Fluorescence, XPS, and TOF-SIMS surface chemical state image analysis of DNA microarrays

Near-edge x-ray absorption fine structure spectra and specific dissociation of small peptoid molecules

In this study, the total ion yield near-edge x-ray absorption fine structure spectra of four similar peptoid molecules, which differ in the numbers and positions of methyl groups, were investigated experimentally and theoretically. At each excitation energy, the intensity and branching ratio of each ionic product were measured. At a few resonant excitation energies, a specific dissociation of the C-CO bond at the nitrogen and oxygen K-edges and of the N-CO bond at the carbon K-edge was dominant, which correlated well with the predicted destination antibonding orbitals of the core electron excitation. These specific dissociation mechanisms of small peptoid molecules could provide insights into similar phenomena that occur in peptide molecules.

Label-Free Imaging of Solid-Phase Peptide Synthesis Products and Their Modifications Tethered in Microspots Using Time-of-Flight Secondary Ion Mass Spectrometry

Time-of-flight secondary ion mass spectrometry is used to analyze solid-phase synthesis products in 60 µm spots of high-density peptide arrays. As a result, a table of specific fragments for the individual detection of amino acids and their side chain protecting groups within peptides is compiled. The specific signal of an amino acid increases linearly as its number increases in the immobilized peptide. Mass-to-charge ratio values are identified that can distinguish between isomers such as leucine and isoleucine. The accessibility of the N-terminus of polyalanine will be studied depending on the number of its residues. The examples provided in the study demonstrate the significant potential of time-of-flight secondary ion mass spectrometry for high-throughput screening of functional groups and their accessibility to chemical reactions occurring simultaneously in hundreds of thousands of microreactors on a single microscope slide.

Multiplexed DNA-functionalized graphene sensor with artificial intelligence-based discrimination performance for analyzing chemical vapor compositions

This study presents a new technology that can detect and discriminate individual chemical vapors to determine the chemical vapor composition of mixed chemical composition in situ based on a multiplexed DNA-functionalized graphene (MDFG) nanoelectrode without the need to condense the original vapor or target dilution. To the best of our knowledge, our artificial intelligence (AI)-operated arrayed electrodes were capable of identifying the compositions of mixed chemical gases with a mixed ratio in the early stage. This innovative technology comprised an optimized combination of nanodeposited arrayed electrodes and artificial intelligence techniques with advanced sensing capabilities that could operate within biological limits, resulting in the verification of mixed vapor chemical components. Highly selective sensors that are tolerant to high humidity levels provide a target for "breath chemovapor fingerprinting" for the early diagnosis of diseases. The feature selection analysis achieved recognition rates of 99% and above under low-humidity conditions and 98% and above under humid conditions for mixed chemical compositions. The 1D convolutional neural network analysis performed better, discriminating the compositional state of chemical vapor under low- and high-humidity conditions almost perfectly. This study provides a basis for the use of a multiplexed DNA-functionalized graphene gas sensor array and artificial intelligence-based discrimination of chemical vapor compositions in breath analysis applications.

Fabrication of gold nanoparticles tethered in heat-cooled calf thymus-deoxyribonucleic acid Langmuir-Blodgett film as effective surface-enhanced Raman scattering sensing platform

SERS active substrate fabricated through self-assembly of Gold nanoparticles on the disjointed networks of Heat-cooled Calf Thymus DNA (HC-Ct DNA) Langmuir-Blodgett (LB) film has been reported. Adsorption kinetics of HC-Ct DNA molecules at the air-water interface has been studied explicitly. The UV-Vis electronic absorption spectra in conjunction with the FESEM images collectively suggest the presence of H- type aggregated domains most likely owing to plane-to-plane self-association of the HC-Ct DNA molecules aligned vertically on the surface of the LB film. Elemental composition and the morphological features of the as-prepared substrate (APS) are explored from XPS analysis and the FESEM, AFM images respectively. The SERS efficacy of the APS has been tested with trace concentrations of 4-Mercaptopyridine molecule. Finally, this SERS active substrate has also been used for the detection of malathion at ultrasensitive concentrations.

Applications of multivariate analysis and unsupervised machine learning to ToF-SIMS images of organic, bioorganic, and biological systems

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging offers a powerful, label-free method for exploring organic, bioorganic, and biological systems. The technique is capable of very high spatial resolution, while also producing an enormous amount of information about the chemical and molecular composition of a surface. However, this information is inherently complex, making interpretation and analysis of the vast amount of data produced by a single ToF-SIMS experiment a considerable challenge. Much research over the past few decades has focused on the application and development of multivariate analysis (MVA) and machine learning (ML) techniques that find meaningful patterns and relationships in these datasets. Here, we review the unsupervised algorithms—that is, algorithms that do not require ground truth labels—that have been applied to ToF-SIMS images, as well as other algorithms and approaches that have been used in the broader family of mass spectrometry imaging (MSI) techniques. We first give a nontechnical overview of several commonly used classes of unsupervised algorithms, such as matrix factorization, clustering, and nonlinear dimensionality reduction. We then review the application of unsupervised algorithms to various organic, bioorganic, and biological systems including cells and tissues, organic films, residues and coatings, and spatially structured systems such as polymer microarrays. We then cover several novel algorithms employed for other MSI techniques that have received little attention from ToF-SIMS imaging researchers. We conclude with a brief outline of potential future directions for the application of MVA and ML algorithms to ToF-SIMS images.

