Fabrication of nanometer-sized protein patterns using atomic force microscopy and selective immobilization

Inkjet Printing: A Viable Technology for Biosensor Fabrication

Printing technology promises a viable solution for the low-cost, rapid, flexible, and mass fabrication of biosensors. Among the vast number of printing techniques, screen printing and inkjet printing have been widely adopted for the fabrication of biosensors. Screen printing provides ease of operation and rapid processing; however, it is bound by the effects of viscous inks, high material waste, and the requirement for masks, to name a few. Inkjet printing, on the other hand, is well suited for mass fabrication that takes advantage of computer-aided design software for pattern modifications. Furthermore, being drop-on-demand, it prevents precious material waste and offers high-resolution patterning. To exploit the features of inkjet printing technology, scientists have been keen to use it for the development of biosensors since 1988. A vast number of fully and partially inkjet-printed biosensors have been developed ever since. This study presents a short introduction on the printing technology used for biosensor fabrication in general, and a brief review of the recent reports related to virus, enzymatic, and non-enzymatic biosensor fabrication, via inkjet printing technology in particular.

Theoretical assessments on the interaction between amino acids and the g-Mg3N2 monolayer: dispersion corrected DFT and DFT-MD simulations

The interaction of a few amino acids (AAs) with the graphene-like magnesium nitride (g-Mg₃N₂) monolayer has been investigated with density functional theory (DFT) simulations. The Mg site was found to cause significant attraction with the polar active sites of AAs. Such AAs, are capable of producing electrostatics bonding with -48.012 (kcal mol^-1) of interaction energy for tyrosine. The good consistency of the DFT interaction energy with the second-order Møller-Plesset method was found. Furthermore, the DFT-MD simulation of the tyrosine/g-Mg₃N₂ system demonstrated that this host-guest system is stable at ambient conditions. The electronic structures and quantum molecular descriptors were calculated, and the results revealed that the g-Mg₃N₂ monolayer is sensitive to the interaction with AAs. Our first-principles outcomes suggest comprehensive visions into the functionalization of g-Mg₃N₂, and anticipate its applicability as an unprecedented nanovector for AAs. In addition, g-Mg₃N₂ nanosheets can be utilized as biosensors for biomolecules detection. These are very hopeful for promising biological and pharmaceutical applications of g-Mg₃N₂.

Single-Molecule Ex Situ Atomic Force Microscopy Allows Detection of Individual Antibody-Antigen Interactions on a Semiconductor Chip Surface

Although in situ atomic force microscopy (AFM) allows single‐molecule detection of antibody–antigen binding, the practical applications of in situ AFM for disease diagnosis are greatly limited, due to its operational complexity and long operational times, including the execution time for the surface chemical/biological treatments in the equipped glass liquid cell. Herein, a method of graphically superimposed alignment that enables ex situ AFM analysis of an immobilized antibody at the same location on a semiconductor chip surface before and after incubation with its antigen is presented. All of the required chemical/biological treatments are executed feasibly using standard laboratory containers, allowing single‐molecule ex situ AFM detection to be conducted with great practicality, flexibility, and versatility. As an example, the analysis of hepatitis B virus X protein (HBx) and its IgG antibody is described. Using ex situ AFM, individual information on the topographical characteristics of the immobilized single and aggregated IgG antibodies on the chip surface is extracted and the data are analyzed statistically. Furthermore, in a statistical manner, the changes in AFM‐measured heights of the individual and aggregated IgG antibodies that occur as a result of changes in conformation upon formation of IgG–HBx complexes are investigated.

Spatially selective binding of green fluorescent protein on designed organosilane nanopatterns prepared with particle lithography

A practical approach for preparing protein nanopatterns has been to design surface templates of nanopatterns of alkanethiols or organosilanes that will selectively bind and localize the placement of biomolecules. Particle lithography provides a way to prepare millions of protein nanopatterns with a few basic steps. For our nanopatterning strategy, organosilanes with methoxy and sulfhydryl groups were chosen as a surface template. Green fluorescent protein (GFP) was selected as a model for patterning. Areas of 2-[methoxy (polyethyleneoxy)6-9propyl]trichlorosilane (MPT-silane) are effective as a matrix for resisting the attachment of proteins, whereas nanopatterns with sulfur groups provide reactive sites for binding linker groups to connect proteins. A protocol with particle lithography was designed to make a surface template of nanopatterns of (3-mercaptopropyl)trimethoxysilane (MPTMS) surrounded by a methoxy terminated matrix. The sulfhydryl groups of the MPTMS nanopatterns were activated with a sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate linker. The activated regions of MPTMS furnished sites for binding GFP. Samples were characterized with atomic force microscopy after successive steps of the patterning protocol to evaluate the selectivity of protein binding. Direct views of the protein bound selectively to designated sites of MPTMS are presented, as evidence of robust and reproducible patterning. Nanoscale patterns of proteins can be used for surfaces of biochips and biosensors, and also for immunochemistry test platforms.

