IGEM:MIT/2006/Notebook/2006-7-5: Difference between revisions
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'''Nanodrop readings following PCR clean-ups: (?? μL for 50 nanograms) | '''Nanodrop readings following PCR clean-ups: (?? μL for 50 nanograms) | ||
#EP cut pSB1A3-1 = | #EP cut pSB1A3-1 = 29.8 ng/μL (2 μL) | ||
#EP cut SAMT = | #EP cut SAMT = 10.4 (5 μL) | ||
#EP cut BAMT = | #EP cut BAMT = 13 ng/μL (4 μL) | ||
#EP cut E0040 = | #EP cut E0040 = 11.7 ng/μL (5 μL) | ||
#XP cut pSB1A3-1 = | #XP cut pSB1A3-1 = 22 ng/μL (2.5 μL) | ||
#XP cut ATF1 = | #XP cut ATF1 = 28.1 ng/μL (2 μL) | ||
#XP cut BSMT = | #XP cut BSMT = 15.7 ng/μL (3.5 μL) | ||
'''We'll do 5 ligations, 10 μL total volume each: | '''We'll do 5 ligations, 10 μL total volume each: | ||
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'''EP cut pSB1A3-1 and EP cut SAMT''' | '''EP cut pSB1A3-1 and EP cut SAMT''' | ||
* μL water | *1.5μL water | ||
*1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | *1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | ||
*.5μL T4 DNA ligase enzyme | *.5μL T4 DNA ligase enzyme | ||
*μL cut SAMT (50ng) | *5μL cut SAMT (50ng) | ||
*μL cut backbone (50ng) | *2μL cut backbone (50ng) | ||
'''EP cut pSB1A3-1 and EP cut BAMT''' | '''EP cut pSB1A3-1 and EP cut BAMT''' | ||
*μL water | *2.5μL water | ||
*1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | *1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | ||
*.5μL T4 DNA ligase enzyme | *.5μL T4 DNA ligase enzyme | ||
*μL cut BAMT (50ng) | *4μL cut BAMT (50ng) | ||
*μL cut backbone (50ng) | *2μL cut backbone (50ng) | ||
'''EP cut pSB1A3-1 and EP cut E0040 (+ Ctrl)''' | '''EP cut pSB1A3-1 and EP cut E0040 (+ Ctrl)''' | ||
*μL water | *1.5μL water | ||
*1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | *1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | ||
*.5μL T4 DNA ligase enzyme | *.5μL T4 DNA ligase enzyme | ||
*μL cut Barry's E0040 part (50ng) | *5μL cut Barry's E0040 part (50ng) | ||
*μL cut backbone (50ng) | *2μL cut backbone (50ng) | ||
'''XP cut pSB1A3-1 and XP cut ATF1''' | '''XP cut pSB1A3-1 and XP cut ATF1''' | ||
*μL water | *4μL water | ||
*1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | *1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | ||
*.5μL T4 DNA ligase enzyme | *.5μL T4 DNA ligase enzyme | ||
*μL cut ATF1 (50ng) | *2μL cut ATF1 (50ng) | ||
*μL cut backbone (50ng) | *2.5μL cut backbone (50ng) | ||
'''XP cut pSB1A3-1 and XP cut BSMT (+ Ctrl)''' | '''XP cut pSB1A3-1 and XP cut BSMT (+ Ctrl)''' | ||
*μL water | *2.5μL water | ||
*1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | *1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells ''strongly'' like wet dog!!) | ||
*.5μL T4 DNA ligase enzyme | *.5μL T4 DNA ligase enzyme | ||
*μL cut BSMT (50ng) | *3.5μL cut BSMT (50ng) | ||
*μL cut backbone (50ng) | *2.5μL cut backbone (50ng) | ||
'''Ligate at room temp for 15 to 20 minutes and then proceed to transformation''' | '''Ligate at room temp for 15 to 20 minutes and then proceed to transformation''' |
Revision as of 11:38, 5 July 2006
BAMT PCR Product Eco/Pst Digest
BEGAN AT 11:15 AM
- We are cutting the BAMT pcr product (using EcoRI and PstI)--
- Total reaction volume is 50μL
- the amount of dna desired is about 800 nanograms
- BAMT pcr product at 58.8 ng/μL -----add 13.6 μL
- we are also going to use Dpn1 only in BAMT cut reaction to destroy dna that is not a pcr product (i.e. get rid of extra template)
- BAMT pcr cleanup product cut reaction:
- 28.9 μL water
- 5 μL NEB buffer 2
- .5 μL BSA
- 13.6 μL BAMT pcr cleanup product (concentration = 50 ng/μL)
- .75 μL Pst1
- .75 μL EcoR1
- .5 μL Dpn 1
- Incubate tube in 37c room for 1-6 hours, then 20 mins at 80deg C to heat inactivate the enzyme, then 4deg forever.
