Imperial/Wet Lab/Protocols/Prot1.5
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__NOTOC__ | __NOTOC__ | ||
= Wet Lab: Protocols: Purification of LuxR = | = Wet Lab: Protocols: Purification of LuxR = | ||
'''Aims:''' | '''Aims:''' | ||
| - | *Through our modeling it has become clear that in order to get the most effective Infecter | + | *Through our modeling it has become clear that in order to get the most effective Infecter Detector system we will need LuxR to be at steady state. This is a fundamental problem with our initial construct because it is unlikely that LuxR will reach steady state under control of the pTet promoter. We are therefore pursuing an alternative where by we will add purified LuxR to the in vitro system. |
| - | *Through literature a protocol | + | *Through literature we found a protocol for purifying LuxR. We are planning to use this as a basis and modify it to suit our needs. |
*For purification of LuxR we require a plasmid that can over express LuxR, we have identified two suitable plasmids and we are currently trying to obtain both. Depending on which one we choose we will have to vary the protocol. | *For purification of LuxR we require a plasmid that can over express LuxR, we have identified two suitable plasmids and we are currently trying to obtain both. Depending on which one we choose we will have to vary the protocol. | ||
<br> | <br> | ||
| Line 32: | Line 33: | ||
====Protocol==== | ====Protocol==== | ||
*Add 0.5 litre of cells (grown to OD 0.5 and induced with AHL) to centrifuge tubes and spin them down at 8000g. | *Add 0.5 litre of cells (grown to OD 0.5 and induced with AHL) to centrifuge tubes and spin them down at 8000g. | ||
| - | *Remove the supernatant and dissolve the pellet in 10ml of Buffer A | + | *Remove the supernatant and dissolve the pellet in 10ml of Buffer A. |
| - | *Sonicate the mixture | + | *Sonicate the mixture. |
*Centrifuge them again at 100 000g and separate the supernatant from the pellet. Keep the supernatant (Tube A). | *Centrifuge them again at 100 000g and separate the supernatant from the pellet. Keep the supernatant (Tube A). | ||
| - | *Resuspend the pellet in water (Tube B)to make up approximately the same volume as in Tube A. | + | *Resuspend the pellet in water (Tube B) to make up approximately the same volume as in Tube A. |
*Remove 100ul of each solution into another two tubes and add SDS page gel loading buffer to them. | *Remove 100ul of each solution into another two tubes and add SDS page gel loading buffer to them. | ||
| - | *Add 2ul of each of the solution to the SDS PAGE | + | *Add 2ul of each of the solution to the SDS PAGE gel and run for 2 hours. |
==Day 3== | ==Day 3== | ||
===Purification=== | ===Purification=== | ||
| - | *This protocol is based on the following protocol from the paper <cite>Synbio2</cite> | + | *This protocol is based on the following protocol from the paper <cite>Synbio2</cite>. |
| - | *It requires the plasmid pMLU117 | + | *It requires the plasmid pMLU117. |
'''Reagents''' | '''Reagents''' | ||
*A Buffer - 50mM Tris-HCL [pH 7.0 at 22°C] 100mM KCL, 50mM NaCl, 2mM EDTA, 2mM dithiothreitol, 10% glycerol, 0.5% Tween 20 | *A Buffer - 50mM Tris-HCL [pH 7.0 at 22°C] 100mM KCL, 50mM NaCl, 2mM EDTA, 2mM dithiothreitol, 10% glycerol, 0.5% Tween 20 | ||
| Line 67: | Line 68: | ||
Add 5 ml of 100% Tween-20 to the mixture. | Add 5 ml of 100% Tween-20 to the mixture. | ||
*AHL stock 1mM | *AHL stock 1mM | ||
| - | C1V1= C2V2 | + | C1V1= C2V2<br> |
| - | 1 x V1= 0.025 x 1000ml | + | 1 x V1= 0.025 x 1000ml<br> |
Add 25ml of the stock solution to the mixture. | Add 25ml of the stock solution to the mixture. | ||
*Give the mixture a good shake. | *Give the mixture a good shake. | ||
