Team:TUDelft/Research Proposal

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='''Research Proposal'''=
 
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__TOC__
 
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=='''Module 1: Delay device'''==
 
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Delayed expression genetic circuit: This kind of circuit has the ability to integrate signals and trigger events after a delay from the initial detection event. There are two approaches to construct a time delay genetic circuit, these are:
 
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#“protein-based” transcriptional regulators
 
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#“RNA-based” posttranscriptional regulators<html><sup id="cite_ref-0" class="reference"><a href="#cite_note-0"><span>[</span>1<span>]</span></a></sup></html>
 
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Based on different literature, we had four different configurations for the time delay genetic circuit. Of the four approaches, two are protein-based and other two are RNA-based.
 
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===Positive Cascade ===
 
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Based on the book of Uri Alon<html><sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span>[</span>2<span>]</span></a></sup></html> and the project requirements, the next scheme can be proposed:<br>[[Image:Positive_feedforward.jpg| <center>Positive cascade overview</center> | thumb | 550px]]<br>
 
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Figure 1: Genes 1 and 3 are present in the cell and they are produced all the time (black). Genes 2 and 4 (green) are in the self destructive plasmid (SDP).<br>
 
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'''Description'''<br>
 
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Protein 1 starts the circuit activating the promoter of gene 2, for proof of concept gene 1 can be changed for a signal molecule. The concentration of protein 2 will increase and achieve the threshold concentration to induce gene 3. As the concentration of protein 3 increases, the induction of gene 4 (restriction enzyme or fluorescent protein) starts.<br>
 
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'''Parameters'''<br>
 
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In order to make a longer or shorter delay the protein production and degradation rates have to be considered. For the former, we can “play” with the ribosome binding site (RBS) and promoter strength. The degradation can be controlled by protein stability, induction of degradation and up-down regulation of degradation enzymes.<br>
 
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'''Biobricks'''<br>
 
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#new RBS
 
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#new transcriptional factors with different stabilities
 
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#new promoters with different strengths<br>
 
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'''Take into account'''<br>
 
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*There are many of biobricks like 1 and 3 in the registry
 
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*Positive feed is always related to leaking problems
 
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*Time frame
 
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*Change LVA tag to decrease degradation<br>
 
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'''Modeling'''<br>
 
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Differential equations involving production rate, degradation rate (and dilution rate)
 
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===Small interfering RNA===
 
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This approach is based on the gene silencing by small interfering RNA explained in Elbashir et al.<html><sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span>[</span>3<span>]</span></a></sup></html> and is given in the following scheme:<br>
 
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[[Image:small_interfering_RNA.jpg | <center> Small interfering RNA approach overview</center> | thumb | 550px]]<br>
 
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Figure 2: Genes 1 and 3 are present in the self destructive plasmid. Gene 2 is present in the cell and is always produced.<br>
 
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'''Description'''<br>
 
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Protein 1 is always produced in the cell and is controlled by the constitutive promoter on gene 2. This protein must be selected carefully since the gene 1 producing the siRNA must be decided based on this protein and the siRNA must be specific for silencing the mRNA of protein 1 without disturbing the other mRNAs of the host organism. The protein 1 will be in excess concentration and hence will inhibit the production of protein 2 (restriction enzyme or fluorescence protein) by repressing the promoter of gene 3. When the production of siRNA is induced by activating the promoter of gene 1, on reaching a threshold it will interfere with the translation of protein 1 and hence the repression of gene 3 is released to produce the protein 2.<br>
 
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'''Parameters and take into account'''<br>
 
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*Protein 1’s stability
 
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*siRNA specificity
 
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*Promoter strength<br>
 
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'''Biobricks'''<br>
 
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#new RBS
 
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#new transcriptional factors with different stabilities
 
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#new promoters with different strengths
 
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#siRNA’s<br>
 
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'''Modeling'''<br>
 
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*Differential equations involving production rate, degradation rate (and dilution rate)
 
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*Interaction siRNA’s - mRNA
 
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===Disadvantages in the approaches above===
 
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In the positive cascade we anticipated that we will encounter the problem of leaky expressions of transcription factors and genes, which may cause drastic effects in an efficient delay system.<br>
 
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For the siRNA approach we could not find literature evidence whether siRNA works in prokaryotes. This causes a major setback in this approach for using it in our host organism E.coli. Because of these disadvantages we felt the other two approaches described as follows in below could be used.
 
