AlanFung:Protocol/Probe Preparation: Difference between revisions
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*iQ SYBR Green Supermix[http://www.bio-rad.com/prd/en/US/adirect/biorad?cmd=catProductDetail&isFromSearch=true&CategoryPath=/Home/Life%20Science%20Research/Products/Amplification%20-%20PCR/Real-Time%20PCR%20Detection%20Systems/MyiQ%20Single-Color%20Real-Time%20PCR%20Detection%20System/&productID=170-8880&Country=US&vertical=LSR]Bio-Rad Cat. 170-8880 | *iQ SYBR Green Supermix[http://www.bio-rad.com/prd/en/US/adirect/biorad?cmd=catProductDetail&isFromSearch=true&CategoryPath=/Home/Life%20Science%20Research/Products/Amplification%20-%20PCR/Real-Time%20PCR%20Detection%20Systems/MyiQ%20Single-Color%20Real-Time%20PCR%20Detection%20System/&productID=170-8880&Country=US&vertical=LSR]Bio-Rad Cat. 170-8880 | ||
*Nuclease-free Water (not DEPC-treated)[https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catProductDetail&productID=AM9937&catID=603437&backButton=true]Ambion Cat. AM9937 | *Nuclease-free Water (not DEPC-treated)[https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catProductDetail&productID=AM9937&catID=603437&backButton=true]Ambion Cat. AM9937 | ||
*QIAquick PCR Purification Kit [ | *QIAquick PCR Purification Kit[http://www1.qiagen.com/Products/DnaCleanup/GelPcrSiCleanupSystems/QIAquickPCRPurificationKit.aspx?r=1745]Qiagen Cat. 28104 | ||
*Cassettes, 1.0 mm [http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catDisplayStyle&catKey=301&filterDispName=Gel%20Casting&filterType=1&OP=filter&filter=ft_1701%2Ff_203601*&_bcs_=H4sIAAAAAAAAAMXOT0vDQBAF8KP7MRYKOUiTSexFKkWqQimCCEHvy2aaLGT%2FsDNJzLd3A5YW8e71%0AMe%2FNL6%2FEe%2FTNoJlkJmuMo9FIf2Ydc9gCTNNUGDcajr5FV2hvgQwjDATooPMW4dzOlWvycx%2F2IfRG%0AKzbeUdGx7cVqJTgOKG5KUZUV3JXVrTg6SplFx7SWtT%2FxpCKuZaZseJB7nYbIR3PhhJ9fv0zb%2BxLM%0A2LrF9FGDakxEzXA5etS22R0%2FD29J9GIo9Gp%2BVoytj3OWolecd8mzEE%2Bqp2sjbBbnAXv55L%2BQ%2FoW2%0AuaZ9A9kYSz3EAQAA] | *Cassettes, 1.0 mm [http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catDisplayStyle&catKey=301&filterDispName=Gel%20Casting&filterType=1&OP=filter&filter=ft_1701%2Ff_203601*&_bcs_=H4sIAAAAAAAAAMXOT0vDQBAF8KP7MRYKOUiTSexFKkWqQimCCEHvy2aaLGT%2FsDNJzLd3A5YW8e71%0AMe%2FNL6%2FEe%2FTNoJlkJmuMo9FIf2Ydc9gCTNNUGDcajr5FV2hvgQwjDATooPMW4dzOlWvycx%2F2IfRG%0AKzbeUdGx7cVqJTgOKG5KUZUV3JXVrTg6SplFx7SWtT%2FxpCKuZaZseJB7nYbIR3PhhJ9fv0zb%2BxLM%0A2LrF9FGDakxEzXA5etS22R0%2FD29J9GIo9Gp%2BVoytj3OWolecd8mzEE%2Bqp2sjbBbnAXv55L%2BQ%2FoW2%0AuaZ9A9kYSz3EAQAA]Invitrogen Cat. NC2010 | ||
*Combs, 1.0 mm 10 well[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&entryPoint=adirect&messageType=catProductDetail&showAddButton=true&productID=NC3010]Invitrogen Cat. NC3010 | *Combs, 1.0 mm 10 well[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&entryPoint=adirect&messageType=catProductDetail&showAddButton=true&productID=NC3010]Invitrogen Cat. NC3010 | ||
*Cassettes, 1.5 mm [http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catDisplayStyle&catKey=301&filterDispName=Gel%20Casting&filterType=1&OP=filter&filter=ft_1701%2Ff_203601*&_bcs_=H4sIAAAAAAAAAMXOT0vDQBAF8KP7MRYKOUiTSexFKkWqQimCCEHvy2aaLGT%2FsDNJzLd3A5YW8e71%0AMe%2FNL6%2FEe%2FTNoJlkJmuMo9FIf2Ydc9gCTNNUGDcajr5FV2hvgQwjDATooPMW4dzOlWvycx%2F2IfRG%0AKzbeUdGx7cVqJTgOKG5KUZUV3JXVrTg6SplFx7SWtT%2FxpCKuZaZseJB7nYbIR3PhhJ9fv0zb%2BxLM%0A2LrF9FGDakxEzXA5etS22R0%2FD29J9GIo9Gp%2BVoytj3OWolecd8mzEE%2Bqp2sjbBbnAXv55L%2BQ%2FoW2%0AuaZ9A9kYSz3EAQAA] | *Cassettes, 1.5 mm [http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catDisplayStyle&catKey=301&filterDispName=Gel%20Casting&filterType=1&OP=filter&filter=ft_1701%2Ff_203601*&_bcs_=H4sIAAAAAAAAAMXOT0vDQBAF8KP7MRYKOUiTSexFKkWqQimCCEHvy2aaLGT%2FsDNJzLd3A5YW8e71%0AMe%2FNL6%2FEe%2FTNoJlkJmuMo9FIf2Ydc9gCTNNUGDcajr5FV2hvgQwjDATooPMW4dzOlWvycx%2F2IfRG%0AKzbeUdGx7cVqJTgOKG5KUZUV3JXVrTg6SplFx7SWtT%2FxpCKuZaZseJB7nYbIR3PhhJ9fv0zb%2BxLM%0A2LrF9FGDakxEzXA5etS22R0%2FD29J9GIo9Gp%2BVoytj3OWolecd8mzEE%2Bqp2sjbBbnAXv55L%2BQ%2FoW2%0AuaZ9A9kYSz3EAQAA]Invitrogen Cat. NC2015 | ||
*Combs, 1.5 mm 2D well[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&productID=NC3502&CID=Search-nc3502]Invitrogen Cat. NC3502 | *Combs, 1.5 mm 2D well[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&productID=NC3502&CID=Search-nc3502]Invitrogen Cat. NC3502 | ||
*N,N,N′,N′-Tetramethylethylenediamine[http://www.sigmaaldrich.com/catalog/ProductDetail.do?N4=T7024|SIGMA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC]Sigma-Aldrich Cat. T7024 | *N,N,N′,N′-Tetramethylethylenediamine[http://www.sigmaaldrich.com/catalog/ProductDetail.do?N4=T7024|SIGMA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC]Sigma-Aldrich Cat. T7024 | ||
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*10 bp DNA Ladder[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&productID=10821015]Invitrogen Cat. 10821-105 | *10 bp DNA Ladder[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&productID=10821015]Invitrogen Cat. 10821-105 | ||
*Novex® TBE-Urea Sample Buffer (2X)[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&productID=LC6876&CID=Search-LC6876]Invitrogen Cat. LC6876 | *Novex® TBE-Urea Sample Buffer (2X)[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&productID=LC6876&CID=Search-LC6876]Invitrogen Cat. LC6876 | ||
*SYBR® Gold nucleic acid gel stain *10,000X concentrate in DMSO[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&productID=S11494&CID=Search-S11494]Invitrogen Cat.S11494 | *SYBR® Gold nucleic acid gel stain *10,000X concentrate in DMSO[http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&productID=S11494&CID=Search-S11494]Invitrogen Cat.S11494 | ||
*EconoTaq Plus 2X Master Mix[http://www.lucigen.com/catalog/index.php?cPath=50_60&pricing] Lucigen Cat. 30035-1 | |||
*3M Sodium Acetate[http://www.teknova.com/product-p/s0298.htm]Teknova Cat. S0298 | |||
*EconoTaq Plus 2X Master Mix [ | |||
*3M | |||
==Overview== | ==Overview== | ||
*Padlock probes production (Agilent Technologies) | |||
*PCR reaction system setup | *PCR reaction system setup | ||
*Probe purification with ethanol precipitation | *Probe purification with ethanol precipitation | ||
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==Procedures== | ==Procedures== | ||
==Step 1: PCR reaction system setup== | ==Step 0: Padlock probe production (Agilent Technologies)== | ||
*Synthesis of long oligonucleotides (~150nt) by inkjet printing on programmable microarray | |||
==Step 1: PCR amplification reaction system setup== | |||
*Thaw Econo Taq on ice | *Thaw Econo Taq on ice | ||
*Prepare strips and tubes on cooling rack | *Prepare strips and tubes on cooling rack | ||
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94C 2M > (94C 30S > 58C 30S > 72C 30S>Plate Read) X16 > 72C 3M > 15C Hold | 94C 2M > (94C 30S > 58C 30S > 72C 30S>Plate Read) X16 > 72C 3M > 15C Hold | ||
==Step 2: | ==Step 2: Amplicons purification with ethanol precipitation== | ||
