Team:Macquarie Australia/Notebook

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PROJECT LAB BOOK


Welcome to the Macquarie University project lab book page!

Here you will find a day-by-day account of our triumphs and failures.

A day-by-day progress for Agrobacterium Tumefaciens Bacteriophytochrome

20th August 2010

Genomic DNA extraction

  • A. tumefaciens genomic DNA extracted using the Invitrogen PureLinkTM Genomic DNA Purification kit as per the manufacturer’s protocols.
  • The extractions were run on a GelRed stained 1% agarose gel and photo taken for visualization (see below).

  • A NanoDrop spectrophotometer reading was also recorded to check the quality of the extracted genomic DNA.

  • The extraction was successful for all A. tumefaciens cell lysate samples (labeled DNA1.1, DNA1.2, DNA2 (See figure below)

  • A. tumefaciens genomic DNA extraction agarose results:

    All four DNA samples show a smear of gDNA. Because the samples were treated with RNase there is no band indicative of RNA visible = SUCCESS!

    FIGURE ONE ***** Results of A. tumefaciens genomic DNA extraction ***

    Figure 1. GelRed stained 1% agarose gel of genomic DNA extraction from A. tumefaciens.

    In lanes 1 and 11 there is a 1kb ladder. In lane 2 is the DNA1.1 flow through, lane 3 is the DNA2.2 flow through, lane 4 is the DNA2.1 flow through and lane 4 in the DNA2.2 flowthrough. All four samples show a smear that is indicative of genomic DNA. The extraction has been successful.

    Nanodrop absorbance readings:

    Genomic DNA sample 260/280 OD ratio Concentration (ng/mL)
    DNA1.1 1.88 351.5
    DNA1.2 1.98 203.1
    DNA2.1 2.14 738.9
    DNA2.2 2.16 709.7

    Overall, the Nanodrop readings show that we have obtained good DNA concentration with minimal protein contamination

    = SUCCESS!


    27th August 2010

    Primer design

  • Various primers were designed manually and using Primer 3 Software package for PCR amplification.
  • The primers were ordered and supplied through XXXXXXXXXXXXXXXXX.
  • There was an array of various primers ordered for amplification of different products. The details of the primers are described below.
  • Fwd and Rvs primers for amplification of the full length A. tumefaciens BphP gene:

    Primer name Primer Sequence
    F1 (AT-FWD-1) 5’-ATG AGT TCA CAT ACG CCG-3’
    R1 (AT-RVS-1) 5’-TCA GGC AAT TTT TTC CTC-3’

    Fwd and Rvs primers for amplification of the full length A. tumefaciens BphP gene for insertion in the operon BEFORE the HO gene:

    Primer name Primer Sequence
    F2 (AT-BHO-F) 5’- AAG GAG ATA TAC ATA TGA TGA GTT CAC ATA CGC CG – 3’
    R3 (AT-BHO-R) 5’- AAG TTG ACA CTC ATA TGA GCC CTC CTT TCA GGC – 3’

    Fwd and Rvs primers for amplification of the full length A. tumefaciens BphP gene:

    Primer name Primer Sequence
    F1 (AT-FWD-1) 5’-ATG AGT TCA CAT ACG CCG-3’
    R1 (AT-RVS-1) 5’-TCA GGC AAT TTT TTC CTC-3’

    Fwd and Rvs primers for amplification of the full length A. tumefaciens BphP gene for insertion in the operon AFTER the HO gene in the operon:

    Primer name Primer Sequence
    F4 (AT-AHO-F) 5’- CCG AAG GCT AGG ATC CAG GAG GGC TGC TAT GAG – 3’
    R2 (AT-AHO-R) 5’- GTT AGC CGG ATC CTC AGG CAA TTT TTT CCT – 3’

    Fwd and Rvs primers for amplification of the full length A. tumefaciens BphP gene for insertion in the operon AFTER the HO gene as well as the addition of a ribosome binding site or Shine Delgano sequence:

