Selective biomolecular nanoarrays for parallel single-molecule investigations

Selective placement of functionalised DNA origami via thermal scanning probe lithography patterning

Here we present a nanopatterning strategy utilising thermal scanning probe lithography (t-SPL) for the precise organisation of DNA origami into nanoarrays. The aim of this approach is to demonstrate control in the fabrication of nanoarray platforms exhibiting single-molecule accuracy. Combining the inherent programmability of DNA origami structures with t-SPL nanopatterning, we demonstrated the controlled immobilisation on surfaces of functionalised DNA origami - as proof of concept we employed gold nanoparticles (AuNPs) and quantum dots (QDs) - at predefined positions and in nanoarray configurations. This method holds great potential for the construction of hetero-functionalised biomolecular nanoarrays with single-molecule control, with applications in bionanotechnology and (nano)materials science.

Single molecule DNA origami nanoarrays with controlled protein orientation

The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.

Single-molecule DNA origami aptasensors for real-time biomarker detection

Here we report the use of DNA nanostructures as platforms to monitor the inherent conformational changes of aptamers upon analyte binding, with single-molecule resolution and real-time capability. An aptasensor designed to sense cortisol was found to suffer from instability in solution, but this was reconciled via a rational design of a single-molecule sensing platform. In this regard, DNA origami was employed to immobilise individual aptasensors on a glass surface and to ensure adequate interaction with their environment, for single-molecule analysis. The strategy presented here can be applied to any aptamer obtained by the destabilisation of a duplex in a SELEX process, and hence employed in the rational design of single-molecule biosensors.

Orthogonal Chemical Functionalization of Au/SiO2/TiW Patterned Substrates

Macropatterned and micropatterned gold/silicon dioxide/titanium tungsten (Au/SiO₂/TiW) substrates were orthogonally functionalized: three different molecules (monovalent silane, thiol, and phosphonic acid) were used to specifically form organolayers on Au, SiO₂, or TiW areas of patterned substrates. The orthogonality of the functionalization (i.e., selective grafting of thiol on Au, phosphonic acid on TiW, and silane on SiO₂) was assessed by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), Fourier transform infrared spectroscopy (FTIR), and contact angle measurements. These results are especially promising for the selective anchoring of targets (e.g., biomolecules, nanoparticles, nanowires, nanotubes, or other nano-objects) onto patterned zones of multimaterial substrates, such as nanosensors or other nanodevices.

Sub-10 nm Resolution Patterning of Pockets for Enzyme Immobilization with Independent Density and Quasi-3D Topography Control

The ability to precisely control the localization of enzymes on a surface is critical for several applications including biosensing, bionanoreactors, and single molecule studies. Despite recent advances, fabrication of enzyme patterns with resolution at the single enzyme level is limited by the lack of lithography methods that combine high resolution, compatibility with soft, polymeric structures, ease of fabrication, and high throughput. Here, a method to generate enzyme nanopatterns (using thermolysin as a model system) on a polymer surface is demonstrated using thermochemical scanning probe lithography (tc-SPL). Electrostatic immobilization of negatively charged sulfonated enzymes occurs selectively at positively charged amine nanopatterns produced by thermal deprotection of amines along the side-chain of a methacrylate-based copolymer film via tc-SPL. This process occurs simultaneously with local thermal quasi-3D topographical patterning of the same polymer, offering lateral sub-10 nm resolution, and vertical 1 nm resolution, as well as high throughput (5.2 × 10⁴ μm²/h). The obtained single-enzyme resolution patterns are characterized by atomic force microscopy (AFM) and fluorescence microscopy. The enzyme density, the surface passivation, and the quasi-3D arbitrary geometry of these patterned pockets are directly controlled during the tc-SPL process in a single step without the need of markers or masks. Other unique features of this patterning approach include the combined single-enzyme resolution over mm² areas and the possibility of fabricating enzymes nanogradients.

