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An electrochemical assay for single nucleotide polymorphisms (SNPs) genotyping is reported. Although electrochemical method is sensitive for DNA detection on surfaces, the ability of surface assay to precisely recognize DNA hybridization event is sacrificed to some extent due to the crowded confined surfaces environments that disfavor DNA hybridization. In the present study, we employed branched tetrahedron structure probes (TSPs) to replace regular linear single stranded DNA capture probes that were immobilized on solid surfaces. This three-dimensional DNA nanostructure lowers the density of immobilized DNA probes on confined surfaces, providing a hybridization environment that is similar to homogenous solution. This TSP-based electrochemical assay reveals excellent performance for SNPs genotyping with concentration as low as 1 nM.