Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals.

Metal-mediated DNA (mmDNA) presents a pathway toward engineering bioinorganic and electronic behavior into DNA devices. Many chemical and biophysical forces drive the programmable chelation of metals between pyrimidine base pairs. Here, we developed a crystallographic method using the three-dimensional (3D) DNA tensegrity triangle motif to capture single- and multi-metal binding modes across granular changes to environmental pH using anomalous scattering. Leveraging this programmable crystal, we determined 28 biomolecular structures to capture mmDNA reactions. We found that silver(I) binds with increasing occupancy in T-T and U-U pairs at elevated pH levels, and we exploited this to capture silver(I) and mercury(II) within the same base pair and to isolate the titration points for homo- and heterometal base pair modes. We additionally determined the structure of a C-C pair with both silver(I) and mercury(II). Finally, we extend our paradigm to capture cadmium(II) in T-T pairs together with mercury(II) at high pH. The precision self-assembly of heterobimetallic DNA chemistry at the sub-nanometer scale will enable atomistic design frameworks for more elaborate mmDNA-based nanodevices and nanotechnologies.

Observation of Flat Bands in Gated Semiconductor Artificial Graphene.

Flat bands near M points in the Brillouin zone are key features of honeycomb symmetry in artificial graphene (AG) where electrons may condense into novel correlated phases. Here we report the observation of van Hove singularity doublet of AG in GaAs quantum well transistors, which presents the evidence of flat bands in semiconductor AG. Two emerging peaks in photoluminescence spectra tuned by backgate voltages probe the singularity doublet of AG flat bands and demonstrate their accessibility to the Fermi level. As the Fermi level crosses the doublet, the spectra display dramatic stability against electron density, indicating interplays between electron-electron interactions and honeycomb symmetry. Our results provide a new flexible platform to explore intriguing flat band physics.

Integrin nanoclusters can bridge thin matrix fibres to form cell-matrix adhesions.

Integrin-mediated cell-matrix adhesions are key to sensing the geometry and rigidity of extracellular environments and influence vital cellular processes. In vivo, the extracellular matrix is composed of fibrous arrays. To understand the fibre geometries that are required for adhesion formation, we patterned nanolines of various line widths and arrangements in single, crossing or paired arrays with the integrin-binding peptide Arg-Gly-Asp. Single thin lines (width ≤30 nm) did not support cell spreading or formation of focal adhesions, despite the presence of a high density of Arg-Gly-Asp, but wide lines (>40 nm) did. Using super-resolution microscopy, we observed stable, dense integrin clusters formed on parallel (within 110 nm) or crossing thin lines (mimicking a matrix mesh) similar to those on continuous substrates. These dense clusters bridged the line pairs by recruiting activated but unliganded integrins, as verified by integrin mutants unable to bind ligands that coclustered with ligand-bound integrins when present in an active extended conformation. Thus, in a fibrous extracellular matrix mesh, stable integrin nanoclusters bridge between thin (≤30 nm) matrix fibres and bring about downstream consequences of cell motility and growth.

Nanoscale Engineering of Closely-Spaced Electronic Spins in Diamond.

Numerous theoretical protocols have been developed for quantum information processing with dipole-coupled solid-state spins. Nitrogen vacancy (NV) centers in diamond have many of the desired properties, but a central challenge has been the positioning of NV centers at the nanometer scale that would allow for efficient and consistent dipolar couplings. Here we demonstrate a method for chip-scale fabrication of arrays of single NV centers with record spatial localization of about 10 nm in all three dimensions and controllable inter-NV spacing as small as 40 nm, which approaches the length scale of strong dipolar coupling. Our approach uses masked implantation of nitrogen through nanoapertures in a thin gold film, patterned via electron-beam lithography and dry etching. We verified the position and spin properties of the resulting NVs through wide-field super-resolution optically detected magnetic resonance imaging.

Improved Glass Surface Passivation for Single-Molecule Nanoarrays.