Surface defective g-C3N4-xClx with unique spongy structure by polarization effect for enhanced photocatalytic removal of organic pollutants

Natural sponge is an ancient marine organism with a single lamellar structure, on which there are abundant porous channels to compose full-fledged spatial veins. Illumined by the natural spongy system, herein, the Cl doped surface defective graphite carbon nitride (g-C₃N_4-xCl_x) was constructed through microwave etching. In this process, microwave with HCl was employed to produce surface defects and peel bulk g-C₃N₄ to form natural spongy structured g-C₃N_4-xCl_x with three-dimensional networks. The spongy structure of the photocatalyst could provide abundant and unobstructed pathways for the transfer and separation of electron-hole pairs, and it was beneficial for photocatalytic reaction. The spongy defective g-C₃N_4-xCl_x achieved excellent degradation of diclofenac sodium (100%), bisphenol A (88.2%), phenol (85.7%) and methylene blue (97%) solution under simulated solar irradiation, respectively. The chlorine atoms were introduced into the g-C₃N₄ skeleton in microwave field with HCl, forming C-Cl bonds and surface polarization field, which could significantly accelerate the separation of photogenerated electrons and holes. As an efficient and universal approach, microwave etching can be generally used to create surface defects for most photocatalysts, which may have potential applications in environmental purification, energy conversion and photodynamic therapy.

Understanding mass spectrometry images: complexity to clarity with machine learning

The application of artificial intelligence and machine learning to hyperspectral mass spectrometry imaging (MSI) data has received considerable attention over recent years. Various methodologies have shown great promise in their ability to handle the complexity and size of MSI data sets. Advances in this area have been particularly appealing for MSI of biological samples, which typically produce highly complicated data with often subtle relationships between features. There are many different machine learning approaches that have been applied to MSI data over the past two decades. In this review, we focus on a subset of non-linear machine learning techniques that have mostly only been applied in the past 5 years. Specifically, we review the use of the self-organizing map (SOM), SOM with relational perspective mapping (SOM-RPM), t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP). While not their only functionality, we have grouped these techniques based on their ability to produce what we refer to as similarity maps. Similarity maps are color representations of hyperspectral data, in which spectral similarity between pixels-that is, their distance in high-dimensional space-is represented by relative color similarity. In discussing these techniques, we describe, briefly, their associated algorithms and functionalities, and also outline applications in MSI research with a strong focus on biological sample types. The aim of this review is therefore to introduce this relatively recent paradigm for visualizing and exploring hyperspectral MSI, while also providing a comparison between each technique discussed.

Controlling orientation, conformation, and biorecognition of proteins on silane monolayers, conjugate polymers, and thermo-responsive polymer brushes: investigations using TOF-SIMS and principal component analysis

Control over orientation and conformation of surface-immobilized proteins, determining their biological activity, plays a critical role in biointerface engineering. Specific protein state can be achieved with adjusted surface preparation and immobilization conditions through different types of protein-surface and protein-protein interactions, as outlined in this work. Time-of-flight secondary ion mass spectroscopy, combining surface sensitivity with excellent chemical specificity enhanced by multivariate data analysis, is the most suited surface analysis method to provide information about protein state. This work highlights recent applications of the multivariate principal component analysis of TOF-SIMS spectra to trace orientation and conformation changes of various proteins (antibody, bovine serum albumin, and streptavidin) immobilized by adsorption, specific binding, and covalent attachment on different surfaces, including self-assembled monolayers on silicon, solution-deposited polythiophenes, and thermo-responsive polymer brushes. Multivariate TOF-SIMS results correlate well with AFM data and binding assays for antibody-antigen and streptavidin-biotin recognition. Additionally, several novel extensions of the multivariate TOF-SIMS method are discussed.

