Precision nanoscale patterning of TLR ligands for improved cancer immunotherapy.

In a recent issue of Nature Nanotechnology, Zeng et al. report that arraying immuno-stimulatory CpG molecules with specific nanoscale spacing on DNA origami nanoparticles enhanced Th1-polarized immune responses. These results highlight spatial presentation of adjuvants as a design strategy to optimize cancer vaccine efficacy, safety, and tolerability.

High-Throughput, Label-Free Detection of DNA Origami in Single-Cell Suspensions Using origamiFISH-Flow.

Structural DNA nanotechnology enables custom fabrication of nanoscale devices and promises diverse biological applications. However, the effects of design on DNA nanostructure (DN)-cell interactions in vitro and in vivo are not yet well-characterized. origamiFISH is a recently developed technique for imaging DNs in cells and tissues. Compared to the use of fluorescent tags, origamiFISH offers label-free and structure-agnostic detection of DNs with significantly improved sensitivity. Here, the origamiFISH technique is extended to quantify DNs in single-cell suspensions, including in nonadherent cells such as subsets of immune cells, via readout by flow cytometry. This method, referred to as origamiFISH-Flow, is high-throughput (e.g., 10 000 cells per second) and compatible with immunostaining for concurrent cell-type and cell-state characterization. It is shown that origamiFISH-Flow provides 20-fold higher signal-to-noise ratio for DN detection compared to dye labeling approaches, leading to the capture of >25-fold more DN+ cells under single-picomolar DN uptake concentrations. Additionally, the use of origamiFISH-Flow is validated to profile the uptake of various DN shapes across multiple cell lines and splenocytes, as well as to quantify in vivo DN accumulation in lymphoid organs. Together, origamiFISH-Flow offers a new tool to interrogate DN interactions with cells and tissues, while providing insights for tailoring their designs in bio-applications.

Universal, label-free, single-molecule visualization of DNA origami nanodevices across biological samples using origamiFISH.

Structural DNA nanotechnology enables the fabrication of user-defined DNA origami nanostructures (DNs) for biological applications. However, the role of DN design during cellular interactions and subsequent biodistribution remain poorly understood. Current methods for tracking DN fates in situ, including fluorescent-dye labelling, suffer from low sensitivity and dye-induced artifacts. Here we present origamiFISH, a label-free and universal method for the single-molecule fluorescence detection of DNA origami nanostructures in cells and tissues. origamiFISH targets pan-DN scaffold sequences with hybridization chain reaction probes to achieve 1,000-fold signal amplification. We identify cell-type- and DN shape-specific spatiotemporal distribution patterns within a minute of uptake and at picomolar DN concentrations, 10,000× lower than field standards. We additionally optimize compatibility with immunofluorescence and tissue clearing to visualize DN distribution within tissue cryo-/vibratome sections, slice cultures and whole-mount organoids. Together, origamiFISH enables the accurate mapping of DN distribution across subcellular and tissue barriers for guiding the development of DN-based therapeutics.

Peptide-Decorated DNA Nanostructures Promote Site-Specific Hydroxyapatite Growth.

The guiding principle for mineralized tissue formation is that mineral growth occurs through the interaction of Ca2+ and phosphate ions with extracellular matrix (ECM) proteins. Recently, nanoengineered DNA structures have been proposed as mimics to ECM scaffolds. However, these principles have not been applied to mineralized tissues. Here, we describe DNA nanostructures, namely, a DNA nanotube and a DNA origami rectangle that are site specifically functionalized with a mineral-promoting "SSEE" peptide derived from ECM proteins present in mineralized tissues. In the presence of Ca2+ and phosphate ions (mineralizing conditions), site-specific calcium phosphate formation occurred on the DNA nanostructures. Amorphous calcium phosphate or hydroxyapatite was formed depending on the incubation time, shape of the DNA nanostructure, and amount of Ca2+ and phosphate ions present. The ability to design and control the growth of hydroxyapatite through nanoengineered scaffolds provides insights into the mechanisms that may occur during crystal nucleation and growth of mineralized tissues and can inspire mineralized tissue regeneration strategies.

Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates.

Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.

Design Verification as Foundation for Advancing DNA Nanotechnology Applications.

Advances in the field of structural DNA nanotechnology have produced a growing number of nanostructures that are now being developed for diverse applications. Often, these nanostructures contain not only nucleic acids but also a myriad of other classes of molecules and materials such as proteins, lipids, sugars, and synthetic polymers. Increasing structural and compositional complexity promises new functional capabilities, but also demands new tools for design verification. Systematically verifying the design of DNA-scaffolded nanomaterials is necessary to identify and to refine their design rules, and to enable the field to progress toward "real world" applications. In this issue of ACS Nano, Bertosin et al. used single-particle cryo-electron microscopy to characterize the structure of multilayer DNA origamis following coating with oligolysine-based polymers, a class of material which has previously been shown to stabilize DNA nanostructures in physiological environments for use in biological applications. This Perspective summarizes their findings, discusses the broader challenges of verifying the design of DNA nanotechnologies incorporating complex materials, and highlights future directions for advancing their applications.

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation.

DNA nanotechnology enables programmable self-assembly of nucleic acids into user-prescribed shapes and dynamics for diverse applications. This work demonstrates that concepts from DNA nanotechnology can be used to program the enzymatic activity of the phage-derived T7 RNA polymerase (RNAP) and build scalable synthetic gene regulatory networks. First, an oligonucleotide-tethered T7 RNAP is engineered via expression of an N-terminally SNAP-tagged RNAP and subsequent chemical coupling of the SNAP-tag with a benzylguanine (BG)-modified oligonucleotide. Next, nucleic-acid strand displacement is used to program polymerase transcription on-demand. In addition, auxiliary nucleic acid assemblies can be used as "artificial transcription factors" to regulate the interactions between the DNA-programmed T7 RNAP with its DNA templates. This in vitro transcription regulatory mechanism can implement a variety of circuit behaviors such as digital logic, feedback, cascading, and multiplexing. The composability of this gene regulatory architecture facilitates design abstraction, standardization, and scaling. These features will enable the rapid prototyping of in vitro genetic devices for applications such as bio-sensing, disease detection, and data storage.

Extrusion of RNA from a DNA-Origami-Based Nanofactory.

Cells often spatially organize biomolecules to regulate biological interactions. Synthetic mimicry of complex spatial organization may provide a route to similar levels of control for artificial systems. As a proof-of-principle, we constructed an RNA-extruding nanofactory using a DNA-origami barrel with an outer diameter of 60 nm as a chassis for integrated rolling-circle transcription and processing of RNA through spatial organization of DNA templates, RNA polymerases, and RNA endonucleases. The incorporation efficiency of molecular components was quantified to be roughly 50% on designed sites within the DNA-origami chassis. Each integrated nanofactory with RNA-producing units, composed of DNA templates and RNA polymerases, produced 100 copies of target RNA in 30 min on average. Further integration of RNA endonucleases that cleave rolling-circle transcripts from concatemers into monomers resulted in 30% processing efficiency. Disabling spatial organization of molecular components on DNA origami resulted in suppression of RNA production as well as processing.

In Vitro Transcriptional Regulation via Nucleic-Acid-Based Transcription Factors.

Cells execute complex transcriptional programs by deploying distinct protein regulatory assemblies that interact with cis-regulatory elements throughout the genome. Using concepts from DNA nanotechnology, we synthetically recapitulated this feature in in vitro gene networks actuated by T7 RNA polymerase (RNAP). Our approach involves engineering nucleic acid hybridization interactions between a T7 RNAP site-specifically functionalized with single-stranded DNA (ssDNA), templates displaying cis-regulatory ssDNA domains, and auxiliary nucleic acid assemblies acting as artificial transcription factors (TFs). By relying on nucleic acid hybridization, de novo regulatory assemblies can be computationally designed to emulate features of protein-based TFs, such as cooperativity and combinatorial binding, while offering unique advantages such as programmability, chemical stability, and scalability. We illustrate the use of nucleic acid TFs to implement transcriptional logic, cascading, feedback, and multiplexing. This framework will enable rapid prototyping of increasingly complex in vitro genetic devices for applications such as portable diagnostics, bioanalysis, and the design of adaptive materials.

Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation.

DNA nanostructures have evoked great interest as potential therapeutics and diagnostics due to ease and robustness of programming their shapes, site-specific functionalizations and responsive behaviours. However, their utility in biological fluids can be compromised through denaturation induced by physiological salt concentrations and degradation mediated by nucleases. Here we demonstrate that DNA nanostructures coated by oligolysines to 0.5:1 N:P (ratio of nitrogen in lysine to phosphorus in DNA), are stable in low salt and up to tenfold more resistant to DNase I digestion than when uncoated. Higher N:P ratios can lead to aggregation, but this can be circumvented by coating instead with an oligolysine-PEG copolymer, enabling up to a 1,000-fold protection against digestion by serum nucleases. Oligolysine-PEG-stabilized DNA nanostructures survive uptake into endosomal compartments and, in a mouse model, exhibit a modest increase in pharmacokinetic bioavailability. Thus, oligolysine-PEG is a one-step, structure-independent approach that provides low-cost and effective protection of DNA nanostructures for in vivo applications.

Controlling DNA-nanoparticle serum interactions.

Understanding the interaction of molecularly assembled nanoparticles with physiological fluids is critical to their use for in vivo delivery of drugs and contrast agents. Here, we systematically investigated the factors and mechanisms that govern the degradation of DNA on the nanoparticle surface in serum. We discovered that a higher DNA density, shorter oligonucleotides, and thicker PEG layer increased protection of DNA against serum degradation. Oligonucleotides on the surface of nanoparticles were highly resistant to DNase I endonucleases, and degradation was carried out exclusively by protein-mediated exonuclease cleavage and full-strand desorption. These results enabled the programming of the degradation rates of the DNA-assembled nanoparticle system from 0.1 to 0.7 h-1 and the engineering of superstructures that can release two different preloaded dye molecules with distinct kinetics and half-lives ranging from 3.3 to 9.8 h. This study provides a general framework for investigating the serum stability of DNA-containing nanostructures. The results advance our understanding of engineering principles for designing nanoparticle assemblies with controlled in vivo behavior and present a strategy for storage and multistage release of drugs and contrast agents that can facilitate the diagnosis and treatment of cancer and other diseases.

Tuning the Drug Loading and Release of DNA-Assembled Gold-Nanorod Superstructures.

The use of DNA to assemble inorganic nanoparticles into superstructures is an emerging strategy to build non-toxic delivery vehicles for targeting diseases in the body. The impact of the core-satellite nanosystem design in mediating drug storage, drug release (via heat), and killing of HeLa cells in culture is investigated.

Engineering the Structure and Properties of DNA-Nanoparticle Superstructures Using Polyvalent Counterions.

DNA assembly of nanoparticles is a powerful approach to control their properties and prototype new materials. However, the structure and properties of DNA-assembled nanoparticles are labile and sensitive to interactions with counterions, which vary with processing and application environment. Here we show that substituting polyamines in place of elemental counterions significantly enhanced the structural rigidity and plasmonic properties of DNA-assembled metal nanoparticles. These effects arose from the ability of polyamines to condense DNA and cross-link DNA-coated nanoparticles. We further used polyamine wrapped DNA nanostructures as structural templates to seed the growth of polymer multilayers via layer-by-layer assembly, and controlled the degree of DNA condensation, plasmon coupling efficiency, and material responsiveness to environmental stimuli by varying polyelectrolyte composition. These results highlight counterion engineering as a versatile strategy to tailor the properties of DNA-nanoparticle assemblies for various applications, and should be applicable to other classes of DNA nanostructures.

DNA assembly of nanoparticle superstructures for controlled biological delivery and elimination.

