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Probing Electron-Induced Bond Cleavage at the Single-Molecule Level Using DNA Origami Templates

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Interdisciplinary Nanoscience Center (iNANO) and Danish National Research Foundation: Centre for DNA Nanotechnology (CDNA), Aarhus University, 8000 Aarhus C, Denmark
Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
§ Center of Advanced Research in Bionanoconjugates and Biopolymers, “Petru Poni” Institute of Macromolecular Chemistry, 700487 Iasi, Romania
Service de Chimie Quantique et Photophysique, Université Libre de Bruxelles, 1050 Brussels, Belgium
Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
# Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark
*Address correspondence to [email protected]; [email protected]
Cite this: ACS Nano 2012, 6, 5, 4392–4399
Publication Date (Web):April 17, 2012
https://doi.org/10.1021/nn3010747
Copyright © 2012 American Chemical Society
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Abstract

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Low-energy electrons (LEEs) play an important role in nanolithography, atmospheric chemistry, and DNA radiation damage. Previously, the cleavage of specific chemical bonds triggered by LEEs has been demonstrated in a variety of small organic molecules such as halogenated benzenes and DNA nucleobases. Here we present a strategy that allows for the first time to visualize the electron-induced dissociation of single chemical bonds within complex, but well-defined self-assembled DNA nanostructures. We employ atomic force microscopy to image and quantify LEE-induced bond dissociations within specifically designed oligonucleotide targets that are attached to DNA origami templates. In this way, we use a highly selective approach to compare the efficiency of the electron-induced dissociation of a single disulfide bond with the more complex cleavage of the DNA backbone within a TT dinucleotide sequence. This novel technique enables the fast and parallel determination of DNA strand break yields with unprecedented control over the DNA’s primary and secondary structure. Thus the detailed investigation of DNA radiation damage in its most natural environment, e.g., DNA nucleosomes constituting the chromatin, now becomes feasible.

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Scheme of the triangular DNA origami structure along with all modified oligonucleotide sequences. This material is available free of charge via the Internet at http://pubs.acs.org.

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