Graphical abstract

In Vivo Molecular Insights into Syntrophic Geobacter Aggregates

Direct interspecies electron transfer (DIET) has been considered as a novel and highly efficient strategy in both natural anaerobic environments and artificial microbial fuel cells. A syntrophic model consisting of Geobacter metallireducens and Geobacter sulfurreducens was studied in this work. We conducted in vivo molecular mapping of the outer surface of the syntrophic community as the interface of nutrients and energy exchange. System for Analysis at the Liquid Vacuum Interface combined with time-of-flight secondary ion mass spectrometry was employed to capture the molecular distribution of syntrophic Geobacter communities in the living and hydrated state. Principal component analysis with selected peaks revealed that syntrophic Geobacter aggregates were well differentiated from other control samples, including syntrophic planktonic cells, pure cultured planktonic cells, and single population biofilms. Our in vivo imaging indicated that a unique molecular surface was formed. Specifically, aromatic amino acids, phosphatidylethanolamine components, and large water clusters were identified as key components that favored the DIET of syntrophic Geobacter aggregates. Moreover, the molecular changes in depths of the Geobacter aggregates were captured using dynamic depth profiling. Our findings shed new light on the interface components supporting electron transfer in syntrophic communities based on in vivo molecular imaging.

Mass spectrometry as a tool to advance polymer science

In contrast to natural polymers, which have existed for billions of years, the first well-understood synthetic polymers date back to just over one century ago. Nevertheless, this relatively short period has seen vast progress in synthetic polymer chemistry, which can now afford diverse macromolecules with varying structural complexities. To keep pace with this synthetic progress, there have been commensurate developments in analytical chemistry, where mass spectrometry has emerged as the pre-eminent technique for polymer analysis. This Perspective describes present challenges associated with the mass-spectrometric analysis of synthetic polymers, in particular the desorption, ionization and structural interrogation of high-molar-mass macromolecules, as well as strategies to lower spectral complexity. We critically evaluate recent advances in technology in the context of these challenges and suggest how to push the field beyond its current limitations. In this context, the increasingly important role of high-resolution mass spectrometry is emphasized because of its unrivalled ability to describe unique species within polymer ensembles, rather than to report the average properties of the ensemble.

Minimal attachment of Pseudomonas aeruginosa to DNA modified surfaces

Extracellular deoxyribonucleic acid (eDNA) exists in biological environments such as those around medical implants since prokaryotic or eukaryotic cells can undergo processes such as autolysis, necrosis, and apoptosis. For bacteria, eDNA has been shown to be involved in biofilm formation and gene transfer and acts as a nutrient source. In terms of biofilm formation, eDNA in solution has been shown to be very important in increasing attachment; however, very little is known about the role played by surface immobilized eDNA in initiating bacterial attachment and whether the nature of a DNA layer (physically adsorbed or covalently attached, and molecular weight) influences biofilm formation. In this study, the authors shed light on the role that surface attached DNA plays in the early biofilm formation by using Si wafers (Si) and allylamine plasma polymer (AAMpp) coated Si wafers to adsorb and covalently immobilize salmon sperm DNA of three different molecular weights. Pseudomonas aeruginosa was chosen to study the bacterial interactions with these DNA functionalized surfaces. Characterization of surface chemistry and imaging of attached bacteria were performed via x-ray photoelectron spectroscopy (XPS), scanning electron microscopy, and epi-fluorescence microscopy. XPS results confirmed the successful grafting of DNA on the AAMpp and Si surfaces, and surprisingly the results showed that the surface attached DNA actually reduced initial bacterial attachment, which was contrary to the initial hypothesis. This adds speculation about the specific role played by DNA in the dynamics of how it influences biofilm formation, with the possibility that it could actually be used to make bacterial resistant surfaces.

Time of flight secondary ion mass spectrometry-A method to evaluate plasma-modified three-dimensional scaffold chemistry

Biopolymers are used extensively in the manufacture of porous scaffolds for a variety of biological applications. The surfaces of these scaffolds are often modified to encourage specific interactions such as surface modification of scaffolds to prevent fouling or to promote a cell supportive environment for tissue engineering implants. However, few techniques can effectively characterize the uniformity of surface modifications in a porous scaffold. By filling the scaffold pores through polymer embedding, followed by analysis with imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS), the distribution and composition of surface chemical species though complex porous scaffolds can be characterized. This method is demonstrated on poly(caprolactone) scaffolds modified with a low-fouling plasma-deposited coating from octafluoropropane via plasma enhanced chemical vapor deposition. A gradient distribution of CF⁺/CF₃⁺ is observed for scaffolds plasma treated for 5 min, whereas a 20 min treatment results in more uniform distribution of the surface modification throughout the entire scaffold. The authors expect this approach to be widely applicable for ToF-SIMS analysis of scaffolds modified by multiple plasma processing techniques as well as alternative surface modification approaches.

