DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation

Abstract

An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

“…(C) Orientation control of single Cy3 and Cy5 molecules on DNA origami with different incorporation strategies. Reproduced with permission from ref . Copyright 2022 American Chemical Society.…”

“…In a recent work of Adamczyk et al, the DNA assembly of single molecules with deterministic position and orientation was demonstrated, as shown in Figure 32C. 496 A fluorophore (Cy3 or Cy5) was doubly linked to a ssDNA staple by leaving a controlled number of unpaired bases in the scaffold, so that a high degree of stretching was applied to the fluorophore to restrain its mobility. By increasing the number of unpaired bases, there was more space for the fluorophore to accommodate and find different sites for interaction with the DNA.…”

Fabrication of 3D Oriented MOF Micropatterns with Anisotropic Fluorescent Properties

“…The anisotropic optical response of encBPY@B94 and postBPY@B94 patterned samples were then assessed via Widefield Fluorescence Microscopy. [32] Both encBPY@B94 and postBPY@B94 were excited with a 488 nm laser, while the detection range was λ > 500 nm (see Experimental section for further details). Polarization-resolved measurements were carried out by rotating the linear polarization of the laser excitation to cover a range of 180°.…”

Dimers of Plasmonic Nanocubes to Reach Single-Molecule Strong Coupling with High Emission Yields

“…Interestingly, both gold and silver nanocubes are compatible with DNA-based self-assembly, which has been shown as an efficient bottom-up strategy for reaching strong coupling at room temperature , and which also allows a control over the orientation of dye molecules. , DNA nanotechnology thus provides all of the required ingredients for producing bright strongly coupled hybrid nanostructures featuring few-photon nonlinearities at room temperature.…”

“…All of the simulations presented in Figure and panels a and b of Figure consider a perfectly centered emitting dipole with an orientation along the dimer axis. While recent self-assembly strategies, in particular using DNA, have shown an excellent position , and orientation , control over fluorescent molecules, it is interesting to consider how robust the appearance of a strong coupling regime will be for an imperfectly centered or oriented transition dipole. Panels c and d of Figure show how the strong coupling figure of merit varies as a function of the off-axis orientation and position of the source dipole, with interparticle spacings of 1 and 2 nm.…”