DataVXACS NanoPaper
journal article·2021-03-23Open access

Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures

Kristina Hübner, Himanshu Joshi, Aleksei Aksimentiev, Fernando D. Stefani, Philip Tinnefeld, Guillermo P. Acuna

ACS Nano· Volume 15· Issue 3
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Source abstract

Abstract

We present a technique to determine the orientation of single fluorophores attached to DNA origami structures based on two measurements. First, the orientation of the absorption transition dipole of the molecule is determined through a polarization-resolved excitation measurement. Second, the orientation of the DNA origami structure is obtained from a DNA-PAINT nanoscopy measurement. Both measurements are performed consecutively on a fluorescence wide-field microscope. We employed this approach to study the orientation of single ATTO 647N, ATTO 643, and Cy5 fluorophores covalently attached to a 2D rectangular DNA origami structure with different nanoenvironments, achieved by changing both the fluorophores' binding position and immediate vicinity. Our results show that when fluorophores are incorporated with additional space, for example, by omitting nucleotides in an elsewise double-stranded environment, they tend to stick to the DNA and to adopt a preferred orientation that depends more on the specific molecular environment than on the fluorophore type. With the aid of all-atom molecular dynamics simulations, we rationalized our observations and provide insight into the fluorophores' probable binding modes. We believe this work constitutes an important step toward manipulating the orientation of single fluorophores in DNA origami structures, which is vital for the development of more efficient and reproducible self-assembled nanophotonic devices.
Source: openalex_inverted_index · Quality: baseline

Research context

Nanomaterials

OpenAlex topics: Advanced biosensing and bioanalysis techniques · DNA and Nucleic Acid Chemistry · Plasmonic and Surface Plasmon Research

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany

Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States

Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina

Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina

Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg CH-1700, Switzerland

Funding

Bundesministerium f?r Bildung und Forschung · Schweizerischer Nationalfonds zur F?rderung der Wissenschaftlichen Forschung · Consejo Nacional de Investigaciones Cient?ficas y T?cnicas · Deutsche Forschungsgemeinschaft · Agencia Nacional de Promoci?n Cient?fica y Tecnol?gica · H2020 Marie Sklodowska-Curie Actions · Max-Planck-Gesellschaft · Alexander von Humboldt-Stiftung · National Science Foundation · Leadership Resource · National Center of Competence in Research Bio-Inspired Materials · Extreme Science and Engineering Discovery Environment

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