Team:SUSTC-Shenzhen-B/lab introduction

From 2012.igem.org

(Difference between revisions)
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                 <h3 class="STYLE10">Objective</h3>
                 <h3 class="STYLE10">Objective</h3>
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                 <p>The goal of our wet lab work is validate our software prediction. There are very limited terminator efficiency data available in literatures, we have designed 100 terminators bioinformatically, and want physically measure the efficiency. By fitting our prediction with experiment results, we can adjust the parameters in our model to make it more accurate.</p>
+
                 <p>The goal of our wet lab work is to validate our software prediction. Since the terminator efficiency data available in literatures is very limited, we designed 100 terminators through the knowledge of terminator structure, and designed an experiment to measure terminator efficiency. By analyzing experiment results, we can adjust the parameters in our model to make it more accurate.</p>
  <h3 class="STYLE10">1, How to measure efficiency:</h3>
  <h3 class="STYLE10">1, How to measure efficiency:</h3>
                 <img src="http://2012.igem.org/wiki/images/6/62/Project.introduction.3JPG.JPG" alt="" class="img_fl img_border" />
                 <img src="http://2012.igem.org/wiki/images/6/62/Project.introduction.3JPG.JPG" alt="" class="img_fl img_border" />
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<p>In figure above, we show our plasmid design to measure terminator efficiency. The terminator to be characterized is flanked by two fluorescent proteins, GFP and RFP. If the terminator is 100% efficient, then, RFP will be transcripted while GFP should not be transcripted. If the terminator is 0% efficienct, then, both RFP and GFP will be transcripted at the same time. We use flow cytometry to measure the fluorescence strength of GFP and RFP. </p>
+
<p>The figure above shows the plasmid designed to measure terminator efficiency. The terminator to be characterized would be flanked by gene sequences of two fluorescent proteins, GFP and RFP. By using flow cytometry, we could measure the fluorescence strength of GFP and RFP, so as to measure the terminator efficiency. </p>
-
The terminator efficiency of a terminator is calculated as:
+
The terminator efficiency of a terminator is calculated with the formula:
<p> E = 1- S/T </p>
<p> E = 1- S/T </p>
-
Here S is the fluorescence strength of GFP with terminator, and T is the fluorescence strenght of GFP without terminator, which is the baseline strength.
+
where S is the fluorescence strength of GFP with terminator, and T is the fluorescence strength of GFP without terminator, which is the baseline strength.
            
            
    
