can soon use this DNA with the assay that we have to identify chitinase activity.
Day 13
The colloidal chitinase particles used in the previous assay test were too large. Redid the assay test with smaller particles. We modified the protocol based on cross references from several other colloidal chitin protocol and decided to increase the volume and chitin to HCl ratio to 1:10. We also increased the incubation period for the 12M HCl and Chitin to 2.5 hrs instead of the original 1 hr. We covered the beaker with foil as it stirred but the vapor form the acid degraded the foil and caused flakes to fall into the foil. We had to scrap it and will remake tomorrow. Also transformed BL21 Cells with complete plasmid and plate 50 μL to LB-AMP plates. Incubate at 37C overnight. Will select colonies and put in shaker O/N.
Day 14
Redid colloidal chitin, select colonies and put in 4 mL LB-AMP and put in shaking incubator (37C O/N)… prepared 10 aliquots: 4 tubes with 2 mL of LB per for clone 1 and 9 to be used for arabinose induction and WB. 2 tubes of 4 mL of LB for miniprep.