*Add in required volume of 100% ethanol, 3M NaOAC and Glycoblue into tray | *Add in required volume of 100% ethanol, 3M NaOAC and Glycoblue into tray | ||
{| border="1" align="center" | {| border="1" align="center" | ||
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*Resuspend the DNA with 100uL RNAse free H2O | *Resuspend the DNA with 100uL RNAse free H2O | ||
==Step 4: Adapter Removal using Lambda Exonuclease & Denaturing == | |||
==Step 4: Adapter Removal== | |||
Exonuclease treatment | Exonuclease treatment | ||
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*Incubate at37C 4h>90C 10m>4C hold Saved as program Alan>EXOAR | *Incubate at37C 4h>90C 10m>4C hold Saved as program Alan>EXOAR | ||
==Step 5:Column purification with Qiaquick== | |||
Purify the reaction with Qiaquick columns | |||
Purify the reaction with | |||
* Add 5X sample volume of PB buffer into each tube, mix well | * Add 5X sample volume of PB buffer into each tube, mix well | ||
* Load mixture onto column | * Load mixture onto column | ||
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* Measure concentration with Nanodrop | * Measure concentration with Nanodrop | ||
==Step 6:USER enzyme digestion== | |||
*Add 40ul ddH2O, 5ul USER, 37C 1h | *Add 40ul ddH2O, 5ul USER, 37C 1h | ||
Latest revision as of 23:27, 17 October 2009
Probe Preparation[edit]
Samples & Materials[edit]
- Nanosep MF Centrifugal Devices[[1]]VWR Cat. 29300-646
- 22G General Use Needles[2]B-D Cat. 305155
- Surgical Blades[3]BD Bard-Parker Cat. 371610
- Nanodrop [4]Thermo Scientific Cat. ND-1000
- Multi-Channel Reagent Reservoirs[5]Heathrow Scientific Cat. HS20521C
- Chromo4 Four-Color Real-Time PCR Detection System[6]Bio-Rad Cat. 359-1590G
- Corning® 15mL PP Centrifuge Tubes[7]Corning Cat. 430791
- Molecular Imager Gel Doc XR+ System[8]Bio-Rad Cat. 170-8170
- OmniPur® Urea[9]EMD Chemicals Inc. Cat. 9530
- USER Enzyme[10]New England Biolabs Cat. M5505L
- DPNII(5KU/ml;1KU/ml)[11]New England Biolabs Cat. R0543T/R0543S
- Lambda Exonuclease[12]New England Biolabs Cat. M0262L
- iQ SYBR Green Supermix[13]Bio-Rad Cat. 170-8880
- Nuclease-free Water (not DEPC-treated)[14]Ambion Cat. AM9937
- QIAquick PCR Purification Kit[15]Qiagen Cat. 28104
- Cassettes, 1.0 mm [16]Invitrogen Cat. NC2010
- Combs, 1.0 mm 10 well[17]Invitrogen Cat. NC3010
- Cassettes, 1.5 mm [18]Invitrogen Cat. NC2015
- Combs, 1.5 mm 2D well[19]Invitrogen Cat. NC3502
- N,N,N′,N′-Tetramethylethylenediamine[20]Sigma-Aldrich Cat. T7024
- TBE Buffer (10X)[21]National Diagnostics Cat. EC-860
- Acrylamide-Bis Solution 40%, 29:1 DNA Sequencing Grade Solution[22]Teknova Cat. A4025
- Ammonium persulfate[23]Sigma-Aldrich Cat. A9164
- Ethanol 200 proof (absolute) [24]Sigma-Aldrich Cat. E7023
- GlycoBlue[25]Ambion Cat. AM9515
- 10 bp DNA Ladder[26]Invitrogen Cat. 10821-105
- Novex® TBE-Urea Sample Buffer (2X)[27]Invitrogen Cat. LC6876
- SYBR® Gold nucleic acid gel stain *10,000X concentrate in DMSO[28]Invitrogen Cat.S11494
- EconoTaq Plus 2X Master Mix[29] Lucigen Cat. 30035-1
- 3M Sodium Acetate[30]Teknova Cat. S0298
Overview[edit]
- Padlock probes production (Agilent Technologies)
- PCR reaction system setup
- Probe purification with ethanol precipitation
- Purify the reaction with Qiaquick columns
- Adapter Removal
- Page Denaturing Gel
- Purify the product from the gel
- Precipitation
- Quantification of DNA using denaturing gel and a quantitative ladder
Procedures[edit]
Step 0: Padlock probe production (Agilent Technologies)[edit]
