Part:BBa_K3453022

Rosewood DmMatK Trigger 1.3

This part is a trigger for sequence-based detection of rosewood. It is a fragment of the MatK gene of Dalbergia maritima var. pubescens (BOLD Acc. n° MADA155-14, MADA063-14, MADA062-14, MADA158-14, MADA065-14, MADA104-14, MADA023-14, MADA071-14, MADA110-14) [1].

Usage and Biology

A toehold switch is an RNA–based device containing a ribosome binding site (RBS) and an ATG start codon embedded in a hairpin structure that blocks translation initiation [2]. The hairpin can be unfolded upon binding of a trigger RNA thereby exposing the RBS and the ATG start codon permitting translation of the reporter protein (Figure 1).

Figure 1. Toehold switches principle.

This part is a trigger for the Rosewood DmMatK Toehold Switch 1.3 (BBa_K3453012) and was designed using the web tool developed by To et al. [3]. It also contains the switch binding site for the Rosewood DmMatK Toehold Switches 1.1 (BBa_K3453011) and 1.4 (BBa_K3453013).

The functionality of this part was tested under controlled of the T7 promoter (BBa_K2150031) and the strong SBa_000587 synthetic terminator (BBa_K3453000) in the composite part BBa_K3453122.

This part proved to be functional: the transcribed rosewood RNA was able to bind to the corresponding toehold switches and a readable output was generated.

Full results are available on the BBa_K3453111, BBa_K3453112 and BBa_K3453113 pages in the registry.

References

[1] Hassold S, Lowry PP 2nd, Bauert MR, Razafintsalama A, Ramamonjisoa L, Widmer A. DNA barcoding of Malagasy rosewoods: towards a molecular identification of CITES-listed Dalbergia species. PLoS One (2016) 11, e0157881.

[2] Green AA, Silver PA, Collins JJ, Yin P. Toehold switches: de-novo-designed regulators of gene expression. Cell (2014) 159, 925-939.

[3] To AC, Chu DH, Wang AR, Li FC, Chiu AW, Gao DY, Choi CHJ, Kong SK, Chan TF, Chan KM, Yip KY. A comprehensive web tool for toehold switch design. Bioinformatics (2018) 34, 2862-2864.

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
  INCOMPATIBLE WITH RFC[1000]

  Illegal BsaI site found at 82