Difference between revisions of "Part:BBa K4268008:Design"

 
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===Design Notes===
 
===Design Notes===
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Golden Gate Assembly Level 1
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The goal of our team's project, Cyanospectre is to create a ghost phage that could be used by synthetic biologists to make genetic engineering of Cyanobacteria easier. We envision that with modification of this virus, it could be used to immobilize target cyanobacteria, or as a viral vector for the delivery of large circuits into a Cyanobacterial chassis.
  
  
 +
We selected a cyanophage, S-TIP37 as the model from which the ghost phage could be built. This phage’s natural host is ''Synechococcus sp WH8109'', a marine Cyanobacteria that has been grown in the lab. We selected this phage based on 1) it has a host that can be grown in the lab, 2) the phage has a relatively small genome making capsid proteins easier to identify, and 3) being a T7-like phage, the structure of its neck region is more simple than that of T4-like phages, making the construction of the ghost phage simpler. We envision that with future modeling, the tail fibers of this ghost phage could be modified to make the virus capable of attaching to and delivering capsid contents to a variety of Salt-water ''Synechococcus sp'' strains employed in synthetic biology as chassis, such as ''Synechococcus sp PCC 11901, UTEX 2973, PCC 7942'' or ''7002''.
 +
----
 +
The
  
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===Source===
 
  
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The coding sequence was derived from the S-TIP37 genome
+
RCF1000 prefix was added to the sequence to facilitate Level 0 cloning via Golden Gate Assembly and the DNA was synthesized by IDT.
 +
 
 +
===Source===
 +
The source of this sequence is from the S-TIP37 genome (Gene ID 54998403 from the NCBI reference assembly NC_048026.1) (HOT80_gp25 Head to Tail Connector [Synechococcus T7-like Phage S-TIP37] - Gene - NCBI, n.d.)
  
 
===References===
 
===References===
 +
The S-TIP37 genome was found on [https://www.genome.jp/entry/rs+NC_048026 GenomeNet]
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 +
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Pearson WR. An introduction to sequence similarity ("homology") searching. Curr Protoc Bioinformatics. 2013 Jun;Chapter 3:Unit3.1. doi: 10.1002/0471250953.bi0301s42. PMID: 23749753; PMCID: PMC3820096.
 +
 +
Pope WH, Weigele PR, Chang J, Pedulla ML, Ford ME, Houtz JM, Jiang W, Chiu W, Hatfull GF, Hendrix RW, King J. Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine synechococcus. J Mol Biol. 2007 May 11;368(4):966-81. doi: 10.1016/j.jmb.2007.02.046. Epub 2007 Feb 22. PMID: 17383677; PMCID: PMC2971696.
 +
 +
U.S. National Library of Medicine. (n.d.). Hot80_gp25 head tail connector [Synechococcus T7-like phage S-tip37] - gene - NCBI. National Center for Biotechnology Information. From https://www.ncbi.nlm.nih.gov/gene/54998403

Revision as of 15:17, 8 October 2022


Head-Tail Connector Transcriptional Unit


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 395
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The goal of our team's project, Cyanospectre is to create a ghost phage that could be used by synthetic biologists to make genetic engineering of Cyanobacteria easier. We envision that with modification of this virus, it could be used to immobilize target cyanobacteria, or as a viral vector for the delivery of large circuits into a Cyanobacterial chassis.


We selected a cyanophage, S-TIP37 as the model from which the ghost phage could be built. This phage’s natural host is Synechococcus sp WH8109, a marine Cyanobacteria that has been grown in the lab. We selected this phage based on 1) it has a host that can be grown in the lab, 2) the phage has a relatively small genome making capsid proteins easier to identify, and 3) being a T7-like phage, the structure of its neck region is more simple than that of T4-like phages, making the construction of the ghost phage simpler. We envision that with future modeling, the tail fibers of this ghost phage could be modified to make the virus capable of attaching to and delivering capsid contents to a variety of Salt-water Synechococcus sp strains employed in synthetic biology as chassis, such as Synechococcus sp PCC 11901, UTEX 2973, PCC 7942 or 7002.

The


RCF1000 prefix was added to the sequence to facilitate Level 0 cloning via Golden Gate Assembly and the DNA was synthesized by IDT.

Source

The source of this sequence is from the S-TIP37 genome (Gene ID 54998403 from the NCBI reference assembly NC_048026.1) (HOT80_gp25 Head to Tail Connector [Synechococcus T7-like Phage S-TIP37] - Gene - NCBI, n.d.)

References

The S-TIP37 genome was found on GenomeNet

Pearson WR. An introduction to sequence similarity ("homology") searching. Curr Protoc Bioinformatics. 2013 Jun;Chapter 3:Unit3.1. doi: 10.1002/0471250953.bi0301s42. PMID: 23749753; PMCID: PMC3820096.

Pope WH, Weigele PR, Chang J, Pedulla ML, Ford ME, Houtz JM, Jiang W, Chiu W, Hatfull GF, Hendrix RW, King J. Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine synechococcus. J Mol Biol. 2007 May 11;368(4):966-81. doi: 10.1016/j.jmb.2007.02.046. Epub 2007 Feb 22. PMID: 17383677; PMCID: PMC2971696.

U.S. National Library of Medicine. (n.d.). Hot80_gp25 head tail connector [Synechococcus T7-like phage S-tip37] - gene - NCBI. National Center for Biotechnology Information. From https://www.ncbi.nlm.nih.gov/gene/54998403