DNA Origami Substrates for Highly Sensitive Surface-Enhanced Raman Scattering

Abstract

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.

FRET efficiency and antenna effect in multi-color DNA origami-based light harvesting systems

“…21,22 Since every staple strand can be addressed and modied individually and separately, different moieties can be arranged with a high local control since the exact position of each staple strand in the DNA origami structure is known. DNA origami structures have been used to create highly sensitive SERS substrates by attaching gold nanoparticle dimers, [23][24][25] to analyze DNA strand breaks induced by low energy electrons 26,27 and UV photons 28 and to arrange different uo-rophores 29,29,30 at precise distances to create nanoscale photonic devices which can be used for example as photonic wires, 15,18 to resolve conformational changes of biomolecules, [31][32][33][34] as logic gates 35,36 and articial light harvesting complexes. 8,10,18 The light harvesting efficiency is in this context typically expressed as an antenna effect (AE), i.e.…”

Ion‐Selective Formation of a Guanine Quadruplex on DNA Origami Structures

“…By means of FRET between two suitable dyes attached to the 3'-and 5'-ends of telomeric DNA we demonstrate that the formation of Gquadruplexes 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.DNA can be folded into almost any 2D and 3D shape by using the DNA origami technique.[1] DNA nanostructures can be decorated with proteins, nanoparticles, fluorescent dyes, and higher-order DNA structures with nanometer precision, and thus they can serve as a versatile tool in analytical science.[2] DNA origami structures can be used as a platform to detect RNA sequences [3] and other molecular species through atomic force microscopy, [4] for few-molecule detection using surface-enhanced Raman scattering (SERS), [5] and to determine the yield of sequence-specific DNA damage.[6]The formation of guanine (G) quadruplex structures from telomeric DNA sequences was also extensively studied using a DNA origami frame and high-speed AFM. [7] Telomeres are located at the ends of eukaryotic chromosomes, and stabilize and protect the genome.…”

Spatial regulation of synthetic and biological nanoparticles by DNA nanotechnology

“…Two groups have proven that this single-molecular fluorescence enhancement effect can be observed in DNA origami-based systems by using a DNA origami pillar structure (Figure 1c) 37 and a simple triangular DNA origami. 38 Similarly, if Raman dyes are placed in the gap, surface-enhanced Raman scattering can be observed 39 if the gap is sufficiently narrow because Raman scattering cross-sections are much smaller than fluorescence cross-sections. In a very recent work, Keyser and co-workers 40 constructed a AuNP pair with a sub-5-nm gap on a multilayer DNA origami platform.…”