I've been trying to double mutate (2 base pair mutation to insert ECOR1 site on my plasmid) on my template DNA using quikchange, I've designed my primers and they have 39 % GC content. The protocol I've been using is as follows for a 25μl reaction volume:
Primer F ACA-TCA-TGT-CTT-ATA-CGA-ATT-CAT-CTT-GGA-AAG-TCC-TCT-CCAC
19.4 n.moles ,I added 194 ul ddH2O,then did 1:10 dilution 90 ul ddH2O and 10 ul stock
primer R GTG-GAG-AGG-ACT-TTC-CAA-GAT-GAA-TTC-GTA-TAA-GAA-GAC-ATG-ATGT
12.5 n.moles ,I added 125 ul ddH2O,then did 1:10 dilution 90 ul ddH2O and 10 ul stock
PCR reaction
2.5 μl DMSO (5% final conc)
2.5 μl 10X Pfu Reaction buffer
0.5 μl 10μM forward primer
0.5 μl 10μM reverse primer
4 ul of 10 ng/μl template DNA
1μl 10mM dNTPs
12 μl dddH2O
Add 0.5 μl Pfu turbo polymerase
PCR cycle
95°C for 1 minute (*1)
95°C for 50 second
58°C for 50 second
68°C for 1min/kb (6.34 minutes)
18 cycles
68 degree 6.5 minutes
hold at 4 degree
added 0.5 ul DPN1 and
Incubated for 1 hour at 37°C
transformed into XL10 gold ultra competent cells and got lots of colonies and when i try to digest my sample with ECOR1 it doesn't cut , failed to mutate site
any ideas would be appreciated.