Metrology of DNA arrays by super-resolution microscopy

Summary form only given, as follows. To counter the rising costs and challenges of semiconductor device scaling, new bottom-up patterning techniques are sought to supplement or replace current top-down lithography techniques. DNA-based techniques such as origami, tiles, and bricks have demonstrated precise control of the size and shape of self-assembled nanostructures, and recent advances in structural DNA nanotechnology have demonstrated the potential for sub-10 nm lithographic patterning with DNA. Beyond the capability for nanoscale patterning, metrology of patterned structures is a crucial capability that poses increasing challenges as the scale of structures decreases. Common high resolution imaging techniques used for DNA nanostructures, such as AFM and TEM, cannot accommodate high throughput characterization. Super-resolution microscopy is being actively developed for biological and DNA-based imaging and is compatible with inline optical metrology techniques for high volume manufacturing. Here, we report a two-step super-resolution methodology for characterizing the periodic structure and quality of 2D DNA origami arrays as proof-of-principle of the ability to incorporate optical defect metrology with DNA-based patterning. Through the integration of DNA-PAINT docking sites with sticky-end hybridization strands6, we demonstrate state-dependent docking sites (defect labels) that deactivate when bound in an array, enabling the acquisition of information on the state of each tile arm in parallel with spatial information. In combination with docking sites near the center of individual structures, ‘crystal-PAINT’ enables step-wise7 characterization of the crystalline structure of arrays and single defect metrology. Using this method, we successfully super-resolved cross-shaped DNA origami tile arrays8 assembled by sticky-end hybridization, identified grain boundaries between individual arrays, and utilized statistical methods to quantify the dimensions and size distribution of tile arrays. With further development in imaging processing, this technique will provide high throughput characterization of self-assembled DNA nanostructures for large-scale origami arrays.