Visualizing molecular distributions for biomaterials applications with mass spectrometry imaging: a review

Mass spectrometry imaging (MSI) is a rapidly emerging field that is continually finding applications in new and exciting areas. The ability of MSI to measure the spatial distribution of molecules at or near the surface of complex substrates makes it an ideal candidate for many applications, including those in the sphere of materials chemistry. Continual development and optimization of both ionization sources and analyzer technologies have resulted in a wide array of MSI tools available, both commercially available and custom-built, with each configuration possessing inherent strengths and limitations. Despite the unique potential of MSI over other chemical imaging methods, their potential and application to (bio)materials science remains in our view a largely underexplored avenue. This review will discuss these techniques enabling high parallel molecular detection, focusing on those with reported uses in (bio)materials chemistry applications and highlighted with select applications. Different technologies are presented in three main sections; secondary ion mass spectrometry (SIMS) imaging, matrix-assisted laser desorption ionization (MALDI) MSI, and emerging MSI technologies with potential for biomaterial analysis. The first two sections (SIMS and MALDI) discuss well-established methods that are continually evolving both in technological advancements and in experimental versatility. In the third section, relatively new and versatile technologies capable of performing measurements under ambient conditions will be introduced, with reported applications in materials chemistry or potential applications discussed. The aim of this review is to provide a concise resource for those interested in utilizing MSI for applications such as biomimetic materials, biological/synthetic material interfaces, polymer formulation and bulk property characterization, as well as the spatial and chemical distributions of nanoparticles, or any other molecular imaging application requiring broad chemical speciation.

Biomedical surface analysis: Evolution and future directions (Review)

This review describes some of the major advances made in biomedical surface analysis over the past 30-40 years. Starting from a single technique analysis of homogeneous surfaces, it has been developed into a complementary, multitechnique approach for obtaining detailed, comprehensive information about a wide range of surfaces and interfaces of interest to the biomedical community. Significant advances have been made in each surface analysis technique, as well as how the techniques are combined to provide detailed information about biological surfaces and interfaces. The driving force for these advances has been that the surface of a biomaterial is the interface between the biological environment and the biomaterial, and so, the state-of-the-art in instrumentation, experimental protocols, and data analysis methods need to be developed so that the detailed surface structure and composition of biomedical devices can be determined and related to their biological performance. Examples of these advances, as well as areas for future developments, are described for immobilized proteins, complex biomedical surfaces, nanoparticles, and 2D/3D imaging of biological materials.

Extracellular matrix-based biomaterial scaffolds and the host response

Extracellular matrix (ECM) collectively represents a class of naturally derived proteinaceous biomaterials purified from harvested organs and tissues with increasing scientific focus and utility in tissue engineering and repair. This interest stems predominantly from the largely unproven concept that processed ECM biomaterials as natural tissue-derived matrices better integrate with host tissue than purely synthetic biomaterials. Nearly every tissue type has been decellularized and processed for re-use as tissue-derived ECM protein implants and scaffolds. To date, however, little consensus exists for defining ECM compositions or sources that best constitute decellularized biomaterials that might better heal, integrate with host tissues and avoid the foreign body response (FBR). Metrics used to assess ECM performance in biomaterial implants are arbitrary and contextually specific by convention. Few comparisons for in vivo host responses to ECM implants from different sources are published. This review discusses current ECM-derived biomaterials characterization methods including relationships between ECM material compositions from different sources, properties and host tissue response as implants. Relevant preclinical in vivo models are compared along with their associated advantages and limitations, and the current state of various metrics used to define material integration and biocompatibility are discussed. Commonly applied applications of these ECM-derived biomaterials as stand-alone implanted matrices and devices are compared with respect to host tissue responses.

Imaging and spectroscopic comparison of multi-step methods to form DNA arrays based on the biotin-streptavidin system

Three multi-step multi-molecular approaches using the biotin-streptavidin system to contact-print DNA arrays on SiO2 surfaces modified with (3-glycidoxypropyl)trimethoxysilane are examined after each deposition/reaction step by atomic force microscopy, X-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry. Surface modification involves the spotting of preformed conjugates of biotinylated oligonucleotides with streptavidin onto surfaces coated with biotinylated bovine serum albumin b-BSA (approach I) or the spotting of biotinylated oligonucleotides onto a streptavidin coating, the latter prepared through a reaction with immobilized b-BSA (approach II) or direct adsorption (approach III). AFM micrographs, quantified by autocorrelation and height histogram parameters (e.g. roughness), reveal uniform coverage after each modification step with distinct nanostructures after the reaction of biotinylated BSA with streptavidin or of a streptavidin conjugate with biotinylated oligonucleotides. XPS relates the immobilization of biomolecules with covalent binding to the epoxy-silanized surface. Protein coverage, estimated from photoelectron attenuation, shows that regarding streptavidin the highest and the lowest immobilization efficiency is achieved by following approaches I and III, respectively, as confirmed by TOF-SIMS microanalysis. The size of the DNA spot reflects the contact radius of the printed droplet and increases with protein coverage (and roughness) prior to the spotting, as epoxy-silanized surfaces are hardly hydrophilic. Representative TOF-SIMS images show sub-millimeter spots: uniform for approach I, doughnut-like (with a small non-zero minimum) for approach II, both with coffee-rings or peak-shaped for approach III. Spot features, originating from pinned contact lines and DNA surface binding and revealed by complementary molecular distributions (all material, DNA, streptavidin, BSA, epoxy, SiO2), indicate two modes of droplet evaporation depending on the details of each applied approach.