Sensitive detection and glycoprofiling of a prostate specific antigen using impedimetric assays

This study presents a proof-of-concept for the development of an impedimetric biosensor for ultra-sensitive glycoprofiling of prostate specific antigen (PSA). The biosensor exhibits three unique characteristics: (1) analysis of PSA with limit of detection (LOD) down to 4 aM; (2) analysis of the glycan part of PSA with LOD down to 4 aM level and; (3) both assays (i.e., PSA quantification and PSA glycoprofiling) can be performed on the same interface due to label-free analysis.

Bottom-up nanofabrication through catalyzed vapor phase HF etching of SiO2

We show that a wide range of inorganic and organic molecules or nanostructures can enhance the vapor phase HF etching of SiO2 resulting in a negative tone pattern transfer to a SiO2 substrate. The templates used in this study include micron- and nanometer-sized NaCl crystals, graphene oxide flakes, and albumin molecules. In all cases, a negative-tone pattern transfer to the underlying SiO2 substrate was obtained. The results suggest that vapor phase HF etching could be a general purpose pattern transfer technique for nanoscale and supramolecular templates.

Nanoscale lithography mediated by surface self-assembly of 16-[3,5-bis(mercaptomethyl)phenoxy]hexadecanoic acid on Au(111) investigated by scanning probe microscopy

The solution-phase self-assembly of bidentate 16-[3,5-bis(mercapto-methyl)phenoxy]hexadecanoic acid (BMPHA) on Au(111) was studied using nano-fabrication protocols with scanning probe nanolithography and immersion particle lithography. Molecularly thin films of BMPHA prepared by surface self-assembly have potential application as spatially selective layers in sensor designs. Either monolayer or bilayer films of BMPHA can be formed under ambient conditions, depending on the parameters of concentration and immersion intervals. Experiments with scanning probe-based lithography (nanoshaving and nanografting) were applied to measure the thickness of BMPHA films. The thickness of a monolayer and bilayer film of BMPHA on Au(111) were measured in situ with atomic force microscopy using n-octadecanethiol as an internal reference. Scanning probe-based nanofabrication provides a way to insert nanopatterns of a reference molecule of known dimensions within a matrix film of unknown thickness to enable a direct comparison of heights and surface morphology. Immersion particle lithography was used to prepare a periodic arrangement of nanoholes within films of BMPHA. The nanoholes could be backfilled by immersion in a SAM solution to produce nanodots of n-octadecanethiol surrounded by a film of BMPHA. Test platforms prepared by immersion particle lithography enables control of the dimensions of surface sites to construct supramolecular assemblies.

Controlled charged amino acids of Ti-binding peptide for surfactant-free selective adsorption

The adsorption mechanism of titanium-binding peptide (TBP) on metal oxide substrates was investigated by evaluating the adsorption behavior of ferritins with various alanine-substituted TBPs. Results revealed that (a) a positively charged amino acid, lysine (K) or arginine (R), in TBP can anchor ferritin to negative zeta-potential substrates, (b) the adsorption force of K is stronger than R, and (c) local electrostatic interactions and flexibility of TBP directly affect adsorption. Based on these findings, selective ferritin adsorption on SiO2 with TiOX patterned surfaces in a surfactant-free condition was demonstrated. Alanine-substituted TBP with one positively charged amino acid (K) and one negatively charged amino acid (D), achieved ferritin-selective adsorption without a surfactant. The importance of controlled electrostatic forces between TBP and a substrate for selective adsorption without a surfactant was clearly demonstrated.

Long-range ordered nanodomains of grafted electroactive molecules

We demonstrate the capability to build zero and one-dimensional electroactive molecular nanostructures ordered over a macroscopic scale and stable under ambient conditions. To realize these arrays, we use the selective grafting of functionalized thiols (juglon and terthiophene based) on a self-organized metallic template. The nanoscale patterning of the molecular conductance is demonstrated and analyzed by scanning tunneling spectroscopy. Finally, the influence of the nanostructuring on electro-chemical properties is measured, paving the way to an all-bottom-up fabrication of nanostructured templates for nanosciences.