| Line 81: | Line 82: | ||
BUFFER A with 1M of NaCl<br> | BUFFER A with 1M of NaCl<br> | ||
| - | Add NaCl and KCl to 1 liter of the general buffer | + | Add NaCl and KCl to 1 liter of the general buffer. |
*NaCl: 1 x 58.442= 5.8442g | *NaCl: 1 x 58.442= 5.8442g | ||
Add 5.8442g of NaCl to the mixture. | Add 5.8442g of NaCl to the mixture. | ||
| Line 90: | Line 91: | ||
Buffer B <br> | Buffer B <br> | ||
| - | Add NaCl and KCl to 1 liter of the general buffer | + | Add NaCl and KCl to 1 liter of the general buffer. |
*NaCl: 0.025x 58.442= 1.4611g | *NaCl: 0.025x 58.442= 1.4611g | ||
Add 1.4611g of NaCl to the mixture. | Add 1.4611g of NaCl to the mixture. | ||
| Line 99: | Line 100: | ||
'''Prepare Cell Lysate''' | '''Prepare Cell Lysate''' | ||
| - | #Colonies of BL21 with over expressing LuxR plasmid should be streaked onto LB-ampicillin plates and grown over night at 37 °C | + | #Colonies of BL21 with over expressing LuxR plasmid should be streaked onto LB-ampicillin plates and grown over night at 37 °C. |
#Colonies were used to inoculate a liter of LB-ampicillin prewarmed at 37 °C, this is grown until an OD<sub>600</sub> of 0.5 is reached, this is then chilled to 28 °C. | #Colonies were used to inoculate a liter of LB-ampicillin prewarmed at 37 °C, this is grown until an OD<sub>600</sub> of 0.5 is reached, this is then chilled to 28 °C. | ||
| - | #AHL 25uM and IPTG to final concentration of 1mM is then added with additional ampicillin (200ug/ml) and the culture continued to grown at 28 °C for 4 hours, this step is when we want to express the LuxR protein and so we need to first induce with IPTG, then add AHL for correct LuxR protein folding and finally a lower temperature to try to prevent inclusion body formation | + | #AHL 25uM and IPTG to final concentration of 1mM is then added with additional ampicillin (200ug/ml) and the culture continued to grown at 28 °C for 4 hours, this step is when we want to express the LuxR protein and so we need to first induce with IPTG, then add AHL for correct LuxR protein folding and finally adjust to a lower temperature to try to prevent inclusion body formation. |
| - | #Cells were harvested by centrifugation at 8000 x g for 10mins at 4 °C and were frozen overnight at -80°C | + | #Cells were harvested by centrifugation at 8000 x g for 10mins at 4 °C and were frozen overnight at -80°C. |
*The following steps were performed at 4 °C: | *The following steps were performed at 4 °C: | ||
#The Cell pellet should be resuspended in 16ml of '''A buffer''' and 25uM AHL. This cell suspension should then be sonicated. | #The Cell pellet should be resuspended in 16ml of '''A buffer''' and 25uM AHL. This cell suspension should then be sonicated. | ||
| Line 109: | Line 110: | ||
'''Chromatography''' | '''Chromatography''' | ||
#The cell extract from 100,000 x g is passed through a 5ml HiTrap herparin column and equilibrated with A buffer and 25uM AHL. Bound proteins are then eluted with a 25ml NaCL step gradient from 0.15 to 1M. | #The cell extract from 100,000 x g is passed through a 5ml HiTrap herparin column and equilibrated with A buffer and 25uM AHL. Bound proteins are then eluted with a 25ml NaCL step gradient from 0.15 to 1M. | ||
| - | #The fractions collected need to see if they contain LuxR. This can be done using SDS-PAGE electrophoresis | + | #The fractions collected need to see if they contain LuxR. This can be done using SDS-PAGE electrophoresis. |
#Now we need to remove the high levels of NaCl from our cell extract. Fractions containing LuxR are then pooled and dialyzed against 500ml of A buffer containing 25uM AHL and 20% (wt/vol) polyethylene glycerol(mw 8000)for four hours. | #Now we need to remove the high levels of NaCl from our cell extract. Fractions containing LuxR are then pooled and dialyzed against 500ml of A buffer containing 25uM AHL and 20% (wt/vol) polyethylene glycerol(mw 8000)for four hours. | ||
