DNA nanostructure decoration: a how-to tutorial.

DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.

Binding, brightness, or noise? Extracting temperature-dependent properties of dye bound to DNA.

We present a method for extracting temperature-dependent thermodynamic and photophysical properties of SYTO-13 dye bound to DNA from fluorescence measurements. Together, mathematical modeling, control experiments, and numerical optimization enable dye binding strength, dye brightness, and experimental noise (or error) to be discriminated from one another. By focusing on the low-dye-coverage regime, the model avoids bias and can simplify quantification. Utilizing the temperature-cycling capabilities and multi-reaction chambers of a real-time PCR machine increases throughput. Significant well-to-well and plate-to-plate variation is quantified by using total least squares to account for error in both fluorescence and nominal dye concentration. Properties computed independently for single-stranded DNA and double-stranded DNA by numerical optimization are consistent with intuition and explain the advantageous performance of SYTO-13 in high-resolution melting and real-time PCR assays. Distinguishing between binding, brightness, and noise also clarifies the mechanism for the increased fluorescence of dye in a solution of double-stranded DNA compared to single-stranded DNA; in fact, the explanation changes with temperature.

Synthesizing the biochemical and semiconductor worlds: the future of nucleic acid nanotechnology.

Since its inception nearly 40 years ago [Kallenbach, et al., Nature, 1983, 305, 829; N. C. Seeman, J. Theoretical Biology, 1982, 99, 237], Nucleic Acid Nanotechnology (NAN) has matured and is beginning to find commercial applications. For the last 20 years, it has been suggested that NAN might be an effective replacement for parts of the semiconductor lithography or protein engineering workflows. However, in that time, these incumbent technologies have made significant advances, and our understanding of NAN's strengths and weaknesses has progressed, suggesting that the greatest opportunities in fact lie elsewhere. Given the commitment of resources necessary to bring new technologies to the market and the desire to use those resources as wisely as possible, we conduct a critical examination of where NAN may benefit from, and provide benefit to, adjacent technologies and compete least with market incumbents. While the accuracy of our conclusions may be limited by our ability to extrapolate from the current state of NAN to its future commercial success, we conclude that the next promising direction is to create a bridge between biology and semiconductor technology. We also hope to stimulate a robust conversation around this technology's capabilities with the goal of building consensus on those research and development efforts that would advance NAN to the greatest effect in real-world applications.

Best practice for improved accuracy: A critical reassessment of van't Hoff analysis of melt curves.

Biomolecular thermodynamics, particularly for DNA, are frequently determined via van't Hoff analysis of optically measured melt curves. Accurate and precise values of thermodynamic parameters are essential for the modeling of complex systems involving cooperative effects, such as RNA tertiary structure and DNA origami, because the uncertainties associated with each motif in a folding energy landscape can compound, significantly reducing the power of predictive models. We follow the sources of uncertainty as they propagate through a typical van't Hoff analysis to derive best practices for melt experiments and subsequent data analysis, assuming perfect signal baseline correction. With appropriately designed experiments and analysis, a van't Hoff approach can provide surprisingly high precision, e.g., enthalpies may be determined with a precision as low as 10-2 kJ ⋅ mol-1 for an 8-base DNA oligomer.

Unmasking the Resolution-Throughput Tradespace of Focused-Ion-Beam Machining.

Focused-ion-beam machining is a powerful process to fabricate complex nanostructures, often through a sacrificial mask that enables milling beyond the resolution limit of the ion beam. However, current understanding of this super-resolution effect is empirical in the spatial domain and nonexistent in the temporal domain. This article reports the primary study of this fundamental tradespace of resolution and throughput. Chromia functions well as a masking material due to its smooth, uniform, and amorphous structure. An efficient method of in-line metrology enables characterization of ion-beam focus by scanning electron microscopy. Fabrication and characterization of complex test structures through chromia and into silica probe the response of the bilayer to a focused beam of gallium cations, demonstrating super-resolution factors of up to 6 ± 2 and improvements to volume throughput of at least factors of 42 ± 2, with uncertainties denoting 95% coverage intervals. Tractable theory models the essential aspects of the super-resolution effect for various nanostructures. Application of the new tradespace increases the volume throughput of machining Fresnel lenses by a factor of 75, enabling the introduction of projection standards for optical microscopy. These results enable paradigm shifts of sacrificial masking from empirical to engineering design and from prototyping to manufacturing.

