Team:Paris/August 15
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{{Paris/Calendar_Links|August 14|August 16}} | {{Paris/Calendar_Links|August 14|August 16}} | ||
- | =='''Transformation of the ligations we did [[Team:Paris/August 14| yesterday]] | + | =Construction of OmpR*+RBS and EnvZ*+RBS= |
+ | I did some digestions (today), ligations (tommorow) and screening (the day after tommorow). | ||
+ | I tried to build : | ||
+ | RBS (B0034) + OmpR* | ||
+ | and | ||
+ | RBS (B0034) + EnvZ* | ||
+ | ==='''Protocol'''=== | ||
+ | {| Border="2" | ||
+ | |align="center"|'''Digestion name''' | ||
+ | |align="center"|'''Template DNA''' | ||
+ | |align="center"|''' Enzymes ''' | ||
+ | |align="center"|'''Volume of DNA''' | ||
+ | |- | ||
+ | |align="center"|D 158 | ||
+ | |align="center"|MP 155.1 - OmpR* | ||
+ | |align="center"|XbaI - PstI | ||
+ | |align="center"|5 µL | ||
+ | |- | ||
+ | |align="center"|D 159 | ||
+ | |align="center"|MP 156.1 - EnvZ* | ||
+ | |align="center"|XbaI - PstI | ||
+ | |align="center"|5 µL | ||
+ | |- | ||
+ | |align="center"|D 102 | ||
+ | |align="center"|MP 100 - B0034 | ||
+ | |align="center"|SpeI - PstI | ||
+ | |align="center"|5 µL | ||
+ | |} | ||
+ | |||
+ | * X µL of Template DNA | ||
+ | * Buffer (n°2) 10X : 3µL | ||
+ | * BSA 100X : 0.3µL | ||
+ | * Pure water qsp 30 µL | ||
+ | * 1 µL of each enzyme | ||
+ | |||
+ | * Incubate during about 3h at 37°C, then 20 minutes at 65°C (to inactivate the enzymes). Then 10°C overnight. | ||
+ | |||
+ | =Creation of a registry of pFliL, pFlhDC, and ''FlhDC''= | ||
+ | ==Transformation of the ligations we did [[Team:Paris/August 14| yesterday]]== | ||
We transformed L 143, L 144 and the negative controls T1 and T2, using Invitrogen's TOP10 chemically competent cells [[Team:Paris/Notebook/Protocols#Transformation|standard protocol]]. | We transformed L 143, L 144 and the negative controls T1 and T2, using Invitrogen's TOP10 chemically competent cells [[Team:Paris/Notebook/Protocols#Transformation|standard protocol]]. | ||
- | == | + | ==PCR amplification of flhDC and its promoter== |
+ | |||
==='''List of PCRs'''=== | ==='''List of PCRs'''=== | ||
{| Border="1" style="text-align: center;" | {| Border="1" style="text-align: center;" | ||
Line 49: | Line 88: | ||
==='''Protocol'''=== | ==='''Protocol'''=== | ||
+ | |||
+ | We followed the [[Team:Paris/Notebook/Protocols#Amplification_of_promoters|standard protocol]] of amplification in Two steps. | ||
+ | PCR program used : | ||
+ | PHUSION2 | ||
+ | |||
==='''Results'''=== | ==='''Results'''=== | ||
- | |||
- | |||
- | ===Measurement of concentration of minipreps | + | |
+ | '''Settings Gel 1%''' | ||
+ | [[Image:KR000170.jpg|thumb|Gel 1%]] | ||
+ | *Ladder 1 kb 10 µL | ||
+ | *4µL Template DNA + 2µL Loading Blue | ||
+ | *1 % Agar | ||
+ | |||
+ | |||
+ | {| style="text-align: center;" border="1" | ||
+ | |- | ||
+ | |'''PCR Name''' | ||
+ | |'''What's in ?''' | ||
+ | |'''Well''' | ||
+ | |'''Expected size''' | ||
+ | |'''Measured size''' | ||
+ | |- | ||
+ | |PCR_138 | ||
