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	=='''Notebook'''==		=='''Notebook'''==
-	==First Week==	+	==Protocols==
-	===Mutation===	+	===Mutations===
		+
		+	'''Ingredients'''
		+
		+	Site directed mutagenesis of 3 plant CYP450 (79A1, 79A2, 79B1).
		+
		+	We aim to destroy restrictionenzymes recognitionsites.
		+
		+	Primers was supplied by ...........
		+
		+
		+	10 μl of 5× reaction buffer
		+
		+	X μl (50 ng) of dsDNA template
		+
		+	X μl (125 ng) of oligonucleotide primer #1
		+
		+	X μl (125 ng) of oligonucleotide primer #2
		+
		+	1 μl of dNTP mix
		+
		+	ddH2O to a final volume of 50 μl
		+
		+	Then add
		+
		+	1 μl of PfuTurbo DNA polymerase (2.5 U/μl)
		+
		+
		+	'''Poly Chain Reaction'''
		+
		+	We ran a PCR to syntesise and amplify our mutated CYP's.
		+
		+
		+	Cycling Parameters for the QuikChange Site-Directed Mutagenesis Method
		+
		+	Segment 1
		+
		+	Cycles 1 Temperature 95°C Time 30 seconds
		+
		+	Segment 2
		+
		+	Cycles 12
		+
		+	Temperature 95°C Time 30 seconds
		+
		+	Temperature 55°C Time 1 minute
		+
		+	Temperature 68°C Time 1 minute/kb of plasmid length
		+
		+
		+	'''Digestion'''
		+
		+	We aim to remove the parentel CYP.
		+
		+	We take advantage of the fact that this CYP is methylated on cytosines. Dpn is a restriction enzyme that cuts DNA which is methylated - therefore our new mutated CYPs remain untouched.
		+
		+	1. Add 1 μl of the Dpn I restriction enzyme (10 U/μl) directly to each amplification reaction.
		+
		+	2. Gently and thoroughly mix each reaction mixture by pipetting the solution up and down
		+	several times. Spin down the reaction mixtures in a microcentrifuge for 1 minute and
		+	immediately incubate each reaction at 37°C (in a heater with lid or in a 37°C room) for 1 hour to digest the parental (i.e., the
		+	nonmutated) supercoiled dsDNA.
		+
		+
		+	'''Source'''
		+
		+	Adapted from
		+	QuikChange™ Site-Directed
		+	Mutagenesis Kit
		+	INSTRUCTION MANUAL
		+
		+
		+	===Competent Cells===
		+
		+	'''E. coli Calcium Chloride competent cell protocol'''
		+
		+	1. Inoculate a single colony into 5mL Lb in 15mL falcon tube. Grow
		+	O/N at 37°C.
		+
		+	2. Use 1mL to inoculate 100mL of LB in 250mL bottle the next morning.
		+
		+	3. Shake at 37°C for 1.5-3hrs until OD600 = 0.4-0.8
		+
		+	Then….
		+	1. Put the cells on ice for 10 mins (keep cold form now on).
		+
		+	2. Collect the cells by centrifugation in the big centrifugue for 10 mins
		+	at 6krpm
		+
		+	3. Decant supernatant and gently resuspend on 10 mL cold 0.1M
		+	CaCl (cells are susceptible to mechanical disruption, so treat them
		+	nicely).
		+
		+	4. Incubate on ice x 20 mins
		+
		+	5. Centrifuge as in 2
		+
		+	6. Discard supernatant and gently resuspend on 5mL cold
		+	0.1MCaCl/15%Glycerol (from a 85% stock)
		+
		+	7. Dispense in microtubes (300μL/tube). Freeze in -80°C.
		+
		+	'''Source:'''
		+
		+	Adapted from
		+	http://www.med.nyu.edu/medicine/labs/blaserlab/Protocols/E-coli_competent_cells_protocol_&_transformation.pdf
		+
		+
		+	===LBamp Plates===
		+
		+	1. 500 ml LB agar and 500 μL amphicilin
		+	2. Pour on plates
		+	3. Leave with the lid half on for 30 minutes at room temperature
		+	4. Put in refrigerator until needed.
		+
		+	===Transformations===
		+
		+	'''Transformation of Ca++ competent cells'''
		+
		+	1. Put 10μL of circular plasmid or all of a ligation reaction of plasmid
		+	DNA in a microtube. Gently add ~50μL of competent cells.
		+
		+	2. Incubate for 30 mins on ice.
		+
		+	3. Heat shock for 45 seconds at 42°C. Put back on ice.
		+
		+	4. Plate the whole lot in LBamp plates
		+
		+	5. Leave the plates at 37°C O/N
	==Second Week==		==Second Week==

