Single molecule protein patterning using hole mask colloidal lithography

Smart Biointerfaces via Click Chemistry-Enabled Nanopatterning of Multiple Bioligands and DNA Force Sensors

Nanoscale biomolecular placement is crucial for advancing cellular signaling, sensor technology, and molecular interaction studies. Despite this, current methods fall short in enabling large-area nanopatterning of multiple biomolecules while minimizing nonspecific interactions. Using bioorthogonal tags at a submicron scale, we introduce a novel hole-mask colloidal lithography method for arranging up to three distinct proteins, DNA, or peptides on large, fully passivated surfaces. The surfaces are compatible with single-molecule fluorescence microscopy and microplate formats, facilitating versatile applications in cellular and single-molecule assays. We utilize fully passivated and transparent substrates devoid of metals and nanotopographical features to ensure accurate patterning and minimize nonspecific interactions. Surface patterning is achieved using bioorthogonal TCO-tetrazine (inverse electron-demand Diels-Alder, IEDDA) ligation, DBCO-azide (strain-promoted azide-alkyne cycloaddition, SPAAC) click chemistry, and biotin-avidin interactions. These are arranged on surfaces passivated with dense poly(ethylene glycol) PEG brushes crafted through the selective and stepwise removal of sacrificial metallic and polymeric layers, enabling the directed attachment of biospecific tags with nanometric precision. In a proof-of-concept experiment, DNA tension gauge tether (TGT) force sensors, conjugated to cRGD (arginylglycylaspartic acid) in nanoclusters, measured fibroblast integrin tension. This novel application enables the quantification of forces in the piconewton range, which is restricted within the nanopatterned clusters. A second demonstration of the platform to study integrin and epidermal growth factor (EGF) proximal signaling reveals clear mechanotransduction and changes in the cellular morphology. The findings illustrate the platform's potential as a powerful tool for probing complex biochemical pathways involving several molecules arranged with nanometer precision and cellular interactions at the nanoscale.

Microarray fabrication techniques for multiplexed bioassay applications

Microarrays are powerful tools for high-throughput bioassays that can extract information from tens of thousands of micro-spots consisting of biomolecules. This information is invaluable to many applications, such as drug discovery and disease diagnostics. Different applications of these microarrays need spots of different shapes, sizes, and chemistries to achieve their goals. Micro/nano-fabrication techniques are used to make microarrays with different feature structures and array densities for required assay procedures. Understanding these fabrication methods is essential to creating an effective microarray. The purpose of this article is to critically review fabrication methods used in recent microarray-based bioassay studies. We summarized commonly used microarray fabrication techniques and filled the gap in recent literature on relevant topics. We discussed recent examples of how microarrays were fabricated and used in a variety of bioassays. Specifically, we examined microarray printing, various microlithography techniques, and microfluidics-based microarray fabrication. We evaluated how their application shaped the fabrication methods and compared their performance based on different applications. In the end, we discussed current challenges and outlined potential future directions. This review addressed the gap in literature and provided important insights for choosing appropriate fabrication techniques towards different applications.

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.

Insight and Recent Advances into the Role of Topography on the Cell Differentiation and Proliferation on Biopolymeric Surfaces

It is well known that surface topography plays an important role in cell behavior, including adhesion, migration, orientation, elongation, proliferation and differentiation. Studying these cell functions is essential in order to better understand and control specific characteristics of the cells and thus to enhance their potential in various biomedical applications. This review proposes to investigate the extent to which various surface relief patterns, imprinted in biopolymer films or in polymeric films coated with biopolymers, by utilizing specific lithographic techniques, influence cell behavior and development. We aim to understand how characteristics such as shape, dimension or chemical functionality of surface relief patterns alter the orientation and elongation of cells, and thus, finally make their mark on the cell proliferation and differentiation. We infer that such an insight is a prerequisite for pushing forward the comprehension of the methodologies and technologies used in tissue engineering applications and products, including skin or bone implants and wound or fracture healing.

Surface patterning techniques for proteins on nano- and micro-systems: a modulated aspect in hierarchical structures

The surface patterning of protein using fabrication or the external functionalization of structures demonstrates various applications in the biomedical field for bioengineering, biosensing and antifouling. This review article offers an outline of the existing advances in protein patterning technology with a special emphasis on the current physical and physicochemical methods, including stencil patterning, trap- and droplet-based microfluidics, and chemical modification of surfaces via photolithography, microcontact printing and scanning probe nanolithography. Different approaches are applied for the biological studies of recent trends for single-protein patterning technology, such as robotic printing, stencil printing and colloidal lithography, wherein the concepts of physical confinement, electrostatic and capillary forces, as well as dielectrophoretics, are summarised to understand the design approaches. Photochemical alterations with diazirine, nitrobenzyl and aryl azide functional groups for the implication of modified substrates, such as self-assembled monolayers functionalized with amino silanes, organosilanes and alkanethiols on gold surfaces, as well as topographical effects of patterning techniques for protein functionalization and orientation, are discussed. Analytical methods for the evaluation of protein functionality are also mentioned. Regarding their selectivity, protein pattering methods will be readily used to fabricate modified surfaces and target-specific delivery systems for the transportation of macromolecules such as streptavidin, and albumin. Future applications of patterning techniques include high-throughput screening, the evaluation of intracellular interactions, accurate screening and personalized treatments.

