Covalent immobilization of native biomolecules onto Au(111) via N-hydroxysuccinimide ester functionalized self-assembled monolayers for scanning probe microscopy

Quantitative epitope analysis reveals drastic 63% reduced immuno-affinity and 60% enhanced transmissibility for SARS-CoV-2 variants

SARS-CoV-2 is the cause of a global pandemic that has led to more than 4 million deaths, continues to spread and holds the world in a tight grip. The virus has developed substantial mutations that undermine the efficacy of current vaccines and monoclonal antibody therapies. Semi-quantitative immuno - and neutralization assays are unable to provide direct quantitative insights about the minute variations of emerging mutants. Here, we develop a quantitative assay that enables synchronous screening of emerging variant epitopes with single amino acid resolution. We report on specific label-free quantitative nanomechanical analysis of pseudovirus spike interaction with ACE2 receptors. Within minutes, we can characterize the B.1.1.7 variant transmissibility due to its 63% increased binding, and measure a 60% reduced efficacy of antibodies towards B.1.351 and P.1 variants. Our technology can assist vaccine development studies, with focus on comparing protection patterns and novel vaccine candidates and tracking of immunity over time.

Nanotechnological immunoassay for rapid label-free analysis of candidate malaria vaccines

Malaria is a life-threatening epidemic disease with half of the world's population at risk. Although its incidence rate has fallen since 2010, this ratio dramatically stalled between 2014 and 2018. New fast and optimized tools in vaccine analysis and seroconversion testing are critically needed. We developed a clinical diagnostic device based on piezo-actuated nanoresonators that perform as quantitative in situ calibrated nano-bio sensors for specific detection of multiple target molecules in serum samples. The immunoassay successfully diagnoses humoral immune responses induced by malaria vaccine candidates and reveals the timeline and stage of the infection. We applied the newly developed strategy to a variety of different samples, from pure antibody/vaccine solutions, to blood samples from clinical trials on both naïve and pre-exposed malaria volunteers from sub-Saharan countries. Our nanomechanical assay provides a direct one-step label-free quantitative immunoassay that is on par with the gold-standard, multi-step enzyme-linked immunosorbent assay (ELISA). We achieve a limit of detection of few pg ml-1, or sub-pM concentrations. The 6 μl sample volume allows more than 50 experiments from one finger prick. Furthermore, we simultaneously detected multiple analytes by differential functionalization of multiple sensors in parallel. The inherent differential read-out with in situ controls reduces false positive results. Due to the faster turnaround time, the minimal volume required and the automatized handling system, this technique has great potential for miniaturization and routine diagnostics in pandemic emergencies.

Opportunities in the Synthesis and Design of Radioactive Thin Films and Nanoparticles

Studies of radioactive isotopes at the liquid-solid or gas-solid interface are enabling a detailed mechanistic understanding of the effects of radioactive decay on physical, biological, and chemical systems. In recent years, there has been a burgeoning interest in using radioactive isotopes for both imaging and therapeutic purposes by attaching them to the surface of colloidal nanoparticles. By merging the field of nanomedicine with the more mature field of internal radiation therapy, researchers are discovering new ways to diagnose and treat cancer. In this Perspective, we discuss state-of-the-art radioactive thin films as applied to both well-defined surfaces and more complex nanoparticles. We highlight the design considerations that are unique to radioactive films, which originate from the damaging and potentially self-destructive emissions produced during radioactive decay, and highlight future opportunities in the largely underexplored area between radioisotope chemistry and nanoscience.

Antibodies Irreversibly Adsorb to Gold Nanoparticles and Resist Displacement by Common Blood Proteins

Gold nanoparticles (AuNPs) functionalized with proteins to impart desirable surface properties have been developed for many nanobiotechnology applications. A strong interaction between the protein and nanoparticle is critical to the formation of a stable conjugate to realize the potential of these emerging technologies. In this work, we examine the robustness of a protein layer adsorbed onto gold nanoparticles while under the stress of a physiological environment that could potentially lead to protein exchange on the nanoparticle surface. The adsorption interaction of common blood plasma proteins (transferrin, human serum albumin, and fibrinogen) and anti-horseradish peroxidase antibody onto AuNPs is investigated by nanoparticle tracking analysis. Our data show that a monolayer of protein is formed at saturation for each protein, and the maximum size increase for the conjugate, relative to the AuNP core, correlates with the protein size. The binding affinity of each protein to the AuNP is extracted from a best fit of the adsorption isotherm to the Hill equation. The antibody displays the greatest affinity (K_d = 15.2 ± 0.8 nM) that is ∼20-65 times stronger than the affinity of the other plasma proteins. Antibody-AuNP conjugates were prepared, purified, and suspended in solutions of blood plasma proteins to evaluate the stability of the antibody layer. An enzyme-mediated assay confirms that the antibody-AuNP interaction is irreversible, and the adsorbed antibody resists displacement by the plasma proteins. This work provides insight into the capabilities and potential limitations of antibody-AuNP-enabled technologies in biological systems.

Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity

Scanning probe microscopy provides a unique window into the morphology, mechanics, and structure of proteins and their complexes on the nanoscale. Such measurements require, however, deposition of samples onto substrates. This process can affect conformations and assembly states of the molecular species under investigation and can bias the molecular populations observed in heterogeneous samples through differential adsorption. Here, we show that these limitations can be overcome with a single-step microfluidic spray deposition platform. This method transfers biological solutions to substrates as microdroplets with subpicoliter volume, drying in milliseconds, a timescale that is shorter than typical diffusion times of proteins on liquid–solid interfaces, thus avoiding surface mass transport and change to the assembly state. Finally, the single-step deposition ensures the attachment of the full molecular content of the sample to the substrate, allowing quantitative measurements of different molecular populations within heterogeneous systems, including protein aggregates.