Photocatalytic nanolithography of self-assembled monolayers and proteins

Self-assembled monolayers of alkylthiolates on gold and alkylsilanes on silicon dioxide have been patterned photocatalytically on sub-100 nm length-scales using both apertured near-field and apertureless methods. Apertured lithography was carried out by means of an argon ion laser (364 nm) coupled to cantilever-type near-field probes with a thin film of titania deposited over the aperture. Apertureless lithography was carried out with a helium-cadmium laser (325 nm) to excite titanium-coated, contact-mode atomic force microscope (AFM) probes. This latter approach is readily implementable on any commercial AFM system. Photodegradation occurred in both cases through the localized photocatalytic degradation of the monolayer. For alkanethiols, degradation of one thiol exposed the bare substrate, enabling refunctionalization of the bare gold by a second, contrasting thiol. For alkylsilanes, degradation of the adsorbate molecule provided a facile means for protein patterning. Lines were written in a protein-resistant film formed by the adsorption of oligo(ethylene glycol)-functionalized trichlorosilanes on glass, leading to the formation of sub-100 nm adhesive, aldehyde-functionalized regions. These were derivatized with aminobutylnitrilotriacetic acid, and complexed with Ni(2+), enabling the binding of histidine-labeled green fluorescent protein, which yielded bright fluorescence from 70-nm-wide lines that could be imaged clearly in a confocal microscope.

Spatially selective surface platforms for binding fibrinogen prepared by particle lithography with organosilanes

We introduce an approach based on particle lithography to prepare spatially selective surface platforms of organosilanes that are suitable for nanoscale studies of protein binding. Particle lithography was applied for patterning fibrinogen, a plasma protein that has a major role in the clotting cascade for blood coagulation and wound healing. Surface nanopatterns of mercaptosilanes were designed as sites for the attachment of fibrinogen within a protein-resistant matrix of 2-[methoxy(polyethyleneoxy)propyl] trichlorosilane (PEG-silane). Preparing site-selective surfaces was problematic in our studies, because of the self-reactive properties of PEG-organosilanes. Certain organosilanes presenting hydroxyl head groups will cross react to form mixed surface multi-layers. We developed a clever strategy with particle lithography using masks of silica mesospheres to protect small, discrete regions of the surface from cross reactions. Images acquired with atomic force microscopy (AFM) disclose that fibrinogen attached primarily to the surface areas presenting thiol head groups, which were surrounded by PEG-silane. The activity for binding anti-fibrinogen was further evaluated using ex situ AFM studies, confirming that after immobilization the fibrinogen nanopatterns retained capacity for binding immunoglobulin G. Studies with AFM provide advantages of achieving nanoscale resolution for detecting surface changes during steps of biochemical surface reactions, without requiring chemical modification of proteins or fluorescent labels.

From the bottom up: dimensional control and characterization in molecular monolayers

Self-assembled monolayers are a unique class of nanostructured materials, with properties determined by their molecular lattice structures, as well as the interfaces with their substrates and environments. As with other nanostructured materials, defects and dimensionality play important roles in the physical, chemical, and biological properties of the monolayers. In this review, we discuss monolayer structures ranging from surfaces (two-dimensional) down to single molecules (zero-dimensional), with a focus on applications of each type of structure, and on techniques that enable characterization of monolayer physical properties down to the single-molecule scale.

Immobilization of proteins on carboxylic acid functionalized nanopatterns

The immobilization of proteins on nanopatterned surfaces was investigated using in situ atomic force microscopy (AFM) and ex situ infrared reflectance-absorption spectroscopy (IRAS). The AFM-based lithography technique of nanografting provided control of the size, geometry, and spatial placement of nanopatterns within self-assembled monolayers (SAMs). Square nanopatterns of carboxylate-terminated SAMs were inscribed within methyl-terminated octadecanethiolate SAMs and activated using carbodiimide/succinimide coupling chemistry. Staphylococcal protein A was immobilized on the activated nanopatterns before exposure to rabbit immunoglobulin G. In situ AFM was used to monitor changes in the topography and friction of the nanopatterns in solution upon protein immobilization. Complementary studies with ex situ IRAS confirmed the surface chemistry that occurred during the steps of SAM activation and subsequent protein immobilization on unpatterned samples. Since carbodiimide/succinimide coupling chemistry can be used for surface attachment of different biomolecules, this protocol shows promise for development of other aqueous-based studies for nanopatterned protein immobilization.

