Difference between revisions of "Part:BBa K4813000"

Revision as of 09:42, 7 October 2023

dTomato fluoresence protein Codon Optimized for E coli

This part encodes a protein called dTomato, which is a red fluorescence protein. It forms a dimer and has a molecular weight of around 27.0 kDa. This protein originates from a species called Discosoma [1].

To enhance its performance for our project, we used IDT codon optimization tools to optimize the sequence. We incorporated this optimized sequence into two composite parts. One part served as a reporter gene for detecting formaldehyde with pFrmR formaldehyde sensing promoter (BBa_K4813003), while the other part (BBa_K4813005) acted as a positive control, where the expression of dTomato was driven by a strong constitutive promoter (BBa_J23100).

Reference

[1] dTomato at fpbase. FPbase. Accessed 20 June 2023 https://www.fpbase.org/protein/dtomato/

[2] tdTomato at fpbase. FPbase. Accessed 20 June 2023 https://www.fpbase.org/protein/tdtomato/

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 15: / Line 15: @@
 <!-- Add more about the biology of this part here
-===Comparing the colouration of optimized dTomato <partinfo>BBa_K4813000</partinfo> and tdTomato <partinfo>BBa_K4813001</partinfo>===
-While the fluorescence protein database indicates that tdTomato exhibits superior fluorescence emission compared to dTomato [2], we don't know if it also applies to their chromoprotein properties. Given that our project focuses on developing a device to monitor formaldehyde levels that can be easily used by the general population without specialized equipment, we are interested in finding a chromoprotein that produces a more pronounced color visible to the naked eye.
+<b>===Usage and Biology===
+Comparing the colouration of optimized dTomato <partinfo>BBa_K4813000</partinfo> and tdTomato <partinfo>BBa_K4813001</partinfo></b>
+While the fluorescence protein database indicates that tdTomato exhibits superior fluorescence emission compared to dTomato [2], we don't know if it also applies to their chromoprotein properties. Given that our project focuses on developing a device to monitor formaldehyde levels that can be easily used by the general population without specialized equipment, we are interested in finding a chromoprotein that produces a more obvious color visible to the naked eye.
 To address this, we have generated two composite parts, one expressing the dTomato part (<partinfo>BBa_K4813002</partinfo>) and the other expressing tdTomato (<partinfo>BBa_K4813004</partinfo>), and subsequently compared their colors as observed by the naked eye.
-[[Image:hkjss-neb-logo.png|450px|thumb|left|'''Figure 1:''' Fermentation of ''E.&nbsp;coli'' KRXwith <partinfo>BBa_K863005</partinfo> (ECOL) in an Infors Labfors Bioreactor, scale: 3&nbsp;L, [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Materials#Autoinduction_medium autoinduction medium] + 60&nbsp;µg/mL chloramphenicol, 37&nbsp;°C, pH&nbsp;7, agitation on cascade to hold pO<sub>2</sub> at 50&nbsp;%, OD<sub>600</sub> measured every 30&nbsp;minutes.]]
+[[https://static.igem.wiki/teams/4813/wiki/logo-png.jpg|200px|]]
+From the figures, the results showed that
-Consequently, we opted to use dTomato for the final assay, as it proved to be more effective in detecting the presence of formaldehyde.
+Consequently, we opted to use dTomato for the final assay, as it proved to be more obvious in detecting the change of colour in ''E. coli'' with the presence of formaldehyde.
-===Usage and Biology===
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