Direct observation and rational design of nucleation behavior in addressable self-assembly

Abstract

SignificanceCurrent efforts aimed at constructing complex supramolecular structures often suffer from low yields or require long assembly protocols. We address these problems by demonstrating a facile strategy for optimizing the nucleation step of a multicomponent self-assembly reaction. By tracking the formation of multisubunit clusters in situ, our experiments show that modifying the critical nucleus required to initiate structure growth can broaden the range of conditions over which self-assembly occurs and, consequently, can dramatically improve the final yield of correctly formed structures. Since varying the design of only a small portion of the target structure optimizes its yield, this strategy provides a practical route to improve the speed and accuracy of self-assembly in biomolecular, colloidal, and nanoparticle systems.

Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand

“…These simulations thus support our hypothesis that the spontaneous nucleation process of DNA bricks is slow and involves thermal fluctuations that overcome a temperature‐dependent free‐energy barrier . At high temperatures, nucleation cannot occur at experimentally reasonable time scales and no product is formed . In contrast, when the P425 seed is included in the reaction mixture, nucleation involving this strand can occur much more readily at higher temperatures, since the strand has longer continuous complementary sections with its neighbours, which allows for favourable bonding without incurring a significant entropic penalty.…”

“…For the large 2D rectangle structure, the seeded structure begins to melt significantly at temperatures higher than those of the unseeded structure in both experiments and Monte Carlo simulations (Figure S20 a–c), indicating that the seed strand provides a stronger protection for the structure, probably due to the decreased nick points (which weaken the base stacking interactions in the case of brick strategy) in its located helix, which may provide a kinetic barrier to the disassembly . Unlike in the assembly process, the disassembly of pre‐assembled structures appears to start at the opposite end of the structure, that is, the one not protected by the seed strand (Figure S20d), while unseeded structures can disassemble from all sides simultaneously, speeding up the disassembly kinetics. This speculation is confirmed by simulation snapshots (inset of Figure S20 b).…”

“…Although in single‐target simulations, the depletion effect is rather more pronounced than in bulk experiments, the behavior of these curves mirrors that of Figure b, with the largest mean cluster size achieved at a higher temperature for systems in which a seed molecule was present. Seed strands lower the free‐energy barrier to nucleation and affect the nucleation behavior itself . An analysis of mean first‐passage times, assuming all remaining terms in the expression for the rate are unchanged, shows a reduction of the height of the nucleation free‐energy barrier by 2.0 k B T at 37 °C when the seed strand is introduced into the system.…”

Lattice models and Monte Carlo methods for simulating DNA origami self-assembly

“…Further, the use of a lattice representation for structural DNA nanotechnology systems has good precedent: a lattice model of DNA bricks was remarkably effective, 23 and unexpectedly yielded near quantitative agreement with experimental measurements of the nucleation kinetics. 24 For simplicity, in this work we consider origami designs in which the angles between helical axes involve only angles that are multiples of 90°in the final structure, so we chose to work with a simple cubic lattice. Contiguous binding domains on a given chain are constrained to occupy adjacent lattice sites.…”

Towards Cytoskeleton Computers. A Proposal

“…Furthermore, DNA is flexible mechanically and coiles up under various influences, while AFs and MTs are the two most mechanically rigid structures seen in cell biology [67,166,128,204,39]. Rigid tube-like [172,68,168] or beam-like [163] structures grown from small sets of DNA strands demonstrate single-filament and network properties similar to actin networks.…”