Team:Dundee/labjournal manu

LABJOURNAL

BioSpray

Our forensic toolkit aims to use synthetic biology approaches to improve on the current methods used by crime scene investigators.

Chromium Detector

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur a tincidunt elit. Aliquam porta nibh at enim luctus, auctor consequat dolor vehicula.

Fingerprint Aging

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur a tincidunt elit. Aliquam porta nibh at enim luctus, auctor consequat dolor vehicula.

22/06 - 28/06

Summary

This week was all about getting started with the newly arrived biobrick BBa_K1058008

Day 1

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 BBa_K1058008 and confirmation of size and sequence.

Day 2

Aim of experiment: To purify BBa_K1058008 for sequence confirmation.

Protocols Used:

Click here to see our miniprep protocol.

Click here to see our sequencing protocol.

Results Miniprep:

Sample Name	Concentration	Unit
Blank	-	-
BBa_K1058008	190.93	ng/µl

Results Sequencing: Figure 1

Next Steps: PCR of parts of BBa_K1058008.

29/06 - 05/07

Summary

During this week, BBa_K1058008 was disassembled into its constituent parts, pChr, and ChrB.

Day 1

Aim of experiment: To break down BBa_K1058008 into the promoter region pChr, and the repressor gene, ChrB, while adding standard prefix and suffix to each. Furthermore optimisation of first 15 codons of ChrB in order to increase the overall rate of transcription. Restriction digest of the respective ends and subsequent ligation of pChr and ChrB into pSB1C3 for submission to registry.

Protocols Used:

Click here to see our PCR protocol.

Click here to see our gel extraction protocol.

Click here to see our restriction digest protocol.

Results:

Figure 2: Agarose gel after PCR of pChr and ChrB.

As can be seen on the image of the gel, PCR of ChrB was not successful. pChr was further processed by restriction digest with EcoRI and PstI

Next Steps: Repeat of PCR of ChrB. Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

06/07 - 12/07

Summary

During this week ligations of pChr and ChrB into pSB1C3 were finalised and the constituent parts of our newly designed chromate sensing system were prepared for ligation and transformation.

Day 1

Aim of experiment: To repeat PCR of ChrB for subsequent ligation into pSB1C3. Ligation of pChr and ChrB into pSB1C3. Transformation of each into a non-pathogenic lab strain of E. coli.

Overnight culture of strain, containing GFPmut2, as a fluorescent reporter for our Chromate sensing system

Protocols Used:

Click here to see our PCR protocol.

The annealing temperature was lowered in order to increase the chances of accomodating a primer that is not 100% complementary. Furthermore different concentrations of DMSO were tested.

Click here to see our gel extraction protocol.

Click here to see our restriction digest protocol.

Click here to see our ligation protocol. Ligations were made in 2:1 and 3:1 ratio.

Click here to see our Overnight culture protocol.

Results:

Figure 3: Agarose gel after PCR of ChrB.

2 bands were extracted from the gel for further characterisation, the strongest band, hence called ChrBs, and the band directly above, hence called ChrBw.

pChr, ChrBs, and ChrBw were ligated into pSB1C3.

pChr-pSB1C3, ChrBs-pSB1C3, and ChrBw-pSB1C3 were transformed into E. coli MC1061.

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 2

Aim of experiment: Purification of GFPmut2 from overnight cultures. Overnight cultures of recombinant MC1061, containing pChr-pSB1C3, ChrBs-pSB1C3, and ChrBw-pSB1C3 respectively. Overnight culture of pUniprom for subsequent ligation of ChrB

Protocols Used:

Miniprep for plasmid purification of overnight culture of GFPmut2.

PCR for amplification of GFPmut2 and ChrB.

Gel extraction of PCR product pf GFPmut2.

Overnight culture of MC1061 containing pChr-pSB1C3, ChrBs-pSB1C3, and ChrBw-pSB1C3 respectively. Furthermore of a strain containing the vector pUniprom.

Results: Figure 5 Since amplification of ChrB was unsuccessful, it will be repeated.

Next Steps: Sequence and size confirmation of pChr-pSB1C3, ChrBs-pSB1C3, and ChrBw-pSB1C3.

Day 3

Aim of experiment: To purify overnight cultures for size and sequence confirmation. Repeat of PCR amplification of pChr and ChrB. Restriction digestes of all parts in order to produce compatible sticky ends.

Protocols Used:

Miniprep of pChr-pSB1C3, ChrBs-pSB1C3, ChrBw-pSB1C3 and pUniprom.

