Probing Heterogeneous Folding Pathways of DNA Origami Self-Assembly at the Molecular Level with Atomic Force Microscopy

Mechanism of DNA origami folding elucidated by mesoscopic simulations

Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

Design principles for accurate folding of DNA origami

We describe design principles for accurate folding of three-dimensional DNA origami. To evaluate design rules, we reduced the problem of DNA strand routing to the known problem of shortest-path finding in a weighted graph. To score candidate DNA strand routes we used a thermodynamic model that accounts for enthalpic and entropic contributions of initial binding, hybridization, and DNA loop closure. We encoded and analyzed new and previously reported design heuristics. Using design principles emerging from this analysis, we redesigned and fabricated multiple shapes and compared their folding accuracy using electrophoretic mobility analysis and electron microscopy imaging. We demonstrate accurate folding can be achieved by optimizing staple routes using our model, and provide a computational framework for applying our methodology to any design.

Sequence-dependent folding of monolayered DNA origami domains

Current models of DNA origami folding can explain the yield of the assembly process and the isomerization of the structure upon the application of mechanical forces. Nevertheless, the role of the sequence in this conformational transformation is still unclear. In this work, we address this question by performing a systematic thermodynamic study of three origami domains that have an identical design but different sequence contents. By comparing the thermal stability of the domains in various settings and measuring the extent of isomerization at equilibrium (both at the global and single-molecule levels), we extract the contribution to folding given by the sequence and propose thermal criton maps of the isomers to rationalize our findings. Our data contribute to a deeper understanding of DNA origami assembly by considering both the topological- and thermal-dependent properties of the sites of initial folding. While the former are responsible for the mechanical aspects of the process, the latter justify the observed sequence-dependent conformational preferences, which appear evident in simple origami structures but remain typically undisclosed in large and more intricate architectures.

Programming rigidity into size-defined wireframe DNA nanotubes

Nanotubes built from DNA hold promise for several biological and materials applications, due to their high aspect ratio and encapsulation potential. A particularly appealing goal is to control the size, shape, and dynamic behaviour of DNA nanotubes with minimal design alteration, as nanostructures of varying morphologies and lengths have been shown to exhibit distinct cellular uptake, encapsulation behaviour, and in vivo biodistribution. Herein, we report a systematic investigation, combining experimental and computational design, to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes. Subtle design changes govern the structure and properties of our nanotubes, which are built from a custom-made, long, and size-defined template strand to which DNA rungs and linkers are attached. Unlike DNA origami, these custom-made strands possess regions with repeating sequences at strategic locations, thereby reducing the number of strands necessary for assembly. Through strand displacement, the nanotubes can be reversibly altered between extended and collapsed morphologies. These design concepts enable fine-tuning of the nanotube stiffness and may pave the way for the development of designer nanotubes for a variety of applications, including the study of cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.

Ion-mediated control of structural integrity and reconfigurability of DNA nanostructures

Nucleic acid-based biomolecular self-assembly enables the creation of versatile functional architectures. Electrostatic screening of the negative charges of nucleic acids is essential for their folding and stability; thus, ions play a critical role in nucleic acid self-assembly in both biology and nanotechnology. However, the ion-DNA interplay and the resulting ion-specific structural integrity and responsiveness of DNA constructs are underexploited. Here, we harness a wide range of mono- and divalent ions to control the structural features of DNA origami constructs. Using atomic force microscopy and Förster resonance energy transfer (FRET) spectroscopy down to the single-molecule level, we report on the global and local structural performance and responsiveness of DNA origami constructs following self-assembly, upon post-assembly ion exchange and post-assembly ion-mediated reconfiguration. We determined the conditions for highly efficient DNA origami folding in the presence of several mono- (Li⁺, Na⁺, K⁺, Cs⁺) and divalent (Ca²⁺, Sr²⁺, Ba²⁺) ions, expanding the range where DNA origami structures can be exploited for custom-specific applications. We then manipulated fully folded constructs by exposing them to unfavorable ionic conditions that led to the emergence of substantial disintegrity but not to unfolding. Moreover, we found that poorly assembled nanostructures at low ion concentrations undergo substantial self-repair upon ion addition in the absence of free staple strands. This reconfigurability occurs in an ion type- and concentration-specific manner. Our findings provide a fundamental understanding of the ion-mediated structural responsiveness of DNA origami at the nanoscale enabling applications under a wide range of ionic conditions.

Regulating the Polymerization of DNA Structures via Allosteric Control of Monomers

Regulation of self-assembly is crucial in constructing structural biomaterials, such as tunable DNA nanostructures. Traditional tuning of self-assembled DNA nanostructures was mainly conducted by introducing external stimuli after the assembly process. Here, we explored the allosteric assembly of DNA structures via introducing external stimuli during the assembly process to produce structurally heterogeneous polymerization products. We demonstrated that ethidium bromide (EB), a DNA intercalator, could increase the left-handed out-of-plane chirality of curved DNA structures. Then, EB and double strands were introduced as competing stimuli to transform monomers into allosteric conformations, leading to three different polymerization products. The steric trap between different polymerization products promoted the polymerized structures to keep their geometric properties, like chirality, under varying intensity of external stimuli. Our strategy harnesses allosteric effects for assembly of DNA-based materials and is expected to expand the design space for advanced control in synthetic materials.