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Published August 2011 | Supplemental Material
Journal Article Open

Programmable molecular recognition based on the geometry of DNA nanostructures


From ligand–receptor binding to DNA hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. DNA retains its position as the best medium with which to create orthogonal, isoenergetic interactions, based on the complementarity of Watson–Crick binding. Here we show that DNA can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions. We show that both binary codes and shape complementarity can serve as a basis for such stacking bonds, and explore their specificity, thermodynamics and binding rules. Orthogonal stacking bonds were used to connect five distinct DNA origami. This work, which demonstrates how a single attractive interaction can be developed to create diverse bonds, may guide strategies for molecular recognition in systems beyond DNA nanostructures.

Additional Information

© 2011 Macmillan Publishers Limited. Received 20 January 2011; Accepted 17 May 2011; Published online 10 July 2011. The authors gratefully acknowledge financial support for the Molecular Programming Project from the US National Science Foundation for Expeditions in Computing (No. 0832824, http://molecular-programming.org) and the Computer and Communication Foundations Emerging Models and Technologies grants No. 0829951 and No. 0622254, the Semiconductor Research Corporation Focus Center on Functional Engineered Nano Architectonics, the Microsoft Corporation and Mark Sims of Nanorex Corporation. S.W. thanks the Benjamin M. Rosen Family Foundation for a graduate fellowship. The authors thank the DNA and Natural Algorithms laboratory, and in particular L. Qian, N. Dabby, D. Doty, R. Schulman and J. Szablowski for comments. Author contributions: S.W. and P.W.K.R. designed the experiments, analysed the data and co-wrote the paper. S.W. wrote the computer programs for designing bond types and performed binary code, shape code and thermodynamics experiments. P.W.K.R. performed cis–trans isomerism experiments.

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Supplemental Material - nchem.1070-s1.pdf

Supplemental Material - nchem.1070-s2.zip

Supplemental Material - nchem.1070-s3.zip

Supplemental Material - nchem.1070-s4.zip


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October 23, 2023