    Primer name Primer Sequence
    F3 (AT-FWD-RBS) 5’- AGG AGG GCT ATG AGT TCA CAT ACG CCG -3’

    Initial PCR

  • The reaction mastermix for the initial PCR was set up as per the following recipe (per sample):
  • Mastermix: Amount per sample (ul)
    Clean H2O 13.75
    10x Buffer 2.00
    Polymerase enzyme 0.25
    dNTP 1.00
    Fwd primer 1.00
    Rvs primer 1.00
    Genomic DNA 1.00
    Total 20.00

    The PCR program was set up as per the following:

    1. 94˚C for 2 minutes
    2. 94˚C for 30 seconds
    3. 60˚C for 30 seconds
    4. 72˚C for 2 minutes & 30 seconds
    5. (This was repeated for another 25 cycles)

    6. 72˚C for 10 minutes
    7. 4˚C to end.

  • Different combinations of the primers were used for the PCR reaction (see below ‘Experimental Design’ section following)
  • Not all possible primer combinations were used due to limitations on the amount of polymerase enzyme available to us
  • The PCR products were run on a 1.2% GelRed stained agarose gel for visualisation (see picture of gel below).
  • Experimental Design – Primer combinations:

    Template DNA Fwd Primer Rvs primer
    DNA1.2 F1 (AT-FWD-1) R1(AT-RVS-1)
    DNA2.2 F1 (AT-FWD-1) R1(AT-RVS-1)
    DNA1.2 F2 (AT-BHO-F) R1(AT-RVS-1)
    DNA2.2 F2 (AT-BHO-F) R1(AT-RVS-1)
    DNA1.2 F3 (AT-FWD-RBS) R1(AT-RVS-1)
    DNA2.2 F3 (AT-FWD-RBS) R1(AT-RVS-1)
    SSH20 (negative control) F1 (AT-FWD-1) R1(AT-RVS-1)

  • A band was seen in lane 6. This lane was using the primer and DNA template combinations of DNA2.2, F3 and R1 primers

    = SUCCESS!!!

  • A PCR product is seen in lane 6 – this is the DNA2.2 template amplified with the F3 (AT-FWD-RBS) and R1 (AT-RVS-1) primers

    = SUCCESS!!

  • FIGURE two ***** Results of the initial PCR ***

    Figure 2. GelRed stained 1.2% agarose gel of initial PCR of A. tumefaciens using various primers.

    In lanes 1 and 11 there is a 1kb ladder. In lane 2 is the DNA1.2 template with F1 and R1 primer pair.

    In lane 3 is the DNA2.2 template with F1 and R1 primer pair. In lane 4 is the DNA1.2 template with F2 and R1 primer pair. In lane 5 is the DNA2.2 template with the F2 and R1 primer pair. In lanes 6 and 7 there is nothing loaded as the wells were damaged. In lane 8 there is the DNA1.2 template with F3 and R1 primer pair. In lane 9 there is the DNA2.2 template with the F3 and R1 primer pair and in lane 10 there is the ssH2O negative control. A product is seen in lane 9 – this is the DNA2.2 template with the F3 and R1 primers! This means that we have a A. tumefaciens bacteriophytochrome product with a ribosome binding sight inserted.


    30th August 2010

    PCR Optimization

  • Now that we have a product obtained by the initial PCR it is time to optimize the PCR conditions using the successful DNA2.2 PCR product obtained from last week and the original DNA2.2 template
  • The reaction mastermix for the PCR was set up as per the following recipe (per sample):
  • Mastermix: Amount per sample (ul)
    Clean H2O 13.75
    10x Buffer 2.00
    Polymerase enzyme 0.25
    dNTP 1.00
    Fwd primer 1.00
    Rvs primer 1.00
    Genomic DNA 1.00
    Total 20.00

    The PCR program was set up as per the following:

    1. 94˚C for 2 minutes
    2. 94˚C for 30 seconds
    3. 60˚C for 30 seconds
    4. 72˚C for 2 minutes & 30 seconds
    5. (This was repeated for another 25 cycles)

    6. 72˚C for 10 minutes
    7. 4˚C to end.

