crosslinking DNA to its binding protein invitro

[Yuval Ebenstein]

Hi Again,
I've been working on this since my last post on the matter in October...
I'm trying to chemically crosslink the CAP (or CRP) DNA binding protein 
to a genomic fragment containing the binding site.
Gel shift confirms I have specific binding and a heparin challenge 
breaks the complex.
An extensive literature search yielded only invivo methods for chemical 
crosslinking, usually for CHIP by incubating with 1% formaldehyde.
However, doing the same invitro, and going up to 5% formaldehyde did not 
give me a complex that survived the heparin so i guess it is not 
crosslinked.
I might be doing something fundamentally wrong (there are no primary 
amines in my samples) or the efficiency is too low to detect in my case. 
I find it hard to believe that there are no protocols for this but I 
haven't found any. Anyway, i'm stuck!
Any help will be greatly appreciated
Cheers
Yuval

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Yuval Ebenstein
Department of Chemistry and Biochemistry, UCLA
Young Hall-2002, 607 Charles E. Young Drive East
Los Angeles, CA 90095-1569
Ph: (310) 794-6685; Fax: (310) 267-4672