Functionalizing DNA origami to investigate and interact with biological systems

DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.

Anion-specific structure and stability of guanidinium-bound DNA origami

While the folding of DNA into rationally designed DNA origami nanostructures has been studied extensively with the aim of increasing structural diversity and introducing functionality, the fundamental physical and chemical properties of these nanostructures remain largely elusive. Here, we investigate the correlation between atomistic, molecular, nanoscopic, and thermodynamic properties of DNA origami triangles. Using guanidinium (Gdm) as a DNA-stabilizing but potentially also denaturing cation, we explore the dependence of DNA origami stability on the identity of the accompanying anions. The statistical analyses of atomic force microscopy (AFM) images and circular dichroism (CD) spectra reveals that sulfate and chloride exert stabilizing and destabilizing effects, respectively, already below the global melting temperature of the DNA origami triangles. We identify structural transitions during thermal denaturation and show that heat capacity changes ΔC_p determine the temperature sensitivity of structural damage. The different hydration shells of the anions and their potential to form Gdm⁺ ion pairs in concentrated salt solutions modulate ΔC_p by altered wetting properties of hydrophobic DNA surface regions as shown by molecular dynamics simulations. The underlying structural changes on the molecular scale become amplified by the large number of structurally coupled DNA segments and thereby find nanoscopic correlations in AFM images.

Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate

DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out.

Strategies for developing DNA-encoded libraries beyond binding assays

DNA-encoded chemical libraries (DELs) have emerged as a powerful technology in drug discovery. The wide adoption of DELs in the pharmaceutical industry and the rapid advancements of DEL-compatible chemistry have further fuelled its development and applications. In general, a DEL has been considered as a massive binding assay to identify physical binders for individual protein targets. However, recent innovations demonstrate the capability of DELs to operate in the complex milieu of biological systems. In this Perspective, we discuss the recent progress in using DNA-encoded chemical libraries to interrogate complex biological targets and their potential to identify structures that elicit function or possess other useful properties. Future breakthroughs in these aspects are expected to catapult DEL to become a momentous technology platform not only for drug discovery but also to explore fundamental biology.

Pharmaceutical applications of framework nucleic acids

DNA is a biological polymer that encodes and stores genetic information in all living organism. Particularly, the precise nucleobase pairing inside DNA is exploited for the self-assembling of nanostructures with defined size, shape and functionality. These DNA nanostructures are known as framework nucleic acids (FNAs) for their skeleton-like features. Recently, FNAs have been explored in various fields ranging from physics, chemistry to biology. In this review, we mainly focus on the recent progress of FNAs in a pharmaceutical perspective. We summarize the advantages and applications of FNAs for drug discovery, drug delivery and drug analysis. We further discuss the drawbacks of FNAs and provide an outlook on the pharmaceutical research direction of FNAs in the future.

DNA nanotechnology-facilitated ligand manipulation for targeted therapeutics and diagnostics

Ligands, mostly binding to proteins to form complexes and catalyze chemical reactions, can serve as drug and probe molecules, as well as sensing elements. DNA nanotechnology can integrate the high editability of DNA nanostructures and the biological activity of ligands into functionalized DNA nanostructures in a manner of controlled ligand stoichiometry, type, and arrangement, which provides significant advantages for targeted therapeutics and diagnostics. As therapeutic agents, multiple- and multivalent-ligands functionalized DNA nanostructures increase ligand-receptor affinity and activate multivalent ligand-receptor interactions, enabling improved regulation of cell signaling and enhanced control of cell behavior. As diagnostic agents, multiple ligands interaction via DNA nanostructures endows DNA nanosensors with high sensitivity and excellent signal transduction capability. Herein, we review the principles and advantages of using DNA nanostructures to manipulate ligands for targeted therapeutics and diagnostics and provide future perspectives.

Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy

DNA origami nanostructures (DONs) are promising substrates for the single-molecule investigation of biomolecular reactions and dynamics by in situ atomic force microscopy (AFM). For this, they are typically immobilized on mica substrates by adding millimolar concentrations of Mg2+ ions to the sample solution, which enable the adsorption of the negatively charged DONs at the like-charged mica surface. These non-physiological Mg2+ concentrations, however, present a serious limitation in such experiments as they may interfere with the reactions and processes under investigation. Therefore, we here evaluate three approaches to efficiently immobilize DONs at mica surfaces under essentially Mg2+-free conditions. These approaches rely on the pre-adsorption of different multivalent cations, i.e., Ni2+, poly-l-lysine (PLL), and spermidine (Spdn). DON adsorption is studied in phosphate-buffered saline (PBS) and pure water. In general, Ni2+ shows the worst performance with heavily deformed DONs. For 2D DON triangles, adsorption at PLL- and in particular Spdn-modified mica may outperform even Mg2+-mediated adsorption in terms of surface coverage, depending on the employed solution. For 3D six-helix bundles, less pronounced differences between the individual strategies are observed. Our results provide some general guidance for the immobilization of DONs at mica surfaces under Mg2+-free conditions and may aid future in situ AFM studies.

DNA origami-based protein networks: from basic construction to emerging applications

Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.

DNA Nanostructures in the Fight Against Infectious Diseases

Throughout history, humanity has been threatened by countless epidemic and pandemic outbreaks of infectious diseases, from the Justinianic Plague to the Spanish flu to COVID-19. While numerous antimicrobial and antiviral drugs have been developed over the last 200 years to face these threats, the globalized and highly connected world of the 21st century demands for an ever-increasing efficiency in the detection and treatment of infectious diseases. Consequently, the rapidly evolving field of nanomedicine has taken up the challenge and developed a plethora of strategies to fight infectious diseases with the help of various nanomaterials such as noble metal nanoparticles, liposomes, nanogels, and virus capsids. DNA nanotechnology represents a comparatively recent addition to the nanomedicine arsenal, which, over the past decade, has made great progress in the area of cancer diagnostics and therapy. However, the past few years have seen also an increasing number of DNA nanotechnology-related studies that particularly focus on the detection and inhibition of microbial and viral pathogens. Herein, a brief overview of this rather young research field is provided, successful concepts as well as potential challenges are identified, and promising directions for future research are highlighted.

Influence of the geometry of fluorescently labelled DNA constructs on fluorescence anisotropy assay

DNA-encoded chemical libraries (DECLs) are powerful tools for modern drug discovery. A DECL is a pooled mixture of small molecule compounds, each of which is tagged with a unique DNA sequence which functions as a barcode. After incubation with a drug target and washing to remove non-binders, the bound molecules are eluted and submitted for DNA sequencing to determine which molecules are binding the target. While the DECL technology itself is ultra-high throughput, the following re-synthesis of identified compounds for orthogonal validation experiments remains the bottleneck. Using existing DNA-small molecule conjugates directly for affinity measurements, as opposed to complete compound resynthesis, could accelerate the discovery process. To this end, we have tested various geometries of fluorescently-labelled DNA constructs for fluorescence anisotropy (FA) experiments. Minimizing the distance between the fluorescent moiety and ligand can maximize the correlation between ligand-protein interaction and corresponding change in fluorophore rotational freedom, thus leading to larger, easier to interpret changes in FA values. However, close proximity can also cause artifacts due to potentially promiscuous interactions between fluorophore and protein. By balancing these two opposite effects, we have identified applicable fluorescently labelled DNA constructs displaying either a single ligand or pairs of fragments for affinity measurement using a FA assay.

Challenges and Perspectives of DNA Nanostructures in Biomedicine

DNA nanotechnology holds substantial promise for future biomedical engineering and the development of novel therapies and diagnostic assays. The subnanometer-level addressability of DNA nanostructures allows for their precise and tailored modification with numerous chemical and biological entities, which makes them fit to serve as accurate diagnostic tools and multifunctional carriers for targeted drug delivery. The absolute control over shape, size, and function enables the fabrication of tailored and dynamic devices, such as DNA nanorobots that can execute programmed tasks and react to various external stimuli. Even though several studies have demonstrated the successful operation of various biomedical DNA nanostructures both in vitro and in vivo, major obstacles remain on the path to real-world applications of DNA-based nanomedicine. Here, we summarize the current status of the field and the main implementations of biomedical DNA nanostructures. In particular, we focus on open challenges and untackled issues and discuss possible solutions.