- Did a PCR cleanup & nanodrop: concentration of digested BAMT = ??ng/μL
- run a gel before moving on to ligation !!
ATF1 PCR Product Xba/Pst Digest
BEGAN AT 11:15 AM
- We are cutting the ATF1 pcr product (using XbaI and PstI)--
- Total reaction volume is 50μL
- the amount of dna desired is about 800 nanograms
- ATF1 pcr product at 30.8 ng/μL -----add 26 μL
- we are also going to use Dpn1 only in ATF1 cut reaction to destroy dna that is not a pcr product (i.e. get rid of extra template)
- ATF1 Digest:
- 16.5 μL water
- 5 μL NEB buffer 3
- .5 μL BSA
- 26 μL ATF1 pcr cleanup product (concentration = 50 ng/μL)
- .75 μL Pst1
- .75 μL XbaI
- .5 μL Dpn 1
- Incubate tube in 37c room for 1-6 hours, then 20 mins at 80deg C to heat inactivate the enzyme, then 4deg forever.
- Did a PCR cleanup & nanodrop: concentration of digested SAMT = ??ng/μL
- run a gel before moving on to ligation !!
BACKBONE pSB1A3-1 bkb Xba/Pst Digest
BEGAN AT 11:15 AM
- 35 μL water
- 5 μL NEB buffer 3
- .5 μL BSA
- 8 μL backbone plasmid
- .75 μL PstI
- .75 μL XbaI
CONTROL (BSMT-BB) Xba/Pst Digest
- 31.58 μL water
- 5 μL NEB buffer 3
- .5 μL BSA
- 11.42 μL BSMT-BB (from BSMT miniprep @ 71ng/μL )
- .75 μL PstI
- .75 μL XbaI
Glycerols and Miniprep of BSMT biobrick
- Did minipreps of A, C, E BSMT liquid cultures to get the BSMT biobrick plasmid.
- Made glycerols of these cells (which contain the BSMT biobrick)
SAMT-BB (J45001), BAMT-BB (J45002), & ATF1-BB (J45006) Ligations
RUN GELS OF DIGESTS TO DOUBLECHECK THAT THEY WORKED!
Nanodrop readings following PCR clean-ups: (?? μL for 50 nanograms)
- EP cut pSB1A3-1 = 29.8 ng/μL (2 μL)
- EP cut SAMT = 10.4 (5 μL)
- EP cut BAMT = 13 ng/μL (4 μL)
- EP cut E0040 = 11.7 ng/μL (5 μL)
- XP cut pSB1A3-1 = 22 ng/μL (2.5 μL)
- XP cut ATF1 = 28.1 ng/μL (2 μL)
- XP cut BSMT = 15.7 ng/μL (3.5 μL)
We'll do 5 ligations, 10 μL total volume each:
- EP cut pSB1A3-1 and EP cut SAMT
- EP cut pSB1A3-1 and EP cut BAMT
- EP cut pSB1A3-1 and EP cut E0040 (+ Ctrl)
- XP cut pSB1A3-1 and XP cut ATF1
- XP cut pSB1A3-1 and XP cut BSMT (+ Ctrl)
EP cut pSB1A3-1 and EP cut SAMT
- 1.5μL water
- 1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells strongly like wet dog!!)
- .5μL T4 DNA ligase enzyme
- 5μL cut SAMT (50ng)
- 2μL cut backbone (50ng)
EP cut pSB1A3-1 and EP cut BAMT
- 2.5μL water
- 1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells strongly like wet dog!!)
- .5μL T4 DNA ligase enzyme
- 4μL cut BAMT (50ng)
- 2μL cut backbone (50ng)
EP cut pSB1A3-1 and EP cut E0040 (+ Ctrl)
- 1.5μL water
- 1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells strongly like wet dog!!)
- .5μL T4 DNA ligase enzyme
- 5μL cut Barry's E0040 part (50ng)
- 2μL cut backbone (50ng)
XP cut pSB1A3-1 and XP cut ATF1
- 4μL water
- 1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells strongly like wet dog!!)
- .5μL T4 DNA ligase enzyme
- 2μL cut ATF1 (50ng)
- 2.5μL cut backbone (50ng)
XP cut pSB1A3-1 and XP cut BSMT (+ Ctrl)
- 2.5μL water
- 1μL T4 DNA ligase buffer (vortex well before adding, make sure it smells strongly like wet dog!!)
- .5μL T4 DNA ligase enzyme
- 3.5μL cut BSMT (50ng)
- 2.5μL cut backbone (50ng)
Ligate at room temp for 15 to 20 minutes and then proceed to transformation