I observed exactly the opposite, PS beads binding to glass rather than
PDMS.  I was told that the beads would bind preferentially to a
hydrophilic surface.  Go figure.

If its purely increasing the hydrophilicity of the PDMS that you're  after.
Either 1. Try running buffer through asap after bonding to the glass
and  keeping it running though until you do your experiments    or
2. Running a reasonably strong ionic solution (NaOH has been
recommended) through the channels BRIEFLY before you do your
experiment.  Strong NaOH will turn your channels opaque if run through
for too long (no idea of time, just info from a colleagues
observations).

The idea is that PDMS' hydrophobicity is changeable and if a polar
solution is in contact with the PDMS then the surface properties of
PDMS will change.  I have observed this myself, but have not
quantified so unfortunately cannot give more of a hint.

Oh one other way is to treat the PDMS with a polar group terminated
silane.  If reacted with rather than adsorbed onto the surface, the
silane should be relatively permanent (though it may still exhibit
some transient decrease in polarity as it 'folds' back into the bulk).

Sorry I couldn't be more specific, but hope this helps.

Dr Matt Davies
Research Assistant
Science & Technology Research Institute
University of Hertfordshire
College Lane
HATFIELD        AL10 9AB
UK

e : m.davies@herts.ac.uk