(by shifalich from rediffmail.com)
Sat Oct 10 09:56:18 EST 2009
The following info was quite useful for me too.
We can't find such details anywhere!!!!
Few months back, I was trying to use pfu but my PCRs did n't work, so I gave up after 2-3 trials. Now, I'll using thse tips.
On Sat, 10 Oct 2009 03:29:11 +0530 wrote
>In article , monika singh wrote:
>i am doing site directed mutagenesis for single amino acid change .i have
>used both stratagene as well as phusion kit but i didnot get the mutation .
>i have also found out that the melting temp. of primers which i am using is
>between 60 to 65 degrees. But according to stratagene primer guidelines it
>should be greater than or equals to 78 degrres. So, this could be the
>possibility of not working of my mutation. also,i have used top 10 cells
>ultra comp cells for transformation. i get the colonies also but it was not
>positive. so, suggest me regarding com cells, pcr conditions ,dpn1 digestion
>so that i can get result
Without doing all kind of controls, you can't know where the problem is.
The calculation of primers melting temperature is somewhat of a joke
as it can vary over 10 degrees in either direction depending on the
program you use. Competent cells have nothing to with it as long as
you do get colonies.
Below is a protocol that I wrote for our lab internal use long ago.
It practically never fails. We've done all kind of mutagenesis with
it, deletions of >1 kbp and insertions of up to 36 bp.
Although the regular QuickChange works, it does not always work
well enough. There are several advantages to the new protocol:
- twice less money spent on primers;
- twice less polymerase is used;
- polymerase with lower error rate is used.
Here is a generic protocol followed by notes and comments that might
Reaction mix (25 ul final)
50 ng template
0.2 uM final single primer
0.2 mM final dNTP mix
2.5 ul 10X Stratagene's PfuUltra II Fusion ("Pfu Fusion" for brevity) buffer
1.0 ul DMSO (or no DMSO)
water to 24.5 ml
0.5 ml of Pfu Fusion
95� 3 min, then 30 cycles:
95� 30 sec
55� 1 min
65� 1 min/kbp template
65� 5 min
- Dpn I treatment and transformation:
Use Fermentas "Quick Digest" DpnI - it is simply a more concentrated
version of the enzyme and it costs the same as regular version. Add
10 ul of the amplification reaction to 0.5 ul DpnI, incubate for 2 hours
in PCR machine at 37�. During incubation, at least once remove the
tube and vortex/spin it again, then continue incubation.
- Electroporate using 1-2 ul of the DpnI-treated reaction, immediately
add 0.5-1 ml SOC, let cells recover for 45 min at 37�, plate 200 and
20 ml (recovery is not absolutely necessary but it does seem to increase
efficiency somewhat). The typical result is several-fold less colonies
than in a "standard" QuickChange reaction, and the efficiency in the
50-90% range. I.e., screen 5-6 clones to be sure to get right one no
NOTES AND COMMENTS
(in no particular order; I am just mentioning everything that I can think
of being worth consideration)
Ideally, it should be a fresh, never frozen miniprep. Freeze/thaw
produces nicks in the plasmid and nicks are killers to the whole
plasmid amplification. It also helps for it to bew "clean" so that
UV measures concentration of the plasmid and not just nucleic
acids with RNA being a major contaminant.
2. The Pfu Fusion polymerase is a new product that is slightly less
expensive than any of the other polymerases we use. It works ~ 4
times faster, makes a bit less errors than Pfu Ultra and its
reaction buffer has pH of ~ 10.0.
3. The method requires only one primer - just write down the
sequence of the sense strand! It's been found in numerous
trials by that desalted primers from IDT work as well as purified
4. Primer design. Keep primer length between 40 and 60 bp.
Try not to exceed 60 bp because above that size IDT forces you
to order 100 nmol scale with the corresponding price increase.
Ideally, you'd want 15-25 bp on either side of the mismatch,
approximately equal melting temperature (TM) for both "arms" of
the primer (but the "right arm", e.g. 3' part, is more significant because
that's where synthesis starts; try to end it with a couple of G/Cs).
The overall primer TM (not counting the mismatched pairs) should
be in the range of 60-70�C (as calculated by IDT's Oligo Analyzer
with default settings). As an example, the most recent primer that
worked 100% to delete 6 bases: Left arm 27 bp/51.1�, right arm
19 bp/53.4�, overall 46 bp/63.8� and it worked with 55� annealing.
5. In linear amplification applications (sequencing, QuikChange),
the larger number of cycles gives better results. 30X has been tried
and works very well. To be sure, 20X also works, although it was
not compared to 30X side by side.
6. Amount of template. The stated 50 ng is simply lifted from what
we find a near optimum for the standard QuickChanges, 100 ng/50 ul,
and was not tested experimentally. In practice, simply using 0.5-2 ul
minipreps (depending on culture volume and on plasmid copy number)
works fine. In theory, advantages of higher template concentration are:
i) more product with less number of cycles, ii) higher chance of priming
when annealing is suboptimal. The theoretical disadvantages of having
too much of the template are: i) introducing more crap into reaction,
some of which might be inhibitory (minipreprs are not clean!), ii) increased
background if the Dpn I treatment is incomplete, iii) increase in the
misprimed side reactions. There is an optimal balance between all
of these factors somewhere... Other things being equal, the best practice
is to have as clean template as possible and that means:
i) don't be greedy with your minipreps; for high copy number plasmids,
1 ml culture is usually sufficient, 3 ml is a lot and more than 3 ml
borders on insanity; ii) use PB solution volume so that it covers
all areas of the column that were in contact with cell lysate; iii) use PE
solution volume so that it covers all areas of the column that were in
contact with PB, and use PE wash TWICE.
7. Annealing temperature. Pfu Fusion seems to be less finicky in terms
of annealing conditions. 2-10 degrees below calculated primer TM have
been found to work in various cases. 55� should work in the vast majority
8. DMSO concentration. DMSO is optional as it rarely makes all or none
difference. Its main effect on the reaction is two-fold: it decreases melting
temperature of DNA duplexes and it reduces primers' secondary structure.
The protocol above uses 4% final. You may also try 0 and 6% as a substitute
to an annealing temperature variance (make sure to mix DMSO well with
other components before adding polymerase).
9. Extension time. Pfu Fusion is quite fast. The default is 60 sec per kbp
at 65�C and it definitely works. Tried alternative is 30 sec at 68�C and,
for sure, it also works. However, in "QuikChange cloning" trials we found
that 65� gives more colonies (perhaps because of the some strand
displacement activity at 68�).
10. Other things that may sometimes be beneficial. Increased concentration
of the primer two-fold, increased concentration of dNTPs two-fold, an
extra 2 mM MgCl2 in the reaction all, in theory, have an effect of increasing
product yield with concomitant slight increase in the error rate (not a big
deal given the error rate of Pfu Fusion).
11. Just like regular QuickChange, the single stranded QuickChange works
for two mutations simultaneously but with reduced efficiency. Make primers
so that they have similar TMs and expect 20-30% of the clones to be double
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