You should add some salt when you anneal!!!
The duplex is highly negatively charged, so adding even a
small amount (like 10mM NaCl) will help with charge
screening, thus making the two strands less repellant to
each other. Buffer is also always a good idea. At low pH
and high temp you'll hydrolyze the glycosidic bonds of your
purines.
Also, depending on how you purified the DNA after synthesis,
the white precipitate may well be other crud - protecting
groups, etc. Did you desalt it at least?
DNA should be very highly soluble, so your complex protocol
should depend mostly on the protein's personality. If it is
also highly soluble, just mix them.
Finally, if you try crystallization with each possible
duplex one at a time, you'll be a post-doc for a very long
time. We usually try at least a half-dozen at a time (with
varying ends), and it usually takes several different
crystal forms to get one that diffracts decently.
Good luck!
Phoebe
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
RNA is really nifty
DNA is over fifty
We have put them
both in one book
Please do take a
really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp
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