Single molecule protein patterning using hole mask colloidal lithography

The ability to manipulate single protein molecules on a surface is useful for interfacing biology with many types of devices in optics, catalysis, bioengineering, and biosensing. Control of distance, orientation, and activity at the single molecule level will allow for the production of on-chip devices with increased biological activity. Cost effective methodologies for single molecule protein patterning with tunable pattern density and scalable coverage area remain a challenge. Herein, Hole Mask Colloidal Lithography is presented as a bench-top colloidal lithography technique that enables a glass coverslip to be patterned with functional streptavidin protein onto patches from 15-200 nm in diameter with variable pitch. Atomic force microscopy (AFM) was used to characterize the size of the patterned features on the glass surface. Additionally, single-molecule fluorescence microscopy was used to demonstrate the tunable pattern density, measure binding controls, and confirm patterned single molecules of functional streptavidin.

Orthogonal chemical functionalization of patterned Au/TiW substrate for selective immobilization of nanoparticles

The evolution of nanobiosensors stresses the need for multi-material nanopatterned surfaces to enhance sensing performances. Titanium tungsten (TiW) has been mastered and routinely implemented in nanoelectronic devices, in a reproducible way and at industrial production scales. Such a material may be envisioned for use in (bio)chemical nanoelectronic sensors, but the surface functionalization of such material has yet to be studied. In the present article, the orthogonal chemical functionalization of patterned Au on TiW substrates has been explored for the first time. Surface functionalizations were assessed by x-ray photoelectron spectroscopy, polarization modulation infrared reflection-absorption spectroscopy and time-of-flight secondary ion mass spectrometry imaging. Au/TiW patterned substrates were functionalized with mercapto-undecamine. Thanks to the orthogonality of thiol/Au versus phosphonic acid/TiW reactions, only the Au features were modified leading to the amine derivatized surface. This allowed for the localizing of carboxy-functionalized nanoparticles by electrostatic interaction on Au with a selectivity above 10 when compared to TiW.

Efficient One-Step PEG-Silane Passivation of Glass Surfaces for Single-Molecule Fluorescence Studies

Surface passivation to inhibit nonspecific interactions is a key requirement for in vitro single-molecule fluorescent studies. Although the standard passivation methods involve the covalent attachment of poly(ethylene glycol) (PEG) in two steps preferably over quartz surfaces, this protocol and improvements thereon require extensive labor and chemicals. Herein, we report an efficient one-step surface grafting of PEG-silane that yields enhanced passivation, as evidenced by reduced nonspecific interactions, over the conventional method at a minimal time and reagent cost and on glass surfaces. Our method is rooted in a mechanistic understanding of the silane reaction with the silanol groups on the glass surface. Single-molecule fluorescence studies with fluorescently tagged proteins and DNA on PEG-silane-functionalized glass surfaces validate the enhanced performance of the method. Combined with atomic force microscopy surface characterization, our study further illustrates that few remaining pinhole defects, plausibly from defects on the glass, on PEG-silane glass-coated surfaces account for the minimal background, where typically no more than one molecule is nonspecifically attached in a given diffraction-limited spot on the surface.

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.

Single-Molecule Patterning via DNA Nanostructure Assembly: A Reusable Platform

Here we describe a facile strategy of general applicability for controlling the immobilization of individual nanomoieties on nanopatterned surfaces with single-molecule control. We combine the ability of DNA nanostructures as programmable platforms, with a one-step Focused Ion Beam nanopatterning, to demonstrate the controlled immobilization of DNA origami functionalized with individual quantum dots (QDs) at predesigned positions on glass coverslips and silicon substrates. Remarkably, the platform developed is reusable after a simple cleaning process, and can be designed to display different geometrical arrangements.

Molecular conformations of DNA targets captured by model nanoarrays

An open question in single molecule nanoarrays is how the chemical and morphological heterogeneities of the solid support affect the properties of biomacromolecules. We generated arrays that allowed individually-resolvable DNA molecules to interact with tailored surface heterogeneities and revealed how molecular conformations are impacted by surface interactions.