Results Miniprep:

Sample Name	Concentration	Unit
Blank	-	-
pUniprom1	55.65	ng/µl
pUniprom2	64.20	ng/µl
pChr1	116.58	ng/µl
pChr2	110.13	ng/µl
pChr3	114.65	ng/µl
pChr4	105.63	ng/µl
ChrBs1	151.18	ng/µl
ChrBs2	108.37	ng/µl
ChrBs3	143.13	ng/µl
ChrBs4	183.27	ng/µl
ChrBw1	116.26	ng/µl
ChrBw2	236.99	ng/µl
ChrBw3	219.21	ng/µl
ChrBw4	208.27	ng/µl

Protocols Used:

PCR for amplification of pChr and ChrB.

Restriction digest for confirmation of size of pChr and ChrB.

Results: Figure 6 Agarose gel for size confirmation.

Protocols Used:

Sequencing of pChr and ChrB that showed expectes sizes.

Results: Figure 7 Confirmed sequence of pChr1.

Results: Figure 8 Confirmed sequence of ChrBw4.

Protocols Used:

Restriction digest of gel purified PCR-products of pChr, ChrB, and GFPmut2, using EcoRI/SpeI, BamHI/HindIII, and XbaI/PstI respecitvely.

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 4

Aim of experiment: To prepare pUniprom for insertion of ChrB.

Protocols Used:

Restriction digest of pUniprom with BamHI and HindIII.

Gel extraction of digested pUniprom

Results: Figure 9

Next Steps: Ligation of ChrB into pUniprom.

Aim of experiment: To amplify ChrB version with first 15 codons optimised for insertion into pUniprom.

Protocols Used:

PCR of optimised ChrB from the sequence confirmed ChrBw4-pSB1C3, adding restriction sites compatible to pUniprom.

Gel extraction of optimised ChrBafter PCR.

Results: Figure 10

Next Steps: Ligation of ChrB and codon optimised ChrB into pUniprom.

Day 5

Aim of experiment: Ligation of ChrB and optimised ChrB into pUniprom. Ligation of pChr and GFPmut2 into pSB1C3

Protocols Used:

Ligation of ChrB and optimised ChrB into pUniprom via BamHI and HindIII restriction sites. Ligation of pChr to GFPmut2 via Spe/Xba link and ligation of pChrGFP construct into pSB1C3 EcoRI/PstI restriction sites.

Results: N/A

Next Steps:Transformation of abovementioned ligations.

13/07 - 19/07

Summary

During this week successful transformations were identifeid and propagated.>

Day 1

Aim of experiment: Transform recombinant vectors into E. coli chassis.

Protocols Used:

Transformation of ChrB-pUniprom, optimised ChrB-pUniprom and pChr-GFPmut2-pSB1C3 into JM110.

Results: Figure 11

Aim of experiment: Backup of digested pSB1C3 for the case that a ligation with 2 inserts does not work.

Protocols Used:

Restriction digest of pSB1C3 with EcoRI/SpeI for subsequent insertion of pChr.

Results:N/A

Next Steps: Store digested plasmid at -20^oC.

Day 2

Aim of experiment: Purification of recombinant vectors for sequence and size confirmation.

Protocols Used:

Overnight culture of JM110 with ChrB-pUniprom, optimised ChrB-pUniprom and pChr-GFPmut2-pSB1C3.

Patch plating of the same colonies.

Results: N/A

Next Steps: Purification of the recombinant plasmids for confirmation of size and sequence.

Day 3

Aim of experiment: Purification of recombinant plasmids for confirmation of size and sequence.

Protocols Used:

Miniprep of ChrB-pUniprom, optimised ChrB-pUniprom and pChr-GFPmut2-pSB1C3.

Results:

Sample Name	Concentration	Unit
Blank	-	-
pSB1C3-pChr-GFPmut2_1	382.32	ng/µl
pSB1C3-pChr-GFPmut2_2	355.31	ng/µl
pSB1C3-pChr-GFPmut2_3	209.85	ng/µl
pSB1C3-pChr-GFPmut2_4	217.57	ng/µl
pUniprom-ChrB-opt_1	150.51	ng/µl
pUniprom-ChrB-opt_2	214.17	ng/µl
pUniprom-ChrB-opt_3	140.85	ng/µl
pUniprom-ChrB-opt_4	115.85	ng/µl
pUniprom-ChrB_1	134.72	ng/µl
pUniprom-ChrB_2	111.41	ng/µl
pUniprom-ChrB_3	111.31	ng/µl
pUniprom-ChrB_4	138.9	ng/µl

Protocols Used:

Restriction digest of ChrB-pUniprom and optimised ChrB-pUniprom with BamHI and HindIII. Restriction digest of pChr-GFPmut2-pSB1C3 with EcoRI/PstI.