Revealing cytokine-induced changes in the extracellular matrix with secondary ion mass spectrometry

Cell-secreted matrices (CSMs), where extracellular matrix (ECM) deposited by monolayer cell cultures is decellularized, have been increasingly used to produce surfaces that may be reseeded with cells. Such surfaces are useful to help us understand cell-ECM interactions in a microenvironment closer to the in vivo situation than synthetic substrates with adsorbed proteins. We describe the production of CSMs from mouse primary osteoblasts (mPObs) exposed to cytokine challenge during matrix secretion, mimicking in vivo inflammatory environments. Time-of-flight secondary ion mass spectrometry data revealed that CSMs with cytokine challenge at day 7 or 12 of culture can be chemically distinguished from one another and from untreated CSM using multivariate analysis. Comparison of the differences with reference spectra from adsorbed protein mixtures points towards cytokine challenge resulting in a decrease in collagen content. This is supported by immunocytochemical and histological staining, demonstrating a 44% loss of collagen mass and a 32% loss in collagen I coverage. CSM surfaces demonstrate greater cell adhesion than adsorbed ECM proteins. When mPObs were reseeded onto cytokine-challenged CSMs they exhibited reduced adhesion and elongated morphology compared to untreated CSMs. Such changes may direct subsequent cell fate and function, and provide insights into pathological responses at sites of inflammation.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

Metal-particle-induced enhancement of the photoluminescence from biomolecule-functionalized carbon nanotubes

The effect of metal particles on the photoluminescence (PL) and the Raman spectra of functionalized SWCNTs in aqueous solutions was systematically investigated by studying three different metal particles (gold, cobalt, and nickel) on three different SWCNT suspensions (DNA-, RNA-, and sodium deoxycholate salt (DOC)-functionalized SWCNTs). Substantial enhancement of the PL intensities was observed, while the Raman spectra remained unchanged, after gold, cobalt, or nickel particles were introduced into RNA-SWCNT aqueous suspensions. Almost the same results were obtained after the same metal particles were added to DNA-SWCNT aqueous suspensions. However, both the PL and the Raman spectra did not exhibit any change at all after the same metal particles were introduced into DOC-SWCNT aqueous suspensions. The unusual PL enhancements observed in this work cannot be accounted for by the three well-known mechanisms in the literature: surface-enhanced Raman scattering effect, Förster resonance energy transfer in a rebundling of isolated SWCNTs, and pH changes of the aqueous solutions.

X-Ray Photoelectron Spectroscopy Investigation of the Nitrogen Species in Photoactive Perfluorophenylazide-Modified Surfaces

X-ray Photoelectron Spectroscopy (XPS) was used to characterize the nitrogen species in perfluorophenylazide (PFPA) self-assembled monolayers. PFPA chemistry is a novel immobilization method for tailoring the surface properties of materials. It is a simple route for the efficient immobilization of graphene, proteins, carbohydrates and synthetic polymers onto a variety of surfaces. Upon light irradiation, the azido group in PFPA is converted to a highly reactive singlet nitrene species that readily undergoes CH insertion and C=C addition reactions. Here, the challenge of characterizing the PFPA modified surfaces was addressed by detailed XPS experimental analyses. The three nitrogen peaks detected in the XPS N1s spectra were assigned to amine/amide (400.5 eV) and azide (402.1 and 405.6 eV) species. The observed 2:1 ratio of the areas from the 402.1 eV to 405.6 eV peaks suggests the assignment of the peak at 402.1 eV to the two outer nitrogen atoms in the azido group and assignment of the peak at 405.6 eV to the central nitrogen atom in the azido group. The azide decomposition as the function of x-ray exposure was also determined. Finally, XPS analyses were conducted on patterned graphene to investigate the covalent bond formation between the PFPA and graphene. This study provides strong evidence for the formation of covalent bonds during the PFPA photocoupling process.

Exploiting end group functionalization for the design of antifouling bioactive brushes

The Diels–Alder reaction between cyclopentadiene and maleimide is exploited to immobilize proteins on the chain-end of polymer brushes.

