I have been trying to do a site directed mutagenesis for single aminoacide change, using QuickChange II Site Directed Mutagenesis Kit.
I have designed my primers using QuickChange Tool. The Tm of the primer is 86 celcius degrees and GC content is %62.5.
I made the following PCR reaction:
2,5ul 10x reaction buffer
25ng DNA template
125ng forward primer
125ng reverse primer
0,5ul 10mM dNTP mix
0.75 ul DMSO
0.5ul Pfu ultra polymerase
dH20
Total reaction volume: 25ul
I then set PCR machine at these conditions and cycled 16 times.:
95 C, 30 secs
95 C, 30 secs
55 C, 1 min
68 C, 7 min (for a 6.5 kb plasmid)
I did the PCR reaction and ran the gel and got a band on the right size.
I then add 0.5ul DpnI and incubate at 37 degree for 1 hour. When I ran the gel after DpnI digestion, I saw no band.
Even I couldn' t see the band after DpnI digestion, I did PCR clean up using a kit.
After PCR clean up, I followed the protocol and did the transformation using DH5a competent cells.
My transformation protocol is:
- Aliquot 40µl of DH5a cells for each transformation into 1.5ml tubes that have been pre-chilled on ice
-Add PCR clean up product to DH5a cells and mix gently
-Incubate the tube on ice for 30 minutes
-Heat shock at 42°C for exactly 45 seconds
-Place tubes on ice for 1:30 minutes
-Add 250µl of pre-warmed (37°C) LB Broth
- Shake at 37°C for 1 hour
-Spread 200µl of each transformation onto LB plates with appropriate
antibiotic
-Allow plates to dry and incubate inverted at 37°C overnight
Result: I got no colonies!
I have been repeating this for the past 2 weeks and getting nothing.
The PCR seems to have worked well. I tried to transform my pre DpnI digested PCR product and got a lot of colonies.
I couldn' t get any colonies after the transformation of post DpnI digested PCR product.
Please, could anyone see where the problem is?
Thanks for any suggestions!
-Didem