The assembly of nanomaterials using DNA can produce complex nanostructures, but the biological applications of these structures remain unexplored. Here, we describe the use of DNA to control the biological delivery and elimination of inorganic nanoparticles by organizing them into colloidal superstructures. The individual nanoparticles serve as building blocks, whose size, surface chemistry and assembly architecture dictate the overall superstructure design. These superstructures interact with cells and tissues as a function of their design, but subsequently degrade into building blocks that can escape biological sequestration. We demonstrate that this strategy reduces nanoparticle retention by macrophages and improves their in vivo tumour accumulation and whole-body elimination. Superstructures can be further functionalized to carry and protect imaging or therapeutic agents against enzymatic degradation. These results suggest a different strategy to engineer nanostructure interactions with biological systems and highlight new directions in the design of biodegradable and multifunctional nanomedicine.

Fluorescence-tagged gold nanoparticles for rapidly characterizing the size-dependent biodistribution in tumor models.

Nanoparticle vehicles may improve the delivery of contrast agents and therapeutics to diseased tissues, but their rational design is currently impeded by a lack of robust technologies to characterize their in vivo behavior in real-time. This study demonstrates that fluorescent-labeled gold nanoparticles can be optimized for in vivo detection, perform pharmacokinetic analysis of nanoparticle designs, analyze tumor extravasation, and clearance kinetics in tumor-bearing animals. This optical imaging approach is non-invasive and high-throughput. Interestingly, these fluorescent gold nanoparticles can be used for multispectral imaging to compare several nanoparticle designs simultaneously within the same animal and eliminates the host-dependent variabilities across measured data. Together these results describe a novel platform for evaluating the performance of tumor-targeting nanoparticles, and provide new insights for the design of future nanotherapeutics.

Nanotoxicology. No signs of illness.

Quantum dots that contain cadmium, selenium and zinc are not toxic to monkeys for periods of up to 90 days, but longer-term studies are needed to determine the ultimate fate of the heavy metals that accumulate in the organs.

A strategy to assemble nanoparticles with polymers for mitigating cytotoxicity and enabling size tuning.

AIM: We aim to develop a facile strategy for assembling nanoparticles within cross-linked polymer micelles that enables tuning of their overall hydrodynamic size and surface charge and to mitigate toxicity. MATERIALS & METHODS: Hydrophobic nanoparticles and amphiphilic co-polymers self-assembled upon solvent-selective precipitation. Size-tunability of the assembled nanostructure was achieved by controlling both the nanoparticle and polymer ratio and the kinetics of the assembly process. RESULTS & CONCLUSION: We were successful in creating polymer shells on the surface of inorganic nanoparticles. The shell thickness could be tuned, and protect the nanoparticles from environmental degradation and minimize the cytotoxicity of inorganic nanoparticles. This strategy provides a method to engineer the interactions of nanoparticles with biological systems, including their targeted delivery to diseased tissues and their safety of use without significantly altering their original materials properties.

Strategies for the intracellular delivery of nanoparticles.

The ability to target contrast agents and therapeutics inside cells is becoming important as we strive to decipher the complex network of events that occur within living cells and design therapies that can modulate these processes. Nanotechnology researchers have generated a growing list of nanoparticles designed for such applications. These particles can be assembled from a variety of materials into desirable geometries and configurations and possess useful properties and functionalities. Undoubtedly, the effective delivery of these nanomaterials into cells will be critical to their applications. In this tutorial review, we discuss the fundamental challenges of delivering nanoparticles into cells and to the targeted organelles, and summarize strategies that have been developed to-date.

Visualizing quantum dots in biological samples using silver staining.

Quantum dot (QD) based contrast agents are currently being developed as probes for bioimaging and as vehicles for drug delivery. The ability to detect QDs, regardless of fluorescence brightness, in cells, tissues, and organs is imperative to their development. Traditional methods used to visualize the distribution of QDs in biological samples mainly rely on fluorescence imaging, which does not account for optically degenerate QDs as a result of oxidative quenching within the biological environment. Here, we demonstrate the use of silver staining for directly visualizing the distribution of QDs within biological samples under bright field microscopy. This strategy involves silver deposition onto the surface of QDs upon reduction by hydroquinone, effectively amplifying the size of QDs until visible for detection. The method can be used to detect non-fluorescent QDs and is fast, simple, and inexpensive.