Past colloquia and seminars


Deterministic Control of the Position and Orientation of Single Molecules in DNA Origami

Academic or specialist Thesis defense

Optical antennas have been revolutionizing the field of nanophononics for over a decade. Constructed from metallic or dielectric nanoparticles, nanoantennas act as transducers between propagating light and localized fields, leading to a remarkable enhancement of light–matter interactions. To date, numerous optical antennas have been demonstrated for various fields, such as sensing, biomedicine or catalysis. Notably, a key driver for plasmonic antenna research is the desire to enhance the sensitivity of fluorescence microscopy at the single molecule level. Specifically, optical antennas can manipulate the photophysical behavior of organic fluorophores. DNA origami technique has proven to be highly efficient for the fabrication of nanoantennas with specific functions involving the arrangement of organic fluorophores and metallic nanoparticles in precise geometries with high positional and stoichiometric control. Given that fluorophores emit fluorescence as electric dipoles, precise control over their orientation becomes crucial in applications with strong orientation-dependent performance. However, controlling both the position and orientation of small molecules in DNA origami has been an open challenge for a long time. This limitation adversely affected the efficiency and reproducibility of nanophotonic devices. In this thesis we have addressed this challenge by developing a method to control the orientation of single dyes. Briefly, we showed that the orientation of Cy5 or Cy3 molecule can be varied from being almost parallel to almost perpendicular with respect to host DNA double-helix within the DNA origami structure by engineering the local environment. Specifically, we achieved this by covalently attaching doubly-linked fluorophores to single-stranded DNA staples and by leaving varying numbers of scaffold bases unpaired. Building upon this foundation, we designed FRET experiments where the orientation of donor and acceptor molecules can be controlled. The results show a clear dependence of FRET efficiency on the orientation of the molecules. Specifically, by independently controlling the orientation of single donor and acceptor molecules, we observed that the average energy transfer efficiency was doubled when the dyes were in a favorable orientation compared to when they were in an unfavorable orientation. Finally, we fabricated optical antennass comprising two gold nanoparticles with a fluorophore strategically positioned between them. Knowing that a parallel oriented dipole to nanoantenna longer axis is reinforced whereas a perpendicularly oriented dipole is canceled out we included in our design a fluorophore with two distinct orientations. Each OA was measured separately in single-molecule fluorescent measurements correlated with scanning electron microscopy, ensuring the precision of fabrication and structural integrity. For those two orientations, the fluorescent enhancement from OA exhibited over a fivefold difference, providing compelling evidence for the significance of orientation. The present study marks a significant milestone, introducing the first nanoantenna with controlled dye’s position and orientation.

When? 17.05.2024 16:00
Where? PER 08 0.51
Chemin du Musée 3
1700 Fribourg
speaker Aleksandra Adamczyk
Groupe Professeur Acuna
Contact Département de Physique
Prof. Acuña
Chemin du Musée 3
1700 Fribourg