A DNA nanoscope via auto-cycling proximity recording

Abstract

Analysis of the spatial arrangement of molecular features enables the engineering of synthetic nanostructures and the understanding of natural ones. The ability to acquire a comprehensive set of pairwise proximities between components would satisfy an increasing interest in investigating individual macromolecules and their interactions, but current biochemical techniques detect only a single proximity partner per probe. Here, we present a biochemical DNA nanoscopy method that records nanostructure features in situ and in detail for later readout. Based on a conceptually novel auto-cycling proximity recording (APR) mechanism, it continuously and repeatedly produces proximity records of any nearby pairs of DNA-barcoded probes, at physiological temperature, without altering the probes themselves. We demonstrate the production of dozens of records per probe, decode the spatial arrangements of 7 unique probes in a homogeneous sample, and repeatedly sample the same probes in different states.

DNA Synthesis by Primer Exchange Reaction Cascades

“…Yin and co‐workers addressed this limitation by introducing primer exchange reaction (PER) cascades for the autonomous synthesis of DNA oligonucleotides of custom length and sequence composition . This synthetic protocol is based on the autocycling proximity recording (APR) mechanism and the toehold exchange reaction . A PER starts with the recognition and binding of a primer (primer a in Figure ) to its complement located on the 3′‐end of a catalytic hairpin molecule.…”

A DNA nanoscope that identifies and precisely localizes over a hundred unique molecular features with nanometer accuracy

“…At the other end of the spectrum, biochemical techniques like Hi-C can discriminate millions of DNA targets on chromosomes by sequencing them, however the contact densities currently obtainable from single nuclei Hi-C experiments preclude synthesizing this information into a structural model of the chromosome, while geometric models synthesized using data from ensemble Hi-C experiments have at best a local resolution of 5 kilobase pairs 6,7 . This fledgling, 'imaging-by-sequencing' field [8][9][10][11][12] has had two main experimental results. Our previous 'auto-cycling proximity recording' (APR) 8 effort demonstrated seven-point reconstructions (spaced ~30 nm apart) from simple, binary proximity data. The subsequent 'DNA microscope', a reaction-diffusion scheme, demonstrated thousands of single particle localizations but only ~10 µm resolution 9 .…”

From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging

“…One application of DNA barcoding is to label and thus track individual molecules as they are manipulated. This concept has been expanded to obtain information beyond tracking particle identities, for example to identifying their interaction partners 7 and spatial positions 8 .…”