Designed DNA Crystal Habit Modifiers

Precision Self-assembly of 3D DNA Crystals Using Microfluidics

Controlling the uniformity in size and quantity of macroscopic three-dimensional (3D) DNA crystals is essential for their integration into complex systems and broader applications. However, achieving such control remains a major challenge in DNA nanotechnology. Here, we present a novel strategy for synthesizing monodisperse 3D DNA single crystals using microfluidic double-emulsion droplets as nanoliter-scale microreactors. These uniformly sized droplets can shrink and swell without leaking their inner contents, allowing the concentration of the DNA solution inside to be adjusted. The confined volume ensures that, once a crystal seed forms, it rapidly consumes the available DNA material, preventing the formation of additional crystals within the same droplet. This approach enables precise control over crystal growth, resulting in a yield of one DNA single crystal per droplet, with a success rate of up to 98.6% ± 0.9%. The resulting DNA crystals exhibit controlled sizes, ranging from 19.3 ± 0.9 μm to 56.8 ± 2.6 μm. Moreover, this method can be applied to the controlled growth of various types of DNA crystals. Our study provides a new pathway for DNA crystal self-assembly and microengineering.

Advancing DNA Structural Analysis: A SERS Approach Free from Citrate Interference Combined with Machine Learning

Surface-enhanced Raman spectroscopy (SERS) has become an indispensable tool for biomolecular analysis, yet the detection of DNA signals remains hindered by spectral interference from citrate ions, which overlap with key DNA features. This study introduces an innovative, ultrasensitive SERS platform utilizing thiol-modified silver nanoparticles (Ag@SDCNPs) that overcomes this challenge by eliminating citrate interference. This platform enables direct, interference-free detection and structural characterization of a wide range of DNA conformations, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), i-motif, hairpin, G-quadruplex, and triple-stranded DNA (tsDNA). Employing calcium ions as aggregating agents and deuterated methanol as an internal standard, the system achieved high spectral quality and reproducibility. Machine learning (ML) techniques, such as linear discriminant analysis (LDA) and t-distributed stochastic neighbor embedding (t-SNE), were utilized for spectral classification, alongside support vector machines (SVM) for predictive modeling, yielding accuracies above 99%. These findings establish a robust and versatile platform for DNA structural analysis, offering transformative potential for applications in clinical diagnostics and biomedical research.

Engineered 3D DNA Crystals: A Molecular Design Perspective

Recent advances in biomolecular self-assembly have transformed material science, enabling the creation of novel materials with unparalleled precision and functionality. Among these innovations, 3D DNA crystals have emerged as a distinctive class of macroscopic materials, engineered through the bottom-up approach by DNA self-assembly. These structures uniquely combine precise molecular ordering with high programmability, establishing their importance in advanced material design. This review delves into the molecular design of engineered 3D DNA crystals, classifying current crystal structures based on "crystal bond orientations" and examining key aspects of in-silico molecular design, self-assembly, and crystal modifications. The functionalization of 3D DNA crystals for applications in crystallization scaffolding, biocatalysis, biosensing, electrical and optical devices, as well as in the emerging fields of DNA computing and data storage are explored. Finally, the ongoing challenges are addressed and future directions to advance the field of engineered 3D DNA crystals are proposed.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

Exploring the Potential of Three-Dimensional DNA Crystals in Nanotechnology: Design, Optimization, and Applications

DNA has been used as a robust material for the building of a variety of nanoscale structures and devices owing to its unique properties. Structural DNA nanotechnology has reported a wide range of applications including computing, photonics, synthetic biology, biosensing, bioimaging, and therapeutic delivery, among others. Nevertheless, the foundational goal of structural DNA nanotechnology is exploiting DNA molecules to build three-dimensional crystals as periodic molecular scaffolds to precisely align, obtain, or collect desired guest molecules. Over the past 30 years, a series of 3D DNA crystals have been rationally designed and developed. This review aims to showcase various 3D DNA crystals, their design, optimization, applications, and the crystallization conditions utilized. Additionally, the history of nucleic acid crystallography and potential future directions for 3D DNA crystals in the era of nanotechnology are discussed.

5'-Phosphorylation Strengthens Sticky-End Cohesions

Sticky-end cohesion plays a critical role in molecular biology and nucleic acid nanotechnology. Although free energy calculations and molecular mechanics can predict these interactions, chemical modification would compromise such predictions. Herein, we have used rationally designed 3D DNA crystals as a tool to experimentally investigate the modulation of 5'-phosphorylation on sticky-end cohesions. We have found that 5'-phosphorylation strengthens the sticky-end cohesion: in a DNA crystal self-assembled exclusively via sticky-end cohesions, 5'-phosphorylation not only promotes the crystallization process, in general, but also accelerates the crystal growth along designed directions. Such a finding allows the fine-tuning of DNA crystallization kinetics and the control of DNA crystal morphology. It also suggests a potential difference in self-assembly kinetics between natural DNA (with 5'-phosphorylation) and synthetic DNA (without 5'-phosphorylation).

Nanoscopic observation of a DNA crystal surface and its dynamic formation and degradation using atomic force microscopy

We report the direct observation of the formation and degradation of tensegrity triangle DNA crystals using atomic force microscopy (AFM). We observed the crystal surface by AFM and characterized the lattice coordination of the assembled triangle units at a molecular level. We visualized dynamic formation and degradation of the crystals and characterized them at nano-scale resolution.

Modulating Self-Assembly of DNA Crystals with Rationally Designed Agents

This manuscript reports a strategy for controlling the crystallization kinetics and improving the quality of engineered self-assembled 3D DNA crystals. Growing large, high-quality biomacromolecule crystals is critically important for determining the 3D structures of biomacromolecules. It often presents a great challenge to structural biologists. Herein, we introduce a rationally designed agent to modulate the crystallization process. Under such conditions, fewer, but larger, crystals that yield diffraction patterns of modestly higher resolution are produced compared with the crystals from conditions without the modulating agent. We attribute the improvement to a smaller number of nuclei and slow growth rate of crystallization. This strategy is expected to be generally applicable for crystallization of other biomacromolecules.

Core-Shell and Layer-by-Layer Assembly of 3D DNA Crystals

A long-standing goal of DNA nanotechnology has been to assemble 3D crystals to be used as molecular scaffolds. The DNA 13-mer, BET66, self-assembles via Crick-Watson and noncanonical base pairs to form crystals. The crystals contain solvent channels that run through them in multiple directions, allowing them to accommodate tethered guest molecules. Here, the first example of biomacromolecular core-shell crystal growth is described, by showing that these crystals can be assembled with two or more discrete layers. This approach leads to structurally identical layers on the DNA level, but with each layer differentiated based on the presence or absence of conjugated guest molecules. The crystal solvent channels also allow layer-specific postcrystallization covalent attachment of guest molecules. Through controlling the guest-molecule identity, concentration, and layer thickness, this study opens up a new method for using DNA to create multifunctional periodic biomaterials with tunable optical, chemical, and physical properties.