Spontaneous Reorganization of DNA-Based Polymers in Higher Ordered Structures Fueled by RNA

Abstract

We demonstrate a strategy that allows for the spontaneous reconfiguration of self-assembled DNA polymers exploiting RNA as chemical fuel. To do this, we have rationally designed orthogonally addressable DNA building blocks that can be transiently deactivated by RNA fuels and subtracted temporarily from participation in the self-assembly process. Through a fine modulation of the rate at which the building blocks are reactivated we can carefully control the final composition of the polymer and convert a disordered polymer in a higher order polymer, which is disfavored from a thermodynamic point of view. We measure the dynamic reconfiguration via fluorescent signals and confocal microscopy, and we derive a kinetic model that captures the experimental results. Our approach suggests a novel route toward the development of biomolecular materials in which engineered chemical reactions support the autonomous spatial reorganization of multiple components.

Autonomous and programmable reorganization of DNA-based polymers using redox chemistry

“…26,34 The DNA tiles also contain a specific overhang single-stranded binding domain of 7-nt to which a 14-nt fuel strand can bind to invade one of the four sticky ends and induce the disassembly of the DNA structure (Figure S1). 26,31,36 It is possible to program different tiles to have the same sticky ends, so that they can co-assemble into the same tubular structure, but different addressable tails so that they can be orthogonally controlled with different fuel strands. 31 Each DNA tile can also be labelled with a different fluorophore (Cy3 for Red, R, tile and Cy5 for Green, G, tile) to independently monitor their distribution in the assembled co-polymer.…”

“…26,31,36 It is possible to program different tiles to have the same sticky ends, so that they can co-assemble into the same tubular structure, but different addressable tails so that they can be orthogonally controlled with different fuel strands. 31 Each DNA tile can also be labelled with a different fluorophore (Cy3 for Red, R, tile and Cy5 for Green, G, tile) to independently monitor their distribution in the assembled co-polymer.…”

“…Indeed, the experimental conditions of the disulfide-reduction reaction we used here to control the assembly/disassembly of DNA polymers are compatible with enzymatic reactions that we had already exploited for the same purpose before. [29][30][31] This makes it in principle possible to control the reconfiguration of DNA structures using two fuel-consuming reactions (enzymatic and redox reactions). Motivated by this possibility we have thus employed one of the DNA tiles described above that is controlled by the disulfide redox reaction together with a different DNA tile controlled by an RNA fuel and an enzyme (RNase H) as fuel consuming unit.…”

“…By coupling these systems with DNA-recognizing enzymes (nucleases, nickases, ligases etc) that are able to inactivate DNA-fuel strands that are used as chemical triggers, it is also possible to introduce temporal control in synthetic devices and self-assembly processes and allow autonomous and controlled reconfiguration. [26][27][28][29][30][31] These examples clearly demonstrate the advantages of using synthetic DNA to create adaptable and reconfigurable synthetic materials. The use of enzymatic reactions to achieve this goal, however, is not without limitations: enzyme activity can be affected by the formed waste products and enzymes can have limited operational stability.…”

Classifying soft self-assembled materials via unsupervised machine learning of defects

“…11 Such dynamical features resulted in a set of intriguing properties that, on the one hand, mimic natural ones, crucial for the functioning of biological tissues (e.g., self-healing, chemotacticity, molecular transport, etc.) [12][13][14][15][16] and, on the other hand, are promising features for the design of new functional materials and nano-technologies 1,[17][18][19][20][21][22][23] A major goal in the study of self-assembled architectures is understanding how changes in the structure of the selfassembling building blocks (input) affect the overall properties of the supramolecular assembled structure (output) (Fig. 1).…”