In addition to being a high-resolution negative-tone electron beam resist, hydrogen silsesquioxane (HSQ) has chemical properties similar to glass, making it useful for integration with biodevice fabrication. The authors demonstrate the use of electron beam patterned HSQ as a solid support for light-directed in situ ssDNA synthesis and ssDNA immobilization, creating submicron HSQ structures (ranging from 1 mu m to 40 nm) that are functionalized with ssDNA. After ssDNA synthesis, the hybridization of Cy-3 labeled complementary strands reveals that the synthesis is indeed localized to the HSQ. They observed relatively low background fluorescence from the supporting silicon substrate or from HSQ where no DNA synthesis was performed. In the course of the experiment they surveyed several materials as support for the HSQ patterning. In addition, the support substrate must be resistant to DNA synthesis. They found that piranha cleaned silicon, glassy carbon, hydrogen plasma treated glassy carbon, and hexamethyldisilazane primed silicon allow little or no synthesis when examined by hybridization with fluorescent labeled complement DNA. This work is relevant to the fabrication of devices that may require submicron patterns of structures functionalized with ssDNA for hybridization assays or DNA self-assembly applications and demonstrates a novel use of a commonly used negative-tone resist.