[RASMB] Protein binding to polymer ( poly(A)-RNA )

[Christoph Brockmann]

Hi Everybody,

I got myself into an interesting problem in that I am trying to 
characterize the binding of a small protein domain to poly(A)-RNA. I am 
getting fairly descent data for defined length RNA oligos using ITC, but 
have serious problems fitting this data to the usual models. It fits, 
but the stoichiometries (although clearly dependend on the polymer 
length) don't make a lot of sense to me.

Is there an established theory that can be used to describe binding 
events with multiple similar binding modes? Since we don't know the 
exact optimal length of the RNA, we are almost certainly using RNAs that 
are either too long or too short, giving rise to multiple register 
binding either way.

Any help would be very much appreciated.

many thanks,
Christoph