Person:

Liu, Di

Though many functional RNAs fold into intricate and precise 3D architectures, it is difficult to acquire their high-resolution structures. Herein, we present a nanoarchitectural strategy for efficient structural determination of RNA-only structures using single-particle cryogenic electron microscopy (cryo-EM). This strategy, termed RNA oligomerization-enabled cryo-EM via installing kissing-loops (ROCK), involves RNA construct engineering to install kissing-loop sequences onto functionally nonessential stems for the homomeric self-assembly into closed nanoarchitectures with multiplied molecular weights and mitigated structural flexibility. ROCK enables the cryo-EM reconstruction of the Tetrahymena group I intron at 2.98 Å resolution overall (2.85 Å for the core), allowing de novo model building of the complete RNA including the previously unknown peripheral domains. ROCK is also applied to two smaller RNAs to produce modest-resolution maps, revealing the conformational change of the Azoarcus group I intron and the bound ligand in the FMN riboswitch. Our work unleashes the largely unexplored potential of cryo-EM in RNA structural studies.

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.