Failure Mechanisms in DNA Self-Assembly: Barriers to Single-Fold Yield.

Understanding the folding process of DNA origami is a critical stepping stone to the broader implementation of nucleic acid nanofabrication technology but is notably nontrivial. Origami are formed by several hundred cooperative hybridization events-folds-between spatially separate domains of a scaffold, derived from a viral genome, and oligomeric staples. Individual events are difficult to detect. Here, we present a real-time probe of the unit operation of origami assembly, a single fold, across the scaffold as a function of hybridization domain separation-fold distance-and staple/scaffold ratio. This approach to the folding problem elucidates a predicted but previously unobserved blocked state that acts as a limit on yield for single folds, which may manifest as a barrier in whole origami assembly.

Analysis and uncertainty quantification of DNA fluorescence melt data: Applications of affine transformations.

Fluorescence-based measurements are a standard tool for characterizing the thermodynamic properties of DNA systems. Nonetheless, experimental melt data obtained from polymerase chain-reaction (PCR) machines (for example) often leads to signals that vary significantly between datasets. In many cases, this lack of reproducibility has led to difficulties in analyzing results and computing reasonable uncertainty estimates. To address this problem, we propose a data analysis procedure based on constrained, convex optimization of affine transformations, which can determine when and how melt curves collapse onto one another. A key aspect of this approach is its ability to provide a reproducible and more objective measure of whether a collection of datasets yields a consistent "universal" signal according to an appropriate model of the raw signals. Importantly, integrating this validation step into the analysis hardens the measurement protocol by allowing one to identify experimental conditions and/or modeling assumptions that may corrupt a measurement. Moreover, this robustness facilitates extraction of thermodynamic information at no additional cost in experimental time. We illustrate and test our approach on experiments of Förster resonance energy transfer (FRET) pairs used study the thermodynamics of DNA loops.

Revealing thermodynamics of DNA origami folding via affine transformations.

Structural DNA nanotechnology, as exemplified by DNA origami, has enabled the design and construction of molecularly-precise objects for a myriad of applications. However, limitations in imaging, and other characterization approaches, make a quantitative understanding of the folding process challenging. Such an understanding is necessary to determine the origins of structural defects, which constrain the practical use of these nanostructures. Here, we combine careful fluorescent reporter design with a novel affine transformation technique that, together, permit the rigorous measurement of folding thermodynamics. This method removes sources of systematic uncertainty and resolves problems with typical background-correction schemes. This in turn allows us to examine entropic corrections associated with folding and potential secondary and tertiary structure of the scaffold. Our approach also highlights the importance of heat-capacity changes during DNA melting. In addition to yielding insight into DNA origami folding, it is well-suited to probing fundamental processes in related self-assembling systems.

So, You Want to Have a Nanofab? Shared-Use Nanofabrication and Characterization Facilities: Cost-of-Ownership, Toolset, Utilization, and Lessons Learned.

Nanofabrication/characterization facilities enable research and development activities across a host of science and engineering disciplines. The collection of tools and supporting infrastructure necessary to construct, image, and measure micro- and nanoscale materials, devices, and systems is complex and expensive to establish, and it is costly to maintain and optimize. As a result, these facilities are typically operated in a shared-use mode. We discuss the key factors that must be considered to successfully create and sustain such facilities. These include the need for long-term vision and institutional commitment, and the hands-on involvement of managers in facility operations. We consider startup, operating, and recapitalization costs, together with algorithms for cost recovery and tool-time allocation. The acquisition of detailed and comprehensive project and tool-utilization data is essential for understanding and optimizing facility operations. Only such a data-driven decision-making approach can maximize facility impact on institutional goals. We illustrate these concepts using the National Institute of Standards and Technology (NIST) NanoFab as our test case, but the methodologies and resources presented here should be useful to all those faced with this challenging task.