Characterization of sample preparation methods of NIH/3T3 fibroblasts for ToF-SIMS analysis

The information that is obtained from single cells during time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis is influenced by the method that was used to prepare the cells. The removal of extracellular media before analysis is necessary, but the rinsing technique should not damage the plasma membrane of the cell. The presence of intracellular salts reduced the secondary ion yield an average of 2.6-fold during Bi3 (+)/C60 (++) depth profiles. Chemical fixation followed by rinsing removed a majority of the intracellular salts, "recovering" the positive secondary ion yields. The formaldehyde-fixation process removed a majority of the intracellular Cl(-), but other key anions were not removed in significant amounts. The data presented here is consistent the anion neutralization mechanism largely responsible for the lower ion yields. All of the organic secondary ions that were detected in the freeze-dried cells were also detected in the formaldehyde-fixed cells, suggesting that the fixation process did not remove any molecular species to an extent that is detectable by ToF-SIMS. Compared to freeze dried cells, well preserved, frozen-hydrated cells showed little increase, or a decreased yield, for most low mass ions, but an increased yield for larger mass fragments. This is consistent with a reduced damage cross section at cryogenic analysis temperatures, although proton donation from water and reduction the salt effects in the presence of water likely also play roles. Numerous ions detected from the frozen-hydrated cells were not detected from the freeze dried cells, however many of these ions were attributed to chemical combinations of water, salts and the ammonium acetate rinsing solution.

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.

High-resolution epifluorescence and time-of-flight secondary ion mass spectrometry chemical imaging comparisons of single DNA microarray spots

DNA microarray assay performance is commonly compromised by spot-spot probe and signal variations as well as heterogeneity within printed microspots. Accurate metrics for captured DNA target signal rely upon uniform spot distribution of both probe and target DNA to yield reliable hybridized signal. While often presumed, this is neither easily achieved nor often proven experimentally. High-resolution imaging techniques were used to determine spot heterogeneity in identical DNA array microspots comprising varied ratios of unlabeled and dye-labeled DNA probes contact-printed onto commercial arraying surfaces. Epifluorescence imaging data for individual array microspots were correlated with time-of-flight secondary ion mass spectrometry (TOF-SIMS) chemical state imaging of the same spots. Epifluorescence imaging intensity distinguished varying DNA density distributed both within a given spot and from spot to spot. TOF-SIMS chemical analysis confirmed these heterogeneous printed DNA distributions by tracking bound Cy3 dye, DNA base, and phosphate specific ion fragments often correlating to fluorescence patterns within identical spots. TOF-SIMS ion fragments originating from probe DNA and Cy3 dye are enriched in microspot centers, correlating with high fluorescence intensity regions. Both TOF-SIMS and epifluorescence support Marangoni flow effects on spot drying, with high-density DNA-Cy3 located in spot centers and nonhomogeneous DNA distribution within printed spots. Microspot image dimensional analysis results for DNA droplet spreading show differing DNA densities across printed spots. The study directly supports different DNA probe chemical and spatial microenvironments within spots that yield spot-spot signal variations known to affect DNA target hybridization efficiencies and kinetics. These variations critically affect probe-target duplex formation and DNA array signal generation.

The influence of nanostructured materials on biointerfacial interactions

Control over biointerfacial interactions in vitro and in vivo is the key to many biomedical applications: from cell culture and diagnostic tools to drug delivery, biomaterials and regenerative medicine. The increasing use of nanostructured materials is placing a greater demand on improving our understanding of how these new materials influence biointerfacial interactions, including protein adsorption and subsequent cellular responses. A range of nanoscale material properties influence these interactions, and material toxicity. The ability to manipulate both material nanochemistry and nanotopography remains challenging in its own right, however, a more in-depth knowledge of the subsequent biological responses to these new materials must occur simultaneously if they are ever to be affective in the clinic. We highlight some of the key technologies used for fabrication of nanostructured materials, examine how nanostructured materials influence the behavior of proteins and cells at surfaces and provide details of important analytical techniques used in this context.

Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond

In this article, it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is shown to break down for a mismatch distance below 5 nt. The behavior of mismatches in the vicinity of the helix edges, and the behavior of tandem mismatches are also investigated. Finally, some thermodynamic outlying sequences are observed and highlighted. These sequences contain combinations of GA mismatches. The analysis of the microarray data reported in this article provides new insights on the DNA hybridization parameters and can help to increase the accuracy of hybridization-based technologies.

ToF-SIMS depth profiling of cells: z-correction, 3D imaging, and sputter rate of individual NIH/3T3 fibroblasts

Proper display of three-dimensional time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging data of complex, nonflat samples requires a correction of the data in the z-direction. Inaccuracies in displaying three-dimensional ToF-SIMS data arise from projecting data from a nonflat surface onto a 2D image plane, as well as possible variations in the sputter rate of the sample being probed. The current study builds on previous studies by creating software written in Matlab, the ZCorrectorGUI (available at http://mvsa.nb.uw.edu/), to apply the z-correction to entire 3D data sets. Three-dimensional image data sets were acquired from NIH/3T3 fibroblasts by collecting ToF-SIMS images, using a dual beam approach (25 keV Bi(3)(+) for analysis cycles and 20 keV C(60)(2+) for sputter cycles). The entire data cube was then corrected by using the new ZCorrectorGUI software, producing accurate chemical information from single cells in 3D. For the first time, a three-dimensional corrected view of a lipid-rich subcellular region, possibly the nuclear membrane, is presented. Additionally, the key assumption of a constant sputter rate throughout the data acquisition was tested by using ToF-SIMS and atomic force microscopy (AFM) analysis of the same cells. For the dried NIH/3T3 fibroblasts examined in this study, the sputter rate was found to not change appreciably in x, y, or z, and the cellular material was sputtered at a rate of approximately 10 nm per 1.25 × 10(13) ions C(60)(2+)/cm(2).

