Carrico:Standard Protocols: Difference between revisions
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{{Template:carrico}} | {{Template:carrico}} | ||
== | <font face="garamond" size="4" style="color:#000000"> | ||
===Ordering oligos through Stony Brook University=== | =='''DNA'''== | ||
==='''Ordering oligos through Stony Brook University'''=== | |||
#Go to [http://www.osa.sunysb.edu/dna/ <span style="color:#2554C7;">DNA Sequencing Facility</span>] | #Go to [http://www.osa.sunysb.edu/dna/ <span style="color:#2554C7;">DNA Sequencing Facility</span>] | ||
#Click on "Custom Oligos" | #Click on "Custom Oligos" | ||
Line 10: | Line 12: | ||
#Click on "Order" | #Click on "Order" | ||
===Guidelines to determine primer sequence for Quikchange=== | ==='''Guidelines to determine primer sequence for Quikchange'''=== | ||
*Between 25 to 45 base pairs | *Between 25 to 45 base pairs | ||
*Desired mutation should be in middle of primer with 10 to 15 bases of correct sequence on both sides | *Desired mutation should be in middle of primer with 10 to 15 bases of correct sequence on both sides | ||
Line 17: | Line 19: | ||
*Melting temperature should be less than or equal to 78°C (Tm = 81.5 + 0.41 (%GC) – 675/N - % mismatch where N = total number of base pairs) | *Melting temperature should be less than or equal to 78°C (Tm = 81.5 + 0.41 (%GC) – 675/N - % mismatch where N = total number of base pairs) | ||
===Gel extracting DNA=== | ==='''Gel extracting DNA'''=== | ||
QIAquick Gel Extraction Kit Protocol (using a microcentrifuge) - [[:Media:QIAquick Gel Extraction Kit Protocol.pdf|<span style="color:#2554C7;">pdf file</span>]] | QIAquick Gel Extraction Kit Protocol (using a microcentrifuge) - [[:Media:QIAquick Gel Extraction Kit Protocol.pdf|<span style="color:#2554C7;">pdf file</span>]] | ||
===Determining DNA template concentration (and amount)=== | ==='''Determining DNA template concentration (and amount)'''=== | ||
#Find absorbance (OD) by: | #Find absorbance (OD) by: | ||
##In a micro cell, pipette 50uL water | ##In a micro cell, pipette 50uL water | ||
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#Go to [http://www.pubquizhelp.34sp.com/other/dnacalculator.html/ DNA Concentration Calculator] | #Go to [http://www.pubquizhelp.34sp.com/other/dnacalculator.html/ DNA Concentration Calculator] | ||
===Purifying DNA=== | ==='''Purifying DNA'''=== | ||
QIAprep Miniprep Protocol - [[:Media:QIAprep Minimprep Protocol.pdf|<span style="color:#2554C7;">pdf file</span>]] | QIAprep Miniprep Protocol - [[:Media:QIAprep Minimprep Protocol.pdf|<span style="color:#2554C7;">pdf file</span>]] | ||
==Protein== | =='''Protein'''== | ||
===Site Specific Incorporation of a Fluorinated Amino Acid in vivo (21st Pair)=== | ==='''Site Specific Incorporation of a Fluorinated Amino Acid in vivo (21st Pair)'''=== | ||
Site Specific Incorporation of a Fluorinated Amino Acid in vivo Protocol - [[:Media:21st Pair Protocol.pdf|<span style="color:#2554C7;">pdf file</span>]] | Site Specific Incorporation of a Fluorinated Amino Acid in vivo Protocol - [[:Media:21st Pair Protocol.pdf|<span style="color:#2554C7;">pdf file</span>]] | ||
==Competent Cells== | =='''Competent Cells'''== | ||
===Making electrocompetent cells=== | ==='''Making electrocompetent cells'''=== | ||
'''Preparation of materials (previous day)''' | '''Preparation of materials (previous day)''' | ||
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#Place aliquots in -80C freezer | #Place aliquots in -80C freezer | ||
===Making chemically competent cells=== | ==='''Making chemically competent cells'''=== | ||
#Start with 5uL cell (-80°C) | #Start with 5uL cell (-80°C) | ||
#Inoculate in 5mL 2XYT (Needs to be VERY STERILE!) | #Inoculate in 5mL 2XYT (Needs to be VERY STERILE!) | ||
Line 106: | Line 108: | ||
#Place tubes in a freezer box & store in -80°C freezer | #Place tubes in a freezer box & store in -80°C freezer | ||
Note: Check transfer efficiency using a known plasmid. | '''Note:''' Check transfer efficiency using a known plasmid. | ||
==Vector NTI== | =='''Vector NTI'''== | ||
===Creating a new plasmid=== | ==='''Creating a new plasmid'''=== | ||
#Open the Vector NTI Explorer program | #Open the Vector NTI Explorer program | ||
Line 120: | Line 122: | ||
#Double-click on newly created plasmid | #Double-click on newly created plasmid | ||
===Creating a gene in a plasmid=== | ==='''Creating a gene in a plasmid'''=== | ||
#Highlight the plasmid you would like edited | #Highlight the plasmid you would like edited | ||
Line 127: | Line 129: | ||
#Select "Save as" | #Select "Save as" | ||
===Changing nucleotides=== | ==='''Changing nucleotides'''=== | ||
#Highlight bases to be changed | #Highlight bases to be changed | ||
#Select "Edit" --> "New" --> "Replace" | #Select "Edit" --> "New" --> "Replace" | ||
#"Save As" a different name | #"Save As" a different name |