Aligned carbon nanotube morphogenesis predicts physical properties of their polymer nanocomposites.

Carbon nanostructure (CNS) based polymer nanocomposites (PNCs) are of interest due to the superior properties of the CNS themselves, scale effects, and the ability to transfer these properties anisotropically to the bulk material. However, measurements of physical properties of such materials are not in agreement with theoretical predictions. Recently, the ability to characterize the 3D morphology of such PNCs at the nanoscale has been significantly improved, with rich, quantitative data extracted from tomographic transmission electron microscopy (TEM). In this work, we use new, nanoscale quantitative 3D morphological information and stochastic modeling to re-interpret experimental measurements of continuous aligned carbon nanotube (A-CNT) PNC properties as a function of A-CNT packing/volume fraction. The 3D tortuosity calculated from tomographic reconstructions and its evolution with volume fraction is used to develop a novel definition of waviness that incorporates the stochastic nature of CNT growth. The importance of using randomly wavy CNTs to model these materials is validated by agreement between simulated and previously-measured PNC elastic moduli. Secondary morphological descriptors such as CNT-CNT junction density and inter-junction distances are measured for transport property predictions. The scaling of the junction density with CNT volume fraction is observed to be non-linear, and this non-linearity is identified as the primary reason behind the previously unexplained scaling of aligned-CNT PNC longitudinal thermal conductivity. By contrast, the measured electrical conductivity scales linearly with volume fraction as it is relatively insensitive to junction density beyond percolation. This result verifies prior hypotheses that electrical conduction in such fully percolated and continuous CNT systems is dominated by the bulk resistivity of the CNTs themselves. This combination of electron tomographic data and stochastic simulations is a powerful method for establishing a predictive capability for nanocomposite structure-property relations, making it an essential aid in understanding and tailoring the next-generation of advanced composites.

Low-Temperature Growth of Carbon Nanotubes Catalyzed by Sodium-Based Ingredients.

Synthesis of low-dimensional carbon nanomaterials such as carbon nanotubes (CNTs) is a key driver for achieving advances in energy storage, computing, and multifunctional composites, among other applications. Here, we report high-yield thermal chemical vapor deposition (CVD) synthesis of CNTs catalyzed by reagent-grade common sodium-containing compounds, including NaCl, NaHCO3 , Na2 CO3 , and NaOH, found in table salt, baking soda, and detergents, respectively. Coupled with an oxidative dehydrogenation reaction to crack acetylene at reduced temperatures, Na-based nanoparticles have been observed to catalyze CNT growth at temperatures below 400 °C. Ex situ and in situ transmission electron microscopy (TEM) reveal unique CNT morphologies and growth characteristics, including a vaporizing Na catalyst phenomenon that we leverage to create CNTs without residual catalyst particles for applications that require metal-free CNTs. Na is shown to synthesize CNTs on numerous substrates, and as the first alkali group metal catalyst demonstrated for CNT growth, holds great promise for expanding the understanding of nanocarbon synthesis.

Subnanometer localization accuracy in widefield optical microscopy.

The common assumption that precision is the limit of accuracy in localization microscopy and the typical absence of comprehensive calibration of optical microscopes lead to a widespread issue-overconfidence in measurement results with nanoscale statistical uncertainties that can be invalid due to microscale systematic errors. In this article, we report a comprehensive solution to this underappreciated problem. We develop arrays of subresolution apertures into the first reference materials that enable localization errors approaching the atomic scale across a submillimeter field. We present novel methods for calibrating our microscope system using aperture arrays and develop aberration corrections that reach the precision limit of our reference materials. We correct and register localization data from multiple colors and test different sources of light emission with equal accuracy, indicating the general applicability of our reference materials and calibration methods. In a first application of our new measurement capability, we introduce the concept of critical-dimension localization microscopy, facilitating tests of nanofabrication processes and quality control of aperture arrays. In a second application, we apply these stable reference materials to answer open questions about the apparent instability of fluorescent nanoparticles that commonly serve as fiducial markers. Our study establishes a foundation for subnanometer localization accuracy in widefield optical microscopy.