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=== Negative Cascade===
 
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Based on Hooshangi et al.<html><sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span>[</span>4<span>]</span></a></sup></html> and the project requirements, the next scheme can be proposed:<br>[[Image:Negative_Feedforward.jpg|center| <center> Negative cascade assembly and overview </center> | thumb | 550px]]<br>
 
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Figure 3: Gene constructs 1 and 3 are present in the cell and they are produced all the time. Gene construct 2 is in the self destructive plasmid (SDP). [[Image:Inhibition_symbol.jpg]] indicates repression.<br>
 
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'''Description'''<br>
 
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IPTG starts the circuit activating (or repressing the repressor of) the promoter of TetR, for proof of concept we have used a signal molecule. The concentration of protein TetR will increase and achieve the threshold concentration to repress gene cI. At this point the production of protein cI stops. As the concentration of protein cI decreases due to its degradation, the repression of GFP gene will no longer exist and the production of GFP starts. In the final circuit it will be replaced by the restriction enzyme gene.<br>
 
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'''Parameters'''<br>
 
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In order to make a longer or shorter delay the protein production and degradation rates have to be considered. For the former, we can “play” with the ribosome binding site (RBS) and promoter strength. The degradation can be controlled by protein stability, induction of degradation and up-down regulation of degradation enzymes.<br>
 
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'''Biobricks'''<br>
 
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#new RBS
 
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#new transcriptional factors with different stabilities
 
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#new promoters with different strengths<br>
 
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'''Take into account'''<br>
 
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*Time frame
 
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*Change LVA tag to decrease degradation<br>
 
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'''Modeling'''<br>
 
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Differential equations involving production rate, degradation rate (and dilution rate)
 
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===Riboregulator===
 
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In bacteria, several factors affect translation initiation, including ribosomal recognition of the mRNA’s RBS and the start codon (AUG). Recognizing the importance of RNA interactions between the ribosome and RBS, and based on work on endogenous riboregulators, Isaacs et al.<html><sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span>[</span>5<span>]</span></a></sup></html> sought to regulate bacterial gene expression by interfering with ribosomal docking at the RBS. From the outset, their objective was to create a modular post transcriptional regulation system that could be integrated into biological networks and implemented with any promoter or gene. This system was already used by Friedland et al.<html><sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span>[</span>6<span>]</span></a></sup></html>.<br>
 
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Circuit 3 that we have in mind is based on the riboregulator and is shown in figure 4.<br>[[Image:Riboregulator_delay.jpg | <center> Riboregulator overview and assembly </center> | thumb | 550px]]<br>
 
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Figure 4: taRNA/RBS (riboregulator) regulated expression of GFP or Restriction endonuclease. Genes key3c, lock3c and cl are on the conjugative plasmid present in all cells. IPTG: signal molecule. GFP/Restriction endonuclease gene is present on the SDP. RBS: ribosome binding site. cr: piece of RNA strand in front of RBS that is complementary to RBS. Key3c is taRNA (trans-activating RNA), could also be small interference RNA, as long as it is complementary to cr. Product could be either GFP/luciferase (for testing) or endonuclease.<br>
 
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'''Description'''<br>
 
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Gene cl is constitutively expressed with lock3c using promoter pTet or pBla while the key3c is inducible by signal molecule IPTG (repressing the repressor LacI) using promoter pLacI. Gene cl is expressed constitutively with the crRNA, lock3c on which the cr part of the RNA binds the RBS directly after transcription, causing RBS to be blocked for the ribosome and therefore blocks the RNA from translation. When pLacI is induced by IPTG, it produces the taRNA molecule, key3c which is complementary to the cr part of the lock3c. When the key3c binds the lock3c it opens the RBS, which makes the crRNA ready for translation. The resulting product (the grey colored folded protein in figure 4) can then induce the gene to produce end-product which may be GFP or endonuclease.<br>
 
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'''Parameters and take into account'''
 
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#taRNA (key3c) should be better complementary to cr (lock3c) than cr to RBS, to make sure that taRNA causes the RBS to open up
 
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#One can play with promoter strengths for genes of key3c and end product
 
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#The degradation rate of cl (the grey colored folded protein in figure 4) can influence the delay time
 
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#Instead of cI inducing end-product expression, it might repress a repressor of a promoter (negative cascade, see figure 3), to get rid of leaky expression
 
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#Take into account “scars”
 
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#Time frame<br>
 
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'''Biobricks'''<br>
 
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#new RBS
 
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#new transcriptional factors with different stabilities
 
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#new promoters with different strengths
 
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#crRNA for each RBS in the registry
 
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#taRNA for each crRNA<br>
 
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'''Modeling'''<br>
 
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*Differential equations involving production rate, degradation rate (and dilution rate)
 
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*Interaction crRNA’s – RBS and crRNA’s – taRNA’s
 
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*Stability of taRNA’s
 
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===Combination of these approaches===
 
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These negative cascade and riboregulator approaches may also be combined if a large delay time is required.
 
