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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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Absolute and arbitrary orientation of single-molecule shapes
DNA origami is a modular platform for the combination of molecular and colloidal components to create optical, electronic, and biological devices. Integration of such nanoscale devices with microfabricated connectors and circuits is challenging: Large numbers of freely diffusing devices must be fixed at desired locations with desired alignment. We present a DNA origami molecule whose energy landscape on lithographic binding sites has a unique maximum. This property enabled device alignment within 3.2° on silica surfaces. Orientation was absolute (all degrees of freedom were specified) and arbitrary (the orientation of every molecule was independently specified). The use of orientation to optimize device performance was shown by aligning fluorescent emission dipoles within microfabricated optical cavities. Large-scale integration was demonstrated with an array of 3456 DNA origami with 12 distinct orientations that indicated the polarization of excitation light.
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- Award ID(s):
- 1636364
- PAR ID:
- 10214340
- Publisher / Repository:
- American Association for the Advancement of Science (AAAS)
- Date Published:
- Journal Name:
- Science
- Volume:
- 371
- Issue:
- 6531
- ISSN:
- 0036-8075
- Page Range / eLocation ID:
- Article No. eabd6179
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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