Primer

Part:BBa_K3658026:Design

Designed by: Yujeong Oh   Group: iGEM20_NYU_Abu_Dhabi   (2020-10-26)


LAMP B3 for Batrachochytrium salamandrivorans (Bsal) ITS region


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
    COMPATIBLE WITH RFC[1000]


Design Notes

When designing the primers, one has to make sure two of them match an exact sequence on the DNA, so that when they are extended, they can form a loop between the primer and the inverse sequence on the new DNA. Lower dG values are usually preferred. We also made sure to check whether F3 and B3 of the set fits into the guide RNA range. For troubleshooting if we did not get enough primers designed: 1. Use a broader range of Tm for primers, but make sure to keep the Tm of F1c/B1c about 3-4 degrees higher than that of F2/B2 and F3/B3 primers. 2. Change the minimum length of F2/B2 and F3/B3 primers to 15 rather than 18. 3. Change the GC rate to 20 or 25 rather than 40.



Source

We found the Bsal ITS region sequence in NCBI and used LAMP primer design software primerexplorer to design the primer.

References