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===Which biobricks we could use===
 
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<table class="table1" border="1" style="text-align: center;">
 
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<tr><th>Part</th><th>Biobrick</th><th>Well</th><th>Plate</th><th>Plasmid</th>><th>Antibiotic</th>><th>Size (bp)</th></tr>
 
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<tr><td>pLac/PLacI</td><td>R0010</td><td>1D</td><td>1</td><td>pSB1A2</td><td>Amp</td><td>200</td></tr>
 
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<tr><td>PBla</td><td>I14018</td><td>18N</td><td>1</td><td>pSB2K3</td><td>Kan</td><td>35</td></tr>
 
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<tr><td>Plambclin</td><td>I12006</td><td>11J</td><td>2</td><td>pSB2K3</td><td>Kan</td><td>82</td></tr>
 
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<tr><td>pTet/Ptet</td><td>R0040</td><td>6I</td><td>1</td><td>pSB1A2</td><td>Amp</td><td>54</td></tr>
 
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<tr><td>key3c</td><td>J23008</td><td>3F</td><td>1</td><td>J23006</td><td>Amp</td><td>94</td></tr>
 
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<tr><td>Lock3c</td><td>J23031</td><td>3L</td><td>1</td><td>J23006</td><td>Amp</td><td>42</td></tr>
 
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<tr><td>GFP</td><td>E0040</td><td>14K</td><td>1</td><td>pSB1A2</td><td>Amp</td><td>720</td></tr>
 
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<tr><td>mRFP1</td><td>E1010</td><td>18F</td><td>1</td><td>pSB2K3</td><td>Kan</td><td>681</td></tr>
 
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<tr><td>cI</td><td>C0051</td><td>4E</td><td>1</td><td>pSB1A2</td><td>Amp</td><td>750</td></tr>
 
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<tr><td>RBS</td><td>B0034</td><td>2M</td><td>1</td><td>pSB1A2</td><td>Amp</td><td>12</td></tr>
 
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<tr><td>T (Double Terminator)</td><td>B0015</td><td>23L</td><td>1</td><td>pSB1AK3</td><td>Amp/Kan</td><td>127</td></tr>
 
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<tr><td>λp-RBS-GFP-T</td><td>S03335</td><td>85</td><td>Box9</td><td>pSB1A2</td><td>Amp</td><td>932</td></tr>
 
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<tr><td>λp-RBS-mRFP1-T</td><td>S03473</td><td>79</td><td>Box9</td><td>pSB1A2</td><td>Amp</td><td>918</td></tr>
 
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<tr><td>RBS - cI - RBS</td><td>K081013</td><td>12D</td><td>2</td><td>pSB1A2</td><td>Amp</td><td>819</td></tr>
 
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<tr><td>TetR</td><td>C0040</td><td>4A</td><td>1</td><td>pSB1A2</td><td>Amp</td><td>660</td></tr>
 
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</table><br>
 
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=='''Module 2: Self Destructive Plasmid'''==
 
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The message that the helper plasmid caries and is delivered by the donor cell to the acceptor cell should disappear in the donor cell, after being passed to the acceptor cell. Therefore we would like to build a plasmid which is able to destruct itself. Therefore the plasmid should be able to degrade itself. This degradation should be inducible.
 
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In order to facilitate the degradation of the plasmid we construct a plasmid whit a I-SceI endonuclease gene which is under control of a Lac promoter. This plasmid also contains several restriction sites of I-SceI in order to start degradation after inducing I-SceI transcription. 
 
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In order to construct the Self Destructive Plasmid (SDP) we build the construct showed in Figure 5 and clone it this construct into a high copy BioBrick assembly plasmid.<br>
 
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[[Image:Construct_SD.jpg|550px]]<br>
 
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'''Figure 5: The construct to be build and cloned into a high copy BioBrick assembly plasmid.'''
 
