Logic Gating by Macrocycle Displacement Using a Double‐Stranded DNA [3]Rotaxane Shuttle

Abstract

Molecular interlocked systems with mechanically trapped components can serve as versatile building blocks for dynamic nanostructures. Here we report the synthesis of unprecedented double-stranded (ds) DNA [2]- and [3]rotaxanes with two distinct stations for the hybridization of the macrocycles on the axle. In the [3]rotaxane, the release and migration of the "shuttle ring" mobilizes a second macrocycle in a highly controlled fashion. Different oligodeoxynucleotides (ODNs) employed as inputs induce structural changes in the system that can be detected as diverse logically gated output signals. We also designed nonsymmetrical [2]rotaxanes which allow unambiguous localization of the position of the macrocycle by use of atomic force microscopy (AFM). Either light irradiation or the use of fuel ODNs can drive the threaded macrocycle to the desired station in these shuttle systems. The DNA nanostructures introduced here constitute promising prototypes for logically gated cargo delivery and release shuttles.

A Protein Rotaxane Controls the Translocation of Proteins Across a ClyA Nanopore

“…DNA has been used to build a variety of nanoscale structures including rotaxanes, [1][2][3] catenenes, 4 reconfigurable three-dimensional objects, 5 biomimetic systems [6][7][8] and chemically fuelled molecular motors. [9][10][11] Proteins possess larger chemical diversity than nucleic acids and are, therefore, attractive building elements in nanotechnology.…”

A Photoregulated DNA‐Based Rotary System and Direct Observation of Its Rotational Movement

“…As ar esult, the azo-rotor moved to ap arallel-stateB/B' form (ON duplex formation at anchorages 3a nd 4). cluded that the azo-rotor was trapped at anchorage 2i nt he perpendicular state since other three single anchoring strands (1,3,4) were all visualized. As showni nF igure2d( Supporting Information Figure S7), all four single anchoring strandso nt he slotted tile could be identified.…”

“…[1] Functional DNA nanostructures can be fabricated to perform tasks such as cargo transportation, [2] logic operations, [3][4][5] and single molecule analysis. [1] Functional DNA nanostructures can be fabricated to perform tasks such as cargo transportation, [2] logic operations, [3][4][5] and single molecule analysis.…”

DNA Origami Rotaxanes: Tailored Synthesis and Controlled Structure Switching

“…[2] Due to the translational and rotational freedom of the enclosed macrocycle, rotaxanes harbor potential as molecular switches and/or molecular cargo shuttles; the movement of which can be dictated by various chemical stimuli including addition of DNA strands, pH changes, and light signals. [3] Intrigued by the potential applications of rotaxanes as stimulus-responsive switches and the diverse conjugation chemistry compatible with DNA nanodevices [4] , several recent investigations have focused on assembly of rotaxanes from DNA. [3b, 5] …”

“…[3] Intrigued by the potential applications of rotaxanes as stimulus-responsive switches and the diverse conjugation chemistry compatible with DNA nanodevices [4] , several recent investigations have focused on assembly of rotaxanes from DNA. [3b, 5] …”