| | Re: Strange results
the mutant oligos, do they have mutations in them or are they the same as the E.coli sequence?
Also you are use 500X the amount of polydidC, which is quite high however should only have a small effect on your binding.
Your protein may be recognizing the cold competitor, or may not be as specific as you thought. Either that, or you may be misrepresenting the cold competitor in several ways:
1) have you compensated for the additional volume? Increased volume decreases the concentration of binding protein and sequence, thus decreasing the frequency of binding
2) have you checked that the cold-competitor/dIdC does not have DNase, or other inhibitory substances such as salts etc that may be inhibiting your reaction?
3) also you may be affecting the pH adding the cold competitor etc
There are many possibilities. have you narrowed it down?