Inhibition of DNA helicase activity determined by SPR

The consequence of small molecule/DNA substrate interaction on the ability of DNA‐processing helicases to function effectively was investigated using surface plasmon resonance (SPR). Several different DNA targets, including various quadruplex‐forming oligonucleotides, were immobilized on SPR sensor chips and kinetics for small molecule/DNA substrate interactions were determined prior to investigation of the effect on DNA helicase activity. SPR is a real‐time measurement and subtle effects related to the difference between duplex DNA unwinding and quadruplex DNA unwinding with the model helicase SV40 large T‐antigen were apparent. In particular, inhibition of quadruplex DNA unwinding was more sensitive to the SPR conditions utilized for observing helicase activity. This may be due to the greater efficiency of T‐ag quadruplex helicase activity in comparison to duplex helicase activity or it may reflect differences in the small molecule/quadruplex DNA interaction. To the extent that the in vivo significance of quadruplex DNA formation is driven by kinetic factors, these results are relevant for determining effective strategies for associated helicase modulation.