Person:

Schaus, Thomas

DNA performs diverse functional roles in biology, nanotechnology, and biotechnology, but current methods for autonomously synthesizing arbitrary single-stranded DNA are limited. Here, we introduce the concept of Primer Exchange Reaction (PER) cascades, which grow nascent single-stranded DNA with user-specified sequences following prescribed reaction pathways. PER synthesis happens in a programmable, autonomous, in situ, and environmentally responsive fashion, providing a platform for engineering molecular circuits and devices with a wide range of sensing, monitoring, recording, signal processing, and actuation capabilities. We experimentally demonstrate a nanodevice that transduces the detection of a trigger RNA into the production of a DNAzyme that degrades an independent RNA substrate, a signal amplifier that conditionally synthesizes long fluorescent strands only in the presence of a particular RNA signal, molecular computing circuits that evaluate logic (AND, OR, NOT) combinations of RNA inputs, and a temporal molecular event recorder that records in the PER transcript the order in which distinct RNA inputs are sequentially detected.

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.

Precise fabrication of semiconducting carbon nanotubes (CNTs) into densely-aligned evenly-spaced arrays is required for the ultra-scaled technology nodes. We report the precise scaling of inter-CNT pitch using a supramolecular assembly method called spatially hindered integration of nanotube electronics (SHINE). Specifically, by using DNA brick crystal based nanotrenches to align DNA-wrapped CNTs through DNA hybridization, we constructed parallel CNT arrays with uniform pitch as small as 10.4 nanometers, at an angular deviation less than 2 degrees and an assembly yield > 95%.

Lithographic scaling of periodic three-dimensional patterns is critical for advancing scalable nanomanufacturing. Current state-of-the-art quadruple patterning or extreme-UV lithography produce line pitch down to around 30 nm, which can be further improved to sub-20 nm through complex post-fabrication processes. Herein, we report the use of three-dimensional (3D) DNA nanostructures to scale the line pitch down to 16.2 nm, around 50 % smaller than current state-of-the-art results. We use a DNA modular epitaxy approach to fabricate scaled 3D DNA masks with prescribed structural parameters (pitch, shape, and critical dimensions) along a designer assembly pathway. Single-run reactive ion etching then transfers the DNA patterns to a Si substrate at a lateral resolution of 7 nm and a vertical resolution of 2 nm. The DNA modular epitaxy-directed lithography achieves smaller pitch than the projected values for advanced technology node in field-effect transistors, and provides a potential complement to the existing lithographic tools towards advanced 3D nanomanufacturing.