Part:BBa_K3657023

DNA Part of an RNA·DNA-DNA triple helix

It was proved by Kunkler et al. that this sequence creates a triple helix with the RNA part (BBa_K3657022) in vitro.

More information available here: iGEM Heidelberg 2020

Usage and Biology

Triple helices are one of the alternative structures formed by nucleic acids. In addition to the Watson-Crick interactions between base pairs, Hoogsteen interactions are crucial for the formation of the triple helix. The binding is sequence specific.

Part Design

You can generate analogical parts yourself as following:

1. Generate a random DNA sequence containing adenine, cytosine and guanine. You sequence should be longer than 19 base pairs and preferably should not contain thymine.
2. Use the following script to generate RNA: link.
   Corresponding bases in the script are the pairs that create strongest bonds according to Kunkler et al.
3. Attention! If you are adding other parts to your RNA, for example hairpins that interact with RNA binding proteins, makes sure that the added parts don't create a stable secondary structure with the triple helix part. Otherwise it may disturb the formation of the triple helix.

References

Kunkler CN, Hulewicz JP, Hickman SC, Wang MC, McCown PJ, Brown JA. Stability of an RNA•DNA-DNA triple helix depends on base triplet composition and length of the RNA third strand. Nucleic Acids Res. 2019; 47(14):7213-7222.

Sequence and Features

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]