  • Again, different combinations of the primers were used for the PCR reaction (see below ‘Experimental Design’ section following)
  • Now that we don’t have a limited enzyme supply, even more primer combinations can be used!!
  • The PCR products were run on a GelRed stained 2% agarose gel using a 100bp ladder for visualization
  • All primer combinations tested worked with bands visible in each lane! The strange band pattern seen in lane 6 is most probably due to non-specific binding.
  • Experimental Design – Primer combinations:

    Template DNA Fwd Primer Rvs primer
    DNA2.2 F1 (AT-FWD-1) R1(AT-RVS-1)
    PCR product (from DNA2.2) F1 (AT-FWD-1) R1(AT-RVS-1)
    DNA2.2 F2 (AT-BHO-F) R1(AT-RVS-1)
    PCR product (from DNA2.2) F2 (AT-BHO-F) R1(AT-RVS-1)
    DNA2.2 F3 (AT-FWD-RBS) R1(AT-RVS-1)
    PCR product (from DNA2.2) F3 (AT-FWD-RBS) R1(AT-RVS-1)
    DNA2.2 F1 (AT-FWD-1) R2 (AT-AHO-R)
    PCR product (from DNA2.2) F1 (AT-FWD-1) R2 (AT-AHO-R)
    DNA2.2 F2 (AT-BHO-F) R2 (AT-AHO-R)
    PCR product (from DNA2.2) F2 (AT-BHO-F) R2 (AT-AHO-R)
    DNA2.2 F3 (AT-FWD-RBS) R2 (AT-AHO-R)
    PCR product (from DNA2.2) F3 (AT-FWD-RBS) R2 (AT-AHO-R)
    ssH2O (-) control F1 (AT-FWD-1) R1 (AT-RVS-1)

    FIGURE THREE ***** PCR optimization results ***

    Figure 3. GelRed stained 2% agarose gel of optimized PCR of A. tumefaciens bacteriophytochrome using various primers. In lanes 1 and 15 there is a 100bp ladder. In lane 2 is the DNA2.2 sample with F1 and R1 primer pair. In lane 3 there is PCR product template (from DNA2.2 sample) with F1 and R1 primer pair. In lane 4 there is DNA sample with F2 and R1 primer pair. In lane 5 is the PCR product (from DNA2.2 sample) with F2 and R1 primer pair. In lane 6 there is DNA2.2 sample with F3 and R1 primer pair. In lane 7 there is PCR product template (from DNA2.2 sample) with F3 and R1 primer pair. In lane 8 there is DNA2.2 sample with F1 and R2 primer pairs. In lane 9 there is PCR product template (from DNA2.2 sample) with F1 and R2 primer pairs. In lane 10 there is DNA2.2 sample with F2 and R2 primer pairs. In lane 11 there is PCR product (from DNA2.2 sample) with F2 and R2 primer pair. In lane 12 there is DNA2.2 sample with F2 and R2 primer pair. In lane 13 there is PCR product (from DNA2.2 sample) with F3 and R2 primer pair. In lane 14 there is ssH2O negative control with F1 and R1 primer pair. All the lanes worked. There is a weird result in lane 7 which is probably due to non-specific binding. = SUCCESS!


    3rd September 2010

    PCR Optimization (using Gradient PCR)

