An ion-controlled four-color fluorescent telomeric switch on DNA origami structures

Abstract

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.

Low‐Energy Electron‐Induced Strand Breaks in Telomere‐Derived DNA Sequences—Influence of DNA Sequence and Topology

“…The human telomere sequence is oriented 5′‐(TTA GGG) n ‐3′ (Telo2N, with n =2) . The reversed oligonucleotide Telo2 contains the same type and number of nucleobases as Telo2N . The strand break cross section for Telo2N was determined relative to Telo2.…”

“…The three strand break cross sections shown in Figure do not follow exactly a linear function, which can be attributed to a change of the secondary structure of the Telo4 sequence. In the presence of monovalent cations, that is, Na + and K + , telomeres can fold into G quadruplexes …”

“…One of the most structurally stable 2D DNA origami shapes is the Rothemund triangle, consisting of three trapezoids that are attached to each other at the corners. It is quite rigid, which results in well‐defined spatial separations of attached entities . Furthermore, the triangles do not tend to aggregate, and adsorb as flat and dispersed monomers on surfaces.…”

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

“…Photonic wires are optical waveguides, in which the light energy is controlled on the nanoscale by transferring it linearly along multiple uorophores from one end to the other end based on FRET. 6,[15][16][17][18][19] Several FRET cascades can be combined in a star-like arrangement to transfer the light energy from the outside (donor molecules) to the center of the photonic network (acceptor dye). By combing these two photonic assemblies (light harvesting complexes with FRET cascades) larger end-to-end distances can be achieved and, above all, a broader range of wavelengths from the electromagnetic spectrum can be absorbed to a higher extent leading to a better light harvesting efficiency for several wavelengths.…”

“…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.…”