SBB09Ntbk-Sadao Ota: Difference between revisions
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'''Cloning PCR, (products are 937bp & 1600bp, )''' | '''Cloning PCR, (products are 937bp & 1600bp, )''' | ||
* 24 uL water | |||
* 3.3 uL Expand 10x Buffer 2 | * 3.3 uL Expand 10x Buffer 2 | ||
* 3.3 uL 10x dNTPs (2 mM in each; 0.2 mM final conc) | * 3.3 uL 10x dNTPs (2 mM in each; 0.2 mM final conc) | ||
Line 26: | Line 26: | ||
* 0.5 uL Expand Polymerase 1 | * 0.5 uL Expand Polymerase 1 | ||
* 0.5 uL Template DNA E.coli 0157:H7 | * 0.5 uL Template DNA E.coli 0157:H7 | ||
* Run this PCR on program 55 | |||
Line 32: | Line 32: | ||
==[[User:Sadao Ota|Sadao Ota]] 15:03, 23 February 2009 (EST)== | ==[[User:Sadao Ota|Sadao Ota]] 15:03, 23 February 2009 (EST)== | ||
<pre> | <pre> | ||
Clean up PCR products | Clean up PCR products | ||
</pre> | </pre> | ||
=== === | === === | ||
'''Regular Zymo Cleanup (removes the polymerase, dNTPs, buffer, and most of the oligonucleotides from a PCR reaction)''' | '''Regular Zymo Cleanup (removes the polymerase, dNTPs, buffer, and most of the oligonucleotides from a PCR reaction)''' | ||
Line 47: | Line 46: | ||
#spin for 90 seconds, full speed to dry. | #spin for 90 seconds, full speed to dry. | ||
#elute with water into a fresh Eppendorf tube, use the same volume of water as the volume of the original reaction | #elute with water into a fresh Eppendorf tube, use the same volume of water as the volume of the original reaction | ||
'''Load to Gel to perform gelation analysis (dead or alive)''' | |||
* mix the eluted DNAs (3 ul) and loading dye (2 ul) | |||
'''EcoRI/BamHI Digest of PCR Products (my PCR products are large enough, so no need to modificate the process)''' | |||
*Set up the following reaction: | |||
8uL of eluted PCR product | |||
1uL of NEB Buffer 2 | |||
0.5uL EcoRI | |||
0.5uL BamHI | |||
*Incubate at 37 degrees on the thermocycler for 1hr | |||
*Run an agarose gel, and melt with 600uL ADB buffer at 55 degrees. ****NOTE: If you are running short of time, this is an acceptable stopping point | |||
Revision as of 23:18, 23 February 2009
Sadao Ota 15:03, 9 February 2009 (EST)
My project is SBB09_20154, to make ag43 Display (short) ag43 Display (long) systems. Designed a oligo M10034 to make Autotransporter protein with promotors and so on (corresponding to amino acids 708-1017). Also, designed another oligo M10035 to make Autotransporter protein only (corresponding to amino acids 517-1017).
- Construction files are M10034 M10035
- Oligonucleotide sequences are Oso001, Oso002, Oso003
Sadao Ota 15:03, 16 February 2009 (EST)
Do PCR with the combination of Oso001&Oso002, and Oso002&Oso003.
Dilute oligonucleotides to be 10 uM
- Add 1 ul of oligo dilution to 9 ul of ddH20
- Mix and spin
Cloning PCR, (products are 937bp & 1600bp, )
- 24 uL water
- 3.3 uL Expand 10x Buffer 2
- 3.3 uL 10x dNTPs (2 mM in each; 0.2 mM final conc)
- 1 uL Oligo Odvs007F (10uM)
- 1 uL Oligo Odvs008rR (10uM)
- 0.5 uL Expand Polymerase 1
- 0.5 uL Template DNA E.coli 0157:H7
- Run this PCR on program 55
Sadao Ota 15:03, 23 February 2009 (EST)
Clean up PCR products
Regular Zymo Cleanup (removes the polymerase, dNTPs, buffer, and most of the oligonucleotides from a PCR reaction)
- Add 180 uL of Zymo ADB buffer (brown bottle) to a 33uL or 50uL reaction.
- Transfer into the Zymo column (small clear guys)
- spin through, discard waste.
- Add 200 uL of PE or Zymo Wash buffer (which is basically 70% ethanol)
- spin through, discard waste.
- Add 200 uL of PE or Zymo Wash buffer
- spin through, discard waste.
- spin for 90 seconds, full speed to dry.
- elute with water into a fresh Eppendorf tube, use the same volume of water as the volume of the original reaction
Load to Gel to perform gelation analysis (dead or alive)
- mix the eluted DNAs (3 ul) and loading dye (2 ul)
EcoRI/BamHI Digest of PCR Products (my PCR products are large enough, so no need to modificate the process)
- Set up the following reaction:
8uL of eluted PCR product 1uL of NEB Buffer 2 0.5uL EcoRI 0.5uL BamHI
- Incubate at 37 degrees on the thermocycler for 1hr
- Run an agarose gel, and melt with 600uL ADB buffer at 55 degrees. ****NOTE: If you are running short of time, this is an acceptable stopping point
- Add 1 ul of oligo dilution to 9 ul of ddH20
- Mix and spin
Cloning PCR, (products are 937bp & 1600bp, )
- 24 uL water
- 3.3 uL Expand 10x Buffer 2
- 3.3 uL 10x dNTPs (2 mM in each; 0.2 mM final conc)
- 1 uL Oligo Odvs007F (10uM)
- 1 uL Oligo Odvs008rR (10uM)
- 0.5 uL Expand Polymerase 1
- 0.5 uL Template DNA E.coli 0157:H7
- Run this PCR on program 55