Article

Effect of DNA Hairpin Loops on the Twist of Planar DNA Origami Tiles

Zhe Li, Lei Wang, Hao Yan, and Yan Liu*
Department of Chemistry and Biochemistry, and the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
School of Pharmaceutical Sciences, Shandong University, Jinan 250012, P. R. China
Langmuir, 2012, 28 (4), pp 1959–1965
DOI: 10.1021/la2037873
Publication Date (Web): November 29, 2011
Copyright © 2011 American Chemical Society
*E-mail: yan_liu@asu.edu.
This article is part of the Bioinspired Assemblies and Interfaces special issue.

Abstract

Abstract Image

The development of scaffolded DNA origami, a technique in which a long single-stranded viral genome is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides, represents an important milestone in DNA nanotechnology. Recent findings have revealed that two-dimensional (2D) DNA origami structures based on the original design parameters adopt a global twist with respect to the tile plane, which may be because the conformation of the constituent DNA (10.67 bp/turn) deviates from the natural B-type helical twist (10.4 bp/turn). Here we aim to characterize the effects of DNA hairpin loops on the overall curvature of the tile and explore their ability to control, and ultimately eliminate any unwanted curvature. A series of dumbbell-shaped DNA loops were selectively displayed on the surface of DNA origami tiles with the expectation that repulsive interactions among the neighboring dumbbell loops and between the loops and the DNA origami tile would influence the structural features of the underlying tiles. A systematic, atomic force microscopy (AFM) study of how the number and position of the DNA loops influenced the global twist of the structure was performed, and several structural models to explain the results were proposed. The observations unambiguously revealed that the first generation of rectangular shaped origami tiles adopt a conformation in which the upper right (corner 2) and bottom left (corner 4) corners bend upward out of the plane, causing linear superstructures attached by these corners to form twisted ribbons. Our experimental observations are consistent with the twist model predicted by the DNA mechanical property simulation software CanDo. Through the systematic design and organization of various numbers of dumbbell loops on both surfaces of the tile, a nearly planar rectangular origami tile was achieved.

DNA sequences, materials and additional AFM results. This material is available free of charge via the Internet at http://pubs.acs.org.

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Received 27 September 2011
Published online 29 November 2011
Published in print 31 January 2012
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