Nucleic Acid Nanotechnology: Innovations Shaping the Future of Biomedicine and Diagnostics

Nucleic acid nanotechnology, which leverages the unique properties of DNA and RNA to design and construct nanoscale architectures and devices, has emerged as a transformative field with profound implications across biomedicine, materials science, and diagnostics. Achieving precise control over the design, synthesis, and functionality of these nucleic acid-based structures is essential to fully realize their potential. Recently, sophisticated methods for manipulating DNA and RNA at the molecular level have driven groundbreaking advances in a wide range of applications, from targeted bioimaging to precision therapeutics. This special issue of Small Methods, titled “Nucleic Acid Nanotechnology” highlights these cutting-edge developments. It features 14 review articles, 22 research papers, and 1 perspective, offering a comprehensive overview of the current state of this rapidly evolving field.

Several articles in this issue explore the self-assembly of DNA into defined structures, with a focus on design principles. Li et al. (smtd.2401455) provide a detailed perspective on engineered 3D DNA crystals from a molecular design standpoint. Their review categorizes current crystal structures based on “crystal bond orientations” and explores key aspects of in-silico molecular design, self-assembly, and crystal modifications. Xiao et al. (smtd.2401649) introduce a series of double-layered tiles, each incorporating two cDAO motifs linked by layered crossovers (LXs). They demonstrate how tile curvature and inter-layer angles can be tuned by programming the positions of LXs in base-length increments. Wang et al. (smtd.2401629) offer a comprehensive review of the precise fabrication of finite-sized DNA origami superstructures, comparing various assembly strategies, such as heterogeneous, self-limited, and templated self-assembly, while critically evaluating their advantages and limitations. Sleiman et al. (smtd.2401477) present an efficient method for automated DNA nanoprinting, advancing the synthesis of covalently branched DNA through hybridization with reactive complementary strands, cross-linking with small molecules, and strand displacement to capture “daughter” products. This method ensures high yields and reuse of the “mother” template, facilitating the precise transfer of DNA strands to various small molecules. Zhang et al. (smtd.2401343) explore the structural dynamics of DNA origami, analyzing how parallel and antiparallel crossovers influence the folding process and stability. Šulc et al. (smtd.2401526) introduce the oxDNA simulation ecosystem to model DNA origami structures, highlighting the need for parameter adjustments based on specific structures, and noting the ecosystem's utility for simpler models but limitations when dealing with complex structures. Liu et al. (smtd.2401401) utilize DNA origami to regulate the crowding of G-quadruplex-hemin complexes, offering insights into how molecular crowding affects DNAzymes and how DNA origami can be employed as a template for designing sensors. Sun et al. (smtd.2400694) review the development of DNA-based conductors, discussing material design and their potential in ultra-scaled electronics. Yuan et al. (smtd.2401102) analyze the thermodynamics and kinetics of nucleic acid-based molecular recognition, providing a framework for rational design in nucleic acid-related applications. Li et al. (smtd.2401631) summarize the common methodological and design principles of DNA nanotechnology and encoded libraries, exploring their synergies for future applications with enhanced functionality.