---

Revision as of 10:58, 27 June 2011

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Contents 1 Notebook 2 Protocols 2.1 Mutations 2.2 Competent Cells 2.3 LBamp Plates 2.4 Transformations 3 Second Week 4 Third Week 5 Fourth Week

Notebook

Protocols

Mutations

Ingredients

Site directed mutagenesis of 3 plant CYP450 (79A1, 79A2, 79B1).

We aim to destroy restrictionenzymes recognitionsites.

Primers was supplied by ...........

10 μl of 5× reaction buffer

X μl (50 ng) of dsDNA template

X μl (125 ng) of oligonucleotide primer #1

X μl (125 ng) of oligonucleotide primer #2

1 μl of dNTP mix

ddH2O to a final volume of 50 μl

Then add

1 μl of PfuTurbo DNA polymerase (2.5 U/μl)

Poly Chain Reaction

We ran a PCR to syntesise and amplify our mutated CYP's.

Cycling Parameters for the QuikChange Site-Directed Mutagenesis Method

Segment 1

Cycles 1 Temperature 95°C Time 30 seconds

Segment 2

Cycles 12

Temperature 95°C Time 30 seconds

Temperature 55°C Time 1 minute

Temperature 68°C Time 1 minute/kb of plasmid length

Digestion

We aim to remove the parentel CYP.

We take advantage of the fact that this CYP is methylated on cytosines. Dpn is a restriction enzyme that cuts DNA which is methylated - therefore our new mutated CYPs remain untouched.

1. Add 1 μl of the Dpn I restriction enzyme (10 U/μl) directly to each amplification reaction.

2. Gently and thoroughly mix each reaction mixture by pipetting the solution up and down several times. Spin down the reaction mixtures in a microcentrifuge for 1 minute and immediately incubate each reaction at 37°C (in a heater with lid or in a 37°C room) for 1 hour to digest the parental (i.e., the nonmutated) supercoiled dsDNA.

Source

Adapted from QuikChange™ Site-Directed Mutagenesis Kit INSTRUCTION MANUAL

Competent Cells

E. coli Calcium Chloride competent cell protocol

1. Inoculate a single colony into 5mL Lb in 15mL falcon tube. Grow O/N at 37°C.

2. Use 1mL to inoculate 100mL of LB in 250mL bottle the next morning.

3. Shake at 37°C for 1.5-3hrs until OD600 = 0.4-0.8

Then…. 1. Put the cells on ice for 10 mins (keep cold form now on).

2. Collect the cells by centrifugation in the big centrifugue for 10 mins at 6krpm

3. Decant supernatant and gently resuspend on 10 mL cold 0.1M CaCl (cells are susceptible to mechanical disruption, so treat them nicely).

4. Incubate on ice x 20 mins

5. Centrifuge as in 2

6. Discard supernatant and gently resuspend on 5mL cold 0.1MCaCl/15%Glycerol (from a 85% stock)

7. Dispense in microtubes (300μL/tube). Freeze in -80°C.

Source:

Adapted from http://www.med.nyu.edu/medicine/labs/blaserlab/Protocols/E-coli_competent_cells_protocol_&_transformation.pdf

LBamp Plates

1. 500 ml LB agar and 500 μL amphicilin 2. Pour on plates 3. Leave with the lid half on for 30 minutes at room temperature 4. Put in refrigerator until needed.

Transformations

Transformation of Ca++ competent cells

1. Put 10μL of circular plasmid or all of a ligation reaction of plasmid DNA in a microtube. Gently add ~50μL of competent cells.

2. Incubate for 30 mins on ice.

3. Heat shock for 45 seconds at 42°C. Put back on ice.

4. Plate the whole lot in LBamp plates

5. Leave the plates at 37°C O/N

Second Week

Third Week

Fourth Week

You should make use of the calendar feature on the wiki and start a lab notebook. This may be looked at by the judges to see how your work progressed throughout the summer. It is a very useful organizational tool as well.