Results: Figure 1

Protocols Used:

Colony PCR of pUniprom-ChrB-opt for elucidation of insert size or presence of insert.

Results: Figure 13 Gel after colony PCR. Colonies 2, 4, 9, and 12 were selected for sequencing.

Next Steps: Confirmation of insert size and sequence of ChrB-opt.

Day 4

Aim of experiment: To prepare ChrB-opt colonies 2, 4, 9, and 12 for sequencing.

Protocols Used:

Click here to see our overnight culture protocol.

Results:N/A

Next Steps: Purification of recombinant plasmids.

Day 5

Aim of experiment: To purify recombinant plasmids for sequence confirmation.

Protocols Used:

Miniprep of ChrB-opt 2, 4, 9, 12.

Results:

Sample Name	Concentration	Unit
Blank	-	-
pUniprom-ChrB-opt_2	255.35	ng/µl
pUniprom-ChrB-opt_4	146.77	ng/µl
pUniprom-ChrB-opt_9	211.91	ng/µl
pUniprom-ChrB-opt_12	181.08	ng/µl

Protocols Used:

Sequencing of ChrB-opt 2, 4, 9, 12.

Results: ChrB showed HindIII restriction sites and was hence cleaved into partial inserts.

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 6

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 7

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Week Beginning 22/06

Summary

This week was all about getting started with the newly arrived biobrick BBa_K1058008

Day 1

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 2

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 3

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 4

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 5

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 6

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 7

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Week Beginning 22/06

Summary

This week was all about getting started with the newly arrived biobrick BBa_K1058008

Day 1

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 2

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 3

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 4

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 5

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 6

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 7

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Week Beginning 22/06

Summary

This week was all about getting started with the newly arrived biobrick BBa_K1058008

Day 1

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 2

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 3

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 4

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 5

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 6

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 7

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Week Beginning 22/06

Summary

This week was all about getting started with the newly arrived biobrick BBa_K1058008

Day 1

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 2

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 3

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 4

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 5

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 6

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 7

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Week Beginning 22/06

Summary

This week was all about getting started with the newly arrived biobrick BBa_K1058008

Day 1

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 2

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 3

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 4

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 5

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 6

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 7

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Week Beginning 22/06

Summary

This week was all about getting started with the newly arrived biobrick BBa_K1058008

Day 1

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 2

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 3

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 4

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 5

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 6

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

Day 7

Aim of experiment: To prepare BBa_K1058008 for sequence confirmation, storage, and further processing.

Protocols Used:

Click here to see our plating protocol.

Click here to see our overnight culture protocol.

Results: N/A

Next Steps: Purification of the Plasmid, containing BBa_K1058008 and confirmation of size and sequence.

×

Plating Protocol

1. Agar plates with required antibiotic were taken out of 4^oC to warm to room temperature.

2. Cells or colonies were picked up from the source with a toothpick under sterile conditions.

3. Fresh agar plates were inoculated with cells on the toothpick.

4. Agar plates were incubated at 4^oC over night.

Close

×

Sequencing Protocol

For sequencing a sample, the following ingredients were added to a microcentrifuge tube:

• Volume of sample equivalent to 550ng DNA
• 2µl of 3mM primer
• Remaining volume of water for a total volume of 30µl

The samples were submitted to DNA sequencing and services.

Close

×

Overnight Culture Protocol

1. Agar plates with required antibiotic were taken out of 4^oC to warm to room temperature.

2. Cells or colonies were picked up from the source with a toothpick under sterile conditions.

3. 5ml of LB medium, supplemented with the required antibiotic, were inoculated with the toothpick.

4. Tubes were incubated at 37^oC in a rotary incubator at 200rpm over night.

Close

×

PCR Protocol

PCR reaction mixtures were set up according to the table below. The length of all sequences used is stated in the Sequences section.

Reactants	Volume (µl)
DNA	1
DMSO	2.5
Forward Primer	0.5
Reverse Primer	0.5
Herculase Buffer	10
dNTP	0.5
Herculase	0.5
H2O	34.5

**PCR Programme**

Elongation time was altered according to the length of the sequences.

Close

×

Colony PCR Protocol

The PCR reaction mixture were set up in multiples of the volumes in table below. The length of all sequences used is stated in the Sequences section.