  • Now that we have the A. tumefaciens bacteriophytochrome product as well as the RBS inserted it is now time for us to amplify the bacteriophytochrome product with the heme oxygenase gene
  • We will be inserting the two genes in two different orientations in the operon
  • We will achieve this using two different primer pairs
    • The first primer pair is F2 (AT-BHO-F) with R3 (AT-BHO-R) [this will insert the bacteriophytchrome gene BEFORE the heme oxygenase gene in the operon]
    • The second primer pair is F4 (AT-AHO-F) with R2 (AT-AHO-R) [this will insert the bacteriophytochrome gene AFTER the heme oxygenase gene in the operon]
  • A technique called gradient PCR will be used here. This PCR includes different annealing temperatures so that the optimum annealing temperature for the primers can be determined.
  • This should also result in reduced non-specific binding that was observed in the previous PCR result
  • The reaction mastermix for the PCR was set up as per the following recipe (per sample):
  • Mastermix: Amount per sample (ul)
    Clean H2O 13.75
    10x Buffer 2.00
    Polymerase enzyme 0.25
    dNTP 1.00
    Fwd primer 1.00
    Rvs primer 1.00
    Genomic DNA 1.00
    Total 20.00

    The PCR program was set up as per the following:

    1. 94˚C for 2 minutes
    2. 94˚C for 30 seconds
    3. 60˚C for 30 seconds
    4. 72˚C for 2 minutes & 30 seconds
    5. (This was repeated for another 25 cycles)

    6. 72˚C for 10 minutes
    7. 4˚C to end.

  • The PCR products were run on a GelRed stained 2% agarose gel using a 1kb ladder for visualization
  • The products were run on a GelRed stained 2% agarose gel for visualization
  • Unfortunately no products were seen
  • Experimental Design – Primer combinations and annealing temperatures:

    Fwd Primer Rvs primer Temp 1 (Degrees Celsius) Temp 2 (Degrees Celsius) Temp 3 (Degrees Celsius) Temp 4 (Degrees Celsius) Temp 5 (Degrees Celsius)
    F2 (AT-BHO-F) R3 (AT-BHO-R) 57.1 58.7 60.6 63.4 64.8
    F4 (AT-AHO-F) R2 (AT-AHO-R) 57.1 58.7 60.6 63.4 64.8

    FIGURE FOUR ***** PCR Optimisation (gradient PCR) results ***

    Figure 4. No product amplification is seen in any lanes. The anticipated product is approximately 1.6 to 3.0kb. The gel had been over run and at the very bottom some bands can be seen but as these are so small they are possibly dimers that are less than 300bp.

    Unfortunately, no products were seen. The anticipated product size was between 1.6kb and 3kb. The gel was over run but the only products that were over run were probably primer dimers, which are less than 300bp in size. = FAIL!


    7th September 2010

    PCR Optimization (using Gradient PCR)

  • The PCR run on 3rd September wasn’t successful so this was repeated
  • This time however, only the PCR product was used as a template in two different dilutions (1:100 and 1:200)
  • Additionally, two different annealing temperatures were used: 60 and 65C
  • The primer pairs used in the previous PCR were also used again for the insertion of the bacteriophytochrome gene and heme oxygenase in different orientations in the operon
  • The reaction mastermix for the PCR was set up as per the following recipe (per sample):
  • Mastermix: Amount per sample (ul)
    Clean H2O 13.75
    10x Buffer 2.00
    Polymerase enzyme 0.25
    dNTP 1.00
    Fwd primer 1.00
    Rvs primer 1.00
    Genomic DNA 1.00
    Total 20.00

    The PCR program was set up as per the following:

    1. 94˚C for 2 minutes
    2. 94˚C for 30 seconds
    3. 60˚C for 30 seconds
    4. 72˚C for 2 minutes & 30 seconds
    5. (This was repeated for another 25 cycles)

    6. 72˚C for 10 minutes
    7. 4˚C to end.

  • The PCR products were run on a GelRed stained 2% agarose gel using a 1kb ladder for visualization
  • Unfortunately, there was no amplification observed in any of the lanes so the picture of this gel is not included = FAIL!
  • Experimental Design – Primer combinations and annealing temperatures:

