DNA Nanotechnology: Enabling technologies and applications

 

Why building with DNA?

 

DNA is a unique polymer. It is the information storage molecule of all known life forms, and can also be used to build up almost arbitrary structures and patterns out of DNA. These structures can be functionalized with a large variety of inorganic nanoparticles, small molecules or large biomolecules such as proteins and antibodies. The diversity of materials, the programmability of interactions, and the spatial control and scalability outperform other technologies for the fabrication of hybrid nanostructures, thus making DNA nanotechnology an invaluable tool for many different disciplines.

Our group is leveraging this unique programmability of DNA to engineer nanoarchitectures and technologies for applications in Biochemistry, Molecular Biology, Nanomedicine, Biophysics and Nanophotonics. Moreover, we are developing a scalable “next-generation” DNA synthesis method.

 

 

DNA-based plasmonic devices

 

The field of plasmonics exploits the interaction of light with nanoscale metallic structures to confine, guide and manipulate light on scales below the diffraction limit. Plasmonic structures exhibit significant potential for applications including quantum optics, sensing and short-distance optical communication (a). Towards this goal, we demonstrated the precise, robust and high-yield assembly of gold nanoparticles on DNA origami templates (b) F. Gür et al. ACS Nano 2016, 5374-5382. More recently, we realized energy propagation through such a self-assembled waveguide to a fluorescent nanodiamond and out coupling of energy. We analyzed the waveguiding at a single-device level by electron energy loss spectroscopy (c) and cathodoluminescence imaging spectroscopy. Our work visually demonstrates the realization of nanometer-precise light manipulation and energy conversion.

preprint: arXiv:1712.09141 [physics] 2017

 

 

Triangulated DNA origami and nanomechanical actuators

In the macroscopic world, stiff and material-efficient structures such as construction cranes and high voltage transmission towers are usually built from triangulated wireframe structures. We extended the DNA origami concept to generate a series of triangulated trusses. These provide defined cavities that we seek to fill with functional elements. Moreover, we are determining biophysical properties such as their bending and torsional stiffness.
Matthies et al. Nano Lett. 2016, 2108-2113.

 

By introducing single-stranded regions edges of the wireframe trusses, the structures are heavily deformed due to the entropic spring forces contracting the single-stranded region. These gaps can be filled by a gap filling polymerase (such as the T4 polymerase). The selective introduction of single-stranded segments (red arrows) curve triangulated trusses. Polymerase-assisted gap filling straightens the trusses.

Agarwal et al. ACS Nano 2018 (in print).

Outlook: This principle shall be the basis for stimuli-responsive mechanical nano devices in photonics or for applications in molecular biology.

 

 

Nanomedicine

Cancer stem cells (CSCs) are responsible for drug resistance, tumor recurrence, and metastasis in several cancer types, making their eradication a primary objective in cancer therapy. In a project lead by Dr. Goncalves, gold nanorods (AuNRs) were functionalized with Nestin-binding peptides that specifically recognize Glioblastoma multiforme (GBM) stem cells for photothermal therapy.

Goncalves et al. Acta Biomaterialia 2017, 58, 12-25.

Goncalves et al. Biomat. Sci. 2018 (in print).

Outlook: We will explore more sophisticated delivery vehicles based on structural DNA nanotechnology for applications in nanomedicine.

 

 

Protection of DNA structures

A main drawback of structural DNA nanotechnology is the instability of structures in biological environments. We developed a protection strategy based on block copolymer micellization which stabilizes DNA structures in biological or low-salt environments.

Agarwal et al. Angew. Chemie 2017, 5460-5464.

 

 

Enzymatic oligonucleotide production

 

Synthetic oligonucleotides are the main cost factor for many studies in DNA nanotechnology, genetics and synthetic biology that require thousands of these at high quality. Inexpensive chip-synthesized oligonucleotide libraries can contain hundreds of thousands of distinct sequences, however only at sub-femtomole quantities per strand. We developed a selective oligonucleotide amplification method with a 10-1000-fold cost-reduction compared to synthetic oligonucleotides or competing amplification methods such as PCR.

Schmidt et al. Nat. Commun. (2015).

 

 

During our work on RCA, we discovered that the RCA efficiency is a function of the template length and shows the same periodicity as B-DNA. Coarse grained molecular dynamics simulations (collaboration with Prof. Jon Doye, Oxford) imply that this bias comes from a varying fraying probability of the last two downstream base pairs. We conclude that an increased strain-promoted fraying probability can increase the polymerization rate compared to a relaxed template. Knowledge of this effect is not only important to make our oligonucleotide amplification method more robust, but also needs to be taken into account for various diagnostic and gene sequencing methods relying on RCA.

Joffroy et al. Nucleic Acids Res 2018, 46 (2), 538–545.

Outlook: We are currently continuing to improve the oligonucleotide amplification method and applying it for new applications in synthetic biology and structural DNA nanotechnology. Furthermore, we will develop means to circumvent it or counterbalance the length-dependent amplification bias.

 

 

Further directions

Several other multi-disciplinary projects are being followed at the interface of Chemistry, Physics, Biology and Electronics. Examples include mechanistic studies of the rolling circle amplification, imaging of biological tissues, bionanomedical applications of DNA origami or single-molecule biophysics of proteins.

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