    
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                 <h3 class="STYLE10">2. Plasmid Construction</h3>
                 <h3 class="STYLE10">2. Plasmid Construction</h3>
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   <p>The goal of BioBrick is to standardize the form of genetic components to allow idempotent reactions where the key structural elements of a component are unchanged by the reactions. So BioBrick provide a standard method of assembling genetic components using specified prefixes and suffixes. Prefixes include EcoRⅠ and XbaⅠ; suffixes include SpeⅠ and PstⅠ.
+
   <p>A goal of synthetic biology is to standardize the form of genetic components to prevent structural elements of components from changing with reactions. It provides a standard method of assembling genetic components using specified prefixes and suffixes. Prefixes include EcoRⅠ and XbaⅠ; suffixes include SpeⅠ and PstⅠ.
   <p>The recognition site of XbaⅠ:</p>
   <p>The recognition site of XbaⅠ:</p>
   <img src="http://2012.igem.org/wiki/images/2/2e/Xba1.JPG" class="img_fl img_border" />
   <img src="http://2012.igem.org/wiki/images/2/2e/Xba1.JPG" class="img_fl img_border" />
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   <img src="http://2012.igem.org/wiki/images/7/77/Spe1.JPG" class="img_fl img_border" />     
   <img src="http://2012.igem.org/wiki/images/7/77/Spe1.JPG" class="img_fl img_border" />     
   <p>(Figure 4)</p>
   <p>(Figure 4)</p>
-
  They have the same cohesive terminus so they can connect together. However, after the combination, neither XbaⅠnor SpeⅠ can recognize this sequence. According to this way can we achieve the goal of BioBricks.
+
<p>The same cohesive terminus enable them to connect with each other. However, after the combination, neither XbaⅠnor SpeⅠis able to recognize this sequence. Through this way we could achieve the goal of building BioBricks. </p>
-
We can see from the picture(Figure 2) that there are 4 standard restriction enzyme cutting sites:  
+
<p>We can see from the picture(Figure 2) that there are 4 standard restriction enzyme cutting sites:  
-
EcoRⅠ, XbaⅠ, SpeⅠ,PstⅠ.
+
EcoRⅠ, XbaⅠ, SpeⅠ,PstⅠ. </p>
   </p>
   </p>
-
   <p>1. Because we will use pstⅠto be the restriction cutting site of terminators, if we want to ligase GFP to the plasmid, this restriction cutting site should be mutated.
+
   <p>(1) As we will use pstⅠto be the restriction cutting site of terminators, if we want to ligase GFP to the plasmid, this restriction cutting site should be mutated.
   <p>The recognition site of PstⅠ:</p>
   <p>The recognition site of PstⅠ:</p>
   <img src="http://2012.igem.org/wiki/images/c/cc/Pst1.JPG" class="img_fl img_border" />  
   <img src="http://2012.igem.org/wiki/images/c/cc/Pst1.JPG" class="img_fl img_border" />  
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   <img src="http://2012.igem.org/wiki/images/c/cc/Afl2.JPG" class="img_fl img_border" />  
   <img src="http://2012.igem.org/wiki/images/c/cc/Afl2.JPG" class="img_fl img_border" />  
     <p>(Figure 6)</p>
     <p>(Figure 6)</p>
-
  Since AflⅡis like PstⅠ,they just have 2 different base-pairs, we use
+
<p> Since AflⅡis similar to PstⅠ,they just have 2 different base pairs, we used these primers:</p>
-
PtoA-F
+
<p>PtoA-F</p>
-
5'-CCACCTGACGTCTAAGAAAC-3'
+
<p>5'-CCACCTGACGTCTAAGAAAC-3'</p>
-
PtoA-R
+
<p>PtoA-R</p>
-
5'-CTTAAGCGGCCGCTACTAGTA-3'
+
<p>5'-CTTAAGCGGCCGCTACTAGTA-3'</p>
-
These primer to mutate the vector.
+
<p>to mutate the vector.</p>
   </p>
   </p>
-
               <p>2. After the mutation is successful, the next step is to connect GFP & RFP to the vector.
+
               <p>(2) After the mutation succeeded, the next step is to connect sequences of GFP & RFP to the vector. These sequences were built by PCR extension.</p>
-
                  The GFP and RFP were built by PCR extension.
+
                   <p>To digest GFP sequence, we used SpeⅠand AflⅡ. We also digested the vector with the same restriction enzyme cutting sites. During the process of base complementary pairing, GFP sequence could be ligated onto the vector with the help of T4 DNA ligase. At the same time, the recognition site of PstⅠ would be added to the vector.</p>
-
                   To digest GFP, we use SpeⅠand AflⅡ. We also digest the vector with the same restriction enzyme cutting sites. During the process of base complementary pairing, GFP can be ligated into the vector with the help of T4 DNA ligase. At the same time, the recognition site of PstⅠ has been added to the vector.
+
                   <p>To digest RFP sequence, we used NotⅠ and SpeⅠ. We also digested the vector with the same restriction enzyme cutting sites. During the process of base complementary pairing, RFP sequence could be ligated onto vector with the help of T4 DNA ligase. At the same time, the recognition site of XbaⅠwould be added to the vector.</p>
-
                   To digest RFP, we use NotⅠ and SpeⅠ. We also digest the vector with the same restriction enzyme cutting sites. During the process of base complementary pairing, RFP can be ligated into vector with the help of T4 DNA ligase. At the same time, the recognition site of XbaⅠ has been added to the vector.
+
                   <p>We can either connect 3 fragments: GFP, RFP sequences and the plasmid at the same time, or connect 2 fragments first and then connect the other one. However, when carrying out the second scheme, we should decide which one to be connected first. According to the picture, GFP should be the one.</p>
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                   We can either connect GFP, RFP and the plasmid these 3 fragments together or connect 2 fragments together first and then connect the other one. However, when we carry out the second scheme, we should consider which one should be connected first. According to the picture, we should connect GFP first.
+
 
-
                   Besides:
+
                   <p>Besides:</p>
-
                   We designed these primers to amplify RFP.
+
                   <p>We designed these primers to amplify RFP.</p>
-
                   R-NPS-F
+
                   <p>R-NPS-F</p>
-
                   5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'
+
                   <p>5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3' </p>
-
                   R-NPS-R
+
                   <p>R-NPS-R</p>
-
                   5'-CGGAGACTAGTCTGCAGATCACATAAGTAAAGTGATAATC-3'
+
                   <p>5'-CGGAGACTAGTCTGCAGATCACATAAGTAAAGTGATAATC-3'</p>
-
                   We designed these primers to amplify GFP.
+
                   <p>We designed these primers to amplify GFP.</p>
-
                   G-SXA-F
+
                   <p>G-SXA-F</p>
-
                   5'-CTAGACTAGTTCTAGAGGCGGACTCACTATAGA-3'   
+
                   <p>5'-CTAGACTAGTTCTAGAGGCGGACTCACTATAGA-3'  </p>
-
                   G-SXA-R
+
                   <p>G-SXA-R</p>
-
                   5'-CCGACTTAAGGGATCCTATAAACGCAG-3'  </p>
+
                   <p>5'-CCGACTTAAGGGATCCTATAAACGCAG-3'  </p>
-
                 <p>3. Until these steps, we have already built the vector well. We decided to use XbaⅠ,PstⅠto digest the vector.  
+
                 <p>(3) Since we built up the vector through the steps before, we decided to use XbaⅠ,PstⅠto digest the vector.</p>
-
                   The terminators were built by PCR extension.
+
                   <p>The terminators were built by PCR extension.</p>
-
                   Then we can ligated terminator into the backbone and transformed into competent cells.
+
                   <p>Then we can ligated terminator into the backbone and transformed into competent cells.</p>
-
                   Characterization devices testing the performance of the terminators utilized fluorescent proteins to measure input and output and altered the arabinose transport system to control inputs. The fluorescence produced by the characterization devices were then measured using flow cytometry to calculate the termination efficiency of the terminators.             </p>
+
                   <p>Characterization devices testing the performance of the terminators utilized fluorescent proteins to measure input and output and altered the arabinose transport system to control inputs. The fluorescence produced by the characterization devices were then measured using flow cytometry to calculate the termination efficiency of the terminators. </p>
<h3 class="STYLE10">3. Fluorescence strength quantification</h3>
<h3 class="STYLE10">3. Fluorescence strength quantification</h3>
-
We used flow cytometer to measured the fluorescence strength. We also used fluorescence microscope to take a picture of bacterial culture.  
+
We used flow cytometer to measured the fluorescence strength. We also used fluorescence microscope to take a picture of bacterial culture.
<br>  
<br>  