    DNA template Dilution Fwd primer Rvs primer Annealing temp (Degrees Celsius)
    PCR product (from DNA2.2) 1:100 F2 (AT-BHO-F) R3 (AT-BHO-R) 60
    PCR product (from DNA2.2) 1:200 F2 (AT-BHO-F) R3 (AT-BHO-R) 60
    PCR product (from DNA2.2) 1:100 F4 (AT-AHO-F) R2 (AT-AHO-R) 60
    PCR product (from DNA2.2) 1:200 F4 (AT-AHO-F) R2 (AT-AHO-R) 60
    PCR product (from DNA2.2) 1:100 F2 (AT-BHO-F) R3 (AT-BHO-R) 65
    PCR product (from DNA2.2) 1:200 F2 (AT-BHO-F) R3 (AT-BHO-R) 65
    PCR product (from DNA2.2) 1:100 F4 (AT-AHO-F) R2 (AT-AHO-R) 65
    PCR product (from DNA2.2) 1:200 F4 (AT-AHO-F) R2 (AT-AHO-R) 65


    10th September 2010

    PCR Optimization (repeated)

  • As we were having trouble with one of the primers annealing we attempted a PCR technique that required a different PCR program to be set
  • The F4 – R2 primer pair were run on the normal PCR program being used for all other PCR’s as these primers were annealing properly
  • The primer pair that we were having difficulty with (F2-R3) required a special PCR program. This would allow for the R3 primer to anneal to the template first for single stranded amplification and then the F2 primer to bind later.

  • The reaction mastermix for the PCR was set up as per the following recipe (per sample):
  • Mastermix: Amount per sample (ul)
    Clean H2O 13.75
    10x Buffer 2.00
    Polymerase enzyme 0.25
    dNTP 1.00
    Fwd primer 1.00
    Rvs primer 1.00
    Genomic DNA 1.00
    Total 20.00

    The first PCR program was set up as per the following:

    1. 94˚C for 2 minutes
    2. 94˚C for 30 seconds
    3. 60˚C for 30 seconds
    4. 72˚C for 2 minutes & 30 seconds
    5. (This was repeated for another 35 cycles)

    6. 72˚C for 10 minutes
    7. 4˚C to end.

    The second PCR program was set up as per the following:

    1. 94˚C for 2 minutes
    2. 94˚C for 30 seconds
    3. 40˚C for 30 seconds
    4. 72˚C for 2 minutes & 30 seconds
    5. (This was repeated for another 4 cycles)

    6. 72˚C for 10 minutes
    7. 4˚C to end.
    8. 4˚C for 5 minutes
    9. 94˚C for 30 seconds
    10. 40˚C for 30 seconds
    11. 72˚C for 2 minutes and 30 seconds
    12. (This was repeated for another 31 cycles)

    13. 72˚C for 10 minutes
    14. 4 ˚C to end
  • The PCR products were run on a GelRed stained 2% agarose gel using a 1kb ladder for visualization
  • Experimental Design – Primer combinations and annealing temperatures:

    Template Primer pair Annealing temp (degrees Celsius) Number of cycles
    F3-R1 PCR product F2-R3 40 4
    F3-R2 PCR product F4-R2 60 35
    F3-R1 PCR product (1:10 dilution) F2-R3 40 4
    F3-R2 PCR product (1:10 dilution) F4-R2 60 35

    FIGURE FIVE ***** PCR optimization (with ssPCR amplification for F2 primer) ***

    Figure 5. GelRed stained 2% agarose gel of optimized PCR using primer pairs for insertion of the heme oxygenase gene and bacteriophytochrome gene. In lanes 1 and 6 there is a 1kb ladder. In lane 2 there is the F3-R1 PCR product amplified with F2-R3 primer pair on the special PCR program allowing for the R3 primer to bind first. In lane 3 there is the F3-R2 PCR product amplified with F4-R2 primer pair on the normal PCR program. In lane 4 there is the F3-R1 PCR product diluted 1:10 amplified with F2-R3 primer pair on the special PCR program allowing for the R3 primer to bind first. In lane 5 there is the F3-R2 PCR product diluted 1:10 amplified with F4-R2 primer pair on the normal PCR program. There is a product band seen in lane 3 – SUCCESS! This is the product with the bacteriophytochrome gene inserted AFTER the heme oxygenase gene.