Single-molecule fluorescence techniques provide a critical tool for probing biomolecular and cellular interactions with unprecedented resolution and precision. Unfortunately, many of these techniques are hindered by a common problem, namely, the nonspecific adsorption of target biomolecules. This issue is mostly addressed by passivating the glass surfaces with a poly(ethylene glycol) (PEG) brush. This is effective only at low concentrations of the probe molecule because there are defects inherent to polymer brushes formed on glass coverslips due to the presence of surface impurities. Tween-20, a detergent, is a promising alternative that can improve surface passivation, but it is incompatible with living cells, and it also possesses limited selectivity for glass background over metallic nanoparticles, which are frequently used as anchors for the probe molecules. To address these issues, we have developed a more versatile method to improve the PEG passivation. A thin film of hydrogen silsesquioxane (HSQ) is spin-coated and thermally cured on glass coverslips in order to cover the surface impurities. This minimizes the formation of PEG defects and reduces nonspecific adsorption, resulting in an improvement comparable to Tween-20 treatment. This approach was applied to single-molecule nanoarrays of streptavidin bound to AuPd nanodots patterned by e-beam lithography (EBL). The fluorescence signal to background ratio (SBR) on HSQ-coated glass was improved by ∼4-fold as compared to PEG directly on glass. This improvement enables direct imaging of ordered arrays of single molecules anchored to lithographically patterned arrays of metallic nanodots.

Directed Assembly of End-Functionalized Single Wall Carbon Nanotube Segments.

A key impediment to the implementation of a nanoelectronics technology based on single wall carbon nanotubes (SWCNTs) is the inability to arrange them in a manner suitable for integration into complex circuits. As a step toward addressing this problem, we explore the binding of fixed-length, end-functionalized SWCNT segments to lithographically defined nanoscale anchors, such that individual SWCNTs can be placed with control over position and orientation. Both monovalent and bivalent bindings are explored using covalent and noncovalent binding chemistries. Placement efficiency is assessed in terms of overall yield of SWCNT binding, as well as binding specificity and the degree of nonspecific binding. Placement yields as high as 93% and 79% are achieved, respectively, for covalent binding and for binding through DNA hybridization. Orientational control of the SWCNT segments is achieved with 95% and 51% efficiency for monovalent and bivalent bindings, respectively. This represents a new approach that could pave the way toward complex SWCNT devices and circuits.

Controlled formation of carbon nanotube junctions via linker-induced assembly in aqueous solution.

Here we present a simple approach for the controlled formation of one-dimensional and multiterminal nanotube junctions. We describe a facile bottom-up strategy for joining the ends of single-walled carbon nanotubes. The geometry of the junctions can be varied and controlled by linker-induced assembly of DNA-wrapped nanotubes.

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.

DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.

DNA double helices containing metal-mediated DNA (mmDNA) base pairs have been constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials has been impractical without a complete lexical and structural description. Here, we explore the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination. We employed the tensegrity triangle to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and elucidated generalized design rules for mmDNA construction. We uncovered two binding modes: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations showed additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates. This article is protected by copyright. All rights reserved.

Nanolithographic control of the spatial organization of cellular adhesion receptors at the single-molecule level.

The ability to control the placement of individual molecules promises to enable a wide range of applications and is a key challenge in nanoscience and nanotechnology. Many biological interactions, in particular, are sensitive to the precise geometric arrangement of proteins. We have developed a technique which combines molecular-scale nanolithography with site-selective biochemistry to create biomimetic arrays of individual protein binding sites. The binding sites can be arranged in heterogeneous patterns of virtually any possible geometry with a nearly unlimited number of degrees of freedom. We have used these arrays to explore how the geometric organization of the extracellular matrix (ECM) binding ligand RGD (Arg-Gly-Asp) affects cell adhesion and spreading. Systematic variation of spacing, density, and cluster size of individual integrin binding sites was used to elicit different cell behavior. Cell spreading assays on arrays of different geometric arrangements revealed a dramatic increase in spreading efficiency when at least four liganded sites were spaced within 60 nm or less, with no dependence on global density. This points to the existence of a minimal matrix adhesion unit for fibronectin defined in space and stoichiometry. Developing an understanding of the ECM geometries that activate specific cellular functional complexes is a critical step toward controlling cell behavior. Potential practical applications range from new therapeutic treatments to the rational design of tissue scaffolds that can optimize healing without scarring. More broadly, spatial control at the single-molecule level can elucidate factors controlling individual molecular interactions and can enable synthesis of new systems based on molecular-scale architectures.

Assembly of heterogeneous functional nanomaterials on DNA origami scaffolds.

