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

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===Source===
 
===Source===
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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.)
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The source of the Head-Tail Connector 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===

Revision as of 16:55, 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.

Level 0 parts BBa_R0085, BBa_B0034, BBa_K4268000 (Head-Tail Connector), and BBa_B0015 are cloned together to form a Level 1 Transcriptional Unit. According to Type IIS Assembly, there will be 5'to 3' fusion sites between each basic part. However, the sequence provided does not contain these sites.

Source

The source of the Head-Tail Connector 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