+ | |gene flhDC | ||
+ | |2 | ||
+ | |992 bp | ||
+ | |style="background: #cbff7B"| 1000 bp | ||
+ | |- | ||
+ | |PCR_140 | ||
+ | |gene flhDC | ||
+ | |3 | ||
+ | |992 bp | ||
+ | |style="background: #cbff7B"| 1000 bp | ||
+ | |- | ||
+ | |PCR_138' | ||
+ | |gene flhDC | ||
+ | |4 | ||
+ | | X | ||
+ | |style="background: #cbff7B"| X | ||
+ | |- | ||
+ | |PCR_133 | ||
+ | |gene flhDC + promoter | ||
+ | |5 | ||
+ | |1227 pb | ||
+ | |style="background: #cbff7B"| 1200 bp | ||
+ | |} | ||
+ | We managed to amplify flhDC ! | ||
+ | |||
+ | '''Settings Gel 2%''' | ||
+ | [[Image:KR000171.jpg|thumb|Gel 2%]] | ||
+ | *Ladder 100 bp 10 µL | ||
+ | *4µL Template DNA + 2µL Loading Blue | ||
+ | *2 % Agar | ||
+ | |||
+ | |||
+ | {| style="text-align: center;" border="1" | ||
+ | |- | ||
+ | |'''PCR Name''' | ||
+ | |'''What's in ?''' | ||
+ | |'''Well''' | ||
+ | |'''Expected size''' | ||
+ | |'''Measured size''' | ||
+ | |- | ||
+ | |PCR_136 | ||
+ | |pflhDC (URI) | ||
+ | |2 | ||
+ | |282 bp | ||
+ | |style="background: #ff6d73"| X | ||
+ | |- | ||
+ | |PCR_137 | ||
+ | |pflhDC | ||
+ | |3 | ||
+ | |428 bp | ||
+ | |style="background: #ff6d73"| X | ||
+ | |- | ||
+ | |PCR_139 | ||
+ | |pflhDC (URI) | ||
+ | |4 | ||
+ | |282 bp | ||
+ | |style="background: #cbff7B"| ~ 300 bp | ||
+ | |- | ||
+ | |PCR_136' | ||
+ | |pflhDC (URI) | ||
+ | |5 | ||
+ | |X | ||
+ | |style="background: #cbff7B"| X | ||
+ | |- | ||
+ | |PCR_137' | ||
+ | |pflhDC | ||
+ | |6 | ||
+ | |X | ||
+ | |style="background: #cbff7B"| X | ||
+ | |} | ||
+ | We managed to amplify the promoter of flhDC | ||
+ | |||
+ | ==Digestions== | ||
+ | After having succeded in amplifying the promoter and the gene of flhDC, we decided to clone it into a plasmid. | ||
+ | The first step is the digestion. | ||
+ | |||
+ | ==='''Protocol'''=== | ||
+ | {| Border="2" | ||
+ | |align="center"|'''Digestion name''' | ||
+ | |align="center"|'''Template DNA''' | ||
+ | |align="center"|''' Enzymes ''' | ||
+ | |align="center"|'''Volume of DNA''' | ||
+ | |- | ||
+ | |align="center"|D 153 | ||
+ | |align="center"|PCR 138 - g flhDC | ||
+ | |align="center"|EcoRI - PstI | ||
+ | |align="center"|5 µL | ||
+ | |- | ||
+ | |align="center"|D 154 | ||
+ | |align="center"|PCR 140 - g flhDC | ||
+ | |align="center"|EcoRI - PstI | ||
+ | |align="center"|5 µL | ||
+ | |- | ||
+ | |align="center"|D 155 | ||
+ | |align="center"|PCR 139 - p flhDC | ||
+ | |align="center"|EcoRI - PstI | ||
+ | |align="center"|5 µL | ||
+ | |- | ||
+ | |align="center"|D 145 | ||
+ | |align="center"|MP122 - pSB1A2 | ||
+ | |align="center"|EcoRI-SpeI | ||
+ | |align="center"|5 µL | ||
+ | |- | ||
+ | |align="center"|D 136 | ||
+ | |align="center"|MP103 - J61002 | ||
+ | |align="center"|EcoRI-SpeI | ||
+ | |align="center"|5 µL | ||
+ | |} | ||
+ | |||
+ | * X µL of Template DNA | ||
+ | * Buffer (n°2) 10X : 3µL | ||
+ | * BSA 100X : 0.3µL | ||
+ | * Pure water qsp 30 µL | ||
+ | * 1 µL of each enzyme | ||
+ | |||
+ | * Incubate during about 3h at 37°C, then 20 minutes at 65°C (to inactivate the enzymes). | ||
