Part:BBa_K4820000:Design

5'-3' 37 base pair oligo capable of binding to human ferritin; biotinylated 3' end

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 SapI.rc site found at 20
  

Design Notes

The paper that we found this sequence in ("Specific repression of b-globin promoter activity by nuclear ferritin") tested the wild type sequence and mutant sequences and it found that the wild type sequence binds to ferritin the best. They also found a recurring motif that they believe assists in binding.

Our design considerations: 1. How long should we make the chain? - we picked the shorter option at 37 bp 2. We made it single strand instead of a double helix to help with the DNA's flexibility - potential increased binding

Source

Sequence is a part of Wild type Human Beta-globin promoter

References

Broyles, R. W., Belegu, V., DeWitt, C., Shah, S. N., Stewart, C. A., Pye, Q. N., & Floyd, R. A. (2001). Specific repression of β-globin promoter activity by nuclear ferritin. Proceedings of the National Academy of Sciences of the United States of America, 98(16), 9145–9150. https://doi.org/10.1073/pnas.151147098

Surguladze, N., Thompson, K. M., Beard, J. L., Connor, J. R., & Fried, M. (2004). Interactions and Reactions of Ferritin with DNA. Journal of Biological Chemistry, 279(15), 14694–14702. https://doi.org/10.1074/jbc.m313348200