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.

Molecular Occupancy of Nanodot Arrays

Single-molecule nanodot arrays, in which a biomolecule of choice (protein, nucleic acid, etc.) is bound to a metallic nanoparticle on a solid substrate, are becoming an increasingly important tool in the study of biomolecular and cellular interactions. We have developed an on-chip measurement protocol to monitor and control the molecular occupancy of nanodots. Arrays of widely spaced nanodots and nanodot clusters were fabricated on glass surfaces by nanolithography and functionalized with fluorescently labeled proteins. The molecular occupancy was determined by monitoring individual fluorophore bleaching events, while accounting for fluorescence quenching effects. We found that the occupancy can be interpreted as a packing problem, and depends on nanodot size and binding ligand concentration, where the latter is easily adjusted to compensate the flexibility of dimension control in nanofabrication. The results are scalable with nanodot cluster size, extending to large area close packed arrays. As an example, the nanoarray platform was used to probe the geometric requirement of T-cell activation at the single-molecule level.

The Orientations of Large Aspect-Ratio Coiled-Coil Proteins Attached to Gold Nanostructures

Methods for patterning biomolecules on a substrate at the single molecule level have been studied as a route to sensors with single-molecular sensitivity or as a way to probe biological phenomena at the single-molecule level. However, the arrangement and orientation of single biomolecules on substrates has been less investigated. Here, the arrangement and orientation of two rod-like coiled-coil proteins, cortexillin and tropomyosin, around patterned gold nanostructures is examined. The high aspect ratio of the coiled coils makes it possible to study their orientations and to pursue a strategy of protein orientation via two-point attachment. The proteins are anchored to the surfaces using thiol groups, and the number of cysteine residues in tropomyosin is varied to test how this variation affects the structure and arrangement of the surface-attached proteins. Molecular dynamics studies are used to interpret the observed positional distributions. Based on initial studies of protein attachment to gold post structures, two 31-nm-long tropomyosin molecules are aligned between the two sidewalls of a trench with a width of 68 nm. Because the approach presented in this study uses one of twenty natural amino acids, this method provides a convenient way to pattern biomolecules on substrates using standard chemistry.

Advances in Functional Assemblies for Regenerative Medicine

The ability to synthesise bioresponsive systems and selectively active biochemistries using polymer-based materials with supramolecular features has led to a surge in research interest directed towards their development as next generation biomaterials for drug delivery, medical device design and tissue engineering.

High speed e-beam lithography for gold nanoarray fabrication and use in nanotechnology

E-beam lithography has been used for reliable and versatile fabrication of sub-15 nm single-crystal gold nanoarrays and led to convincing applications in nanotechnology. However, so far this technique was either too slow for centimeter to wafer-scale writing or fast enough with the so-called dot on the fly (DOTF) technique but not optimized for sub-15 nm dots dimension. This prevents use of this technology for some applications and characterization techniques. Here, we show that the DOTF technique can be used without degradation in dots dimension. In addition, we propose two other techniques. The first one is an advanced conventional technique that goes five times faster than the conventional one. The second one relies on sequences defined before writing which enable versatility in e-beam patterns compared to the DOTF technique with same writing speed. By comparing the four different techniques, we evidence the limiting parameters for the writing speed. Wafer-scale fabrication of such arrays with 50 nm pitch allowed XPS analysis of a ferrocenylalkyl thiol self-assembled monolayer coated gold nanoarray.

Enzymatic reactions on immobilised substrates

This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.

