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Revision as of 09:33, 26 October 2012

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Week 25: 15 october - 21 october

GFP modification

15 October

• 3rd time growing JM109 containing our biobricks BBa_K883702 (GFP coil with an IPTG induced promoter) and BBa_K883703 (GFP coil + His tag with an IPTG induced promoter) and induce expression with IPTG with new medium

-> no GFP production could be seen

16 October

• to check if there are any colonies showing green fluorescence on the original plate (of the transformation on 21.September GFPcoil; GFPcoil + his tag in Bba_J04500 (IPTG induced promoter) in JM109), colonies where picked randomly and plated on agarplates containing IPTG next to the selection antibiotic

-> some colonies containing GFPcoil with an IPTG induced promoter show green fluorescence

Figure 1: 3 colonies containing GFPcoil with an IPTG induced promoter show a slight green colour in normal daylight'

• plate the JM109 samples that where used for sending the bricks in to the registry - containing BBa_K883702(GFPcoil with IPTG induced promoter) and BBa_K883703 (GFPcoil + His tag with IPTG induced promoter) on agarplates containing IPTG next to the selection antibiotic

-> culture containing BBa_K883702(GFPcoil with IPTG induced promoter) shows green fluorescence

Figure 2: BBa_K883702(GFPcoil with IPTG induced promoter)in JM109 [left] shows some green fluorescence whereas for BBa_K883703 (GFPcoil + His tag with IPTG induced promoter) in JM109 [right] no fluorescence can be seen '

• grow colonies containing the biobricks BBa_K883702 BBa_K883703 BBa_K883701 and BBa_K883700

• grow colonies containing BBa_K883702 and BBa_K883703 in duplo once with IPTG in the medium and once adding IPTG (fresh stock solution) to the culture at OD=0.6

• miniprep of the colonies containing BBa_K883702 BBa_K883703 BBa_K883701 and BBa_K883700

• 2nd try to send the bricks BBa_K883702 BBa_K883703 BBa_K883701 and BBa_K883700 in for sequencing

-> sequencing revealed that BBa_K883702 and BBa_K883703 had the expected sequence but BBa_K883701 and BBa_K883700 where faulty - therefore we deleted these two bricks from the registry

18 October

• transformation of BBa_K883702 with BL21 (producing strain) - plating the transformants on plates containing IPTG

19 October

• colony PCR of the transformation BBa_K883702 with BL21 using sequencing primers and plating the picked colonies again on a plate containing IPTG

-> all the colonies picked had the correct insert and showed fluorescence under the UV light

Figure 3: the transformation was successful since all the colonies on the plate show slight green fluorescence.'

Figure 4: the colony PCR shows that all picked colonies had the correct insert size. Bba_I13522 was used as a positive control and reference.'

• transformation of BBa_K883703 (GFPcoil + his tag + IPTG promoter) with BL21 (producing strain)

• digestion of BBa_K883702 as well as BBa_K883703 and ligation with the pSB1C3 backbone (originating from BBa_J04450). These constructs where than transformed with DH5α and plated on plate containing IPTG.

• plate JM109 containing the faulty brick BBa_K883700 and BBa_K883701 again to check if there are different colonies present containing different inserts

-> on the plate containg BBa_K883700 there where even red colonies growing on the plate (from original plasmid BBa_J04450 of the pSB1C3 backbone and encode for RFP with a constitutive promoter) so clearly there was a mistake done with picking single colonies from the tranformants

21 October

• innoculate 2x45ml medium with 10ml culture containing GFPcoil with an IPTG promoter. After an OD of around 0.5 was reached IPTG was added and the batch was incubated overnight

-> no fluorescence could be seen in the fluid or the pellet

• Colony PCR of the transformation from 19. October (BBa_K883703 (GFPcoil + his tag + IPTG promoter) with BL21; BBa_K883702 and BBa_K883703 in the pSB1C3 backbone

Figure 5: some of the picked colonies had an insert of the right size.'

Figure 6: transformation of the ligation of BBa_K883702 with the pSB1C3 backbone in DH5α. The red colonies contain the original plasmid BBa_J04450 of the pSB1C3 backbone and encode for RFP with a constitutive promoter, the green colonies contain the successful ligation product with the RFP encoding gene cut out and the GFPcoil + IPTG promoter ligated into the backbone (examples marked with an arrow). The circled ones are picked colonies'

-> comapring these two outcomes together it can be concluded that colony nr. 1 of the GFPcoil in pSB1C3 backbone in DH5α transformants (first lane second row in figure 5; left arrow to the circle in picture 6) has the correct insert and the GFP is functioning

• pick white colonies from the plate with JM109 containing the faulty brick BBa_K883700 and BBa_K883701 (from 19.october) and plate them again to seperate the cultures

Hepatitis B inside modification

15 October

• PCR check of the PCR fragment obtained on 27.August

Figure 7: The purified PCR fragment contains fragments of the correct size as well as a bigger fragment. The nonpurified sample shows only a smear.'

• ligation of the PCR product in pJET

• transformation with DH5α

-> there was growth on the negative control plate

CCMV K-coil frameshift correction

Directly after the European Jamboree we ordered two new primers to correct the frameshifts of the CCMV wt K-coil construct and the CCMV Δ26 K-coil construct. With these two primers we are able to repeat our extension-PCR scheme. To prevent new and unwanted frameshifts the primers were designed to anneal at the [http://partsregistry.org/Part:BBa_K883000 BBa_K883000] which is coding for the wildtype coat protein of CCMV and has a confirmed DNA-sequence. Additionally the resulting constructs were checked with Expasy translate to find unnecessary STOP-codons.

CCMV wt K-coil FW1: 5' TGGTGGTGGTTCTGGTGGTGGTGGTTCTGCTGCTGCTATGGGTACAGTCGGAACAGG 3'

CCMV Δ26 K-coil FW1: 5'TGGTGGTGGTTCTGGTGGTGGTGGTTCTGCTGCTGCTGTGGTCCAACCTGTTATTGTAGA 3'

PCR step I PCR step II PCR step III PCR step IV

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