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Description
One of the main advantages of DNA nanotechnology is that colloidal nanoparticles and fluorophores can be positioned with nanometric precision. In order to fully manipulate the interaction between these species it is necessary to not only control their relative position but also their relative orientation. In this work, we study the orientation of Cy5 fluorophores incorporated in an innovative way using two independent measurements carried out in a standard wide-field fluorescence microscope. Our results show that single fluorophores attached with two anchoring points can adopt different orientations on a DNA-origami, from perpendicular to aligned with the double-helix depending on the number of bases removed from the complimentary sequence.