Bifunctional nanoarrays for probing the immune response at the single-molecule level

Bifunctional nanoarrays were created to simulate the immunological synapse and probe the T-cell immune response at the single-molecule level. Sub-5 nm AuPd nanodot arrays were fabricated using both e-beam and nanoimprint lithography. The nanoarrays were then functionalized by two costimulatory molecules: antibody UCHT1 Fab, which binds to the T-cell receptor (TCR) and activates the immune response, bound to metallic nanodots; and intercellular adhesion molecule-1, which enhances cell adhesion, on the surrounding area. Initial T-cell experiments show successful attachment and activation on the bifunctional nanoarrays. This nanoscale platform for single-molecule control of TCR in living T-cells provides a new approach to explore how its geometric arrangement affects T-cell activation and behavior, with potential applications in immunotherapy. This platform also serves as a general model for single-molecule nanoarrays where more than one molecular species is required.

Robustly passivated, gold nanoaperture arrays for single-molecule fluorescence microscopy

The optical confinement generated by metal-based nanoapertures fabricated on a silica substrate has recently enabled single-molecule fluorescence measurements to be performed at physiologically relevant background concentrations of fluorophore-labeled biomolecules. Nonspecific adsorption of fluorophore-labeled biomolecules to the metallic cladding and silica bottoms of nanoapertures, however, remains a critical limitation. To overcome this limitation, we have developed a selective functionalization chemistry whereby the metallic cladding of gold nanoaperture arrays is passivated with methoxy-terminated, thiol-derivatized polyethylene glycol (PEG), and the silica bottoms of those arrays are functionalized with a binary mixture of methoxy- and biotin-terminated, silane-derivatized PEG. This functionalization scheme enables biotinylated target biomolecules to be selectively tethered to the silica nanoaperture bottoms via biotin-streptavidin interactions and reduces the nonspecific adsorption of fluorophore-labeled ligand biomolecules. This, in turn, enables the observation of ligand biomolecules binding to their target biomolecules even under greater than 1 μM background concentrations of ligand biomolecules, thereby rendering previously impracticable biological systems accessible to single-molecule fluorescence investigations.

Low-cost fabrication of centimetre-scale periodic arrays of single plasmid DNA molecules

We report the development of a low-cost method to generate a centimetre-scale periodic array of single plasmid DNA molecules of 11 kilobase pairs. The arrayed DNA molecules are amenable to enzymatic and physical manipulations.

DNA as a molecular wire: distance and sequence dependence

Functional nanowires and nanoelectronics are sought for their use in next generation integrated circuits, but several challenges limit the use of most nanoscale devices on large scales. DNA has great potential for use as a molecular wire due to high yield synthesis, near-unity purification, and nanoscale self-organization. Nonetheless, a thorough understanding of ground state DNA charge transport (CT) in electronic configurations under biologically relevant conditions, where the fully base-paired, double-helical structure is preserved, is lacking. Here, we explore the fundamentals of CT through double-stranded DNA monolayers on gold by assessing 17 base pair bridges at discrete points with a redox active probe conjugated to a modified thymine. This assessment is performed under temperature-controlled and biologically relevant conditions with cyclic and square wave voltammetry, and redox peaks are analyzed to assess transfer rate and yield. We demonstrate that the yield of transport is strongly tied to the stability of the duplex, linearly correlating with the melting temperature. Transfer rate is found to be temperature-activated and to follow an inverse distance dependence, consistent with a hopping mechanism of transport. These results establish the governing factors of charge transfer speed and throughput in DNA molecular wires for device configurations, guiding subsequent application for nanoscale electronics.

Temperature dependence of electrochemical DNA charge transport: influence of a mismatch

Charge transfer through DNA is of interest as DNA is both the quintessential biomolecule of all living organisms and a self-organizing element in bioelectronic circuits and sensing applications. Here, we report the temperature-dependent properties of DNA charge transport in an electronically relevant arrangement of DNA monolayers on gold under biologically relevant conditions, and we track the effects of incorporating a CA single base pair mismatch. Charge transfer (CT) through double stranded, 17mer monolayers was monitored by following the yield of electrochemical reduction of a Nile blue redox probe conjugated to a modified thymine. Analysis with cyclic voltammetry and square wave voltammetry shows that DNA CT increases significantly with temperature, indicative of more DNA bridges becoming active for transport. The mismatch was found to attenuate DNA CT at lower temperatures, but the effect of the mismatch diminished as temperature was increased. Voltammograms were analyzed to extract the electron transfer rate k(0), the electron transfer coefficient α, and the redox-active surface coverage Γ*. Arrhenius behavior was observed, with activation energies of 100 meV for electron transfer through well-matched DNA. Single CA mismatches increased the activation energy by 60 meV. These results have clear implications for sensing applications and are evaluated with respect to the prominent models of DNA CT.