The DNA template is made in the following way:

1. Agar plates with required antibiotic were taken out of 4^oC to warm to room temperature.
2. A numbered grid according to the desired number of PCR reactions is drawn on the back of the plate.
3. Cells or colonies were picked up from the source with a toothpick under sterile conditions.
4. Each colony is transferred to a 30µl aliquot of sterile water.
5. With the same toothpick the grid with the respctive number on the plate was inoculated.
6. • The plate was incubated at 37^oC overnight.
   • The inoculated water-aliquots were boiled for 10min, then centrifuged at 13300rpm for 10min.
7. The supernatant of this preparation is the DNA fraction for the subsequent PCR reaction.

Reactants	Volume (µl)
DNA	5
DMSO	1
Forward Primer	0.5
Reverse Primer	0.5
+Mg Buffer	2
dNTP	0.2
Taq-polymerase	0.2
H2O	10.6

15µl of the reaction mixture was aliquoted into separate PCR tubes. 5µl of DNA fraction was added to each respective tube in order to have a total reaction volume of 20µl per tube.

**PCR Programme**

Elongation time was altered according to the length of the sequences.

Close

×

Miniprep Protocol

1. 5ml bacterial overnight culture was pelleted by stepwise centrifugation in 1.5ml microcentrifuge tubes at 13300rpm for 3 minutes at room temperature.

2. Pelleted bacterial cells were resuspended in 250µl of Buffer P1.

3. 250µl of Buffer P2 was added and mixed thoroughly by inverting the tube 4-6 times until solution became clear.

4. 350µl of Buffer N3 was added and immediately and thoroughly mixed by inverting the tube 4-6 times.

5. The mixture was centrifuged for 10 minutes at 13300rpm in a microcentrifuge.

6. The supernatant was applied to a QIAprep spin column by pipetting.

7. 500µl of Buffer PB was added to the QIAprep spin column and centrifuged for 1 minute. The flow-through was discarded.

8. 750µl of Buffer PE was added to the QIAprep spin column and centrifuged for 1 minute. The flow-through was discarded.

9. The QIAprep spin column was spun for an additional minute to remove residual wash buffer.

10. The QIAprep spin column was placed in a clean 1.5ml microcentrifuge and the DNA eluted by adding 30µl of H2O to the QIAprep spin column and centrifuging for 1 minute.

Close

×

Gel Extraction Protocol

1. The desired DNA fragment was excised from the agarose gel with a clean, sharp scalpel.

2. The gel slice was transferred into a microcentrifuge tube. 700µl of Buffer QG was added.

3. The gel slice was incubated in a water bath at 50°C for 10 min (or until the gel slice has completely dissolved). The tube was vortexed every 2–3 min to help dissolve gel.

4. After the gel slice had been dissolved completely, the color of the mixture was checked that it was yellow (similar to Buffer QG without dissolved agarose). If the color of the mixture was orange or violet, 10 μl 3 M sodium acetate, pH 5.0 would be added, and mixed. The color of the mixture would turn yellow.

5. 230µl of isopropanol was added to the sample and mixed.

6. A QIAquick spin column was placed in a 2ml collection tube. The sample was applied to the QIAquick spin column and centrifuged for 1 minute. The flow-through was discarded.

7. 500µl of QG buffer was added to the QIAquick spin column and centrifuged for 1 minute. The flow-through was discarded.

8. 750µl of Buffer PE was added to the QIAquick spin column and centrifuged for 1 minute. The flow-through was discarded.

9. The QIAprep spin column was spun for an additional minute to remove residual wash buffer.

10. The QIAprep spin column was placed in a clean 1.5ml microcentrifuge and the DNA eluted by adding 30µl of H2O to the QIAprep spin column and centrifuging for 1 minute.

Close

×

Restriction Digest Protocol

Restriction digests were set up according to the table below. The appropriate reaction and restriction enzymes that were used is stated in the Journal section.

	Post Plasmid Purification	Post PCR	gBlock
DNA	1mg	50µl	100ng
Cutsmart Buffer (µl)	6	6	6
Water (µl)	As required	1	As required
Enzyme 1 (µl)	1.5	1.5	1.5
Enzyme 2 (µl)	1.5	1.5	1.5
Total Volume (µl)	30	60	30

The digests were incubated at 37^oC for 3 hours.
Note that when performing plasmid digestions, 2.5µl of alkaline phosphatase and 2.5µl of its buffer were added at the 2 hour and 2.5 hour mark.

Close