DNA Nanotechnology; A platform for sensing

S. Buckhout-White, M.G. Ancona, E.R. Goldman, I.L. Medintz
Naval Research Laboratory,
United States

Keywords: DNA nanostructures, FRET, sensing


DNA nanostructures represent an interesting intersection of nanotechnology, chemistry and biology. With much of the research in this area focusing on the development of novel structures, nano-machines and actuation, the use of DNA as a sensing platform provides an exciting area of exploration. For an effective DNA-based beacon one needs not only a strong signal, but also the ability to affect a large signal change. Building from our prior work with DNA-based amplifying Förster resonant energy transfer (FRET) dendrimers we have investigated ways to modify these networks through dynamic re-organization of their underlying DNA scaffold[1]. Specifically, with our branched dendrimer we dynamically augment the FRET pathways through appropriate toehold-mediated strand displacements that either add or remove particular dyes. In one case the removal of a single dye results in a 5-fold difference in the intensity of the final acceptor dye. Another system investigated for use in biosensing was based on circularizing the FRET pathway in order to produce a photonic logic gate that processes single-stranded linker inputs[2]. With three linkers as inputs we have demonstrated a molecular switch capable of dynamic switching from one output set to the other. We have explored multiple dye sets using the same DNA structural configuration and have been able to achieve unique spectral output depending on the dye-triad chosen[3]. This flexibility allows for a wide range of application once these logic-enhanced beacons are applied to a sensing platform. This system has also been successfully used to sensing restriction enzymes, again allowing for three unique inputs. A final system investigated examines the feasibility of sensing long complex DNA plasmids through use of the principles of DNA origami. We simplify the system, by limiting ourselves to 10 assembly strands. By integrating a DNA based amplification reaction; hybridization chain reaction [4]; we can assemble columns of gold nanoparticles when the assembly strands bind to the long target DNA. This amplification scheme in conjunction with the plasmonic enhancement of the gold nanoparticles substantially increases the sensitivity of the system. References 1. Buckhout-White, S., et al., Assembling programmable FRET-based photonic networks using designer DNA scaffolds. Nat Commun, 2014. 5. 2. Buckhout-White, S., et al., A triangular three-dye DNA switch capable of reconfigurable molecular logic. RSC Advances, 2014. 4(90): p. 48860-48871. 3. Buckhout-White, S., et al., Expanding molecular logic capabilities in DNA-scaffolded multiFRET triads. Rsc Advances, 2016. 6(100): p. 97587-97598. 4. Dirks, R.M. and N.A. Pierce, Triggered amplification by hybridization chain reaction. Proceedings of the National Academy of Sciences of the United States of America, 2004. 101(43): p. 15275-15278.