Triple Helix Formation in a Topologically Controlled DNA Nanosystem

Abstract

In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace.

Triplex DNA Nanostructures: From Basic Properties to Applications

“…Thereconfiguration of duplex DNAstructures into triplex assemblies was followed by AFM at the single-molecule level by the deposition of the functional DNAunits in an origami frame (Figure 14 A). [87] Then ucleic acids 60 and 61 were deposited on the origami frames and hybridized with the short nucleic acids 62, 62', 63,and 63' to rigidify the linear parallel duplex structure in the frame.T he domains aand bin60 and 61 included the base sequences that can form, in the presence of the auxiliary strand 64,the T·A-T and C + ·G-C triplexes that bridge the parallel duplexes into an X-shaped crosslinked structure. Figure 14 Bdepicts the AFM images of the parallel linear duplexes within the frame prior to the addition of the auxiliary strand 64 (panel I) and after addition of the auxiliary strand 64 (panel II).…”

Triplex-forming oligonucleotides: a third strand for DNA nanotechnology

“…Binding of the TFO results in the association of the two duplexes running along the centre of the frame into an X-shaped structure that is visualised by AFM. Adapted from ( 93 ) with permission. ( D ) Triplex- directed scaffolding of a tensegrity triangle crystal with a cyanine dye.…”

“…The Sugiyama and Endo groups have also examined triplex formation within the context of a DNA origami structure ( 93 ). The goal of this study was not to demonstrate its targeted modification of the structure per se but to visualise the process of triplex formation itself.…”

Triplex‐DNA‐Nanostrukturen: von grundlegenden Eigenschaften zu Anwendungen

“…Die Rekonfiguration von Duplex‐DNA‐Strukturen zu Triplex‐Aggregaten wurde durch AFM auf der Einzelmolekülebene beobachtet, indem die funktionellen DNA‐Einheiten in einem Origamirahmen platziert wurden (Abbildung A) . Die Nukleinsäuren 60 und 61 wurden auf den Origamirahmen positioniert und mit den kurzen Nukleinsäuren 62 , 62 ′, 63 und 63 ′ hybridisiert, um die lineare parallele Duplexstruktur in dem Rahmen zu versteifen.…”