Binding response measurements were corrected for non-specific control chip responses used to determine equilibrium and kinetic binding parameters, using Biacore Biaevaluation software.
Light emission was recorded as mean arbitrary light units/cycle over 60 min. SPR data were analysed using the curve fitting software Origin 7.0 (OriginLab Corporation, Northampton, MA, USA) and Biaevaluation software to determine the k on and k off rate constants and binding parameters, using both first and second order kinetic models.
The interaction mechanism was predicted through molecular modeling first, then the binding parameters were confirmed using a series of spectroscopic methods, including fluorescence spectroscopy, UV visible absorbance spectroscopy, circular dichroism (CD) spectroscopy and Fourier transform infrared (FT-IR) spectroscopy.
Overall, the binding parameters inferred using QPMEME systematically indicated less drift than the parameters inferred using the weight matrix, with the best overall performance when the SELEX data set was used to train the algorithm.
Data were analysed and binding parameters calculated using the supplied software.
For the large-scale radial flow capsule, the CFD model quantitatively predicts breakthrough data using binding parameters independently determined using the small-scale axial flow capsule, identifying structural irregularities within the membrane pleats as an important source of band broadening.
Δ S° is the standard change in entropy upon binding was calculated from determined equilibrium parameters using the equation: − RTLn KA)=Δ G°=Δ H° − TΔ S°, where R is the universal gas constant (1.9872 cal·mol−1·K−1), T is the temperature in Kelvin, KA is the association constant.
Nucleotide binding was measured using a standard filter-binding assay.
To test this hypothesis, we compared the DNA binding parameters of doxorubicin and doxorubicinol using a binding displacement assay described in Methods.
