I'm trying to determine Kd values for protein:RNA binding using tryptophan fluorescence.
Buffer:
10mM HEPES (pH 7.5)
100mM NaCL
4mM MgCl2
1mM TCEP
[protein] = 0.25uM; RNA is titrated in 0 - 4uM.
Instruments used:
-Perkin Elmer LS 55
-Varian Cary Eclipse
Fluoresence quenching data is corrected for the inner filter effect ad fit to a quadratic equation.
Problem:
Im measuring Kd's in the nM range for my protein:RNA complex, but when I titrate RNA into BSA or lysozyme as negative controls, I also measure nM Kds. Same goes for my protein:poly-dIdC.
This is very confusing. Why would I be measuring such tight binding amongst molecules that should have no specific binding?
I've increased [NaCl] to 250 nM (to reduce non-specific binding), conducted the experiment in 25% glycerol (to reduce collisional quenching), neither have alleviated the issue.
Can anyone provide rationale for my results and suggest experiment to separate the specific vs. non-specific interactions that may be leading to my results?
thanks.