Light-directed nanosynthesis: near-field optical approaches to integration of the top-down and bottom-up fabrication paradigms

The integration of top-down (lithographic) and bottom-up (synthetic chemical) methodologies remains a major goal in nanoscience. At larger length scales, light-directed chemical synthesis, first reported two decades ago, provides a model for this integration, by combining the spatial selectivity of photolithography with the synthetic utility of photochemistry. This review describes attempts to realise a similar integration at the nanoscale, by employing near-field optical probes to initiate selective chemical transformations in regions a few tens of nm in size. A combination of near-field exposure and an ultra-thin resist yields exceptional performance: in self-assembled monolayers, an ultimate resolution of 9 nm (ca. λ/30) has been achieved. A wide range of methodologies, based on monolayers of thiols, silanes and phosphonic acids, and thin films of nanoparticles and polymers, have been developed for use on metal and oxide surfaces, enabling the fabrication of metal nanowires, nanostructured polymers and nanopatterned oligonucleotides and proteins. Recently parallel lithography approaches have demonstrated the capacity to pattern macroscopic areas, and the ability to function under fluid, suggesting exciting possibilities for surface chemistry at the nanoscale.

Nanobiochips

The actual progress towards biological chip devices consisting of nanostructured functional entities is summarized. The practical aspects of molecular nanobiochips are discussed, including the main surface chemistry platforms, as well as conventional and unconventional fabrication tools. Several successful biological demonstrations of the first generation of nanobiochip devices (mainly, different nanoarrays) are highlighted with the aim of revealing the potential of this technology in life sciences, medicine, and related areas.

Cell fluidics: producing cellular streams on micropatterned synthetic surfaces

Patterning cell-adhesive molecules on material surfaces provides a powerful tool for controlling and guiding cell locomotion and migration. Here we report fast, reliable, easy to implement methods to fabricate large patterns of proteins on synthetic substrates to control the direction and speed of cells. Two common materials exhibiting very different protein adsorption capacities, namely, polystyrene and Teflon, were functionalized with micrometric stripes of laminin. The protein was noncovalently immobilized onto the surface by following either lithographically controlled wetting (LCW) or micromolding in capillaries (MIMIC). These techniques proved to be sufficiently mild so as not to interfere with the protein adhesion capability. Cells adhered onto the functionalized stripes and remained viable for more than 20 h. During this time frame, cells migrated along the lanes and the dynamics of motion was strongly affected by the substrate surface chemistry and culturing conditions. In particular, enhanced mismatches of cell adhesive properties obtained by the juxtaposition of bare and laminin-functionalized Teflon caused cells to move slowly and their movement to be highly confined. The patterning procedure was also effective at guiding migration on conventional cell culture dishes that were functionalized with laminin patterns, even in the presence of serum proteins, although to a lesser extent compared to that for Teflon. This work demonstrates the possibility of creating well-defined, long-range cellular streams on synthetic substrates by pursuing straightforward functionalizing techniques that can be implemented for a broad class of materials under conventional, long-time cell-culturing conditions. The procedure effectively confines cells to migrate along predefined patterns and can be implemented in different biomedical and biotechnological applications.

Automated scanning probe lithography with n-alkanethiol self assembled monolayers on Au(111): Application for teaching undergraduate laboratories

Controllers for scanning probe instruments can be programmed for automated lithography to generate desired surface arrangements of nanopatterns of organic thin films, such as n-alkanethiol self-assembled monolayers (SAMs). In this report, atomic force microscopy (AFM) methods of lithography known as nanoshaving and nanografting are used to write nanopatterns within organic thin films. Commercial instruments provide software to control the length, direction, speed, and applied force of the scanning motion of the tip. For nanoshaving, higher forces are applied to an AFM tip to selectively remove regions of the matrix monolayer, exposing bare areas of the gold substrate. Nanografting is accomplished by force-induced displacement of molecules of a matrix SAM, followed immediately by the surface self-assembly of n-alkanethiol molecules from solution. Advancements in AFM automation enable rapid protocols for nanolithography, which can be accomplished within the tight time restraints of undergraduate laboratories. Example experiments with scanning probe lithography (SPL) will be described in this report that were accomplished by undergraduate students during laboratory course activities and research internships in the chemistry department of Louisiana State University. Students were introduced to principles of surface analysis and gained "hands-on" experience with nanoscale chemistry.