+ | Then 10°C overnight. | ||
+ | |||
+ | =Construction of pLas-TetR-GFP tripart & rbs-LasR-dble ter= | ||
+ | |||
+ | ==Measurement of concentration of minipreps== | ||
[[Team:Paris/Notebook/Protocols#Concentration of the Miniprep|standard protocol]] | [[Team:Paris/Notebook/Protocols#Concentration of the Miniprep|standard protocol]] | ||
{| border="1" style="text-align: center" | {| border="1" style="text-align: center" | ||
- | |Digestion | + | |'''Digestion''' |
- | |Miniprep used | + | |'''Miniprep used''' |
- | |Concentration (µg/mL) | + | |'''Concentration (µg/mL)''' |
- | |ratio 260/280 | + | |'''ratio 260/280''' |
|- | |- | ||
|D146 | |D146 | ||
Line 74: | Line 253: | ||
|} | |} | ||
- | + | ==Digestion== | |
- | + | ||
[[Team:Paris/Notebook/Protocols#Digestion|Protocol Digestion]] | [[Team:Paris/Notebook/Protocols#Digestion|Protocol Digestion]] | ||
- | == | + | ==Ligation== |
[[Team:Paris/Notebook/Protocols#Ligation|Protocol Ligation]] | [[Team:Paris/Notebook/Protocols#Ligation|Protocol Ligation]] | ||
{| border="1" style="text-align: center" | {| border="1" style="text-align: center" | ||
- | |Ligation name | + | |'''Ligation name''' |
- | |Insert | + | |'''Insert''' |
- | |Vector | + | |'''Vector''' |
|- | |- | ||
|L150 | |L150 | ||
Line 106: | Line 284: | ||
|} | |} | ||
+ | =PCR screening of cloning of E0240, flhD, flhC and pflhDC+flhDC= | ||
==Analysis of yesterday PCR screening== | ==Analysis of yesterday PCR screening== | ||
+ | '''Electrophoresis''' | ||
+ | *1% agarose gel | ||
+ | *10 µL loaded | ||
+ | |||
Gel 1 [[Image:KR000163.jpg|200px|]] | Gel 1 [[Image:KR000163.jpg|200px|]] | ||
Gel 2 [[Image:KR000162.jpg|200px|]] | Gel 2 [[Image:KR000162.jpg|200px|]] | ||
Gel 3 [[Image:KR000164.jpg|200px|]] | Gel 3 [[Image:KR000164.jpg|200px|]] | ||
+ | {| border="1" style="text-align: center" | ||
+ | |colspan="18"|'''Gel n°1''' | ||
+ | |- | ||
+ | |'''well n°''' | ||
+ | |1 | ||
+ | |2 | ||
+ | |3 | ||
+ | |4 | ||
+ | |5 | ||
+ | |6 | ||
+ | |7 | ||
+ | |8 | ||
+ | |9 | ||
+ | |10 | ||
+ | |11 | ||
+ | |12 | ||
+ | |13 | ||
+ | |14 | ||
+ | |15 | ||
+ | |16 | ||
+ | |17 | ||
+ | |- | ||
+ | |'''sample''' | ||
+ | |1 kb DNA ladder | ||
+ | |positive control 1<br> E0240 | ||
+ | |positive control 2<br> pSB3K3 | ||
+ | |negative control | ||
+ | |colspan="8"|'''E0240 in pSB3K3''' | ||
+ | |100 bp DNA ladder | ||
+ | |colspan="4"|'''FlhD in pSB1A2''' | ||
+ | |- | ||
+ | |'''clone''' | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |L139.1 | ||
+ | |L139.2 | ||
+ | |L139.3 | ||
+ | |L139.4 | ||
+ | |L139.5 | ||
+ | |L139.6 | ||
+ | |L139.7 | ||
+ | |L139.8 | ||
+ | | | ||
+ | |L140.1 | ||
+ | |L140.2 | ||
+ | |L140.3 | ||
+ | |L140.4 | ||
+ | |- | ||
+ | |'''expected size''' | ||
+ | | | ||
+ | | | ||
+ | |316 bp | ||
+ | |0 kb | ||
+ | |colspan="8"|1192 bp | ||
+ | | | ||
+ | |colspan="4"|589 bp | ||
+ | |- | ||
+ | |'''measured size''' | ||
+ | | | ||
+ | |1,1 kb | ||
+ | |1 kb | ||
+ | |0 kb | ||
+ | |style="background: #cbff7B"|1,5 kb<br>'''1,1 kb'''<br>0,6 kb | ||
+ | |0,6 kb | ||
