Hierarchical Assembly of DNA Nanostructures Based on Four-Way Toehold-Mediated Strand Displacement

Abstract

Because of its attractive cost and yield, hierarchical assembly, in which constituent structures of lower hierarchy share a majority of components, is an appealing approach to scale up DNA self-assembly. A few strategies have already been investigated to combine preformed DNA nanostructures. In this study, we present a new hierarchical assembly method based on four-way toehold-mediated strand displacement to facilitate the combination of preformed DNA structural units. Employing such a method, we have constructed a series of higher-order structures composed of 5, 7, 9, 11, 13, and 15 preformed units respectively.

DNA dynamics and computation based on toehold-free strand displacement

“…On the other hand, toehold mediated strand displacement has enabled many DNA dynamic systems [5][6][7] , including switchable devices 8,9 , walkers [10][11][12][13][14][15] , triggered amplification 16,17 , and circuits 12,18,19 . Especially, there are a few examples of dynamic megadalton DNA nanostructures in which the paired segments with toeholds make the systems switchable from one state to another [20][21][22][23][24][25] .…”

DNA‐Based Chemical Reaction Networks

“…This synthetic computing platform holds great potential for reconstituting a split enzyme for targeted prodrug activation. Yin and co‐workers took advantage of single‐stranded tiles to assemble preformed DNA nanostructure units into structures of higher order . In this work, four‐way toehold‐mediated SDRs initiated the combination of preformed DNA structural units once the overhanging toeholds were recognized.…”

“…To date, materials obtained throughD NA-programmable chemical synthesis have been extended to organicc ompounds, biomacromolecules,p roteins, DNA nanostructures, ands oforth. [48,50,[52][53][54]…”

“…On the basis of this principle, a series of higher order structures were constructed. To date, materials obtained through DNA‐programmable chemical synthesis have been extended to organic compounds, biomacromolecules, proteins, DNA nanostructures, and so forth …”

Current-Voltage Characteristics of a Self-Assembled DNA

“…Seeman converted the DNA molecule (unidimensional structure) into 2D and 3D complex asymmetric structures named self-assembled DNA, where single strands of DNA were hybridized to form stable crosses. This self-arrangement of branched artificial DNA is useful for designing and constructing electronic nanodevices [3 -8] for its high nanoscale precision [9][10][11]. The self-assembled DNA has an accuracy at the nanoscale regime, i. e., a much higher resolution than conventional lithography.…”