Regulation of local structure and composition of binary disulfide and thiol self-assembled monolayers using nanografting

Nanografting is used to create spatial confinement, which enables regulation of self-assembly reaction pathways and outcome. The degree and outcome of this regulation is revealed using binary self-assembled monolayers (SAMs) of organothiols and disulfides. In naturally grown systems, these SAMs have more complex morphology when compared with corresponding binary alkanethiol SAMs. Taller molecules form nanodomains of ellipsoidal cap in shape. These domains arrange in various irregular geometries, including 1D worm-like and 2D branches. This observation differs from binary alkanethiol SAMs, where nanodomains are separated and randomly dispersed. During nanografting, more homogeneous morphology was observed compared with naturally grown layers. By varying nanoshaving speed, the nanodomain structure can be regulated from randomly dispersed to more heterogeneous and, finally, to near natural growth. This trend is very similar to mixed alkanethiol systems, where the domain size and separation increase with increasing speed. Different from the alkanethiol systems, the observed structural variations are due to the changes in surface composition, in addition to domain size, shape, and arrangement.

Biomimetic nanopatterns as enabling tools for analysis and control of live cells

It is becoming increasingly evident that cell biology research can be considerably advanced through the use of bioengineered tools enabled by nanoscale technologies. Recent advances in nanopatterning techniques pave the way for engineering biomaterial surfaces that control cellular interactions from the nano- to the microscale, allowing more precise quantitative experimentation capturing multi-scale aspects of complex tissue physiology in vitro. The spatially and temporally controlled display of extracellular signaling cues on nanopatterned surfaces (e. g., cues in the form of chemical ligands, controlled stiffness, texture, etc.) that can now be achieved on biologically relevant length scales is particularly attractive enabling experimental platform for investigating fundamental mechanisms of adhesion-mediated cell signaling. Here, we present an overview of bio-nanopatterning methods, with the particular focus on the recent advances on the use of nanofabrication techniques as enabling tools for studying the effects of cell adhesion and signaling on cell function. We also highlight the impact of nanoscale engineering in controlling cell-material interfaces, which can have profound implications for future development of tissue engineering and regenerative medicine.

Native serotonin membrane receptors recognize 5-hydroxytryptophan-functionalized substrates: enabling small-molecule recognition

Recognition of small diffusible molecules by large biomolecules is ubiquitous in biology. To investigate these interactions, it is important to be able to immobilize small ligands on substrates; however, preserving recognition by biomolecule-binding partners under these circumstances is challenging. We have developed methods to modify substrates with serotonin, a small-molecule neurotransmitter important in brain function and psychiatric disorders. To mimic soluble serotonin, we attached its amino acid precursor, 5-hydroxytryptophan, via the ancillary carboxyl group to oligo(ethylene glycol)-terminated alkanethiols self-assembled on gold. Anti-5-hydroxytryptophan antibodies recognize these substrates, demonstrating bioavailability. Interestingly, 5-hydroxytryptophan-functionalized surfaces capture membrane-associated serotonin receptors enantiospecifically. By contrast, surfaces functionalized with serotonin itself fail to bind serotonin receptors. We infer that recognition by biomolecules evolved to distinguish small-molecule ligands in solution requires tethering of the latter via ectopic moieties. Membrane proteins, which are notoriously difficult to isolate, or other binding partners can be captured for identification, mapping, expression, and other purposes using this generalizable approach.

Single protein molecule mapping with magnetic atomic force microscopy

Understanding the structural organization and distribution of proteins in biological cells is of fundamental importance in biomedical research. The use of conventional fluorescent microscopy for this purpose is limited due to its relatively low spatial resolution compared to the size of a single protein molecule. Atomic force microscopy (AFM), on the other hand, allows one to achieve single-protein resolution by scanning the cell surface using a specialized ligand-coated AFM tip. However, because this method relies on short-range interactions, it is limited to the detection of binding sites that are directly accessible to the AFM tip. We developed a method based on magnetic (long-range) interactions and applied it to investigate the structural organization and distribution of endothelin receptors on the surface of smooth muscle cells. Endothelin receptors were labeled with 50-nm superparamagnetic microbeads and then imaged with magnetic AFM. Considering its high spatial resolution and ability to "see" magnetically labeled proteins at a distance of up to 150 nm, this approach may become an important tool for investigating the dynamics of individual proteins both on the cell membrane and in the submembrane space.