In response to the growing demand for high-resolution imaging and sensitive detection methods, several papers in this issue examine how DNA nanotechnology is advancing these techniques. Zhao et al. (smtd.2401303) explore the broad potential of DNA-encoded fluorescent signals for biological imaging, detailing the design of DNA-based probes for targeted labeling and multiplexed detection. Hong et al. (smtd.2401279) push the boundaries of bioimaging by demonstrating how programmable DNA reactions can control the localization and activation of fluorescent molecules, enhancing the capabilities of fluorescence microscopy. Li et al. (smtd.2401531) introduce a novel method for imaging RNA species with high spatial precision, using enzymatic activation of hybridization chain reactions to target microRNAs within mitochondria. Han et al. (smtd.2401559) expand upon this approach, developing a DNA origami-based CRISPR/dCas9 system for real-time genomic visualization and tracking in living cells. Jungmann et al. (smtd.2401799) present a DNA-PAINT-based method for imaging protein interactions, enabling the direct visualization of ligand-receptor binding at single-protein resolution, which offers new insights into cell signaling. Liu et al. (smtd.2402095) developed DNA switches integrated with electrochemical sensors to detect microRNA, advancing the field of biosensing. Wei et al. (smtd.2401416) discuss methods for improving sequencing accuracy through custom primers, facilitating faster and more specific tests. Gu et al. (smtd.2401236) present the fusion of allosteric ribozymes with CRISPR-Cas12a to create efficient diagnostics for small molecule targets. Song et al. (smtd.2401041) investigate DNA nanostructures in activating cGAS-STING signaling pathways. Fu et al. (smtd.2401733) review methods for faster single-stranded nucleic acid detection in point-of-care diagnostics, offering solutions for bedside DNA-based diagnostic results. Sia et al. (smtd.2401988) introduce a method to improve DNA amplification using PCR for better clinical testing. Sun et al. (smtd.2401389) highlight the potential of DNA-assisted nanoparticle separation in diagnostic assays.

A significant portion of this issue is dedicated to advancing therapeutic applications of DNA nanotechnology. Yang et al. (smtd.2400349) study a novel aptamer-based approach for tumor-specific degradation of microRNA, proposing a RIBOTAC strategy for precise cancer therapy. Tan et al. (smtd.2400551) review the potential of exosomes enhanced with aptamers for targeted theranostics, emphasizing their role in precise cancer treatment and diagnostics. Ahn et al. (smtd.2400902) investigate strategies to improve the delivery of oligonucleotide therapeutics across the blood-brain barrier, focusing on protein corona-assisted DNA cubes for enhanced drug transport. Zhang et al. (smtd.2401286) explore the development of new polymers for gene delivery, specifically GalNAc-modified poly(β-amino esters) for effective genetic material delivery. Jiang et al. (smtd.2401514) examine chemical engineering strategies for applying DNAzymes in biosensing and gene therapy, with a focus on enhancing DNAzyme stability, activity, and target specificity. Wang et al. (smtd.2401160) report on a methyl-engineered DNAzyme for monitoring alkyltransferase activity and self-sufficient gene regulation. Li et al. (smtd.2401600) developed an innovative in vitro selection strategy using a pre-structured DNA library to generate high-affinity dimeric aptamers for the SARS-CoV-2 spike protein, which could be pivotal for future therapeutic applications. Yang et al. (smtd.2401712) synthesize a series of cholesterol-derived mannopolypeptide and cholesterol-conjugated mannose derivatives for the construction of mannosylated LNPs for efficient mRNA delivery.

This issue also explores critical issues related to the safe and effective translation of DNA nanotechnology. Yang et al. (smtd.2401007) investigate the pharmacokinetics, immunogenicity, and immunotoxicity of DNA nanoparticles, finding a favorable safety profile for potential therapeutic use. Sugimoto et al. (smtd.2401630) screen 179 compounds to identify those that suppress RNA accumulation in neuroblastoma cells, providing insights for therapeutic strategies targeting neurodegenerative diseases. Chao et al. (smtd.2401360) review advancements in tetrahedral nucleic acid frameworks for biomedical applications. Zuo et al. (smtd.2401476) examine the nucleophilic reactions of phosphorothioate oligonucleotides, highlighting their use in drug delivery and fluorescent labeling. Roh et al. (smtd.2401881) develop methods for reconfiguring RCA-originated DNA-MgPPi micro hybrids into multifunctional DNA-metal nanohybrids with potential applications in drug delivery and photothermal therapy. Liu et al. (smtd.2401572) stress the importance of studying aptamer binding and dissociation constants, which are crucial for optimizing aptamer-based applications. Weizmann et al. (smtd.2401113) provide an opinion on how DNA nanotechnology can advance topoisomerase research, proposing areas for further integration with biology.

This special issue of Small Methods offers a comprehensive platform to showcase the diversity and significant advancements in nucleic acid nanotechnology. By highlighting innovative methods and applications, it aims to stimulate further research and foster collaboration in this exciting and rapidly expanding field.

The authors declare no conflict of interest.