Stanford/BIOE44:Module 5:Day3

M5: Day 2 - Continue Building

Freezer Stocks of Synthesized Parts

Materials

• 5mL overnight culture
• sterile 60% glycerol
• 3 cryovials, labelled

Procedure

1. Label your cryovials: part name, plasmid, date, your initials.
2. Add 500ul of sterile 60% glycerol to each of your cryovials.
3. Add 1.5mL of overnight culture to each cryovial. (Its easiest to use a 5ml pipette, take up 4.5mL of culture then drop 1.5mL into each tube)
4. Invert tubes several times to mix.
5. Put in freezer box in -80C freezer. (Usually one tube is kept as the working stock and the other two are kept as back ups in a separate freezer.)

PCR amplifying your parts

Your primers have arrived! This is the packing list that comes with the primers when they are delievered. It has a lot of useful information.

We will use this polymerase: Pfx50 DNA polyermase It is higher fidelity than TAQ (which means it makes less mistakes).

PCR mix (taken from Pfx50 manual)

Component	Volume	Final Conc.
10X Pfx50 buffer	5ul	1X
10mM dNTPs	1.5ul	300uM
fwd primer		300nM
rev primer		300nM
Template		1-100pg
Pfx50 polymerase	1ul
Water
Total volume	50ul

PCR Protocol (taken from Pfx50 manual)

Cycles	Temp	Time
1x	94C	2 min
35x	94C	15s
	60-68C (Tm primers - 2C)	30s
	68C	30s per kb
1x	68C	5 min
1x	15C	forever

I0500 troubleshooting

I0500 gel

When I0500 (in pSB2K3) is digested with EcoRI & PstI a large smear is produced. When the same construct is digested with SpeI & PstI, a smear, albeit smaller, is also produced.

Smears are caused by a whole bunch of pieces of DNA that are only slightly different in size. This can be caused by degradation of DNA products. Multiple people have had this happen when they digested this vector. What could be happening? Why would digestion with different enzymes change the smear?

Troubleshooting ideas

1. Run uncut and single cut plasmids to see if there is even an intact plasmid.
2. Try inoculating I0500 from different sources in case the source has been contaminated.