Difference between revisions of "Part:BBa K4268000:Design"

(→‎Design Notes)
(→‎Design Notes)
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===Design Notes===
 
===Design Notes===
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''Synechococcus sp WH 8109'', was decided as the desired cyanobacterial species that SUNY_Oneonta iGEM would like to target, S-TIP 37 is the infecting cyanophage of this cyanobacterial species. Although S-TIP 37's genome has been fully sequenced there is little experimental evidence of research on the genome, thus resulting in many hypothetical proteins whose functions are unknown. To better characterize these putative genes, a series of bioinformatic tools were employed.
  
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''Synechococcus sp PCC 11901'', was decided as the desired cyanobacterial species that SUNY_Oneonta iGEM would like to focus on? S-TIP 37 is the infecting cyanophage of this cyanobacterial species. However, the genome has not undergone full sequencing and many of its genes remain hypothetical proteins. Thus, in comparison to Syn-5, another T7-like phage that has been fully sequenced, was needed. Both S-TIP 37 and Syn-5 are structurally and genetically similar allowing the team to distinguish the genes needed for producing the phage shell.
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SUNY_Oneonta iGEM identified another T7-like phage that has had considerable research done with its genome, Syn-5. The structural and genomic similarities between the Syn-5 and S-TIP 37, allowed direct comparisons to be drawn between the two.  
  
  
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*Restriction sites were removed/altered to ensure RCF10 and RCF1000 compatibility
 
*Restriction sites were removed/altered to ensure RCF10 and RCF1000 compatibility
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name,
 +
  
 
*To complete Level 0 Golden Gate Assembly, the sequence contains SapI sites at the ends
 
*To complete Level 0 Golden Gate Assembly, the sequence contains SapI sites at the ends

Revision as of 22:15, 25 September 2022


S-TIP37 Head-Tail Connector


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 346
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Synechococcus sp WH 8109, was decided as the desired cyanobacterial species that SUNY_Oneonta iGEM would like to target, S-TIP 37 is the infecting cyanophage of this cyanobacterial species. Although S-TIP 37's genome has been fully sequenced there is little experimental evidence of research on the genome, thus resulting in many hypothetical proteins whose functions are unknown. To better characterize these putative genes, a series of bioinformatic tools were employed.

SUNY_Oneonta iGEM identified another T7-like phage that has had considerable research done with its genome, Syn-5. The structural and genomic similarities between the Syn-5 and S-TIP 37, allowed direct comparisons to be drawn between the two.


Insert poster table comparison

Upon the isolation of the Head-Tail Connector sequence, the following edits were made:

  • Restriction sites were removed/altered to ensure RCF10 and RCF1000 compatibility

name,


  • To complete Level 0 Golden Gate Assembly, the sequence contains SapI sites at the ends

Source

The source of this sequence is from the S-TIP37 genome (GenBanK: NC_048026.1)

References

The S-TIP37 genome was found on GenomeNet