One on each side: gold nanoparticles (AuNPs) and semiconducting quantum dots (QDs) are integrated on a single DNA origami scaffold. Streptavidin-functionalized QDs bind to biotin anchors on one side of the DNA origami, while DNA-coated AuNPs bind through DNA hybridization to single-stranded DNA on the other side of the scaffold. This approach offers a new path toward the organization of complex systems consisting of disparate materials.

Selective biomolecular nanoarrays for parallel single-molecule investigations.

The ability to direct the self-assembly of biomolecules on surfaces with true nanoscale control is key for the creation of functional substrates. Herein we report the fabrication of nanoscale biomolecular arrays via selective self-assembly on nanopatterned surfaces and minimized nonspecific adsorption. We demonstrate that the platform developed allows for the simultaneous screening of specific protein-DNA binding events at the single-molecule level. The strategy presented here is generally applicable and enables high-throughput monitoring of biological activity in real time and with single-molecule resolution.

Robust pattern transfer of nanoimprinted features for sub-5-nm fabrication.

We explore the limits of a simple and facile process for transferring low aspect ratio, high-resolution features defined by nanoimprint lithography. The process involves postimprint deposition of an angle-evaporated hard mask. This widens the process window for residual resist removal and facilitates easy liftoff. An added benefit is a concomitant reduction of feature size. A postliftoff annealing step produces high pattern uniformity and additional feature size reduction. The process is extremely robust, and it enables relatively straightforward fabrication of sub-5-nm spherical structures. It is extendible to rectilinear patterns as well.

Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology.

DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication and self-assembling properties. Recently we discovered that by intercalating Ag+ in polycytosine-mismatch oligonucleotides, the resulting C-Ag+-C duplexes are able to conduct charge efficiently. To map the functionality and biostability of this system, we built and characterized internally-functionalized DNA nanowires through non-canonical, Ag+-mediated base pairing in duplexes containing cytosine-cytosine mismatches. We assessed the thermal and chemical stability of ion-coordinated duplexes in aqueous solutions and conclude that the C-Ag+-C bond forms DNA duplexes with replicable geometry, predictable thermodynamics, and tunable length. We demonstrated continuous ion chain formation in oligonucleotides of 11-50 nucleotides (nt), and enzyme ligation of mixed strands up to six times that length. This construction is feasible without detectable silver nanocluster contaminants. Functional gene parts for the synthesis of DNA- and RNA-based, C-Ag+-C duplexes in a cell-free system have been constructed in an Escherichia coli expression plasmid and added to the open-source BioBrick Registry, paving the way to realizing the promise of inexpensive industrial production. With appropriate design constraints, this conductive variant of DNA demonstrates promise for use in synthetic biological constructs as a dynamic nucleic acid component and contributes molecular electronic functionality to DNA that is not already found in nature. We propose a viable route to fabricating stable DNA nanowires in cell-free and synthetic biological systems for the production of self-assembling nanoelectronic architectures.

Full control of ligand positioning reveals spatial thresholds for T cell receptor triggering.

Elucidating the rules for receptor triggering in cell-cell and cell-matrix contacts requires precise control of ligand positioning in three dimensions. Here, we use the T cell receptor (TCR) as a model and subject T cells to different geometric arrangements of ligands, using a nanofabricated single-molecule array platform. This comprises monovalent TCR ligands anchored to lithographically patterned nanoparticle clusters surrounded by mobile adhesion molecules on a supported lipid bilayer. The TCR ligand could be co-planar with the supported lipid bilayer (2D), excluding the CD45 transmembrane tyrosine phosphatase, or elevated by 10 nm on solid nanopedestals (3D), allowing closer access of CD45 to engaged TCR. The two configurations resulted in different T cell responses, depending on the lateral spacing between the ligands. These results identify the important contributions of lateral and axial components of ligand positioning and create a more complete foundation for receptor engineering for immunotherapy.

Emerging many-body effects in semiconductor artificial graphene with low disorder.

The interplay between electron-electron interactions and the honeycomb topology is expected to produce exotic quantum phenomena and find applications in advanced devices. Semiconductor-based artificial graphene (AG) is an ideal system for these studies that combines high-mobility electron gases with AG topology. However, to date, low-disorder conditions that reveal the interplay of electron-electron interaction with AG symmetry have not been achieved. Here, we report the creation of low-disorder AG that preserves the near-perfection of the pristine electron layer by fabricating small period triangular antidot lattices on high-quality quantum wells. Resonant inelastic light scattering spectra show collective spin-exciton modes at the M-point's nearly flatband saddle-point singularity in the density of states. The observed Coulomb exchange interaction energies are comparable to the gap of Dirac bands at the M-point, demonstrating interplay between quasiparticle interactions and the AG potential. The saddle-point exciton energies are in the terahertz range, making low-disorder AG suitable for contemporary optoelectronic applications.

