Difference between revisions of "Part:BBa K3453011"

Revision as of 22:26, 3 October 2020

Rosewood DmMatK Toehold Switch 1.1

This part is a toehold switch sensor for sequence-based detection of rosewood. It targets a fragment of the MatK gene of Dalbergia maritima var. pubescens (BBa_K3453020).

Usage and Biology

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

This part is a toehold switch sensor that targets a fragment of the MatK gene of Dalbergia maritima var. pubescens (BBa_K3453020). It was designed using the web tool developed by To et al. [2] and follows the architecture of the Series B of toehold switch sensors for Zika virus detection [3] and of the BioBits™ toeholds[4].

Its corresponding trigger sequence is BBa_K3453021.

The functionality of this part was tested using sfGFP-LVAtag (BBa_K2675006) as a reporter. The expression was controlled by the T7 promoter (BBa_K2150031) and the strong SBa_000587 synthetic terminator (BBa_K3453000) in the composite part BBa_K3453111.

This part proved to be functional: a readable output was generated only in the presence of rosewood RNA.

Full results are available on the BBa_K3453111 page in the registry.

References

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

[2] 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.

[3] Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O'Connor DH, Gehrke L, Collins JJ. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell (2016) 165, 1255-1266.

[4] Huang A, Nguyen PQ, Stark JC, Takahashi MK, Donghia N, Ferrante T, Dy AJ, Hsu KJ, Dubner RS, Pardee K, Jewett MC, Collins JJ. BioBits™ Explorer: A modular synthetic biology education kit. Sci Adv (2018) 4, eaat5105.

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_K3453011 short</partinfo>
-This part is a toehold switch sensor for sequence-based detection of rosewood. It targets a fragment of the MatK gene of ''Dalbergia maritima'' var. ''pubescens'' ([[Part:BBa_K3453020|BBa_K3453020]]) (BOLD Acc. n° MADA155-14, MADA063-14, MADA062-14, MADA158-14, MADA065-14, MADA104-14, MADA023-14, MADA071-14, MADA110-14) [1].
+This part is a toehold switch sensor for sequence-based detection of rosewood. It targets a fragment of the MatK gene of ''Dalbergia maritima'' var. ''pubescens'' ([[Part:BBa_K3453020|BBa_K3453020]]).
 ===Usage and Biology===
-TO DO
+A toehold switch is an RNA–based device containing a ribosome binding site (RBS) embedded in a hairpin structure that blocks translation initiation [1]. The hairpin can be unfolded upon binding of a trigger RNA therefore exposing the RBS and permitting translation of the reporter protein.
+This part is a toehold switch sensor that targets a fragment of the MatK gene of ''Dalbergia maritima'' var. ''pubescens'' ([[Part:BBa_K3453020|BBa_K3453020]]).
+It was designed using the web tool developed by To ''et al.'' [2] and follows the architecture of the Series B of toehold switch sensors for Zika virus detection [3] and of the BioBits™ toeholds[4].
+Its corresponding trigger sequence is [[Part:BBa_K3453021|BBa_K3453021]].
+The functionality of this part was tested using sfGFP-LVAtag ([[Part:BBa_K2675006|BBa_K2675006]]) as a reporter. The expression was controlled by 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_K3453111|BBa_K3453111]].
+This part proved to be functional: a readable output was generated only in the presence of rosewood RNA.
+Full results are available on the [[Part:BBa_K3453111|BBa_K3453111]] page 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.
+[1] Green AA, Silver PA, Collins JJ, Yin P. Toehold switches: de-novo-designed regulators of gene expression. Cell (2014) 159, 925-939.
 [2] 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.
+[3] Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O'Connor DH, Gehrke L, Collins JJ. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell (2016) 165, 1255-1266.
+[4] Huang A, Nguyen PQ, Stark JC, Takahashi MK, Donghia N, Ferrante T, Dy AJ, Hsu KJ, Dubner RS, Pardee K, Jewett MC, Collins JJ. BioBits™ Explorer: A modular synthetic biology education kit. Sci Adv (2018) 4, eaat5105.
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