Problem analyzing polymer/DNA conjugates

Daniel Käsmayr daniel.kaesmayr at
Tue Jan 17 06:33:14 EST 2006

Dear folks,

I would like to ask for some advice or just some crazy ideas:

I am in the process of creating polymer-DNA-conjugates. The polymers
are multifunctional and should be coupled to 10+ single strand DNA
oligos, either via peptide bond or thiol/maleimide reactions. My major
problem is the purification/analytic of the conjugates as their
structure is highly branched (the polymers are either linear -
creating brush type conjugates - or star shaped - creating dendronized
conjugates). It seems there are two major problems:

a) detecting bands is very difficult as EtBr will not really stain
single stranded DNA as well. SybrGold is better, but:
b) the polymers and their conjugates do not behave as expected in a
SDS-PAGE - they do not penetrate the gel at all or just barely scratch
the gel at the pockets. It seems that there are some species migrating
in 3% AA gels - but as you all know these are a pain to handle and

Does anyone out there have an idea which method might be useful to
solve this problem?



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