DNA

Part:BBa_K4636016:Design

Designed by: Ping-yu Yang   Group: iGEM23_NTHU-Taiwan   (2023-10-11)

Splint_4771_18

Design

For optimal efficiency in circularizing our target RNA, we have considered various design factors based on references[1]. Here are the design considerations:
(1) Keep the GC content below 50% to facilitate the dissociation between DNA-RNA hybrid.
(2) Tm value around 37°C.
(3) Ensure that the splint is no longer than 20 base pairs, as longer splints may result in a lower combination rate.
(4) To prevent non-specific binding, the splint should not be smaller than 10 base pairs.
(5) The entropy predicted by RNAfold should be close to 1.
(6) Ensure that there are no secondary structures in the splint.

Reference

1. An, R., Li, Q., Fan, Y., Li, J., Pan, X., Komiyama, M., & Liang, X. (2017). Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration. Nucleic acids research, 45(15), e139. https://doi.org/10.1093/nar/gkx553

Source


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]