Determining the binding mode and binding affinity constant of tyrosine kinase inhibitor PD153035 to DNA using optical tweezers

Research highlights: → PD153035 is a DNA intercalator and intercalation occurs only under very low salt concentration. → The minimum distance between adjacent bound PD153035 ∼ 11 bp. → Binding affinity constant for PD153035 is 1.18(±0.09) x 104 (1/M). → The change of binding free energy of PD153035-DNA interaction is -5.49 kcal mol-1 at 23 ± 0.5 oC. -- Abstract: Accurately predicting binding affinity constant (KA) is highly required to determine the binding energetics of the driving forces in drug-DNA interactions. Recently, PD153035, brominated anilinoquinazoline, has been reported to be not only a highly selective inhibitor of epidermal growth factor receptor but also a DNA intercalator. Here, we use a dual-trap optical tweezers to determining KA for PD153035, where KA is determined from the changes in B-form contour length (L) of PD153035-DNA complex. Here, L is fitted using a modified wormlike chain model. We found that a noticeable increment in L in 1 mM sodium cacodylate was exhibited. Furthermore, our results showed that KA = 1.18(±0.09) x 104 (1/M) at 23 ± 0.5 oC and the minimum distance between adjacent bound PD153035 ∼ 11 bp. We anticipate that by using this approach we can determine the complete thermodynamic profiles due to the presence of DNA intercalators.