Daniel:Notebook/ComboLock/2016-7-28: Difference between revisions
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==Buffers== | ==Buffers== | ||
'''KLN Mix''' | '''KLN Mix''' | ||
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{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | ||
|- style="background-color:#D8E4BC;font-size:12pt;font-weight:bold" align="center" | |- style="background-color:#D8E4BC;font-size:12pt;font-weight:bold" align="center" | ||
| width=" | | width="200" height="40" | Reagent | ||
| width="65" | Stock Conc | | width="65" | Stock Conc | ||
| width="72" | Final Amount | | width="72" | Final Amount | ||
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|- style="background-color:#D9D9D9;font-size:12pt" | |- style="background-color:#D9D9D9;font-size:12pt" | ||
| height="15" valign="bottom" | Phusion HF DNA | | height="15" valign="bottom" | Phusion HF DNA Polymerase | ||
| align="center" valign="bottom" | 2000 U/mL | | align="center" valign="bottom" | 2000 U/mL | ||
| align="center" valign="bottom" | 6.4U | | align="center" valign="bottom" | 6.4U |
Revision as of 20:40, 28 July 2016
Phusion Test
Hemo Klentaq has strand displacement activity, which could be a potential (big) problem for latch-padlock circularization. Therefore, on Chris and Andrew's recommendation I will try a test using Phusion instead of Hemo Klentaq.
Buffers
KLN Mix
Reagent | Stock | uL added |
Amp Ligase Buffer | 10X | 2 |
dNTPs | 100 uM | 2 |
Hemo Klentaq | NA | 4 |
Amp Ligase | 5 U/uL | 2 |
nfH2O | NA | 10 |
Phusion Buffer
Reagent | Stock Conc | Final Amount | 1x Vol (uL) | MM Vol (4.1x) (uL) |
NAD+ | 5 mM | 40 nmol | 8 | 32.8 |
dNTP | 1 mM | 600 pmol | 0.6 | 2.46 |
Betaine | 5 M | 15 umol | 3 | 12.3 |
10X AmpLigase Buffer | 10X | 1X | 2 | 8.2 |
Amp Ligase | 5 U/uL | 10 U | 2 | 8.2 |
Phusion HF DNA Polymerase | 2000 U/mL | 6.4U | 3.2 | 13.12 |
nf H2O | 1.2 | 4.92 | ||
Total | 20 | 82 |
Protocol
- C-Probe Hybridization
- Measure cell concentrations in cell counter
- Human - 3.05E5 cells/mL; Mouse - 9.75E5 cells/mL (from 7-25-2016)
- Add cells to a new tube such that there are 30000 cells present per sample
- Human- 350 uL (3 samples) uL; Mouse- 30 uL
- Pellet cells via centrifugation at 600g for 3 min
- Wash with 200 uL wash buffer and pellet cells via centrifugation at 600g for 3 min
- Add 100 uL 50% hematoxylin (filtered) and pellet cells via centrifugation at 600g for 3 min
- Wash once with 200 uL wash buffer and pellet cells via centrifugation at 600g for 3 min
- Wash 2 times with 200 uL wash buffer prime and pellet cells via centrifugation at 600g for 3 min
- Pellet cells via centrifugation at 600g for 3 min
- Combine 0.5 uL of each C probe into a 0.2 mL tube with 2 uL nfH2O
- Heat C probes to 90C for 5 min; Chill probes on ice to quench
- Add probes to CPH buffer according to sample matrix, 1 uL probe mix per sample
- Incubate probes at 40C for 1 hour with vigorous agitation
- Wash three times with 200 uL wash buffer and pelleting at 600xg for 3 min
- Incubate cells for 20 min at 40C in 200 uL stringent wash buffer
- Latch and Padlock Hybridization
- Pellet at 600xg for 3 min and remove supernatant
- Resuspend pellet in 100 uL LPH buffer with 100 nM Padlock0001-68
- Incubate for 30 min at 37C
- Wash twice with 100 uL wash buffer by pelleting cells at 600xg for 3 min
- Incubate cells for 20 min at 40C in 150 uL stringent wash buffer
- Resuspend pellet in 100 uL LPH buffer with 100 nM Latch0001
- For sample 3, use 10 uL 100 uM Latch0001 (10 uM final concentration)
- Incubate for 30 min at 37C
- Wash twice with 200 uL wash buffer by pelleting cells at 600xg for 3 min
- Incubate cells for 20 min at 40C in 200 uL stringent wash buffer
- Resuspend with 20 uL 1x Amp Ligase buffer and transfer to a 0.2 mL tube
- Circularization
- Prepare 20 uL KLN mix
- Prepare
- Add 2 uL KLN mix to 20 uL of reaction
- Incubate at 55C overnight (XX hours)
- Continued tomorrow
C Probes-VIM (C1+C2) | C Probes-SOD1 (C1+C2) | U87MG | 3T3 Cells | Treatment | |
Sample 1 | X | X | X | Klentaq | |
Sample 2 | X | X | X | Phusion | |
Sample 3 | X | Phusion | |||
Sample 4 | X | X | X | Phusion | |
Sample 5 | X | X | Phusion |