Quantitative Assessment of Tip Effects in Single-Molecule High-Speed Atomic Force Microscopy Using DNA Origami Substrates

High-speed atomic force microscopy (HS-AFM) is widely employed in the investigation of dynamic biomolecular processes at a single-molecule level. However, it remains an open and somewhat controversial question, how these processes are affected by the rapidly scanned AFM tip. While tip effects are commonly believed to be of minor importance in strongly binding systems, weaker interactions may significantly be disturbed. Herein, we quantitatively assess the role of tip effects in a strongly binding system using a DNA origami-based single-molecule assay. Despite its femtomolar dissociation constant, we find that HS-AFM imaging can disrupt monodentate binding of streptavidin (SAv) to biotin (Bt) even under gentle scanning conditions. To a lesser extent, this is also observed for the much stronger bidentate SAv-Bt complex. The presented DNA origami-based assay can be universally employed to quantify tip effects in strongly and weakly binding systems and to optimize the experimental settings for their reliable HS-AFM imaging.

Multivalent glycan arrays

Glycan microarrays have become a powerful technology to study biological processes, such as cell-cell interaction, inflammation, and infections. Yet, several challenges, especially in multivalent display, remain. In this introductory lecture we discuss the state-of-the-art glycan microarray technology, with emphasis on novel approaches to access collections of pure glycans and their immobilization on surfaces. Future directions to mimic the natural glycan presentation on an array format, as well as in situ generation of combinatorial glycan collections, are discussed.

Deformation-Resistant, Double-Layer DNA Self-Assembled Nanoraft with High Positioning Precision

The precise control and localization of a single entity on a stiff and rigid interface are crucial for exploring interentity interactions. A critical challenge for the precise positioning of a single entity on a substrate lies in how to construct a solid and flat interface with high positioning precision. Herein, we developed a solid DNA self-assembled nanoraft with high conformational stability by constructing a double-layer DNA origami. Compared with conventional single-layer DNA origami, the double-layer nanoraft showed higher deformation resistance capability with the nanorafts possessing higher structural integrity. Further, we analyzed the deformability of these two DNA origamis by structural reconstruction simulation, the results of which were significantly consistent with transmission electron microscopy experimental results. Using the deformation-resistant DNA self-assembled nanoraft, we achieved the precise positioning of single-stranded DNA probes on the DNA nanointerface by visualizing the AuNPs captured by the probes. Compared with the interface constructed by single-layer DNA origami, the distance between AuNPs on the two-layer DNA origami was more approximate to the theoretical value that we designed. The rigid nanointerface with high deformation resistance capability thus provides a powerful means for facilitating the self-assembly of heterogeneous elements with precisely controlled spacing and position.

Prescribing DNA Origami Patterns via Scaffold Decoration

DNA origami has rapidly emerged as a powerful technique to fabricate user-defined DNA nanostructures. However, the ability to custom-make patterns on DNA origami template is hampered by the heavy workload and high cost of changing staple DNA (up to several hundred strands per set). Here, a scaffold-decorated DNA origami method is developed by prescribing the pattern information to the scaffold DNA. For each pixel of an origami, a designed "pixel strand" (P-strand) is hybridized to the scaffold, strongly preoccupying a specific position and competing with invading staples in a mild origami assembly. To fabricate a new origami pattern, the P-strand set needs to be replaced with a universal staple set. The yield of thus-fabricated DNA origami patterns is comparable to a conventional DNA origami with canonical method. One-pot fabrication of three different nanopatterns in a single test-tube is further demonstrated. Also, dynamic switch of the pattern is shown. This method provides a generic approach and offers large flexibility for scaling up the nanofabrication with DNA origami by kinetically modulating the reaction pathway of the staples with the scaffold DNA, which represents a novel route in the self-assembly of complex biomolecular systems.

A dual signal amplification strategy combining thermally initiated SI-RAFT polymerization and DNA-templated silver nanoparticles for electrochemical determination of DNA