TOF-SIMS imaging of adsorbed proteins on topographically complex surfaces with Bi(3) (+) primary ions

Although previous studies have demonstrated that TOF-SIMS is a powerful method for the characterization of adsorbed proteins due to its specificity and surface sensitivity, it was unclear from earlier work whether the differences between proteins observed on uniform flat surfaces were large enough to facilitate clear image contrast between similar proteins in small areas on topographically complex samples that are more typical of biological tissues. The goal of this study was to determine whether Bi(3) (+) could provide sufficiently high sensitivity to provide clear identification of the different proteins in an image. In this study, 10 μm polystyrene microspheres were adsorbed with one of three different proteins, human serum albumin (HSA), bovine serum albumin (BSA), and hemoglobin. Spheres coated with HSA were then mixed with spheres coated with either BSA (a very similar protein) or hemoglobin (a dramatically different protein), and deposited on silicon substrates. Fluorescent labeling was used to verify the SIMS results. With maximum autocorrelation factors (MAF) processing, images showed clear contrast between both the very different proteins (HSA and hemoglobin) and the very similar proteins (HSA and BSA). Similar results were obtained with and without the fluorescent labels. MAF images were calculated using both the full spectrum and only characteristic amino acid fragments. Although better image contrast was obtained using the full spectrum, differences between the spheres were still evident when only the amino acid fragments were included in the analysis, suggesting that we are truly observing differences between the proteins themselves. These results demonstrate that TOF-SIMS, with a Bi(3) (+) primary ion, is a powerful technique for characterizing interfacial proteins not only on large uniform surfaces, but also with high spatial resolution on the topographically complex samples typical in biological analysis.

Supported lipid bilayer microarrays created by non-contact printing

Arrays of supported lipid bilayers (SLBs) provide great potential for future drug development and multiplexed biological research, but are difficult to prepare due to the sensitivity of both the lipid and protein structural arrangement to air exposure. A novel way to produce arrays of SLBs is presented based on non-contact dispensing of vesicles to a substrate through a thin surface confined water film. The approach presents many degrees of freedom since it is not limited to a specific substrate, lipid composition, linker or controlled environment. The method allows adjustment of spot size (180-360 μm) by repeated dispensing as well as control over the composition of the spots and subsequent analytes. SLB formation by vesicle adsorption and rupture allows for incorporation of membrane proteins through pre-formed proteoliposomes. Dispensing through a dip-and-rinse water film avoids contamination, disruptive drying and the need for complex buffer compositions. Furthermore, no humidity control is necessary which simplifies the production step and prolongs the life-time of the spotting system. We characterize the method with respect to control over spot size, bilayer mobility and the formation process as well as demonstrate the possibility to fuse bilayer spots with subsequently added vesicles. Since complex lipid compositions and multiple spotting nozzles can be used, this novel technique is expected to be a promising platform for future applications, e.g. patterning to monitor peptide/protein-lipid interactions, for glycomics using glycolipids or lipopolysaccharides, and to study mixing of spatially confined lipid membranes.

Controlled density patterning of tolylterpyridine-tagged oligonucleotides

An efficient surface anchoring strategy of tolylterpyridine-tagged DNA single strands (ssDNA-ttpy) synthesized on gold electrodes is reported. The method is based on exchange reactions between Fe(II)bis-terpyridine complexed SAMs and ssDNA-ttpy, and allows efficient hybrydization of the cDNA strands. Moreover, by using low-current focused ion beam lithography, micropatterned arrays are obtained, homogeneously covered with ssDNA-ttpy. The surface adsorption kinetics of ssDNA-ttpy, as well as its hybridization efficiency, was monitored by in situ quartz crystal microbalance with dissipation monitoring (QCM-D) technique. The effective confinement of the ssDNA-ttpy at the micrometer level has been monitored by time of flight secondary ion mass spectrometry (ToF-SIMS) and ellipsometric surface imaging experiments, providing laterally resolved chemical and topographic mapping.

