We used AGE analysis to monitor origami denaturation at specific temperatures using the following as signals: (i) the release of the Cy5-labeled staple 1, which migrates below the 0.5 kb dsDNA marker; (ii) the decrease of the Cy5 signal in the origami; and (iii) the conversion of the origami into the faster migrating ssDNA scaffold. Where appropriate, AGE analysis was supported by TEM imaging of the heat-treated nanostructures.