+ | |0,6 kb | ||
+ | |0,6 kb | ||
+ | |0,6 kb | ||
+ | |0,6 kb | ||
+ | |0,6 kb | ||
+ | |0,6 kb | ||
+ | | | ||
+ | |0,4 kb<br>0,3 kb | ||
+ | |0,4 kb<br>0,3 kb | ||
+ | |0,4 kb<br>0,3 kb | ||
+ | |0,4 kb<br>0,3 kb | ||
+ | |} | ||
+ | {| border="1" style="text-align: center" | ||
+ | |colspan="18"|'''Gel n°2''' | ||
+ | |- | ||
+ | |'''well n°''' | ||
+ | |1 | ||
+ | |2 | ||
+ | |3 | ||
+ | |4 | ||
+ | |5 | ||
+ | |6 | ||
+ | |7 | ||
+ | |8 | ||
+ | |9 | ||
+ | |10 | ||
+ | |11 | ||
+ | |12 | ||
+ | |13 | ||
+ | |14 | ||
+ | |15 | ||
+ | |16 | ||
+ | |17 | ||
+ | |- | ||
+ | |'''sample''' | ||
+ | |1 kb DNA ladder | ||
+ | |positive control 1<br> E0240 | ||
+ | |positive control 2<br> pSB3K3 | ||
+ | |negative control | ||
+ | |colspan="4"|'''FlhD in pSB1A2''' | ||
+ | |100 bp DNA ladder | ||
+ | |colspan="8"|'''FlhC in pSB1A2''' | ||
+ | |- | ||
+ | |'''clone''' | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |L140.5 | ||
+ | |L140.6 | ||
+ | |L140.7 | ||
+ | |L140.8 | ||
+ | | | ||
+ | |L141.1 | ||
+ | |L141.2 | ||
+ | |L141.3 | ||
+ | |L141.4 | ||
+ | |L141.5 | ||
+ | |L141.6 | ||
+ | |L141.7 | ||
+ | |L141.8 | ||
+ | |- | ||
+ | |'''expected size''' | ||
+ | | | ||
+ | | | ||
+ | |316 bp | ||
+ | |0 kb | ||
+ | |colspan="4"|589 bp | ||
+ | | | ||
+ | |colspan="8"|817 bp | ||
+ | |- | ||
+ | |'''measured size''' | ||
+ | | | ||
+ | |1,1 kb | ||
+ | |1 kb | ||
+ | |0 kb | ||
+ | |0,3 kb | ||
+ | |0,3 kb | ||
+ | |0,3 kb | ||
+ | |0,3 kb | ||
+ | | | ||
+ | |style="background: #cbff7B"|0,8 kb | ||
+ | |style="background: #cbff7B"|0,8 kb | ||
+ | |style="background: #cbff7B"|0,8 kb | ||
+ | |style="background: #cbff7B"|0,8 kb | ||
+ | |style="background: #cbff7B"|0,8 kb | ||
+ | |style="background: #cbff7B"|0,8 kb | ||
+ | |0,3 kb | ||
+ | |style="background: #cbff7B"|0,8 kb | ||
+ | |} | ||
+ | {| border="1" style="text-align: center" | ||
+ | |colspan="18"|'''Gel n°3''' | ||
+ | |- | ||
+ | |'''well n°''' | ||
+ | |1 | ||
+ | |2 | ||
+ | |3 | ||
+ | |4 | ||
+ | |5 | ||
+ | |6 | ||
+ | |7 | ||
+ | |8 | ||
+ | |9 | ||
+ | |10 | ||
+ | |11 | ||
+ | |12 | ||
+ | |13 | ||
+ | |14 | ||
+ | |15 | ||
+ | |16 | ||
+ | |17 | ||
+ | |- | ||
+ | |'''sample''' | ||
+ | |1 kb DNA ladder | ||
+ | |positive control 1<br> E0240 | ||
+ | |positive control 2<br> pSB3K3 | ||
+ | |negative control | ||
+ | |colspan="8"|'''FlhDC+promotor in pSB1A2''' | ||
+ | |100 bp DNA ladder | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | |'''clone''' | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |L142.1 | ||
+ | |L142.2 | ||
+ | |L142.3 | ||
+ | |L142.4 | ||
+ | |L142.5 | ||
+ | |L142.6 | ||
+ | |L142.7 | ||
+ | |L142.8 | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | |'''expected size''' | ||
+ | | | ||
+ | | | ||
+ | |316 bp | ||
+ | |0 kb | ||
+ | |colspan="8"|1403 bp | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | |'''measured size''' | ||
+ | | | ||
+ | |1,1 kb | ||
+ | |1 kb | ||
+ | |0 kb | ||
+ | |0,3 kb<br>0,4 kb | ||
+ | |0,3 kb<br>0,4 kb | ||
+ | |0,3 kb<br>0,4 kb | ||
+ | |0,3 kb<br>0,4 kb | ||
