Concepedia

Design and Characterization of Programmable DNA Nanotubes

Paul W. K. Rothemund, Axel Ekani-Nkodo, Nick Papadakis, Ashish Kumar, Deborah Kuchnir Fygenson, Erik Winfree

Journal of the American Chemical Society · 2004 · 514 citations · 37 references

TL;DR

DNA self‑assembly offers a programmable bottom‑up route to complex nanostructures, yet the factors controlling the geometry of DNA nanotubes remain poorly understood. The authors set out to report and characterize a new type of nanotube constructed from DNA double‑crossover (DAE‑E) tiles. They assembled these tiles into tubes and measured their dimensions, persistence length, and pattern‑display capabilities. The resulting tubes are 7–20 nm in diameter, 4–10 tiles in circumference, grow up to 50 μm with a ~4 μm persistence length, can display diverse patterns, and their structure is governed by sticky‑end stacking, face identity, tile design, and is captured by a simple B‑form DNA geometry‑energy model.

Abstract

DNA self-assembly provides a programmable bottom-up approach for the synthesis of complex structures from nanoscale components. Although nanotubes are a fundamental form encountered in tile-based DNA self-assembly, the factors governing tube structure remain poorly understood. Here we report and characterize a new type of nanotube made from DNA double-crossover molecules (DAE-E tiles). Unmodified tubes range from 7 to 20 nm in diameter (4 to 10 tiles in circumference), grow as long as 50 μm with a persistence length of ∼4 μm, and can be programmed to display a variety of patterns. A survey of modifications (1) confirms the importance of sticky-end stacking, (2) confirms the identity of the inside and outside faces of the tubes, and (3) identifies features of the tiles that profoundly affect the size and morphology of the tubes. Supported by these results, nanotube structure is explained by a simple model based on the geometry and energetics of B-form DNA.