Revision as of 13:15, 10 August 2010 by RachelBoyd (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

Contents 1 Transformation of pVeg and lacI 1.1 Results/Aims 1.2 Discussion 1.3 Conclusion 2 Transformation of lacI 2.1 Aims 2.2 Materials and Protocol 2.3 Result 3 Amplification of Pspac_oid promoter by PCR 3.1 Aim 3.2 Materials and Protocol 3.2.1 PCR 3.3 Discussion 3.4 Conclusion 4 Amplification of Pspac_oid promoter by PCR 4.1 Aim 4.2 Materials and Protocol 4.2.1 PCR 4.3 Discussion 4.4 Conclusion 5 Gel Electrophoresis for Amplified Pspac_oid promoter 5.1 Aim 5.2 Materials and Protocol 5.3 Result 5.4 Discussion 5.5 Conclusion 6 Transformation of hyperspank and spoVG 6.1 Aim 6.2 Materials and Protocol

Transformation of pVeg and lacI

Results/Aims

• There are colonies on all 3 plates for pVeg.

• For lacI, there is only one colony on one of the normal plates and more on the concentrated one.

Discussion

• For pVeg, we will set up an overnight broth culture from the colonies for plasmid extraction
• To show that we have sucessfully transformed from lacI, we will select 4 colonies and plate them on a section of an agar plate as well as setting up overnight broth cultures.

Conclusion

Please refer to 10.08.10.

Transformation of lacI

Aims

To transform some competent E.coli DH5α with the ligation products: 1:3, 1:5 and the vector from the ligation on 06.08.10.

Materials and Protocol

Please refer to Transformation of E.coli.

Result

Please refer to 10.08.10 for result.

Amplification of Pspac_oid promoter by PCR

Aim

The aim of this experiment is to amplify Pspac_oid promoter fragment from plasmid pMutin4 for the construction of rocF BioBrick with the help of 2 different Phusion PCR.

Materials and Protocol

Please refer to PCR for Phusion PCR protocol. The details for the 4 PCR reactions are mentioned below:

PCR

Tube	Part to be amplified	DNA fragment consisting the part	Forward primer	Reverse Primer	Melting Temperature (Tm in °C)	Size of the fragment (in bp)	Extension time* (in seconds)
1	Pspacoid Promoter	pMutin4	P1P1 forward	P2P1 reverse	58	106 approx.	15
2	Pspacoid Promoter	pMutin4	P1P1 forward	P2P1 reverse	59	106 approx.	15

Table 1: Table represents 4 different Phusion PCR reactions for the amplification of Pspac_oid promoter, so that it can be ligated together with other fragments for the construction of rocF with the help of Gibson Cloning method.

• The extension rate of the Phusion polymerase is 1Kb/ 30 seconds. Thus the extension time of each and every PCR reaction is slightly different.
• For learning about the rocF fragments, please refer to the Cloning strategy for rocF.

Discussion

All the 2 Phusion PCR reactions were done however, gel electrophoresis will be done later today, to check whether the fragments have actually amplified or not.

Conclusion

Today afternoon, we would be running gel electrophoresis to check the outcome of the 2 PCR reactions and later all the fragments will be ligated with help of Gibson protocol if the fragments have amplified.

Amplification of Pspac_oid promoter by PCR

Aim

The aim of this experiment is to amplify Pspac_oid promoter fragment from plasmid pMK-RQ containing Biobrick kinA and plasmid pMK-RQ containing stochastic switch developed by Team Newcastle 2009 for the construction of rocF BioBrick with the help of 4 different Phusion PCR.

Materials and Protocol

Please refer to PCR for Phusion PCR protocol. The details for the 2 PCR reactions are mentioned below:

PCR

Tube	Part to be amplified	DNA fragment consisting the part	Forward primer	Reverse Primer	Melting Temperature (Tm in °C)	Size of the fragment (in bp)	Extension time* (in seconds)
1	Pspacoid Promoter	Plasmid containing kinA	P1P1 forward	P2P1 reverse	58	106 approx.	15
2	Pspacoid Promoter	Plasmid containing kinA	P1P1 forward	P2P1 reverse	59	106 approx.	15
3	Pspacoid Promoter	Plasmid containing stochastic switch	P1P1 forward	P2P1 reverse	58	106 approx.	15
1	Pspacoid Promoter	Plasmid containing stochastic switch	P1P1 forward	P2P1 reverse	59	106 approx.	15

Table 2: Table represents 2 different Phusion PCR reactions for the amplification of Pspac_oid promoter, so that it can be ligated together with other fragments for the construction of rocF with the help of Gibson Cloning method.

• The extension rate of the Phusion polymerase is 1Kb/ 30 seconds. Thus the extension time of each and every PCR reaction is slightly different.
• For learning about the rocF fragments, please refer to the Cloning strategy for rocF.

Discussion

All the 4 Phusion PCR reactions were done however, gel electrophoresis will be done later today, to check whether the fragments have actually amplified or not.

Conclusion

Today afternoon, we would be running gel electrophoresis to check the outcome of the 4 PCR reactions and later all the fragments will be ligated with help of Gibson protocol if the fragments have amplified.

Gel Electrophoresis for Amplified Pspac_oid promoter

Aim

The aim of the experiment is to perform gel electrophoresis for the two PCR reactions Pspac_oid promoter amplified from plasmid pMutin4 and from plasmid pMK-RQ containing Biobrick kinA and plasmid pMK-RQ containing stochastic switch developed by Team Newcastle 2009 which took place today morning and thus confirm that they were successful.

Materials and Protocol

Please refer to: Gel electrophoresis.

Result

Figure 1: Gel electrophoresis of the lacI and Pspac_oid promoter.

• Lane 1: 1kb DNA ladder
• Lane 2: Plamid pMutin4 containing Pspac_oid promoter
• Lane 3: Plamid pMutin4 containing Pspac_oid promoter
• Lane 4: Plamid pMK-RQ (kinA BioBrick) containing Pspac_oid promoter
• Lane 5: Plamid pMK-RQ (kinA BioBrick) containing Pspac_oid promoter
• Lane 6: Plamid pMK-RO (stchastic switch BioBrick) containing Pspac_oid promoter
• Lane 7: Plamid pMK-RO (stchastic switch BioBrick) containing Pspac_oid promoter
• Lane 8: 100bp DNA ladder

	Pspac_oid pormoter
Size of the Fragment (in bp)	148 approx.

Table 3: Table represents the size of the Pspac_oid fragment represented as bands on the gel in all the lanes.

Discussion

We found two bands in the all lanes out of which one is of approximately of 150 bp is size and the other band is of 80 bp approximately in size.

Conclusion

This experiment shows that the PCR reaction was not perfectly successful for the Pspac_oid fragment. The problem is that there are 2 fragments on the gel instead of 1 and the second band which of 80bp in size might be corresponding to primer dimers. When we checked the primer sequence again, we found that there is a high complementarity within the primers itself and thus the amplification of the Pspac_oid fragment is not taking place at a desired rate. The first band present on the gel can be of the Pspac_oid fragment and thus tomorrow 10th August, 2010, we would be doing gel extraction for the fragment and will check whether these fragments are of Pspac_oid or not.

Transformation of hyperspank and spoVG

Aim

To transform competent E.coli DH5α with hyperspank and spoVG.

Materials and Protocol

Please refer to transformation of E.coli.