High-throughput single-molecule analysis of DNA-protein interactions by tethered particle motion

Tethered particle motion (TPM) monitors the variations in the effective length of a single DNA molecule by tracking the Brownian motion of a bead tethered to a support by the DNA molecule. Providing information about DNA conformations in real time, this technique enables a refined characterization of DNA-protein interactions. To increase the output of this powerful but time-consuming single-molecule assay, we have developed a biochip for the simultaneous acquisition of data from more than 500 single DNA molecules. The controlled positioning of individual DNA molecules is achieved by self-assembly on nanoscale arrays fabricated through a standard microcontact printing method. We demonstrate the capacity of our biochip to study biological processes by applying our method to explore the enzymatic activity of the T7 bacteriophage exonuclease. Our single molecule observations shed new light on its behaviour that had only been examined in bulk assays previously and, more specifically, on its processivity.

Quantum dot nanoarrays: self-assembly with single-particle control and resolution

The develpoment of a highly selective immobilization strategy for the self-assembly of quantum dots (QDs) from solution on lithographically defined, biochemically functionalized metal nanopatterns is presented. Nanosale control is achieved for the formation of predominantly single-particle structures consisting of a QD coupled to a metal nanoparticle, and assembled into an ordered nanoarray.

Label-free electrical detection of pyrophosphate generated from DNA polymerase reactions on field-effect devices

We introduce a label-free approach for sensing polymerase reactions on deoxyribonucleic acid (DNA) using a chelator-modified silicon-on-insulator field-effect transistor (SOI-FET) that exhibits selective and reversible electrical response to pyrophosphate anions. The chemical modification of the sensor surface was designed to include rolling-circle amplification (RCA) DNA colonies for locally enhanced pyrophosphate (PPi) signal generation and sensors with immobilized chelators for capture and surface-sensitive detection of diffusible reaction by-products. While detecting arrays of enzymatic base incorporation reactions is typically accomplished using optical fluorescence or chemiluminescence techniques, our results suggest that it is possible to develop scalable and portable PPi-specific sensors and platforms for broad biomedical applications such as DNA sequencing and microbe detection using surface-sensitive electrical readout techniques.

Single-molecule protein arrays enabled by scanning probe block copolymer lithography

The ability to control the placement of individual protein molecules on surfaces could enable advances in a wide range of areas, from the development of nanoscale biomolecular devices to fundamental studies in cell biology. Such control, however, remains a challenge in nanobiotechnology due to the limitations of current lithographic techniques. Herein we report an approach that combines scanning probe block copolymer lithography with site-selective immobilization strategies to create arrays of proteins down to the single-molecule level with arbitrary pattern control. Scanning probe block copolymer lithography was used to synthesize individual sub-10-nm single crystal gold nanoparticles that can act as scaffolds for the adsorption of functionalized alkylthiol monolayers, which facilitate the immobilization of specific proteins. The number of protein molecules that adsorb onto the nanoparticles is dependent upon particle size; when the particle size approaches the dimensions of a protein molecule, each particle can support a single protein. This was demonstrated with both gold nanoparticle and quantum dot labeling coupled with transmission electron microscopy imaging experiments. The immobilized proteins remain bioactive, as evidenced by enzymatic assays and antigen-antibody binding experiments. Importantly, this approach to generate single-biomolecule arrays is, in principle, applicable to many parallelized cantilever and cantilever-free scanning probe molecular printing methods.