#After dialysis the sample was diluted 1:1 with a KCL and NaCL free version of A buffer plus 25uM AHL, this gives a final salt concentration of 75mM. | #After dialysis the sample was diluted 1:1 with a KCL and NaCL free version of A buffer plus 25uM AHL, this gives a final salt concentration of 75mM. | ||
#Now we need to prepare a SP column, this needs to be equilibrated with buffer B and 25uM AHL.Then the sample can be run through and washed with B buffer. | #Now we need to prepare a SP column, this needs to be equilibrated with buffer B and 25uM AHL.Then the sample can be run through and washed with B buffer. | ||
#Finally, to remove the bound protein the SP column can be eluted with 100ml linear NaCl gradients of 0.075 to 0.5M. To test fraction content and purity of LuxR, SDS-PAGE can be carried out. | #Finally, to remove the bound protein the SP column can be eluted with 100ml linear NaCl gradients of 0.075 to 0.5M. To test fraction content and purity of LuxR, SDS-PAGE can be carried out. | ||
Latest revision as of 02:09, 27 October 2007
Wet Lab: Protocols: Purification of LuxR
Aims:
- Through our modeling it has become clear that in order to get the most effective Infecter Detector system we will need LuxR to be at steady state. This is a fundamental problem with our initial construct because it is unlikely that LuxR will reach steady state under control of the pTet promoter. We are therefore pursuing an alternative where by we will add purified LuxR to the in vitro system.
- Through literature we found a protocol for purifying LuxR. We are planning to use this as a basis and modify it to suit our needs.
- For purification of LuxR we require a plasmid that can over express LuxR, we have identified two suitable plasmids and we are currently trying to obtain both. Depending on which one we choose we will have to vary the protocol.
Day 1
Growing up of cells and Induction of LuxR Production
Day 2
Initial Testing for LuxR solubility
Equipments
- Stripettes
- 2ml Eppendorf tubes
- Sonicator
- Beakers
- Ice
- Polyacrylamide gel tank and Electrophoretic Equipment
Reagents
- Buffer A
- SDS buffers
- Loading dye
- DNA marker
Protocol
- Add 0.5 litre of cells (grown to OD 0.5 and induced with AHL) to centrifuge tubes and spin them down at 8000g.
- Remove the supernatant and dissolve the pellet in 10ml of Buffer A.
- Sonicate the mixture.
- Centrifuge them again at 100 000g and separate the supernatant from the pellet. Keep the supernatant (Tube A).
- Resuspend the pellet in water (Tube B) to make up approximately the same volume as in Tube A.
- Remove 100ul of each solution into another two tubes and add SDS page gel loading buffer to them.
- Add 2ul of each of the solution to the SDS PAGE gel and run for 2 hours.
Day 3
Purification
- This protocol is based on the following protocol from the paper Synbio2.
- It requires the plasmid pMLU117.
Reagents
- A Buffer - 50mM Tris-HCL [pH 7.0 at 22°C] 100mM KCL, 50mM NaCl, 2mM EDTA, 2mM dithiothreitol, 10% glycerol, 0.5% Tween 20
- B Buffer - 50mM Tris-HCL [pH 7.0 at 22°C] 50mM KCL, 25mM NaCl, 2mM EDTA, 2mM dithiothreitol, 10% glycerol, 0.5% Tween 20
- 25uM solution AHL
- 1 Litre LB-amp
- NaCl gradients
Equipment
- Temp controlled Centrifuge
- SP column
- LB amp plates
Protocol
Making up Buffers
General Buffer
Total Volume: 1 litre
- Tris-HCl: 0.05 x 131.4= 6.57g
Add 6.57g of Tris-HCl to a minimum amount of distilled water to dissolve it. Then add enough concentrated HCL to bring it to pH 7.0. Then top it up to 870ml with distilled water.
