A biochemical DNA nanoscopethat identifies and localizes over a hundred unique features with nanometer accuracy

Techniques that can spatially localize molecular-scale features while discriminating between many targets would be highly valued in studying nanoscale processes. Here, we present a biochemical DNA nanoscope, an ‘imaging by sequencing’ technique that begins by labeling points with unique barcoded primers. The primers are extended and meet in random pairs, such that the length of the intervening sequence encodes the distance between primers. The records are then identified with massively parallel next-gen sequencing using the MinION (Oxford Nanopore Technologies). Finally, the obtained reads are demultiplexed and the pattern is algorithmically reconstructed by minimizing the total error between measured and reconstructed distances. This enables unique, “full color” identification of every feature on a DNA origami testbed with ~ 2 nm average accuracy (RMS deviation), thus combining state-of-the-art accuracy (e.g, EM, SRM, and AFM) with the ability to label and identify 100 or more targets. We demonstrate the technique on many geometries in an ensemble manner, with many copies of the same origami structure.

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