Detection of target-probe oligonucleotide hybridization using synthetic nanopore resistive pulse sensing

Despite the plethora of DNA sensor platforms available, a portable, sensitive, selective and economic sensor able to rival current fluorescence-based techniques would find use in many applications. In this research, probe oligonucleotide-grafted particles are used to detect target DNA in solution through a resistive pulse nanopore detection technique. Using carbodiimide chemistry, functionalised probe DNA strands are attached to carboxylated dextran-based magnetic particles. Subsequent incubation with complementary target DNA yields a change in surface properties as the two DNA strands hybridize. Particle-by-particle analysis with resistive pulse sensing is performed to detect these changes. A variable pressure method allows identification of changes in the surface charge of particles. As proof-of-principle, we demonstrate that target hybridization is selectively detected at micromolar concentrations (nanomoles of target) using resistive pulse sensing, confirmed by fluorescence and phase analysis light scattering as complementary techniques. The advantages, feasibility and limitations of using resistive pulse sensing for sample analysis are discussed.

► We describe a novel method using resistive pulse sensing to selectively detect short target DNAs.► Discrimination of probe DNA-grafted particles and particles after incubation with target DNA. ► To our knowledge we report the first use of the variable pressure method for target DNA detection. ► Changes in surface charge upon hybridization allow identification of particle groups. ► Complementary techniques, zeta potential and fluorescence are used to confirm expected results.