Abstract: A method of detecting a pathogen uses a 3D nanochannel device having top and bottom chambers, and a plurality of nanochannels. The method also includes functionalizing a nanochannel by coupling an oligonucleotide probe to an inner surface thereof. The method further includes adding a lysis buffer and patient sample to the top chamber. Moreover, the method includes extracting an oligonucleotide from the patient sample. In addition, the method includes placing top and bottom electrodes in the top and bottom chambers respectively and applying an electrophoretic bias therethrough. The method also includes applying a selection bias across first and second gating nanoelectrodes to direct flow of the oligonucleotide through the nanochannel. Moreover, the method includes applying a sensing bias through a sensing nanoelectrode. In addition, the method includes detecting an output current from the sensing nanoelectrode, and analyzing the output current from the sensing nanoelectrode to detect the oligonucleotide.