- Synthesis of long oligonucleotides (~150nt) by inkjet printing on programmable microarray
Step 1: PCR amplification reaction system setup[edit]
- Thaw Econo Taq on ice
- Prepare strips and tubes on cooling rack
- Add in Content in table to tubes accordinly
Content | Volume | X24 | X48 | X72 | X96 | 1.5 mL Tube |
Jan_09_CPG_D40809 (10uM) | 0.2uL | 4.8uL | 9.6uL | 14.4uL | 19.2uL | 2.4uL |
Econo Taq | 50uL | 1250uL | 2400uL | 3600uL | 4800uL | 650uL |
AP1V6 AP2V6 Mix (50uM) | 0.4uL | 9.6uL | 19.2uL | 28.8uL | 38.4uL | 4.8uL |
RNAse free H2O | 50uL | 1200uL | 2400uL | 3600uL | 4800uL | 600uL |
50X SYBG I | 0.4uL | 9.6uL | 19.2uL | 28.8uL | 38.4uL | 4.8uL |
Total Volume | 101uL | 2424uL | 4848uL | 7272uL | 9696uL | 1212uL |
- Mix content in 1.5 mL tube vortex and spin down in the order of water>SYBR Green>Primer >template>econotaq
- Aliquot 105uL using P200 pipette to strip tubes on cooling rack
- Seal strips with strip caps
- Place into Real Time PCR
- Perform
94C 2M > (94C 30S > 58C 30S > 72C 30S>Plate Read) X16 > 72C 3M > 15C Hold
Step 2: Amplicons purification with ethanol precipitation[edit]
- Add in required volume of 100% ethanol, 3M NaOAC and Glycoblue into tray
Content | Volume Needed | Volume |
100% Ethanol | 2.5X Sample Volume | 6000uL |
3M NaOAC | 0.1X Sample Volume | 240uL |
Glycoblue | 1/300X Sample Volume | 8uL |
Sample | Sample Volume | 2400uL |
Total Volume | 8648uL |
- Mix all content by repeat pipetting using multichannel pipette
- Pool all 24 wells PCR product into tray using multichannel pipette(P300)
- Mix all content by repeat pipetting using multichannel pipette
- Aliquot about 3750uL to 2 x 15mL tube
- Store in -80C for more than 20 mins or forever
- Turn on Centrifuge fix temperature at 4C, place a tube of 75% ethanol into 4C fridge
- Centrifuge frozen 15mL tubes at 3000rpm for 20m at 4C
- Remove all liquid CAUTION: DO NOT DISCARD BLUE PELLET AT THE BOTTOM OF THE TUBE
- Add in 750uL cold 75% Ethanol, mix by repeat pipetting and transfer to a 1.5mL tube
- Centrifuge at 10,000rpm for 5min at 4C
- Remove all liquid, air dry sample for 5min or until samples dried out
- Resuspend the DNA with 100uL RNAse free H2O
Step 4: Adapter Removal using Lambda Exonuclease & Denaturing[edit]
Exonuclease treatment
- Add in 3uL Lambda Exonuclease (5K/mL) for sample concentration around 100ng/uL NOTE: If sample too concentrated, dilute sample to about 100ng/uL per tube
- Add in (1/10 of total volume) 6uL 10X Exo buffer
- Incubate at37C 4h>90C 10m>4C hold Saved as program Alan>EXOAR
Step 5:Column purification with Qiaquick[edit]
Purify the reaction with Qiaquick columns
- Add 5X sample volume of PB buffer into each tube, mix well
- Load mixture onto column
- Centrifuge at 14,000rpm for 1min
- Discard flow through and add 750uL PE buffer to each column
- Repeat Centrifuge
- Discard flow through
- Repeat centrifuge
- Transfer columns to clean 1.5mL tubes
- Place the column/tube assemblies on bench top wait for 2min
- Add in 50uL EB buffer to each column (For nicking enzyme probes add in 100ul of ddH2O) let stand for 5 min
- Repeat centrifuge
- Measure concentration with Nanodrop
Step 6:USER enzyme digestion[edit]
- Add 40ul ddH2O, 5ul USER, 37C 1h
- Add 10ul 10x DpnII buffer, 5ul RE-DpnII-ns2 guide oligo,
94C 2min -> 37C 3min -> add 5ul DpnII -> 37C 6h -> 75C 20min -> 4c hold Purified with Qiaquick
Incubation with USER enzyme:
- Add 5ul DpNII 10x buffer and 2 uL of USER (1K/ml)enzyme incubate for 2 hours on 37C.