Advanced printing and deposition methodologies for the fabrication of biosensors and biodevices

Advanced printing and deposition methodologies are revolutionising the way biological molecules are deposited and leading to changes in the mass production of biosensors and biodevices. This revolution is being delivered principally through adaptations of printing technologies to device fabrication, increasing throughputs, decreasing feature sizes and driving production costs downwards. This review looks at several of the most relevant deposition and patterning methodologies that are emerging, either for their high production yield, their ability to reach micro- and nano-dimensions, or both. We look at inkjet, screen, microcontact, gravure and flexographic printing as well as lithographies such as scanning probe, photo- and e-beam lithographies and laser printing. We also take a look at the emerging technique of plasma modification and assess the usefulness of these for the deposition of biomolecules and other materials associated with biodevice fabrication.

Confocal detection of planar homogeneous and heterogeneous immunosorbent assays

Optically sectioned detection of fluorescence immunoassays using a confocal microscope enables the creation of both homo- and heterogeneous planar format assays. We report a set assays requiring optically sectioned detection using a model system and analysis procedures for separating signals of a surface layer from an overlying solution. A model sandwich assay with human immunoglobulin G as the target antigen is created on a glass substrate. The prepared surfaces are exposed to antigen and a FITC-labeled secondary antibody. The resulting preparations are either read directly to provide a homogeneous assay or after wash steps, giving a heterogeneous assay. The simplicity of the object shapes arising from the planar format makes the decomposition of analyte signals from the thin film bound to the surface and overlayer straightforward. Measured response functions of the thin film and overlayer fit well to the Cauchy-Lorentz and cumulative Cauchy-Lorentz functions, respectively, enabling the film and overlayer to be separated. Under the conditions used, the detection limits for the homogeneous and heterogeneous forms of the assay are 2.2 and 5.5 ng/ml, respectively. Planar format, confocally read fluorescence assays enable wash-free detection of antigens and should be applicable to a wide range of assays involving surface-bound species.

A nanoengineering approach for investigation and regulation of protein immobilization

It is known that protein attachment to surfaces depends sensitively upon the local structure and environment of the binding sites at the nanometer scale. Using nanografting and reversal nanografting, both atomic force microscopy (AFM)-based lithography techniques, protein binding sites with well-defined local environments are designed and engineered with nanometer precision. Three proteins, goat antibiotin immunoglobulin G (IgG), lysozyme, and rabbit immunoglobulin G, are immobilized onto these engineered surfaces. Strong dependence on the dimension and spatial distribution of protein binding sites are revealed in antibody recognition, covalent attachment via primary amine residues and surface-bound aldehyde groups. This investigation indicates that AFM-based nanolithography enables the production of protein nanostructures, and more importantly, protein-surface interactions at a molecular level can be regulated by changing the binding domains and their local environment at nanometer scale.

Nanopatterning of fibronectin and the influence of integrin clustering on endothelial cell spreading and proliferation

Investigating stages of maturation of cellular adhesions to the extracellular matrix from the initial binding events to the formation of small focal complexes has been challenging because of the difficulty in fabricating the necessary nanopatterned substrates with controlled biochemical functionality. We present the fabrication and characterization of surfaces presenting fibronectin nanopatterns of controlled size and pitch that provide well-defined cellular adhesion sites against a nonadhesive polyethylene glycol background. The nanopatterned surfaces allow us to control the number of fibronectin proteins within each adhesion site from 9 to 250, thereby limiting the number of integrins involved in each cell-substrate adhesion. We demonstrate the presence of fibronectin on the nanoislands, while no protein was observed on the passivated background. We show that the cell adheres to the nanopatterns with adhesions that are much smaller and more evenly distributed than on a glass control. The nanopattern influences cellular proliferation only at longer times, but influences spreading at both early and later times, indicating adhesion size and adhesion density play a role in controlling cell adhesion and signaling. However, the overall density of fibronectin on all patterns is far lower than on homogeneously coated control surfaces, showing that the local density of adhesion ligands, not the average density, is the important parameter for cell proliferation and spreading.