A highly sensitive method is described for determination of DNA. It is based on dual signal amplification, viz. (a)DNA-templated metal deposition, and (b) thermally initiated surface-initiated reversible addition-fragmentation chain transfer (SI-RAFT) polymerization. A peptide nucleic acid (PNA) with a terminal thiol group was grasped onto a gold electrode by self-assembly. The modified electrode serves as a probe to selectively capture target DNA (tDNA). In the next step, Zr(IV) ions are bound to the phosphate groups of the tDNA. A chain-transfer agent (CTA) for thermally initiated SI-RAFT polymerization, 4-cyano-4-(phenylcarbonothioylthio)pentanoic acid (CPAD), was immobilized on tDNA by conjugation of the carboxy group to Zr(IV) ions. Subsequently, numerous monomers of glycosyloxyethyl methacrylate (GEMA) were connected to the CPAD by thermally initiated SI-RAFT polymerization with azobisisobutyronitrile (AIBN) serving as the free-radical thermal initiator. Afterwards, hydroxyl groups of the GEMA were oxidized to aldehyde groups reacting with sodium periodate, and silver nanoparticles were further introduced on the surface of electrode via "silver mirror reaction". This results in a large electrochemical signal amplification. Under optimized conditions, the electrochemical signal (best measured at a working potential of 0 V vs. SCE (KCl; 3 M)) increases linearly with the logarithm of tDNA concentration in the 10 to 10⁶ aM concentration range. The detection limit is as low as 5.6 aM (~34 molecules in a 10 μL sample). This is lower by factors between 2 and 1800 times than detection limits of most other ultra-sensitive electrochemical DNA assays. Graphical abstractSchematic representation of a dual signal amplification strategy combining thermally initiated surface-initiated reversible addition-fragmentation chain transfer polymerization (SI-RAFT) and DNA-templated silver nanoparticles for electrochemical determination of DNA.

Enhancing the stability of DNA origami nanostructures: staple strand redesign versus enzymatic ligation

DNA origami structures have developed into versatile tools in molecular sciences and nanotechnology. Currently, however, many potential applications are hindered by their poor stability, especially under denaturing conditions. Here we present and evaluate two simple approaches to enhance DNA origami stability. In the first approach, we elevated the melting temperature of nine critical staple strands by merging the oligonucleotides with adjacent sequences. In the second approach, we increased the global stability by enzymatically ligating all accessible staple strand ends directly. By monitoring the gradual urea-induced denaturation of a prototype triangular DNA origami modified by these approaches using atomic force microscopy, we show that rational redesign of a few, critical staple strands leads to a considerable increase in overall stability at high denaturant concentration and elevated temperatures. In addition, enzymatic ligation yields DNA nanostructures with superior stability at up to 37 °C and in the presence of 6 M urea without impairing their shape. This bio-orthogonal approach is readily adaptable to other DNA origami structures without the need for synthetic nucleotide modifications when structural integrity under harsh conditions is required.

Bioapplications of DNA nanotechnology at the solid-liquid interface

DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.

Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability

DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.

Quantitative Measurement of Spatial Effects of DNA Origami on Molecular Binding Reactions Detected using Atomic Force Microscopy

DNA origami is a ubiquitous nanostructure that can be used as a universal scaffold for constructing molecular motors, nanosensors, nanodrugs, and optical devices. Understanding the inherent heterogeneity of DNA origami structures is crucial for optimizing the design of high-efficiency nanosized-devices. Here, we investigated the spatial effects of the DNA origami on binding reactions using atomic force microscopy. Protein complexes formed more efficiently at the vertex and rim than on the surface of the DNA origami; surprisingly, the maximum difference in biotin-streptavidin binding efficiency was over 80%, and the change in the binding rate was approximately 40-fold, suggesting the presence of distinct microenvironments at different locations of the DNA origami. Our findings are not only useful for the potential applications of the DNA origami, but also for clarifying differences in nanomaterials caused by nonuniform distribution or defects.

DNA nanostructures: A versatile lab-bench for interrogating biological reactions

At its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches - including atomic force microscopy - by isolating, arranging and contextualising biological systems at the single molecule level. This review explores the state-of-the-art of DNA-based nanoscale tools employed to enhance and tune the interrogation of biological reactions, the study of spatially distributed pathways, the visualisation of enzyme interactions, the application and detection of forces to biological systems, and biosensing platforms.

Create Nanoscale Patterns with DNA Origami

Structural deoxyribonucleic acid (DNA) nanotechnology offers a robust platform for diverse nanoscale shapes that can be used in various applications. Among a wide variety of DNA assembly strategies, DNA origami is the most robust one in constructing custom nanoshapes and exquisite patterns. In this account, the static structural and functional patterns assembled on DNA origami are reviewed, as well as the reconfigurable assembled architectures regulated through dynamic DNA nanotechnology. The fast progress of dynamic DNA origami nanotechnology facilitates the construction of reconfigurable patterns, which can further be used in many applications such as optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.