Observation of Dirac bands in artificial graphene in small-period nanopatterned GaAs quantum wells.

Charge carriers in graphene behave like massless Dirac fermions (MDFs) with linear energy-momentum dispersion 1, 2 , providing a condensed-matter platform for studying quasiparticles with relativistic-like features. Artificial graphene (AG)-a structure with an artificial honeycomb lattice-exhibits novel phenomena due to the tunable interplay between topology and quasiparticle interactions 3-6 . So far, the emergence of a Dirac band structure supporting MDFs has been observed in AG using molecular 5 , atomic 6, 7 and photonic systems 8-10 , including those with semiconductor microcavities 11 . Here, we report the realization of an AG that has a band structure with vanishing density of states consistent with the presence of MDFs. This observation is enabled by a very small lattice constant (a = 50 nm) of the nanofabricated AG patterns superimposed on a two-dimensional electron gas hosted by a high-quality GaAs quantum well. Resonant inelastic light-scattering spectra reveal low-lying transitions that are not present in the unpatterned GaAs quantum well. These excitations reveal the energy dependence of the joint density of states for AG band transitions. Fermi level tuning through the Dirac point results in a collapse of the density of states at low transition energy, suggesting the emergence of the MDF linear dispersion in the AG.

Spatial Control of Biological Ligands on Surfaces Applied to T Cell Activation.

In this chapter, we present techniques, based on molecular-scale nanofabrication and selective self-assembly, for the presentation of biomolecules of interest (ligands, receptors, etc.) on a surface with precise spatial control and arbitrary geometry at the single-molecule level. Metallic nanodot arrays are created on glass coverslips and are then used as anchors for the immobilization of biological ligands via thiol linking chemistry. The nanodot size is controlled by both lithography and metallization. The reagent concentration in self-assembly can be adjusted to ensure single-molecule occupancy for a given dot size. The surrounding glass is backfilled by a protein-repellent layer to prevent nonspecific adsorption. Moreover, bifunctional surfaces are created, whereby a second ligand is presented on the background, which is frequently a requirement for simulating complex cellular functions involving more than one key ligand. This platform serves as a novel and powerful tool for molecular and cellular biology, e.g., to study the fundamental mechanisms of receptor-mediated signaling.

The Functional Response of Mesenchymal Stem Cells to Electron-Beam Patterned Elastomeric Surfaces Presenting Micrometer to Nanoscale Heterogeneous Rigidity.

Cells directly probe and respond to the physicomechanical properties of their extracellular environment, a dynamic process which has been shown to play a key role in regulating both cellular adhesive processes and differential cellular function. Recent studies indicate that stem cells show lineage-specific differentiation when cultured on substrates approximating the stiffness profiles of specific tissues. Although tissues are associated with a range of Young's modulus values for bulk rigidity, at the subcellular level, tissues are comprised of heterogeneous distributions of rigidity. Lithographic processes have been widely explored in cell biology for the generation of analytical substrates to probe cellular physicomechanical responses. In this work, it is shown for the first time that that direct-write e-beam exposure can significantly alter the rigidity of elastomeric poly(dimethylsiloxane) substrates and a new class of 2D elastomeric substrates with controlled patterned rigidity ranging from the micrometer to the nanoscale is described. The mechanoresponse of human mesenchymal stem cells to e-beam patterned substrates was subsequently probed in vitro and significant modulation of focal adhesion formation and osteochondral lineage commitment was observed as a function of both feature diameter and rigidity, establishing the groundwork for a new generation of biomimetic material interfaces.

Control of DNA origami inter-tile connection with vertical linkers.

This communication describes a new method that enables high yield assembly along both of the two-dimensional edges of DNA origami tiles by controlling the Mg(2+) concentration; high Mg(2+) concentrations promote linkage connections between the vertical edges of the tiles. As a demonstration, DNA origami dimers assembled from two rectangular origami along the vertical edges are used as scaffolds for the double sided assembly of gold nanoparticles with different inter-particle spacings.