Micrometer and nanometer scale patterning using the photo-fries rearrangement: toward selective execution of molecular transformations with nanoscale spatial resolution

The photolithographic modification of monolayers provides a versatile and powerful means of fabricating functionalized nanostructured surfaces. In this contribution, we present photosensitive thiol-bearing aryl ester groups which are capable of undergoing the so-called photo-Fries rearrangement to yield hydroxyketones. Phenyl 16-mercaptohexadecanoate was prepared by a three-step synthesis. This molecule undergoes a photoisomerization reaction upon illumination with UV light at ca. 250 nm. Subsequently this molecule was applied as a self-assembled monolayer on gold. Following photochemical modification, the adsorbates were selectively derivatized to yield amino-functionalized surfaces using a simple two-step reaction. This reaction was monitored by X-ray photoelectron spectroscopy and contact angle measurements and friction force microscopy. Micrometer-scale patterned surfaces were produced using a contact mask in conjunction with a frequency-doubled argon ion laser (lambda=244 nm). Near-field optical exposure was carried out by coupling the laser to a scanning near-field optical microscope and yielded nanometer-scale resolution. Following derivatization, the resulting structures were analyzed by friction force microscopy. Clear contrast was observed in the friction signal following surface modification.

Ligand-induced structural changes in maltose binding proteins measured by atomic force microscopy

We use atomic force microscopy (AFM) based force-compression measurements to probe the ligand-induced functional conformational changes in surface-immobilized dicysteine-terminated maltose binding proteins (dicys-MBPs). The proteins are immobilized at well-defined locations directly on Au substrates using the previously reported technique of nanografting. By measuring the difference between the ligand-free and ligand-bound mechanical work performed by the AFM-tip during the protein compression, we determine the open-closed transition energy for dicys-MBPs to be DeltaE0 = (8 +/- 4) Kcal/mol. We also compare the binding kinetics of two different ligands (maltose and maltotriose) to dicys-MBPs by performing AFM-friction measurements. We show that our results are consistent with a simple model for the surface-immobilized dicys-MBPs: the protein consists of two rigid lateral lobes connected by a hinge-loaded spring.

Nanobiotechnology and Cell Biology: Micro- and Nanofabricated Surfaces to Investigate Receptor-Mediated Signaling

Advances in microfabrication and nanofabrication are opening new opportunities to investigate complicated questions of cell biology in ways not before possible. In particular, the spatial regulation of cellular processes can be examined by engineering the chemical and physical environment to which the cell responds. Lithographic methods and selective chemical modification schemes can provide biocompatible surfaces that control cellular interactions on the micron and submicron scales on which cells are organized. Combined with fluorescence microscopy and other approaches of cell biology, a widely expanded toolbox is becoming available. This review illustrates the potential of these integrated engineering tools, with an emphasis on patterned surfaces, for investigating fundamental mechanisms of receptor-mediated signaling in cells. We highlight progress made with immune cells and in particular with the IgE receptor system, which has been valuable for developing technology to gain new information about spatial regulation in signaling events.

Atomic force microscopy-derived nanoscale chip for the detection of human pathogenic viruses

Native-protein nanolithography (NPNL) was used to fabricate stable bioactive arrays of viral receptor spots. The arrays were specific for the cognate virus and devoid of nonspecific protein and virus adsorption under physiologic conditions. The spot size ranged from 200 nm x 200 nm to 2 microm x 2 microm and up to 3 x 3 spots were arranged per array. With proper force adjustment in the patterning experiments, His(6)-tagged bovine serum albumin (BSA) molecules were selectively removed from the underlying self-assembled monolayer (SAM) while leaving the latter intact. Injection of His(6)-tagged very low density lipoprotein receptor (VLDLR-His(6)) constructs resulted in specific, oriented binding to the Ni(2+)-loaded bis-(nitrolotriacetic acid) (bis-NTA) groups to the re-exposed SAM areas. The arrays of viral receptors were used for the detection of human rhinovirus particles (serotype 2; HRV2) under native conditions by topographical imaging at high signal-to-noise ratio. The kinetic on-rate of the HRV2-VLDLR interaction was derived from the time-dependent binding of the virions to the VLDL receptor spots. No significant binding was observed for the major group virus HRV14 that uses the unrelated receptor ICAM-1.

Structural characterization of aldehyde-terminated self-assembled monolayers

The structure of aldehyde-terminated alkanethiol self-assembled monolayers (SAMs) on Au(111) is investigated using scanning tunneling microscopy (STM), atomic force microscopy (AFM), and density functional theory (DFT) calculations. For the first time, the structures of aldehyde-terminated SAMs are revealed with molecular resolution. SAMs of 11-mercapto-1-undecanal exhibit the basic (radical3xradical3)R30 degrees periodicity and form various c(4x2) superstructures upon annealing. In conjunction with DFT studies, the models of the (radical3xradical3)R30 degrees and the c(4x2) superstructures are constructed. In comparison with alkanethiol SAMs, the introduction of aldehyde-termini results in smaller domain size, lower degree of long-range order, large coverage of disordered areas, and higher density of missing molecules and other point defects within domains of closely packed molecules. The origin of these structural differences is mainly attributed to the strong dipole-dipole interactions among the aldehyde termini.

