Abstract
The selectivity of Watson-Crick base pairing has allowed the design of DNA-based functional materials bearing an unprecedented level of accuracy. Examples include DNA origami, made of tiles assembling into arbitrarily complex shapes, and DNA coated particles featuring rich phase behaviors. Frequently, the realization of conceptual DNA-nanotechnology designs has been hampered by the lack of strategies for effectively controlling relaxations. In this article, we address the problem of kinetic control on DNA-mediated interactions between Brownian objects. We design a kinetic pathway based on toehold-exchange mechanisms that enables rearrangement of DNA bonds without the need for thermal denaturation, and test it on suspensions of DNA-functionalized liposomes, demonstrating tunability of aggregation rates over more than 1 order of magnitude. While the possibility to design complex phase behaviors using DNA as a glue is already well recognized, our results demonstrate control also over the kinetics of such systems.
Highlights
We introduce an interaction scheme based on Toehold Exchange Mechanism (TEM) that enables direct control over the aggregation kinetics of colloidal units
We propose a new mechanism to control the kinetics of DNA mediated interactions
This is tested on liposomes that are functionalized with three different types of DNA thethers, two of which (A1 and A2) compete to bind the third (B)
Summary
D NA nanotechnology has capitalized on the availability of a large library of oligomers that, in view of the selective nature of the Watson−Crick pairing, enable a large number of specific interactions to work simultaneously.[2,3] In systems of DNA ”bricks”, this extreme selectivity makes it possible to design arbitrarily complex aggregates that selfassemble from short DNA strands with an unprecedented level of accuracy.[4,5] The impact on engineering composite materials has been just as significant, with DNA-mediated interactions[6−8] being used to design complex phase behaviors in DNA-coatedcolloid (DNACC) systems,[9−12] to engineer ultrasensitive detectors[13,14] and microscopic walkers,[15,16] or to create new biomimetic structures like DNA functionalized liposomes[17−20] or artificial pores.[21]. The straightforward approach to design kinetically accessible experiments consists of finely tuning environmental variables, temperature, to a sweet spot where binding/ unbinding rates and interaction potentials are both suitable for reversible self-assembly.[24,25] This strategy lacks flexibility and it is difficult to implement due to the high sensitivity of DNAmediated interactions to temperature changes, which narrows down the window of suitable experimental conditions. Wang et al.[26] demonstrated that a high-density coating of weakly attractive DNA tethers facilitates equilibration over a broader range of temperatures. In these systems, kinetic behavior remains intimately connected to the thermodynamic ground state: neither can be changed without affecting the other. Toehold-mediated strand-displacement mechanisms have been widely applied in DNA nanotechnology to enable isothermal control over the kinetics of DNA bonds.[27−29] In the simplest implementation, a short single-stranded DNA
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