Enhanced durability of carbon nanotube grafted hierarchical ceramic microfiber-reinforced epoxy composites.

As carbon nanotube (CNT) infused hybrid composites are increasingly identified as next-generation aerospace materials, it is vital to evaluate their long-term structural performance under aging environments. In this work, the durability of hierarchical, aligned CNT grafted aluminoborosilicate microfiber-epoxy composites (CNT composites) are compared against baseline aluminoborosilicate composites (baseline composites), before and after immersion in water at 25 °C (hydro) and 60 °C (hydrothermal), for extended durations (90 d and 180 d). The addition of CNTs is found to reduce water diffusivities by approximately 1.5 times. The mechanical properties (bending strength and modulus) and the damage sensing capabilities (DC conductivity) of CNT composites remain intact regardless of exposure conditions. The baseline composites show significant loss of strength (44 %) after only 15 d of hydrothermal aging. This loss of mechanical strength is attributed to fiber-polymer interfacial debonding caused by accumulation of water at high temperatures. In situ acoustic and DC electrical measurements of hydrothermally aged CNT composites identify extensive stress-relieving micro-cracking and crack deflections that are absent in the aged baseline composites. These observations are supported by SEM images of the failed composite cross-sections that highlight secondary matrix toughening mechanisms in the form of CNT pullouts and fractures which enhance the service life of composites and maintain their properties under accelerated aging environments.

Molecular Precision at Micrometer Length Scales: Hierarchical Assembly of DNA-Protein Nanostructures.

Robust self-assembly across length scales is a ubiquitous feature of biological systems but remains challenging for synthetic structures. Taking a cue from biology-where disparate molecules work together to produce large, functional assemblies-we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method. This process simultaneously shapes the structure at the nanoscale and directs the large-scale geometry. The DNA skeleton guides the assembly of RecA protein filaments, which provides rigidity at the micrometer scale. We use our modular design strategy to assemble tetrahedral, rectangular, and linear shapes of defined dimensions. This method enables the robust construction of complex assemblies, greatly extending the range of DNA-based self-assembly methods.

Giant Surface Conductivity Enhancement in a Carbon Nanotube Composite by Ultraviolet Light Exposure.

Carbon nanotube composites are lightweight, multifunctional materials with readily adjustable mechanical and electrical properties-relevant to the aerospace, automotive, and sporting goods industries as high-performance structural materials. Here, we combine well-established and newly developed characterization techniques to demonstrate that ultraviolet (UV) light exposure provides a controllable means to enhance the electrical conductivity of the surface of a commercial carbon nanotube-epoxy composite by over 5 orders of magnitude. Our observations, combined with theory and simulations, reveal that the increase in conductivity is due to the formation of a concentrated layer of nanotubes on the composite surface. Our model implies that contacts between nanotube-rich microdomains dominate the conductivity of this layer at low UV dose, while tube-tube transport dominates at high UV dose. Further, we use this model to predictably pattern conductive traces with a UV laser, providing a facile approach for direct integration of lightweight conductors on nanocomposite surfaces.

Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging.