+ | |0,3 kb<br>0,4 kb | ||
+ | |0,3 kb<br>0,4 kb | ||
+ | |style="background: #cbff7B"|'''1,4 kb'''<br>0,4 kb<br>0,3 kb | ||
+ | |0,3 kb<br>0,4 kb | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |} | ||
=Starting the construction of the Promoter characterization plasmid= | =Starting the construction of the Promoter characterization plasmid= | ||
- | |||
- | + | ||
+ | ==Measurement of concentration of minipreps== | ||
[[Team:Paris/Notebook/Protocols#Concentration of the Miniprep|standard protocol]] | [[Team:Paris/Notebook/Protocols#Concentration of the Miniprep|standard protocol]] | ||
Line 187: | Line 610: | ||
|} | |} | ||
- | + | ==Digestion== | |
[[Team:Paris/Notebook/Protocols#Digestion|Protocol Digestion]] | [[Team:Paris/Notebook/Protocols#Digestion|Protocol Digestion]] | ||
{| border="1" style="text-align: center" | {| border="1" style="text-align: center" | ||
+ | |Name | ||
|Plasmid | |Plasmid | ||
|Description | |Description | ||
Line 197: | Line 621: | ||
|Enzymes | |Enzymes | ||
|- | |- | ||
+ | | | ||
|MP3 | |MP3 | ||
- | |B0015 (double terminator B0010-B0012) | + | |B0015 (double terminator B0010-B0012) - FV |
|4 | |4 | ||
|EcoRI and XbaI | |EcoRI and XbaI | ||
|- | |- | ||
- | | | + | |D164 |
- | | | + | |MP101 |
+ | |promoter J23101 - BV | ||
|1 | |1 | ||
- | | | + | |SpeI and PstI |
|- | |- | ||
+ | |D161 | ||
|MP104 | |MP104 | ||
- | |PTet (Tet promoter) | + | |PTet (Tet promoter) - BV |
|1 | |1 | ||
|SpeI and PstI | |SpeI and PstI | ||
|- | |- | ||
- | | | + | |D162 |
- | | | + | |MP114 |
+ | |TetR - FI | ||
|1 | |1 | ||
- | | | + | |EcoRI and SpeI |
|- | |- | ||
+ | |D163 | ||
|MP143 | |MP143 | ||
- | |gfp generator | + | |gfp generator - BI |
|2 | |2 | ||
|SpeI and PstI | |SpeI and PstI | ||
|} | |} |
Latest revision as of 18:06, 4 September 2008
Construction of OmpR*+RBS and EnvZ*+RBSI did some digestions (today), ligations (tommorow) and screening (the day after tommorow). I tried to build : RBS (B0034) + OmpR* and RBS (B0034) + EnvZ* Protocol
Creation of a registry of pFliL, pFlhDC, and FlhDCTransformation of the ligations we did yesterdayWe transformed L 143, L 144 and the negative controls T1 and T2, using Invitrogen's TOP10 chemically competent cells standard protocol. PCR amplification of flhDC and its promoterList of PCRs
ProtocolWe followed the standard protocol of amplification in Two steps. PCR program used : PHUSION2 ResultsSettings Gel 1%
We managed to amplify flhDC ! Settings Gel 2%
We managed to amplify the promoter of flhDC DigestionsAfter having succeded in amplifying the promoter and the gene of flhDC, we decided to clone it into a plasmid. The first step is the digestion. Protocol
Then 10°C overnight. Construction of pLas-TetR-GFP tripart & rbs-LasR-dble terMeasurement of concentration of minipreps
DigestionLigation
PCR screening of cloning of E0240, flhD, flhC and pflhDC+flhDCAnalysis of yesterday PCR screeningElectrophoresis
Starting the construction of the Promoter characterization plasmidMeasurement of concentration of minipreps
Digestion
|