Revision as of 16:41, 26 October 2012

Title

Introduction to the Lab Work

Objective

The goal of our wet lab work is to validate our software prediction. Since the terminator efficiency data available in literatures is very limited, we designed 100 terminators through the knowledge of terminator structure, and designed an experiment to measure terminator efficiency. By analyzing experiment results, we can adjust the parameters in our model to make it more accurate.

1, How to measure efficiency:

The figure above shows the plasmid designed to measure terminator efficiency. The terminator to be characterized would be flanked by gene sequences of two fluorescent proteins, GFP and RFP. By using flow cytometry, we could measure the fluorescence strength of GFP and RFP, so as to measure the terminator efficiency.

The terminator efficiency of a terminator is calculated with the formula:

E = 1- S/T

where S is the fluorescence strength of GFP with terminator, and T is the fluorescence strength of GFP without terminator, which is the baseline strength.

2. Plasmid Construction

A goal of synthetic biology is to standardize the form of genetic components to prevent structural elements of components from changing with reactions. It provides a standard method of assembling genetic components using specified prefixes and suffixes. Prefixes include EcoRⅠ and XbaⅠ; suffixes include SpeⅠ and PstⅠ.

The recognition site of XbaⅠ:

(Figure 3)

The recognition site of SpeⅠ:

(Figure 4)

The same cohesive terminus enable them to connect with each other. However, after the combination, neither XbaⅠnor SpeⅠis able to recognize this sequence. Through this way we could achieve the goal of building BioBricks.

We can see from the picture(Figure 2) that there are 4 standard restriction enzyme cutting sites: EcoRⅠ, XbaⅠ, SpeⅠ,PstⅠ.

(1) As we will use pstⅠto be the restriction cutting site of terminators, if we want to ligase GFP to the plasmid, this restriction cutting site should be mutated.

The recognition site of PstⅠ:

(Figure 5)

The recognition site of AflⅡ:

(Figure 6)

Since AflⅡis similar to PstⅠ,they just have 2 different base pairs, we used these primers:

PtoA-F

5'-CCACCTGACGTCTAAGAAAC-3'

PtoA-R

5'-CTTAAGCGGCCGCTACTAGTA-3'

to mutate the vector.

(2) After the mutation succeeded, the next step is to connect sequences of GFP & RFP to the vector. These sequences were built by PCR extension.

To digest GFP sequence, we used SpeⅠand AflⅡ. We also digested the vector with the same restriction enzyme cutting sites. During the process of base complementary pairing, GFP sequence could be ligated onto the vector with the help of T4 DNA ligase. At the same time, the recognition site of PstⅠ would be added to the vector.

To digest RFP sequence, we used NotⅠ and SpeⅠ. We also digested the vector with the same restriction enzyme cutting sites. During the process of base complementary pairing, RFP sequence could be ligated onto vector with the help of T4 DNA ligase. At the same time, the recognition site of XbaⅠwould be added to the vector.

We can either connect 3 fragments: GFP, RFP sequences and the plasmid at the same time, or connect 2 fragments first and then connect the other one. However, when carrying out the second scheme, we should decide which one to be connected first. According to the picture, GFP should be the one.

Besides:

We designed these primers to amplify RFP.

R-NPS-F

5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'

R-NPS-R

5'-CGGAGACTAGTCTGCAGATCACATAAGTAAAGTGATAATC-3'

We designed these primers to amplify GFP.

G-SXA-F

5'-CTAGACTAGTTCTAGAGGCGGACTCACTATAGA-3'

G-SXA-R

5'-CCGACTTAAGGGATCCTATAAACGCAG-3'

(3) Since we built up the vector through the steps before, we decided to use XbaⅠ,PstⅠto digest the vector.

The terminators were built by PCR extension.

Then we can ligated terminator into the backbone and transformed into competent cells.

Characterization devices testing the performance of the terminators utilized fluorescent proteins to measure input and output and altered the arabinose transport system to control inputs. The fluorescence produced by the characterization devices were then measured using flow cytometry to calculate the termination efficiency of the terminators.

3. Fluorescence strength quantification

We used flow cytometer to measured the fluorescence strength. We also used fluorescence microscope to take a picture of bacterial culture.
South University of Science and Technology of China