Multifocus microscopy (MFM) allows high-resolution instantaneous three-dimensional (3D) imaging and has been applied to study biological specimens ranging from single molecules inside cells nuclei to entire embryos. We here describe pattern designs and nanofabrication methods for diffractive optics that optimize the light-efficiency of the central optical component of MFM: the diffractive multifocus grating (MFG). We also implement a "precise color" MFM layout with MFGs tailored to individual fluorophores in separate optical arms. The reported advancements enable faster and brighter volumetric time-lapse imaging of biological samples. In live microscopy applications, photon budget is a critical parameter and light-efficiency must be optimized to obtain the fastest possible frame rate while minimizing photodamage. We provide comprehensive descriptions and code for designing diffractive optical devices, and a detailed methods description for nanofabrication of devices. Theoretical efficiencies of reported designs is ≈90% and we have obtained efficiencies of > 80% in MFGs of our own manufacture. We demonstrate the performance of a multi-phase MFG in 3D functional neuronal imaging in living C. elegans.

Trade-off between the Mechanical Strength and Microwave Electrical Properties of Functionalized and Irradiated Carbon Nanotube Sheets.

Carbon nanotube (CNT) sheets represent a novel implementation of CNTs that enable the tailoring of electrical and mechanical properties for applications in the automotive and aerospace industries. Small molecule functionalization and postprocessing techniques, such as irradiation with high-energy particles, are methods that can enhance the mechanical properties of CNTs. However, the effect that these modifications have on the electrical conduction mechanisms has not been extensively explored. By characterizing the mechanical and electrical properties of multiwalled carbon nanotube (MWCNT) sheets with different functional groups and irradiation doses, we can expand our insights into the extent of the trade-off that exists between mechanical strength and electrical conductivity for commercially available CNT sheets. Such insights allow for the optimization of design pathways for engineering applications that require a balance of material property enhancements.

Nanomanufacturing: A Perspective.

Nanomanufacturing, the commercially scalable and economically sustainable mass production of nanoscale materials and devices, represents the tangible outcome of the nanotechnology revolution. In contrast to those used in nanofabrication for research purposes, nanomanufacturing processes must satisfy the additional constraints of cost, throughput, and time to market. Taking silicon integrated circuit manufacturing as a baseline, we consider the factors involved in matching processes with products, examining the characteristics and potential of top-down and bottom-up processes, and their combination. We also discuss how a careful assessment of the way in which function can be made to follow form can enable high-volume manufacturing of nanoscale structures with the desired useful, and exciting, properties.

The Nanolithography Toolbox.

This article introduces in archival form the Nanolithography Toolbox, a platform-independent software package for scripted lithography pattern layout generation. The Center for Nanoscale Science and Technology (CNST) at the National Institute of Standards and Technology (NIST) developed the Nanolithography Toolbox to help users of the CNST NanoFab design devices with complex curves and aggressive critical dimensions. Using parameterized shapes as building blocks, the Nanolithography Toolbox allows users to rapidly design and layout nanoscale devices of arbitrary complexity through scripting and programming. The Toolbox offers many parameterized shapes, including structure libraries for micro- and nanoelectromechanical systems (MEMS and NEMS) and nanophotonic devices. Furthermore, the Toolbox allows users to precisely define the number of vertices for each shape or create vectorized shapes using Bezier curves. Parameterized control allows users to design smooth curves with complex shapes. The Toolbox is applicable to a broad range of design tasks in the fabrication of microscale and nanoscale devices.

Noncontact conductivity and dielectric measurement for high throughput roll-to-roll nanomanufacturing.

Advances in roll-to-roll processing of graphene and carbon nanotubes have at last led to the continuous production of high-quality coatings and filaments, ushering in a wave of applications for flexible and wearable electronics, woven fabrics, and wires. These applications often require specific electrical properties, and hence precise control over material micro- and nanostructure. While such control can be achieved, in principle, by closed-loop processing methods, there are relatively few noncontact and nondestructive options for quantifying the electrical properties of materials on a moving web at the speed required in modern nanomanufacturing. Here, we demonstrate a noncontact microwave method for measuring the dielectric constant and conductivity (or geometry for samples of known dielectric properties) of materials in a millisecond. Such measurement times are compatible with current and future industrial needs, enabling real-time materials characterization and in-line control of processing variables without disrupting production.