Interlocked DNA nanostructures controlled by a reversible logic circuit.

Tao Li,Michael Famulok,Finn Lohmann

doi:10.1038/ncomms5940

Abstract

DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems.

Highlights

DNA nanostructures constitute attractive devices for logic computing and nanomechanics
Interlocked nanoarchitectures made of dsDNAs provide an ideal platform for combining nanomechanical devices with molecular computing
This change in mobility can be visualized by native polyacrylamide gel electrophoresis and is indicated by the appearance of a slower band accompanied by the disappearance of the [3]pseudocatenane band (Fig. 2c, lane 2 versus lane 1)

Summary

Introduction

DNA nanostructures constitute attractive devices for logic computing and nanomechanics. The G-quadruplex only forms when preceded by the assembly of the i-motif The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. On addition of toehold release oligodeoxynucleotides (ROs), the interlocked and immobile nanocircles comprising the [3]pseudocatenane architecture become mobile This causes the C-rich regions in the head-motifs to form a bimolecular i-motif structure under acidic conditions. We employ this interlocked DNA architecture to construct a reversible logic circuit via monitoring its programmable assembly by fluorescence quenching (FQ) and fluorescence resonance energy transfer (FRET). The designed logic circuit is further used to control a DNAzyme nanoswitch built on the difference in robustness between the bimolecular i-motif and G-quadruplex structures on the head-motifs of the interlocked DNA architecture

Methods

Results

Conclusion