DNA nanotechnology holds great promise
for the fabrication of novel
plasmonic nanostructures and the potential to carry out single-molecule
measurements using optical spectroscopy. Here, we demonstrate for
the first time that DNA origami nanostructures can be exploited as
substrates for surface-enhanced Raman scattering (SERS). Gold nanoparticles
(AuNPs) have been arranged into dimers to create intense Raman scattering
hot spots in the interparticle gaps. AuNPs (15 nm) covered with TAMRA-modified
DNA have been placed at a nominal distance of 25 nm to demonstrate
the formation of Raman hot spots. To control the plasmonic coupling
between the nanoparticles and thus the field enhancement in the hot
spot, the size of AuNPs has been varied from 5 to 28 nm by electroless
Au deposition. By the precise positioning of a specific number of
TAMRA molecules in these hot spots, SERS with the highest sensitivity
down to the few-molecule level is obtained.
DNA origami nanostructures are a versatile tool that can be used to arrange functionalities with high local control to study molecular processes at a single-molecule level. Here, we demonstrate that DNA origami substrates can be used to suppress the formation of specific guanine (G) quadruplex structures from telomeric DNA. The folding of telomeres into G-quadruplex structures in the presence of monovalent cations (e.g. Na(+) and K(+)) is currently used for the detection of K(+) ions, however, with insufficient selectivity towards Na(+). By means of FRET between two suitable dyes attached to the 3'- and 5'-ends of telomeric DNA we demonstrate that the formation of G-quadruplexes on DNA origami templates in the presence of sodium ions is suppressed due to steric hindrance. Hence, telomeric DNA attached to DNA origami structures represents a highly sensitive and selective detection tool for potassium ions even in the presence of high concentrations of sodium ions.
The folding of single-stranded telomeric DNA into guanine (G) quadruplexes is a conformational change that plays a major role in sensing and drug targeting. The telomeric DNA can be placed on DNA origami nanostructures to make the folding process extremely selective for K(+) ions even in the presence of high Na(+) concentrations. Here, we demonstrate that the K(+)-selective G-quadruplex formation is reversible when using a cryptand to remove K(+) from the G-quadruplex. We present a full characterization of the reversible switching between single-stranded telomeric DNA and G-quadruplex structures using Förster resonance energy transfer (FRET) between the dyes fluorescein (FAM) and cyanine3 (Cy3). When attached to the DNA origami platform, the G-quadruplex switch can be incorporated into more complex photonic networks, which is demonstrated for a three-color and a four-color FRET cascade from FAM over Cy3 and Cy5 to IRDye700 with G-quadruplex-Cy3 acting as a switchable transmitter.
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