Difference between revisions of "Part:BBa K3407002:Design"
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===Design Notes=== | ===Design Notes=== | ||
− | + | The gene was amplified by PCR from Bacillus subtilis strain 168, which has the ATCC6051 genome that is the same strain as NCCB 70064, also same as KTCC 1028. Mini-3 amino acid sequence was retrieved from UniProt (UniProt ID: O31418), introduced as a query in tBlastn from NCBI against B. subtilis ATCC 6051 genome and the resulting mini3 sequence (GenBank: CP011115.1) was used as a template for the design of the primers. | |
+ | Primers were designed to have a melting temperature of 59-60 ºC. Overhangs with BglBricks Prefix and Suffix were added, along with a His-tag in the Reverse primer for a C-terminal-tagged protein. Designed to be cloned through Gibson Assembly. The primers used were the following: | ||
+ | M3-039 (mini3-Fw) | ||
+ | 5’ - gaattcaaaagatcttttaagaaggagatatacatATGCTTGAATTTGATACGATAAAAGATTCTAAGCAG - 3’ | ||
+ | |||
+ | M3-040 (mini3-Rv) | ||
+ | |||
+ | 5’ - tttatttgatgcctggagatccttactcgagtttggatccTTAGTGGTGGTGGTGATGGTGGTCGCTTTTTACGCTGGTTTCCTCTGTTGCTGACTCATTTGTTTTCCTCC - 3’ | ||
===Source=== | ===Source=== | ||
− | Genomic | + | Genomic DNA from <i>B. subtilis</i> strain 168. |
+ | Plasmid used pBbE8c backbone from BglBricks. pBbE8c-RFP was a gift from Jay Keasling (Addgene plasmid # 35269; http://n2t.net/addgene:35269; RRID:Addgene_35269) <html><a href="#1">[1]</a></html> | ||
+ | Please refer to the Addgene page for more information about licences associated with the use of the plasmid. | ||
===References=== | ===References=== | ||
+ | <html> | ||
+ | |||
+ | <head> | ||
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+ | <title>Ordered List</title> | ||
+ | |||
+ | </head> | ||
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+ | <style> | ||
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+ | ol li { | ||
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+ | counter-increment: OrderedList; | ||
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+ | list-style: none; | ||
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+ | } | ||
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+ | ol li :before { | ||
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+ | content: "[" counter(OrderedList) "]"; | ||
+ | |||
+ | } | ||
+ | |||
+ | </style> | ||
+ | <html> | ||
+ | <ol> | ||
+ | |||
+ | <li> | ||
+ | <a id="1" href="https://jbioleng.biomedcentral.com/articles/10.1186/1754-1611-5-12" target="_blank"> | ||
+ | BglBrick vectors and datasheets: A synthetic biology platform for gene expression. Lee TS, Krupa RA, Zhang F, Hajimorad M, Holtz WJ, Prasad N, Lee SK, Keasling JD. J Biol Eng. 2011 Sep 20;5:12. 10.1186/1754-1611-5-12 PubMed 21933410</a> | ||
+ | </li> | ||
+ | </ol> | ||
+ | </html> |
Latest revision as of 00:11, 28 October 2020
Mini-3: a small dsRNA restriction enzyme.
- 10INCOMPATIBLE WITH RFC[10]Illegal XbaI site found at 339
Illegal PstI site found at 193 - 12INCOMPATIBLE WITH RFC[12]Illegal PstI site found at 193
- 21COMPATIBLE WITH RFC[21]
- 23INCOMPATIBLE WITH RFC[23]Illegal XbaI site found at 339
Illegal PstI site found at 193 - 25INCOMPATIBLE WITH RFC[25]Illegal XbaI site found at 339
Illegal PstI site found at 193 - 1000COMPATIBLE WITH RFC[1000]
Design Notes
The gene was amplified by PCR from Bacillus subtilis strain 168, which has the ATCC6051 genome that is the same strain as NCCB 70064, also same as KTCC 1028. Mini-3 amino acid sequence was retrieved from UniProt (UniProt ID: O31418), introduced as a query in tBlastn from NCBI against B. subtilis ATCC 6051 genome and the resulting mini3 sequence (GenBank: CP011115.1) was used as a template for the design of the primers. Primers were designed to have a melting temperature of 59-60 ºC. Overhangs with BglBricks Prefix and Suffix were added, along with a His-tag in the Reverse primer for a C-terminal-tagged protein. Designed to be cloned through Gibson Assembly. The primers used were the following:
M3-039 (mini3-Fw)
5’ - gaattcaaaagatcttttaagaaggagatatacatATGCTTGAATTTGATACGATAAAAGATTCTAAGCAG - 3’
M3-040 (mini3-Rv)
5’ - tttatttgatgcctggagatccttactcgagtttggatccTTAGTGGTGGTGGTGATGGTGGTCGCTTTTTACGCTGGTTTCCTCTGTTGCTGACTCATTTGTTTTCCTCC - 3’
Source
Genomic DNA from B. subtilis strain 168. Plasmid used pBbE8c backbone from BglBricks. pBbE8c-RFP was a gift from Jay Keasling (Addgene plasmid # 35269; http://n2t.net/addgene:35269; RRID:Addgene_35269) [1] Please refer to the Addgene page for more information about licences associated with the use of the plasmid.
References