Annealing of DpnII oligo and incubation with DpnII.
- add 6ul of 10X DpnII buffer and 2uL RE-DpnIIs guide oligo (100uM)
- Perform 94C 5m > 60C 5m > 0.1C/sec to 37C > add 4ul of DpnII restriction enzyme -> 37C 2 hours > 4C hold
- Qiaquick column purification
- Elute with 60uL EB Buffer
Step 5: Page Denaturing Gel[edit]
- Prepare a 2D well denaturing gel by scraping off the gel residue outside and peel of the sticker at the back of gel
- Load 2 gels into the gel running module
- Add in fresh 0.5X TBE buffer to the inside core full the outer core up to the metal line
- Pre-run the gel for 30 min at 200V
- Dilute sample to no more than 40ng/uL
- Dilute TBE-Urea sample buffer (2X) to 1X in each tube.
For 2 gels; Mix 0.5 uL Invitrogen 10bp ladder with 4.5 uL dH2O, 5 uL 2x TBE-Urea sample buffer For 4 gels; Mix 0.5 uL Invitrogen 10bp ladder with 9.5 uL ddH2O, 10uL 2X TBE-Urea sample buffer
- Denature samples and ladder at 75C for 7 min, then quickly transfer to cooling rack, wait for 5 mins
- Flush the wells very well with P1000 & P200 pipette to remove all urea.
NOTE: DO NOT TOUCH THE TUBE WITH YOUR HANDS IN THE FOLLOWING STEP, GRAB THE CAP
- Load the samples into the wells, run at 200V for 30 min.
- Stain gel with 4uL SYBR Gold in ~100 mL of TBE in clean tray.
- Place tray on an orbital shaker for ~5 min.
Step 6: Purify the product from the gel[edit]
- Prepare two gel shearing assemblies by placing a 0.5 mL tube within another 1.5 mL Non-Stick tube. Use G20 needle to punch a small hole at the bottom of the 0.5 mL tube. Use two assemblies for each PAGE gel.
- Cut out the correct band (85-92 nt in this case), chop the band into small slices, split into two half and transfer each half to one shearing assembly.
- Centrifuge at top speed > 12000 rpm for 2 min to sheer the gel, remove the 0.5 mL tube.
- Add 400 uL clean 1x TE buffer in the 1.5 mL tube. Tape the tubes on a vortexer, place the vortexer in 37C incubator, shake the tubes at low speed for 1 hour. Alternatively, can keep the tubes in 4C fridge overnight.
- Spin down all tubes at 13,000rpm for 2min
- In the PCR hood, transfer the liquid layer of the gel mix to Nanosep columns, spin for 3 min at top speed (15,000 rpm), and then transfer supernatant to 1.5mL tube.
Step 7: Precipitation[edit]
Turn on centrifuge let it cool down to 4C
- Add 0.1x total volume of 3M sodium acetate and 2.5x total volume 100% ethanol.
- Add 1uL Glycoblue vortex and spin down so that one can precipitate better and see the DNA.
- Freeze in -80C for 20 min, spin at 10,000 rpm for 20 min at 4C, discard supernatant with pipette.
- Add 500 uL of 75% ethanol to wash DNA, spin at 10,000 rpm for 5 min at 4C, discard supernatant and aspirate with (P1000 pipette) let dry for 5 mins spindown ad aspirate with P200 pipette.
- Let dry in hood ~ 10 min.
- Add 20 uL of water(totally) to the tube to resolve the DNA in, leave at least 15 min.
Store at 4C if needed, spin down before proceeding
Step 8: Quantification of DNA using denaturing gel and a quantitative ladder[edit]
Combine all tubes into a 1.5mL tube
1. Add 4uL of 5ng/uL 90-mer, 4ul of H2O and 8 uL of 2x TBE-Urea buffer 2. Dilute sample 10x (1uL sample + 9 uL of water) so total is 10uL of sample, and add 10 uL of 2x TBE buffer 3. Denature the DNA with loading dye on thermalcycler 75C for 7 min, quickly transfer to cooling rack, wait for 1 min. 4. Use 6% 10 well TBU gel, add 0.5x TBE buffer, flush the wells very well to remove all urea. 5. Pre-run the gel at 200V for 10 min, then load the samples into the wells, run at 200V for 30 min. Load the ladder as 8, 4, 2, 1 uL, and load the samples as 10, 5, 2.5 uL. 6. Stain the gel with 5 uL SYBR gold in ~100 mL of TBE in clean tray. Place the tray on an orbital shaker for 5 min. Then quantify the gel to calculate the % yield.