Difference between revisions of "Part:BBa K3453043"

Latest revision as of 21:38, 26 October 2020

Rosewood DmRbcL Trigger 1.3

This part is a trigger for sequence-based detection of rosewood. It is a fragment of the RbcL 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 DmRbcL Toehold Switch 1.3 (BBa_K3453033) and was designed using the web tool developed by To et al. [3]. It also contains the switch binding site for the Rosewood DmRbcL Toehold Switch 2.1 (BBa_K3453034).

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_K3453143.

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_K3453133 and BBa_K3453134 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
COMPATIBLE WITH RFC[1000]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K3453043 short</partinfo>
-to do
+This part is a trigger for sequence-based detection of rosewood. It is a fragment of the RbcL 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].
-<!-- Add more about the biology of this part here
 ===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).
+[[File: T--Evry_Paris-Saclay--toehold-switch.png|600px]]
+Figure 1. Toehold switches principle.
+This part is a trigger for the Rosewood DmRbcL Toehold Switch 1.3 ([[Part:BBa_K3453033|BBa_K3453033]]) and was designed using the web tool developed by To ''et al.'' [3]. It also contains the switch binding site for the Rosewood DmRbcL Toehold Switch 2.1 ([[Part:BBa_K3453034|BBa_K3453034]]).
+The functionality of this part was tested under controlled of the T7 promoter ([[Part:BBa_K2150031|BBa_K2150031]]) and the strong SBa_000587 synthetic terminator ([[Part:BBa_K3453000|BBa_K3453000]]) in the composite part [[Part:BBa_K3453143|BBa_K3453143]].
+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 [[Part:BBa_K3453133|BBa_K3453133]] and [[Part:BBa_K3453134|BBa_K3453134]] 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.
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