Gene expression depends on epigenetic factors, which can be influenced by the polymer dynamics of DNA. To observe these nanoscale dynamics despite the limited resolution of video light microscopy, we are developing a method to magnify them mechanically. Our approach involves creating a nanoscale instrument called a “DNA nunchuck:” a pair of DNA nanotubes that are connected by a dsDNA linker, so that the bending of the linker at any given time can be magnified by the orientations of the nanotubes. Because the nanotubes are densely labeled with fluorophores, the changes in their orientations can be observed by video fluorescence microscopy, allowing conclusions to be drawn about the dynamic behavior of the linker strand. The original nunchuck design consisted of two DNA nanotubes labeled with identical fluorophores, but to distinguish the two “arms” of the nunchuck, later designs utilized nanotubes labeled with dissimilar fluorophores. However, neither labeling scheme allowed the arms to be distinguished during dynamic imaging, because only one wavelength of light can be observed in each frame of video. To solve this problem, we designed nunchucks where one arm contained twice as many Cy3 fluorophores as the other, allowing them to be distinguished by fluorescence intensity. The placement of these additional flurophores, however, interfered with nanotube formation, resulting in a mere 7% yield of two-toned nunchucks. Here, we describe how we increased this yield to 19% by lowering the temperature of nanotube formation by one degree Celsius, and demonstrate their potential utility in the study of DNA dynamics.