The Bumpy Road to Stem Cell Therapies: Rational Design of Surface Topographies to Dictate Stem Cell Mechanotransduction and Fate

Cells sense and respond to a variety of physical cues from their surrounding microenvironment, and these are interpreted through mechanotransductive processes to inform their behavior. These mechanisms have particular relevance to stem cells, where control of stem cell proliferation, potency, and differentiation is key to their successful application in regenerative medicine. It is increasingly recognized that surface micro- and nanotopographies influence stem cell behavior and may represent a powerful tool with which to direct the morphology and fate of stem cells. Current progress toward this goal has been driven by combined advances in fabrication technologies and cell biology. Here, the capacity to generate precisely defined micro- and nanoscale topographies has facilitated the studies that provide knowledge of the mechanotransducive processes that govern the cellular response as well as knowledge of the specific features that can drive cells toward a defined differentiation outcome. However, the path forward is not fully defined, and the "bumpy road" that lays ahead must be crossed before the full potential of these approaches can be fully exploited. This review focuses on the challenges and opportunities in applying micro- and nanotopographies to dictate stem cell fate for regenerative medicine. Here, key techniques used to produce topographic features are reviewed, such as photolithography, block copolymer lithography, electron beam lithography, nanoimprint lithography, soft lithography, scanning probe lithography, colloidal lithography, electrospinning, and surface roughening, alongside their advantages and disadvantages. The biological impacts of surface topographies are then discussed, including the current understanding of the mechanotransductive mechanisms by which these cues are interpreted by the cells, as well as the specific effects of surface topographies on cell differentiation and fate. Finally, considerations in translating these technologies and their future prospects are evaluated.

Toward the Development of Rapid, Specific, and Sensitive Microfluidic Sensors: A Comprehensive Device Blueprint

Recent advances in nano/microfluidics have led to the miniaturization of surface-based chemical and biochemical sensors, with applications ranging from environmental monitoring to disease diagnostics. These systems rely on the detection of analytes flowing in a liquid sample, by exploiting their innate nature to react with specific receptors immobilized on the microchannel walls. The efficiency of these systems is defined by the cumulative effect of analyte detection speed, sensitivity, and specificity. In this perspective, we provide a fresh outlook on the use of important parameters obtained from well-characterized analytical models, by connecting the mass transport and reaction limits with the experimentally attainable limits of analyte detection efficiency. Specifically, we breakdown when and how the operational (e.g., flow rates, channel geometries, mode of detection, etc.) and molecular (e.g., receptor affinity and functionality) variables can be tailored to enhance the analyte detection time, analytical specificity, and sensitivity of the system (i.e., limit of detection). Finally, we present a simple yet cohesive blueprint for the development of high-efficiency surface-based microfluidic sensors for rapid, sensitive, and specific detection of chemical and biochemical analytes, pertinent to a variety of applications.

Multifunctional Structured Platforms: From Patterning of Polymer-Based Films to Their Subsequent Filling with Various Nanomaterials

There is an astonishing number of optoelectronic, photonic, biological, sensing, or storage media devices, just to name a few, that rely on a variety of extraordinary periodic surface relief miniaturized patterns fabricated on polymer-covered rigid or flexible substrates. Even more extraordinary is that these surface relief patterns can be further filled, in a more or less ordered fashion, with various functional nanomaterials and thus can lead to the realization of more complex structured architectures. These architectures can serve as multifunctional platforms for the design and the development of a multitude of novel, better performing nanotechnological applications. In this work, we aim to provide an extensive overview on how multifunctional structured platforms can be fabricated by outlining not only the main polymer patterning methodologies but also by emphasizing various deposition methods that can guide different structures of functional nanomaterials into periodic surface relief patterns. Our aim is to provide the readers with a toolbox of the most suitable patterning and deposition methodologies that could be easily identified and further combined when the fabrication of novel structured platforms exhibiting interesting properties is targeted.

Antibody Printing Technologies

Antibody microarrays are routinely employed in the lab and in the clinic for studying protein expression, protein-protein, and protein-drug interactions. The microarray format reduces the size scale at which biological and biochemical interactions occur, leading to large reductions in reagent consumption and handling times while increasing overall experimental throughput. Specifically, antibody microarrays, as a platform, offer a number of different advantages over traditional techniques in the areas of drug discovery and diagnostics. While a number of different techniques and approaches have been developed for creating micro and nanoscale antibody arrays, issues relating to sensitivity, cost, and reproducibility persist. The aim of this review is to highlight current state-of the-art techniques and approaches for creating antibody arrays by providing latest accounts of the field while discussing potential future directions.