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

Abstract

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.

Photoresponsive Formation of an Intermolecular Minimal G‐Quadruplex Motif

“…Fora nother recent example of ion selectivity in Gquadruplexes and possible application in nanotechnology,see also Ref. [36].Cation selectivity has also been reported for the thrombin-binding aptamer G-quadruplex, [37] whose G-tetrad core adopts the same folding topology as we have determined for GG-Az1-GG (see Figure 4a nd the corresponding discussion). We propose that the smaller size of the Na + ion is not optimal to coordinate all eight O6 atoms in the two-tetrad cavity,which is necessary to keep the GG-Az1-GG in astable quadruplex structure.F urthermore,t he azobenzene linkers may introduce additional strain to the ionic channel, leading to the observed ion selectivity.…”

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.…”

A Versatile Multiple Target Detection System Based on DNA Nano-assembled Linear FRET Arrays

“…DNA nanotechnology has been seen as a fast evolving field in recent years due to the unique physicochemical properties, its specific ability to noncovalently self-assemble into complex yet predictable structures, and easy access to building-block oligomeric components via customizable, automated synthetic chemistry that allows for multiple site-specific chemical modifications17181920212223. DNA-based architectures and functional devices are currently playing an increasing role under investigation including molecular scale biosensors2425262728293031.…”