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<table class="table1" border="1" style="text-align: center;">
 
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<tr><td>[[Image:p-lacI.jpg]]</td><td>p-lacI</td><td>[[Image:I-SceI restriction site.jpg]]</td><td>I-SceI restriction site</td></tr>
 
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<tr><td>[[Image:p-tetR.jpg]]</td><td>p-tetR</td><td>[[Image:GFP with LVA tag.jpg]]</td><td>GFP with LVA tag</td></tr>
 
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<tr><td>[[Image:Constitutive promoter.jpg]]</td><td>Constitutive promoter</td><td>[[Image:TetR.jpg]]</td><td>TetR</td></tr>
 
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<tr><td>[[Image:Ribosomal binding site.jpg]]</td><td>Ribosomal binding site</td><td>[[Image:I-SceI.jpg]]</td><td>I-SceI</td></tr>
 
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<tr><td>[[Image:Terminator.jpg]]</td><td>Terminator</td></tr>
 
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</table><br>
 
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In order to build this construct 6 other constructs should be built, assembly of these constructed will result to the above showed construct. We like to use in the first place already existing BioBricks. Since there is no I-SceI restriction site available as BioBrick, we should standardize this restriction site. The half-life time of the GFP-LVA is 40-80 minutes. This short half-life is useful for this project. After constructing the SDP we would like to induce the transcription of this GFP and stop the induction. At the time that the signal of the GFP disappears we induce the transcription endonuclease and in order to check if the plasmid is degraded we induce the transcription of the GFP once again.
 
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'''For more information on the cloning strategy of constructing self destructive plasmid check the [[Team:TUDelft/Cloning Strategy|cloning strategy]] page'''
 
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===Checking the Self Destructive Plasmid===
 
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In order to check the activity of SDP some experiments should be done.
 
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During the assembly of the construct several control experiments will be done. After building a construct, the construct will be checked by PCR and agarose gel electrophoresis to check the length of the construct. Verification forward primer(VF2) and verification reverse (VR) will be used.
 
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The expression and activity of I-SceI will be checked by an Assay.  The construct showed in figure.10 will be used to check the expression of I-SceI. The same plasmid or other vectors containing I-SceI recognition site could be used to check the activity of the endonuclease. Incubating this plasmid with expressed and purified I-SceI and agarose gel electrophoresis will show if the endonuclease is active. These results will be compared with activity of commercial available I-SceI homing endonuclease.
 
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The expression of TetR will be checked by expression TetR from the in figure.9 showed construct. Western Blot analysis should show if TetR is expressed.
 
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='''References'''=
 
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<ol><li id="cite_note-0"><cite id="CITEREFSmolke2009" class="article" style="font-style: normal;">
 
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Smolke C, 2009. [http://www.ncbi.nlm.nih.gov/pubmed/19478174 It’s the DNA That Counts]. Science, 324:1156-1157.</cite>
 
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<li id="cite_note-1"><cite id="CITEREFSystemBio2006" class="book" style="font-style: normal;">
 
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An introduction to systems biology: design principles of biological circuits. Uri Alon, Publisher CRC Press, 2006, pp 41-69.[http://en.wikipedia.org/wiki/Special:BookSources/1584886420 ISBN 1584886420]</cite>
 
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<li id="cite_note-2"><cite id="CITEREFElbashir2001" class="article" style="font-style: normal;">
 
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Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T., 2001. [http://www.ncbi.nlm.nih.gov/pubmed/11373684 Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells]. Nature, 411(6836):494-498.</cite>
 
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<li id="cite_note-3"><cite id="CITEREFSmolke2009" class="article" style="font-style: normal;">
 
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Hooshangi S, Thiberge S, Weiss R, 2005. [http://www.ncbi.nlm.nih.gov/pubmed/15738412 Ultrasensitivity and noise propagation in a synthetic transcriptional cascade]. PNAS, 102,10 :3581–3586.</cite>
 
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<li id="cite_note-4"><cite id="CITEREFIsaacs2006" class="article" style="font-style: normal;">
 
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Isaacs F, Dwyer d and Collins J, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16680139 RNA synthetic biology]. Nature Biotech., 24:545-554.</cite>
 
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<li id="cite_note-5"><cite id="CITEREFFriedland2009" class="article" style="font-style: normal;">
 
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Friedland A, Lu T, Wang X, Shi D, Church G and Collins J, 2009. [http://www.ncbi.nlm.nih.gov/pubmed/19478183 Synthetic Gene Networks That Count]. Science, 324:1199-1202.</cite>
 
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<li id="cite_note-6"><cite id="CITEREFThorsted1998" class="article" style="font-style: normal;">
 
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Thorsted, P. B., D. P. Macartney, P. Akhtar, A. S. Haines, N. Ali, P. Davidson, T. Stafford, M. J. Pocklington, W. Pansegrau, B. M. Wilkins, E. Lanka, and C. M. Thomas. 1998. [http://www.ncbi.nlm.nih.gov/nuccore/113911681?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum Complete sequence of the IncPbeta  plasmid R751: implications for evolution and organisation of the IncP backbone]. J. Mol. Biol. 282:969-990.</cite>
 
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Latest revision as of 10:33, 7 October 2009