Difference between revisions of "Part:BBa K2973000"

 
(11 intermediate revisions by 3 users not shown)
Line 3: Line 3:
 
<partinfo>BBa_K2973000 short</partinfo>
 
<partinfo>BBa_K2973000 short</partinfo>
  
This composite part consists of T7 Promoter(BBa_J64997) and T7 Terminator(BBa_K731721), Ribosomal Binding Site(BBa_B0034), CDS of β-lactamase without the signal peptide. β-lactamase (EC 3.5.2.6) is a small monomeric enzyme(29kDa) that is produced by bacteria and gives them resistance to antibiotics with &#946;-lactam ring because of its ability to hydrolyze the amide bond in the &#946;-lactam ring. This ability can be exploited in order to use β-lactamase as a protein reporter by providing the enzyme with its chromogenic substrate Nitrocefin. Nitrocefin is a chromogenic cephalosporin first reported in 1972 as a novel and straightforward substrate used to detect bacteria resistant to &#946;-lactam antibiotics. Normally, a nitrocefin solution has a yellow color, but after its hydrolysis by β-lactamase, the color of the solution turns red, allowing that way the detection of the enzyme.
+
This composite part consists of T7 Promoter(<partinfo>BBa_J64997</partinfo>)and T7 Terminator(<partinfo>BBa_K731721</partinfo>), Ribosomal Binding Site(<partinfo>BBa_B0034</partinfo>), CDS of β-lactamase without the signal peptide. β-lactamase (EC 3.5.2.6) is a small monomeric enzyme(29kDa) that is produced by bacteria and gives them resistance to antibiotics with the &#946;-lactam ring because of its ability to hydrolyze the amide bond in the &#946;-lactam ring. This ability can be exploited in order to use β-lactamase as a protein reporter by providing the enzyme with its chromogenic substrate Nitrocefin. Nitrocefin is a chromogenic cephalosporin first reported in 1972 as a novel and straightforward substrate used to detect bacteria resistant to &#946;-lactam antibiotics. Normally, a nitrocefin solution has a yellow color, but after its hydrolysis by β-lactamase, the color of the solution turns red, allowing that way the detection of the enzyme.
  
 
===Usage and Biology===
 
===Usage and Biology===
Line 10: Line 10:
 
This part was used as a <b>positive control</b> for our <i>in vitro</i> protein synthesis experiments.
 
This part was used as a <b>positive control</b> for our <i>in vitro</i> protein synthesis experiments.
  
In order to test the sensitivity of our regulatory system we performed experiments by adding different concentrations of trigger and reducing the time of the <i>in vitro</i> protein synthesis reaction.
+
In order to test the sensitivity of our regulatory system we performed experiments by adding different concentrations of the trigger and reducing the time of the <i>in vitro</i> protein synthesis reaction.
The <i>in vitro</i> transcription/ translation reactions were done using the PURExpress® In Vitro Protein Synthesis kit. A reaction without a trigger sequence was included, as a negative control and a leakage measure. Furthermore, in order to reduce the cost of the reaction, we lowered the reaction volume from 25 to 7 μL.
+
The <i>in vitro</i> transcription/ translation reactions were done using the PURExpress® <i>In Vitro</i> Protein Synthesis kit. A reaction without a trigger sequence was included, as a negative control and a leakage measure. Furthermore, in order to reduce the cost of the reaction, we lowered the reaction volume from 25 to 7 μL.
  
Firstly, we tested the functionality of our regulatory system by adding following concentrations of trigger:
+
Firstly, we tested the functionality of our regulatory system by adding the following concentrations of trigger:
  
 
• <b>0.3nM</b> (Fig 2.)
 
• <b>0.3nM</b> (Fig 2.)
Line 35: Line 35:
 
</html>
 
</html>
  
<b>Figure 1.</b> Enzymatic assay of β-lactamase with nitrocefin as its substrate, when expressed from a non-regulated and a toehold-regulated construct in a cell free system. Error bars correspond to standard deviation of n=2 replicates. Blank was subtracted. After the 3-hour incubation in the cell-free system, the chromogenic substrate of β-lactamase, nitrocefin, was added and an additional 45-minute enzymatic assay was performed in the plate reader, at 37oC.
+
<b>Figure 1.</b> Enzymatic assay of β-lactamase with nitrocefin as its substrate, when expressed from a non-regulated and a toehold-regulated construct in a cell-free system. Error bars correspond to the standard deviation of n=2 replicates. Blank was subtracted. After the 3-hour incubation in the cell-free system, the chromogenic substrate of β-lactamase, nitrocefin, was added and an additional 45-minute enzymatic assay was performed in the plate reader, at 37 &#8451;.
  
