DNA

Part:BBa_K4636011:Design

Designed by: Lo-Chueh, Chu   Group: iGEM23_NTHU-Taiwan   (2023-10-11)


Probe_0004771_11


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

The sequence we designed can be separated into two parts: The binding sequence and the extension sequence. (See Figure 1 for details of probe sequence.)


Figure 1. Probe design compose of binding sequence and extension sequence.

Binding sequence is mainly a feasible binding sites for cDNA of hsa_circ_0004771. We use blast to confirm that its specificity is high enough. In addition, we also have the following considerations:
(1) GC content is between 40%~60%.
(2) Tm value is around 40°C.
(3) Finally, we refer to the paper[1] and add two AA sequences as extension sequences at the 3’ end of the sequence. AA sequence is between the binding sequence and gold nanoparticle.
(4) The avoidance of self-dimer is also important for primer design.

Reference

1. Ali, M. M., Kanda, P., Aguirre, S. D., & Li, Y. (2011). Modulation of DNA-modified gold-nanoparticle stability in salt with concatemeric single-stranded DNAs for colorimetric bioassay development. Chemistry (Weinheim an der Bergstrasse, Germany), 17(7), 2052–2056. https://doi.org/10.1002/chem.201002677