Attaching DNA to surfaces facilitates spatial organization and enables the advantages of surface chemistry to be combined with the well-understood rules governing DNA assembly, transcription and translation. Now, a team led by Friedrich Simmel at the Technical University of Munich, Germany, have developed a photocleavable-DNA-based resist that can be used for lithographic patterning and compartmentalized gene expression (Angew. Chem. Int. Ed.; 2018).

Credit: Wiley

The process involves attaching a DNA-based resist to a surface at one end via a biotinylated polyethylene glycol (PEG) linker. The DNA strand forms a hairpin loop containing a nitrophenyl moiety that can be cleaved by UV light or a beam of electrons, creating a site for ‘toe-hold-mediated’ strand exchange. A second complementary DNA strand can then be attached to this free site, thereby providing a route to selectively functionalize the surface with a cargo such as a fluorophore or gene. Using a mask to protect select areas of the surface from UV light enables spatial control over where the DNA-resist is cleaved and therefore where the surface is functionalized. By using multiple masks and controlling exposure times, Simmel and colleagues were able to fabricate surfaces functionalized with different cargos. This approach is a ‘positive-tone’ lithographic process, enabling functionalization of the surface in areas where the DNA is cleaved and avoiding the drawbacks of ‘negative-tone’ pattern transfer; for example, unwanted modification of the background.

To demonstrate the effectiveness of the DNA-resist the team replicated the expressionist oil painting ‘Tiger’ by Franz Marc. This was achieved by designing a mask that they then split into separate masks for red, green and blue. Patterning a functionalized surface with the three colour masks and subsequently attaching partner DNA strands conjugated with red, green and blue fluorophores gave rise to a fluorescence image of the Tiger painting (pictured, left). The team also showed that the approach could be used to fabricate spatially distributed genetic circuits. To do this they used their lithographic method to immobilize three different linear genes that each encoded a different fluorescent protein. Cell-free expression of the encoded proteins enabled the production of fluorescent protein gradients (pictured, right).