Sub-100 nm patterning of supported bilayers by nanoshaving lithography

Sub-100 nm wide supported phospholipid bilayers (SLBs) were patterned on a planar borosilicate substrate by AFM-based nanoshaving lithography. First, a bovine serum albumin monolayer was coated on the glass and then selectively removed in long strips by an AFM tip. The width of vacant strips could be controlled down to 15 nm. Bilayer lines could be formed within the vacant strips by vesicle fusion. It was found that stable bilayers formed by this method had a lower size limit of approximately 55 nm in width. This size limit stems from a balance between a favorable bilayer adhesion energy and an unfavorable bilayer edge energy.

Scanning probe-based fabrication of 3D nanostructures via affinity templates, functional RNA, and meniscus-mediated surface remodeling

Developing generic platforms to organize discrete molecular elements and nanostructures into deterministic patterns on surfaces is one of the central challenges in the field of nanotechnology. Here we review three applications of the atomic force microscope (AFM) that address this challenge. In the first, we use two-step nanografting to create patterns of self-assembled monolayers (SAMs) to drive the organization of virus particles that have been either genetically or chemically modified to bind to the SAMs. Virus-SAM chemistries are described that provide irreversible and reversible binding, respectively. In the second, we use similar SAM patterns as affinity templates that have been designed to covalently bind oligonucleotides engineered to bind to the SAMs and selected for their ability to mediate the subsequent growth of metallic nanocrystals. In the final application, the liquid meniscus that condenses at the AFM tip-substrate contact is used as a physical tool to both modulate the surface topography of a water soluble substrate and guide the hierarchical assembly of Au nanoparticles into nanowires. All three approaches can be generalized to meet the requirements of a wide variety of materials systems and thereby provide a potential route toward development of a generic platform for molecular and materials organization.

Achieving precision and reproducibility for writing patterns of n-alkanethiol self-assembled monolayers with automated nanografting

Nanografting is a high-precision approach for scanning probe lithography, which provides unique advantages and capabilities for rapidly writing arrays of nanopatterns of thiol self-assembled monolayers (SAMs). Nanografting is accomplished by force- induced displacement of molecules of a matrix SAM, followed immediately by the self-assembly of n-alkanethiol ink molecules from solution. The feedback loop used to control the atomic force microscope tip position and displacement enables exquisite control of forces applied to the surface, ranging from pico to nanonewtons. To achieve high-resolution writing at the nanoscale, the writing speed, direction, and applied force need to be optimized. There are strategies for programing the tip translation, which will improve the uniformity, alignment, and geometries of nanopatterns written using open-loop feedback control. This article addresses the mechanics of automated nanografting and demonstrates results for various writing strategies when nanografting patterns of n-alkanethiol SAMs.

The investigation of Protein A and Salmonella antibody adsorption onto biosensor surfaces by atomic force microscopy

The investigation of Protein A and antibody adsorption on surfaces in a biological environment is an important and fundamental step for increasing biosensor sensitivity and specificity. The atomic force microscope (AFM) is a powerful tool that is frequently used to characterize surfaces coated with a variety of molecules. We used AFM in conjunction with scanning electron microscopy to characterize the attachment of protein A and its subsequent binding to the antibody and Salmonella bacteria using a gold quartz crystal. The rms roughness of the base gold surface was determined to be approximately 1.30 nm. The average step height change between the solid gold and protein A layer was approximately 3.0 +/- 1.0 nm, while the average step height of the protein A with attached antibody was approximately 6.0 +/- 1.0 nm. We found that the antibodies did not completely cover the protein A layer, instead the attachment follows an island model. Salt crystals and water trapped under the protein A layer were also observed. The uneven adsorption of antibodies onto the biosensor surface might have led to a decrease in the sensitivity of the biosensor. The presence of salt crystals and water under the protein A layer may deteriorate the sensor specificity. In this report, we have discussed the application and characterization of protein A bound to antibodies which can be used to detect bacterial and viral pathogens.