 
<html>
 
  <head>
 
      <title>HTML img Tag</title>
 
  </head>
 
 
  <body>
 
      <img src="https://static.igem.org/mediawiki/parts/9/93/Pure_3_hours_15.png" width="660"
 
        height="460">
 
  </body>
 
</html>
 
 
<b>Figure 2.</b> Enzymatic assay of β-lactamase with nitrocefin as its substrate, when expressed from a non-regulated and a toehold-regulated construct in a cell free system. Error bars correspond to standard deviation of n=2 replicates. Blank was subtracted. Incubation time = 3 hours. After the 3-hour incubation in the cell-free system, the chromogenic substrate of β-lactamase, nitrocefin, was added and an additional 15-minute enzymatic assay was performed in the plate reader, at 37oC
 
 
 
Since PURExpress’ incubation time is the most time-consuming part of our project, we sought to lower the incubation time and assess the performance of the cell-free system and its sensitivity. We performed a <b>1-hour</b> <i>in vitro</i> protein synthesis reaction, with all the other conditions remaining the same. Again, a gradient of trigger concentrations was included to measure the system’s sensitivity.
 
 
The trigger concentrations that were tested are listed below:
 
 
• <b>3nM</b>
 
 
• <b>7nM</b>
 
 
• <b>16nM</b>
 
 
• <b>50nM</b>
 
 
• <b>75nM</b>
 
 
After the <b>1-hour</b> incubation in the cell-free system, we added a chromogenic substrate of β-lactamase, nitrocefin, and performed an additional 15-minute enzymatic assay in the plate reader, at 37oC.
 
 
 
<html>
 
  <head>
 
      <title>HTML img Tag</title>
 
  </head>
 
 
  <body>
 
      <img src="https://static.igem.org/mediawiki/parts/2/20/1hour.png" width="640"
 
        height="460">
 
  </body>
 
</html>
 
 
<b>Figure 3.</b> Enzymatic assay of β-lactamase with nitrocefin as its substrate, when expressed from a non-regulated and a toehold-regulated construct in a cell free system. Blank was subtracted. Incubation time = 1 hour
 
  
  

Latest revision as of 12:28, 21 October 2019


T7-RBS-β-Lactamase-No Signal peptide

This composite part consists of T7 Promoter(BBa_J64997)and T7 Terminator(BBa_K731721), Ribosomal Binding Site(BBa_B0034), CDS of β-lactamase without the signal peptide. β-lactamase (EC 3.5.2.6) is a small monomeric enzyme(29kDa) that is produced by bacteria and gives them resistance to antibiotics with the β-lactam ring because of its ability to hydrolyze the amide bond in the β-lactam ring. This ability can be exploited in order to use β-lactamase as a protein reporter by providing the enzyme with its chromogenic substrate Nitrocefin. Nitrocefin is a chromogenic cephalosporin first reported in 1972 as a novel and straightforward substrate used to detect bacteria resistant to β-lactam antibiotics. Normally, a nitrocefin solution has a yellow color, but after its hydrolysis by β-lactamase, the color of the solution turns red, allowing that way the detection of the enzyme.

Usage and Biology

Documentation

This part was used as a positive control for our in vitro protein synthesis experiments.

In order to test the sensitivity of our regulatory system we performed experiments by adding different concentrations of the trigger and reducing the time of the in vitro protein synthesis reaction. The in vitro transcription/ translation reactions were done using the PURExpress® In Vitro Protein Synthesis kit. A reaction without a trigger sequence was included, as a negative control and a leakage measure. Furthermore, in order to reduce the cost of the reaction, we lowered the reaction volume from 25 to 7 μL.

Firstly, we tested the functionality of our regulatory system by adding the following concentrations of trigger:

0.3nM (Fig 2.)

3nM (Fig 2.)

7nM (Fig 1., Fig 2.)

75nM (Fig 1.)


HTML img Tag

Figure 1. Enzymatic assay of β-lactamase with nitrocefin as its substrate, when expressed from a non-regulated and a toehold-regulated construct in a cell-free system. Error bars correspond to the standard deviation of n=2 replicates. Blank was subtracted. After the 3-hour incubation in the cell-free system, the chromogenic substrate of β-lactamase, nitrocefin, was added and an additional 45-minute enzymatic assay was performed in the plate reader, at 37 ℃.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 851
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]