Primer

Part:BBa_K4479002:Design

Designed by: Alston Lo, Ruochen Liu, Xinyi Xuan   Group: iGEM22_Toronto   (2022-10-12)


FIP LAMP Primer for Oak Wilt 1


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

We ranked our FIP primer based on the following criteria: 1. Distance between F2 and F3 primer: 0 - 60 nt 2. Distance between F2 and B2 primer: 120 - 160 nt 3. Distance between F1c and F2 primer: 40 - 60 nt 4. Distance between F1c and B1c primer: 0 - 100 nt 5. Length of F1c primer: 15 - 25 bp 6. Length of F2 primer: 15 - 25 bp 7. GC Content: 40 - 60% 8. Melting temperature for F1c primer: 60 - 68℃ 9. Melting temperature for F2 primer: 55 - 63℃ 10. Melting temperature difference between F1c and B1c primers: ≤ 5℃ 11. Melting temperature difference between F2 and B2 primers: ≤ 5℃

Other criteria for extra marks: 1. No runs of 3 or more of one base (i.e ACCC) 2. No dinucleotide repeats (i.e ATATATAT) 3. Avoid forward and reverse primers having complementary sequences 4. Avoid more than three bases that complement within the primer



Source

The part was designed with the Primer Explorer software and then it was ranked against primers provided by the GLAPD software using computer models by our Drylab team. The criteria for ranking were: Primer Distance, Primer Length, GC Content, Melting Temperature, and Melting Temperature Difference. The target sequence it originated from is MG270170.1.

References