Difference between revisions of "Part:BBa K346007:Experience"

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(→‎Applications of BBa_K346007)
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===Applications of BBa_K346007===
 
===Applications of BBa_K346007===
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'''• Aim – to verify Assembly Standard 10 compliance<br>'''
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'''  • Method:'''
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'''Standard restriction digest and gel electrophoresis'''
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''Escherichia coli'' bacterial culture containing plasmids BBa_K346007 (coding region of Ag43 only), was inoculated overnight in LB-chloramphenicol medium in a shaking water bath at 370C. Plasmid mini preps were conducted with a Qiagen plasmid mini prep kit. Single and double restriction digests were carried out accordingly:
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[[File:Restriction_digest_table.jpg]]
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Restriction digests with EcoRI, XbaI, SpeI and PstI was performed to linearize the vector and to confirm the existence of unique restriction sites, as required by the iGEM biobrick Assembly standard 10 rules. Double restriction digests with EcoRI plus PstI and XbaI plus SpeI were performed to separate the BBa_K346007 insert from the pSB1C3 plasmid backbone. Digests were incubated at 370C for 2 hours and analysed by gel electrophoresis. Theoretical maps were used to calculate the expected sizes of the fragments and to compare them against the gel electrophoresis results.
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'''  • Result:'''
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[[File:restriction_digest_on_BBa_K346007.jpg]]
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Figure 1. Gel electrophoresis on standard restriction digests of BBa_K346007.
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Restriction digests were separated on a 0.8% agarose gel. Lane 1; NEB 1 kb size standards ladder, Lane 2; uncut plasmid, Lanes 3-6; plasmid cut with either EcoRI, XbaI, SpeI or PstI respectively, Lane 7; plasmid cut with EcoRI+PstI, Lane 8; plasmid cut with XbaI+SpeI.
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[[File:Fragment sizes_BBa_K346007.jpg]]
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Figure 2.Fragment sizes resulted from standard restriction digests on BBa_K346007.
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• Conclusion
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The pSB1C3-BBa_K346007 construct was shown to contain 6 additional PstI sites, as found in the wild-type gene of Antigen 43.
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This part is the basic part of BBa_K759001 Biobrick, which we have also shown that contains the same PstI sites (see Experience section of BBa_K759001).
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Thus we conclude that the BioBrick BBa_K346007 originally deposited with iGEM did not meet assembly standard 10, and the
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6 native PstI sites present in Ag43 had not in fact been removed as stated in the original documentation.
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Based on the results mentioned above, pSB1C3- BBa_K759001 has been chosen as the subject for removal of the PstI sites to ensure that an Ag43 BioBrick is created that meets Assembly Standard 10 requirements (see the RFC10 compatible version of this Biobrick created by 2014 iGEM Aberdeen team:BBa_K1352000)
  
 
===User Reviews===
 
===User Reviews===

Revision as of 23:39, 3 October 2014

This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K346007

• Aim – to verify Assembly Standard 10 compliance


• Method:


Standard restriction digest and gel electrophoresis

Escherichia coli bacterial culture containing plasmids BBa_K346007 (coding region of Ag43 only), was inoculated overnight in LB-chloramphenicol medium in a shaking water bath at 370C. Plasmid mini preps were conducted with a Qiagen plasmid mini prep kit. Single and double restriction digests were carried out accordingly:

Restriction digest table.jpg

Restriction digests with EcoRI, XbaI, SpeI and PstI was performed to linearize the vector and to confirm the existence of unique restriction sites, as required by the iGEM biobrick Assembly standard 10 rules. Double restriction digests with EcoRI plus PstI and XbaI plus SpeI were performed to separate the BBa_K346007 insert from the pSB1C3 plasmid backbone. Digests were incubated at 370C for 2 hours and analysed by gel electrophoresis. Theoretical maps were used to calculate the expected sizes of the fragments and to compare them against the gel electrophoresis results.


• Result:

File:Restriction digest on BBa K346007.jpg

Figure 1. Gel electrophoresis on standard restriction digests of BBa_K346007.

Restriction digests were separated on a 0.8% agarose gel. Lane 1; NEB 1 kb size standards ladder, Lane 2; uncut plasmid, Lanes 3-6; plasmid cut with either EcoRI, XbaI, SpeI or PstI respectively, Lane 7; plasmid cut with EcoRI+PstI, Lane 8; plasmid cut with XbaI+SpeI.


File:Fragment sizes BBa K346007.jpg Figure 2.Fragment sizes resulted from standard restriction digests on BBa_K346007.

• Conclusion

The pSB1C3-BBa_K346007 construct was shown to contain 6 additional PstI sites, as found in the wild-type gene of Antigen 43. This part is the basic part of BBa_K759001 Biobrick, which we have also shown that contains the same PstI sites (see Experience section of BBa_K759001).

Thus we conclude that the BioBrick BBa_K346007 originally deposited with iGEM did not meet assembly standard 10, and the 6 native PstI sites present in Ag43 had not in fact been removed as stated in the original documentation.

Based on the results mentioned above, pSB1C3- BBa_K759001 has been chosen as the subject for removal of the PstI sites to ensure that an Ag43 BioBrick is created that meets Assembly Standard 10 requirements (see the RFC10 compatible version of this Biobrick created by 2014 iGEM Aberdeen team:BBa_K1352000)

User Reviews

UNIQ1f8f73cd3ee8dc0d-partinfo-00000000-QINU

••••

Kenta

Aggregation was confirmed in the construct of BBa_K759001. But this part contains 6 PstI recognition sites in the 883-888, 1441-1446, 2041-2046, 2665-2670, 2936-2941, 2989-2994 bp regions at the time of 2012.

UNIQ1f8f73cd3ee8dc0d-partinfo-00000002-QINU