An attractive strategy to improve the energy transfer properties of synthetic dye networks is to optimize the excitonic coupling between the dyes to increase energy transfer rates. To explore this possibility, we investigate the use of J-like cyanine dye dimers (Cy3 and Cy5 dimers) on DNA duplexes as energy transfer relays in molecular photonic wires. This approach is based on using the collective emission dipole of a J-dimer to enhance the FRET rate between the dimer relay and a remote acceptor dye. Experimentally, we find that in room temperature aqueous buffer conditions the dimer relay provided no benefit in energy transfer quantum yield relative to a simple monomer relay. Further investigation led us to determine that enhanced non-radiative relaxation, non-ideal dye orientation within the dimer, and unfavorable dye orientation between the dimer and the acceptor dye limit energy transfer through the dimer relay. We hypothesized that non-radiative relaxation was the largest factor, and demonstrated this by placing the sample in a viscous solvent or cooling the sample, which dramatically improved energy transfer through the J-like dimer relay. Similar to how the formation of DNA-templated J-like dimers has improved, the practical use of J-like dimers to optimize energy transfer quantum efficiency will require improvements in the ability to control orientation between dyes to reach its full potential.
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Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching
Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.
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- Award ID(s):
- 1648655
- NSF-PAR ID:
- 10340536
- Date Published:
- Journal Name:
- International Journal of Molecular Sciences
- Volume:
- 23
- Issue:
- 14
- ISSN:
- 1422-0067
- Page Range / eLocation ID:
- 7690
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/ijms23147690