Revision as of 20:42, 14 July 2009
Carrico Lab at Stony Brook
Home Lab Members Recipes Standard Protocols Publications Links
DNA
Ordering oligos through Stony Brook University
- Go to DNA Sequencing Facility
- Click on "Custom Oligos"
- Click on "Ordering" link at bottom of page
- Log-in
- Click on "Order"
Guidelines to determine primer sequence for Quikchange
- Between 25 to 45 base pairs
- Desired mutation should be in middle of primer with 10 to 15 bases of correct sequence on both sides
- Minimum GC content = 40%
- Should terminate in one or more C or G bases
- Melting temperature should be less than or equal to 78°C (Tm = 81.5 + 0.41 (%GC) – 675/N - % mismatch where N = total number of base pairs)
Gel extracting DNA
QIAquick Gel Extraction Kit Protocol (using a microcentrifuge) - pdf file
Determining DNA template concentration (and amount)
- Find absorbance (OD) by:
- In a micro cell, pipette 50uL water
- BLANK at 260nm (remember to turn both vis & UV lamps on and wait 5 minutes)
- Pipette out 5uL water
- Pipette in 5uL DNA template
- Place micro cell in spectrophotometer & READ (remember light pathway for placement)
- Clean micro cell by washing with 2mL water followed by 2mL methanol/ethanol from wash bottles
- Go to DNA Concentration Calculator
Purifying DNA
QIAprep Miniprep Protocol - pdf file
Protein
Site Specific Incorporation of a Fluorinated Amino Acid in vivo (21st Pair)
Site Specific Incorporation of a Fluorinated Amino Acid in vivo Protocol - pdf file
Competent Cells
Making electrocompetent cells
Preparation of materials (previous day)
- Sterilize 2x 500mL LB media in 2L flasks and 2L DI water
- Sterilize at least 50 Eppendorf tubes, 200uL pipette tips and 1000uL pipette tips
- Wash 4 large centrifuge bottles and sterilize with ethanol (do NOT use autoclave)
- Place dry capped bottles and sterilized water in Cold Room on 6th floor
- Sterile filter 10% glycerol solution and place in Cold Room on 6th floor
- Assemble the following:
- 200uL and 1000uL pipettors and sterile tips
- Pipetboy
- At least 10 disposable 10mL pipettes
- Large round dewar
- Sterile tubes
- 1 large Eppendorf tube rack
- 1 sterile 50mL Falcon tube
Preparation of cells
- Grow 2x 5mL starter cultures of the cells to be made competent overnight
- Inoculate 1L (2x 500mL in 2L flasks) LB broth with starter cultures
- Grow at 37C to an OD(600) of 0.5-0.8 (at this point, cells should be in log-phase growth)
- Transfer flasks to an ice bucket and chill on ice 15-30min
- Move to cold room
- Transfer cells to large centrifuge bottles
- Balance and centrifuge at 4C and 4000rpm (~4000g) for 12 minutes
- Immediately place bottles back on ice and (in cold room) empty supernatant
- Resuspend pellets in an equal volume of sterilized water using the Pipetboy and disposable pipettes
- Centrifuge at 4C and 4000rpm for 12 minutes
- Pour off supernatant
- Resuspend pellets in ~10mL sterile water each
- Consolidate from 4 bottles to 2 bottles
- Fill up bottles to ~350mL, balance and centrifuge
- Pour off supernatant
- Resuspend pellets in ~10mL cold sterile 10% glycerol solution and transfer to 50mL Falcon tube
- Balance a second Falcon tube with water
- Spin Falcon tubes at 4C and 7800 rpm (6500g) for 20min
- Resuspend to a final volume of ~2mL cold 10% glycerol
- Aliquot into Eppendof tubes (50uL each)
- Flash freeze in liquid Nitrogen bath
- Place aliquots in -80C freezer
Making chemically competent cells
- Start with 5uL cell (-80°C)
- Inoculate in 5mL 2XYT (Needs to be VERY STERILE!)
- Leave overnight in incubator at 37°C
- Mix 500uL from overnight & 50mL 2XYT using pipette boy
- Incubate at 37°C & 250rpm until OD readings of 0.600 (~2.5hr)
- Note: E. coli strains generally double after ½ hour
- Place on ice for 30 minutes
- While “on ice,” make CaCl2 (& glycerol) solutions
- 30mL 50mM CaCl2 (dilute from 1M CaCl2)
- 7mL 50mM CaCl2 & 20% glycerol
- Centrifuge at 4°C, 3000rpm for 15 minutes
- Resuspend in 25mL 50mM CaCl2 (makes cells permeable)
- Use pipette boy to be extra sterile
- Do NOT mix too much
- Place on ice for 60 minutes
- Centrifuge at 2000rpm for 10 minutes
- Resuspend in 5mL 50mM CaCl2 & 20% glycerol
- In Ice Room on 6th floor, aliquot 105uL into 600uL eppendorfs
- Flash freeze with liquid nitrogen in deuer
- Place tubes in a freezer box & store in -80°C freezer
Note: Check transfer efficiency using a known plasmid.
Vector NTI
Creating a new plasmid
- Open the Vector NTI Explorer program
- Click on the "New" icon
- Fill-in "Name"
- Under the "Sequence" tab, click on "Edit Sequence"
- Paste-in the sequence
- Select "OK"
- Double-click on newly created plasmid
Creating a gene in a plasmid
- Highlight the plasmid you would like edited
- Select "Edit" --> "New" --> "Add feature"
- Select the name of the plasmid
- Select "Save as"
Changing nucleotides
- Highlight bases to be changed
- Select "Edit" --> "New" --> "Replace"
- "Save As" a different name