Difference between revisions of "Part:BBa K2054004:Design"

Revision as of 03:54, 28 October 2016

Oligo 4 of DNA Tetrahedral Nanostructure

Design Notes

This device was modified from a recent publication about in vivo synthesis and self-assembly of DNA nanostructures. We made use of the technique described in the article to synthesize oligos for our tetrahedral nanostructure, where the sequences are generated by a software called Tiamat. This device will enable the single-stranded DNA oligo 4 to be synthesized inside cells. The ssDNA oligos produced can be purified and used to form our tetrahedral nanostructure, which consists of 5 oligos.

Below show our tetrahedral nanostructure and the sequence of the oligos.

Construction and production of ssDNA The design is based on the literature mentioned and contains:

a strong promoter BBa_J23100 from the Registry of standard biobricks a ‘r_oligo’ region that contains the sequence of our desired oligos and more (see below); a terminator BBa_B0054, which is also from the Registry;

The ‘r_oligo’ region will transcribe a product that contains a non-coding RNA (ncRNA) and a HIV-Terminator-Binding Site (HTBS) that exhibit a 3’-hairpin structure:

The HTBS serves as a terminator in this gene, where the HIV reverse transcriptase binds. During the reverse transcription, the binding of HIVRT initiates the elongation, which is aided by another RT murine leukemia reverse transcriptase (MLRT). RNase H then cleaves specifically the ncRNA-DNA linkages, which leaves the desired ssDNA to hang, but still attached to the HTBS on its 5’ end. RNase A then breaks to release the desired ssDNA. The following diagram summarizes the in vivo conversion.

Source

Elbaz, J., Yin, P., & Voigt, C. A. (2016). Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nature communications, 7.

References

Elbaz, J., Yin, P., & Voigt, C. A. (2016). Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nature communications, 7.