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Annealing palindromic linkers

Peter Ashby p.r.ashby at dundee.MAPS.ac.uk
Tue Jan 16 10:57:18 EST 2001

In article <3a63fb84$1 at news.unibe.ch>, "Bruno Cenni" 
<bruno.removethis.cenni at removethis.insel.ch> wrote:

> Hi all,
> we're (expectedly) having troubles cloning a linker into a plasmid. This
> linker consists of two complementary 33 bp oligos that after annealing 
> have
> open restriction enzyme sites at their ends. The problems comes probably
> from the fact that the oligos contain two complementary inverted 6 bp
> recognition sites thus giving a palindrome (spaced by 3 bp). Any 
> suggestions
> on conditions to increase the proper annealing of the oligos without too
> much of the self-annealing and stem-loop formation?

Are your oligos phosphorylated? it makes quite a difference when doing 
this and I would suspect that before assuming your oligos haven't 
annealed. A cheap way to achieve this is to make your oligos overlapping 
and then cut them after annealing.


Peter Ashby
Wellcome Trust Biocentre
University of Dundee
Dundee, Scotland
Reverse the spam and remove to email me.

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