Blunt end Ligation

Martin Kennedy mkennedy at
Sat Mar 19 04:24:38 EST 1994

In article <9403151925.AA13581 at>, anjali at writes:
> I have a 11.2 kb plasmid which has a 1.8 kb luciferase gene as the reporter.
> I want to delete a 2.1 kb fragment from this plasmid (which is not a part
> of the reporter) which is released as a Xho1-Nde1 fragment. The resulting
> backbone of 9.1 kb was run on an agarose gel and purified. The ends were 
> end filled using Klenow(confirmed by adding radioactivity in the reaction)
> and then blunt end ligated. I got about 100-150 transformants (when transformed
> in DH5a). On doing a colony hyb. with luciferase only 7 transformants picked
> up. These transformants did not pick with the deleted 2.1 kb fragment.
> What are the rest of the transformants? 
> The restriction pattern of these "positives" is absolutely weird. I'm not
> even getting the right size on linearization which should be 9.1 kb instead
> it is giving a band in the 5-6 kb region.
> Can anybody tell me what is the problem? And also suggest me modified 
> protocols which should be followed at any step?
> Anjali.


I don't know what your problem is, but when I do this kind of deletion I always
fill the ends before running on a gel (Klenow is very sensitive to agarose
contaminants) - just add dNTPs and Klenow for 20 minutes before you run your
reaction products.  It works much better, and I wouldn't bother with the
isotope.  The other modification you ought to try is to heat kill the ligase
and treat the ligation mix with XhoI or NdeI, or both, before transforming.  I
usually make the ligation up to 100ul with RE buffer, cut, then transform about
10% of it.  Alternatively, just add one of the restriction enzymes into your
ligation.  This way you ought to get 100% genuine deletion derivatives.


NNNN   NN  Martin A Kennedy (E-mail = mkennedy at  ZZZZZZZ  
NN NN  NN       Cytogenetic and Molecular Oncology Unit          ZZZ
NN  NN NN           Christchurch School of Medicine            ZZZ
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