Composite

Part:BBa_K3725020

Designed by: Alice Hou, Michelle Jing, Monica Cho, Janet Standeven, Megan McSweeney   Group: iGEM21_Lambert_GA   (2021-09-29)
Revision as of 03:10, 21 October 2021 by Pranavkanthala (Talk | contribs)


Overview
The F. oxysporum f.sp. lycopersici toehold part is designed to be used in conjunction with the T7 F. oxysporum f.sp. lycopersici trigger in order to express GFP as a part of the engineered toehold switch system. The described structure was designed using NUPACK (Nucleic Acid Package) software’s Design feature. This was done by finding a unique gene of the P. cryptogea species that encodes for pathogenicity: the FRP1 gene. After inputting the FRP1 gene sequence into the NUPACK software using an input code given by Takashi et. al., pairs of trigger sequences and switch sequences were outputted. The trigger sequences given were 36 base-pair long sequences from the FRP1 gene, and the switch sequences given were reverse complementary to the trigger sequences. The pairs were ordered by normalized ensemble defect, so the pair with the lowest normalized ensemble defect was used. We ordered the insert in a pUCIDT Amp plasmid from Integrated DNA Technologies.
Description
The F. oxysporum f.sp. lycopersici toehold part is designed to be used in conjunction with the T7 F. oxysporum f.sp. lycopersici trigger in order to express GFP as a part of the engineered toehold switch system. The described structure was designed using NUPACK (Nucleic Acid Package) software’s Design feature. This was done by finding a unique gene of the P. cryptogea species that encodes for pathogenicity: the FRP1 gene. After inputting the FRP1 gene sequence into the NUPACK software using an input code given by Takashi et. al., pairs of trigger sequences and switch sequences were outputted. The trigger sequences given were 36 base-pair long sequences from the FRP1 gene, and the switch sequences given were reverse complementary to the trigger sequences. The pairs were ordered by normalized ensemble defect, so the pair with the lowest normalized ensemble defect was used. We ordered the insert in a pUCIDT Amp plasmid from Integrated DNA Technologies.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 784


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Categories
Parameters
None