Surface characterization of carbohydrate microarrays

Carbohydrate microarrays are essential tools to determine the biological function of glycans. Here, we analyze a glycan array by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to gain a better understanding of the physicochemical properties of the individual spots and to improve carbohydrate microarray quality. The carbohydrate microarray is prepared by piezo printing of thiol-terminated sugars onto a maleimide functionalized glass slide. The hyperspectral ToF-SIMS imaging data are analyzed by multivariate curve resolution (MCR) to discern secondary ions from regions of the array containing saccharide, linker, salts from the printing buffer, and the background linker chemistry. Analysis of secondary ions from the linker common to all of the sugar molecules employed reveals a relatively uniform distribution of the sugars within the spots formed from solutions with saccharide concentration of 0.4 mM and less, whereas a doughnut shape is often formed at higher-concentration solutions. A detailed analysis of individual spots reveals that in the larger spots the phosphate buffered saline (PBS) salts are heterogeneously distributed, apparently resulting in saccharide concentrated at the rim of the spots. A model of spot formation from the evaporating sessile drop is proposed to explain these observations. Saccharide spot diameters increase with saccharide concentration due to a reduction in surface tension of the saccharide solution compared to PBS. The multivariate analytical partial least squares (PLS) technique identifies ions from the sugars that in the complex ToF-SIMS spectra correlate with the binding of galectin proteins.

Molecular mechanisms in morpholino-DNA surface hybridization

Synthetic nucleic acid mimics provide opportunity for redesigning the specificity and affinity of hybridization with natural DNA or RNA. Such redesign is of great interest for diagnostic applications where it can enhance the desired signal against a background of competing interactions. This report compares hybridization of DNA analyte strands with morpholinos (MOs), which are uncharged nucleic acid mimics, to the corresponding DNA-DNA case in solution and on surfaces. In solution, MO-DNA hybridization is found to be independent of counterion concentration, in contrast to DNA-DNA hybridization. On surfaces, when immobilized MO or DNA "probe" strands hybridize with complementary DNA "targets" from solution, both the MO-DNA and DNA-DNA processes depend on ionic strength but exhibit qualitatively different behaviors. At lower ionic strengths, MO-DNA surface hybridization exhibits hallmarks of kinetic limitations when separation between hybridized probe sites becomes comparable to target dimensions, whereas extents of DNA-DNA surface hybridization are instead consistent with limits imposed by buildup of surface (Donnan) potential. The two processes also fundamentally differ at high ionic strength, under conditions when electrostatic effects are weak. Here, variations in probe coverage have a much diminished impact on MO-DNA than on DNA-DNA hybridization for similarly crowded surface conditions. These various observations agree with a structural model of MO monolayers in which MO-DNA duplexes segregate to the buffer interface while unhybridized probes localize near the solid support. A general perspective is presented on using uncharged DNA analogues, which also include compounds such as peptide nucleic acids (PNA), in surface hybridization applications.

Immobilized antibody orientation analysis using secondary ion mass spectrometry and fluorescence imaging of affinity-generated patterns

This study assesses the capability of high-resolution surface analytical tools to distinguish immobilized antibody orientations on patterned surfaces designed for antibody affinity capture. High-fidelity, side-by-side copatterning of protein A (antibody Fc domain affinity reagent) and fluorescein (antibody Fab domain hapten) was achieved photolithographically on commercial amine-reactive hydrogel polymer surfaces. This was verified from fluorescence imaging using fluorescently labeled protein A and intrinsic fluorescence from fluorescein. Subsequently, dye-labeled murine antifluorescein antibody (4-4-20) and antibody Fab and Fc fragments were immobilized from solution onto respective protein A- and fluorescein- copatterned or control surfaces using antibody-ligand affinity interactions. Fluorescence assays support specific immobilization to fluorescein hapten- and protein A-patterned regions through antigen-antibody recognition and natural protein A-Fc domain interactions, respectively. Affinity-based antibody immobilization on the two different copatterned surfaces generated side-by-side full antibody "heads-up" and "tails-up" oriented surface patterns. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis, sensitive to chemical information from the top 2 to 3 nm of the surface, provided ion-specific images of these antibody patterned regions, imaging and distinguishing characteristic ions from amino acids enriched in Fab domains for antibodies oriented in "heads-up" regions, and ions from amino acids enriched in Fc domains for antibodies oriented in "tails-up" regions. Principal component analysis (PCA) improved the distinct TOF-SIMS amino acid compositional and ion-specific surface mapping sensitivity for each "heads-up" versus "tails-up" patterned region. Characteristic Fab and Fc fragment immobilized patterns served as controls. This provides first demonstration of pattern-specific, antibody orientation-dependent surface maps based on antibody domain- and structure-specific compositional differences by TOF-SIMS analysis. Since antibody immobilization and orientation are critical to many technologies, orientation characterization using TOF-SIMS could be very useful and convenient for immobilization quality control and understanding methods for improving the performance of antibody-based surface capture assays.