Single-stranded DNA (ssDNA) can be designed to assemble into duplexes and other high-order structures through Watson-Crick hydrogen bonds. Incorporation of unnatural nucleobases or binding with small molecules can also introduce new interactions that give rise to novel DNA assemblies. However, the methods for determining the conformational properties of DNA assemblies are still very limited. Here we develop a new strategy for probing conformational polymorphism of different DNA assemblies. By installing poly(dC)30 tails to the ends of individual ssDNA that assemble into duplex, triplex, or other complex structures, we are able to observe different current blockade patterns corresponding to specific DNA nanostructures when the DNA assemblies are lodged inside α-hemolysin vestibule. We can also monitor the disassembly of the DNA nanostructures in solution. This method complements the existing traditional technologies such as circular dichroism spectroscopy, fluorescence labeling, and NMR spectroscopy, and shows distinct advantages of high accuracy and general applicability.