- EDTA: 0.002 x 372.24= 0.744g
Add 0.744g of EDTA to the mixture.
- DTT: 0002 x 154.3= 0.309g
- 10% glycerol
Add 100ml of 100% glycerol to the mixture.
- 0.5% of Tween-20
Add 5 ml of 100% Tween-20 to the mixture.
- AHL stock 1mM
C1V1= C2V2
1 x V1= 0.025 x 1000ml
Add 25ml of the stock solution to the mixture.
- Give the mixture a good shake.
BUFFER A
Add NaCl and KCl to 1 liter of the general buffer.
- NaCl: 0.05 x 58.442= 2.922g
Add 2.922g of NaCl to the mixture.
- KCl: 0.1 x 74.55= 7.455g
Add 7.455g of KCl to the mixture.
- Give it a good shake.
BUFFER A with 1M of NaCl
Add NaCl and KCl to 1 liter of the general buffer.
- NaCl: 1 x 58.442= 5.8442g
Add 5.8442g of NaCl to the mixture.
- KCl: 0.1 x 74.55= 7.455g
Add 7.455g of KCl to the mixture.
- Give it a good shake.
Buffer B
Add NaCl and KCl to 1 liter of the general buffer.
- NaCl: 0.025x 58.442= 1.4611g
Add 1.4611g of NaCl to the mixture.
- KCl: 0.05 x 74.55= 3.7275g
Add 3.7275g KCl to the mixture.
- Give it a good shake.
Prepare Cell Lysate
- Colonies of BL21 with over expressing LuxR plasmid should be streaked onto LB-ampicillin plates and grown over night at 37 °C.
- Colonies were used to inoculate a liter of LB-ampicillin prewarmed at 37 °C, this is grown until an OD600 of 0.5 is reached, this is then chilled to 28 °C.
- AHL 25uM and IPTG to final concentration of 1mM is then added with additional ampicillin (200ug/ml) and the culture continued to grown at 28 °C for 4 hours, this step is when we want to express the LuxR protein and so we need to first induce with IPTG, then add AHL for correct LuxR protein folding and finally adjust to a lower temperature to try to prevent inclusion body formation.
- Cells were harvested by centrifugation at 8000 x g for 10mins at 4 °C and were frozen overnight at -80°C.
- The following steps were performed at 4 °C:
- The Cell pellet should be resuspended in 16ml of A buffer and 25uM AHL. This cell suspension should then be sonicated.
- After sonication the lysate was centrifuged at 20,000 x g for 10 min. After this, remove the supernatant and centrifuge again at 100,000 x g for 1.5h.
Chromatography
- The cell extract from 100,000 x g is passed through a 5ml HiTrap herparin column and equilibrated with A buffer and 25uM AHL. Bound proteins are then eluted with a 25ml NaCL step gradient from 0.15 to 1M.
- The fractions collected need to see if they contain LuxR. This can be done using SDS-PAGE electrophoresis.
- Now we need to remove the high levels of NaCl from our cell extract. Fractions containing LuxR are then pooled and dialyzed against 500ml of A buffer containing 25uM AHL and 20% (wt/vol) polyethylene glycerol(mw 8000)for four hours.
- After dialysis the sample was diluted 1:1 with a KCL and NaCL free version of A buffer plus 25uM AHL, this gives a final salt concentration of 75mM.
- Now we need to prepare a SP column, this needs to be equilibrated with buffer B and 25uM AHL.Then the sample can be run through and washed with B buffer.
- Finally, to remove the bound protein the SP column can be eluted with 100ml linear NaCl gradients of 0.075 to 0.5M. To test fraction content and purity of LuxR, SDS-PAGE can be carried out.