Manual sample deposition on a substrate can introduce artifacts in quantitative AFM measurements. Here the authors present a microfluidic spray device for reliable deposition of subpicoliter droplets which dry out in milliseconds after landing on the surface, thereby avoiding protein self-assembly.

Nanomechanical clinical coagulation diagnostics and monitoring of therapies

Clinical coagulation diagnostics often requires multiple tests. Coagulation times are a first indication of an abnormal coagulation process, such as a coagulation factor deficiency. To determine the specific deficient factor, additional immuno- and/or enzyme assays are necessary. Currently, every clinical laboratory has to normalize their assays (international normalized ratio, INR), and therefore, certain variability within the clinical analytics exists. We report a novel strategy for a quick, reliable and quantitative diagnosis of blood coagulation diseases (e.g. haemophilia) and for monitoring factor replacement and anticoagulant therapies (e.g. heparin treatment). We exploit nano-oscillations of microcantilevers for real-time measurements of the evolving blood plasma clot strength (viscosity). The sensors are oscillated at multiple high resonance mode numbers, in order to minimise the oscillation amplitude (a few nanometers), to provide direct internal control and to increase the quality factor. Along with the activated thromboplastin time (aPTT) and prothrombin time (PT) other parameters important for thrombosis diagnostics can be obtained, including the final clot strength and the fibrinolysis time. We demonstrate the dependence of the parameters on factor deficiencies and we diagnose a specific factor deficiency through an integrated and quantitative in situ immunoassay. This approach does not require continuous calibration since it delivers an absolute quantity (clot strength). The low sample volume required (a few μl) and the ability to measure different parameters within the same test (PT, aPTT and global coagulation assay) make the presented technique a versatile point-of-care device for clinical coagulation diagnostics.

The Anatomy of a Nonfaradaic Electrochemical Biosensor

Point-of-care (POC) testing has revolutionized diagnostic healthcare, bringing medical results directly and immediately to the patient. With faster diagnostics, more immediate clinical management decisions can be made. POC tests most often use a dipstick or swab format to detect the presence of a pathogen, disease, or other relevant biomarker. In these formats, the POC tests eliminate the need for complex lab equipment and trained personnel to collect, process, and analyze sample data for simple diagnostics. However, these tests cannot satisfy all clinical needs, because accurate quantitative results are needed. The present study serves as a template for designing a nonfaradaic electrochemical biosensor toward quantitative POC diagnostics. We focus on investigating the most important parameters when constructing a nonfaradaic biosensor through both mathematical modeling and electrochemical measurements. Furthermore, we demonstrate quantitative affinity biosensing of a model protein toward developing a POC device.

Chemical modification of antibodies enables the formation of stable antibody–gold nanoparticle conjugates for biosensing

Antibody-modified gold nanoparticles (AuNPs) are central to many novel and emerging biosensing technologies due to the specificity provided by antibody–antigen interactions and the unique properties of nanoparticles.

Label-Free Protein and Pathogen Detection Using the Atomic Force Microscope

The atomic force microscope (AFM) uses a sharp micron-scale tip to scan and amplify surface features, providing exceptionally detailed topographical information with magnification on the order of ×106. This instrument is used extensively for quality control in the computer and semiconductor industries and is becoming a progressively more important tool in the biological sciences. Advantages of the AFM for biological application include the ability to obtain information in a direct, label-free manner and the ability to image in solution, providing real-time data acquisition under physiologically relevant conditions. A novel application of the AFM currently under development combines its surface profiling capabilities with fixed immuno-capture using antibodies immobilized in a nanoarray format. This provides a distinctive platform for direct, label-free detection and characterization of viral particles and other pathogens.

Cytotoxicity of folic acid conjugated hollow silica nanoparticles toward Caco2 and 3T3 cells, with and without encapsulated DOX

Hollow silica nanoparticles of two sizes with and without a folic acid targeting ligand were synthesized. Fickian diffusion of the antitumor drug doxorubicin hydrochloride (DOX) was demonstrated by the produced nanoparticles, achieving a cumulative release of 73% and 45% for 215 nm and 430 nm particles respectively over a period of 500 h. The hollow silica nanoparticles presented a time and dose dependent toxicity, selective to human epithelial colorectal adenocarcinoma (Caco2) cells, over mouse embryonic fibroblast (3T3) cells. At 24h Caco2 cell viability was reduced to 66% using pure hollow silica at a concentration of 50 μg mL(-1), while that of 3T3 cells remained at 94% under the same conditions. The selective cytotoxicity of hollow silica nanoparticles was further enhanced by conjugation of folic acid and incorporation of DOX: at 24h and an equivalent DOX concentration of 0.5 μg mL(-1), viable Caco2 cells were reduced to 45% while 3T3 cells were reduced to 83%. Interestingly the equivalent dose of free DOX was more toxic to 3T3 than to Caco2 cells, reducing the 3T3 viability to 72% and the Caco2 viability to 80%, which is likely due to the presence of the p-glycoprotein pumps in Caco2 cells. Folic acid conjugation served to enhance the viability of both cell lines in this work. Careful optimization of the folate content should further improve the cell specificity of the hollow silica nanoparticles, thus providing a viable targeting platform for cancer therapy.

Succinimidyl ester surface chemistry: implications of the competition between aminolysis and hydrolysis on covalent protein immobilization

N-Hydroxysuccinimide (NHS) ester terminal groups are commonly used to covalently couple amine-containing biomolecules (e.g., proteins and peptides) to surfaces via amide linkages. This one-step aminolysis is often performed in buffered aqueous solutions near physiological pH (pH 6 to pH 9). Under these conditions, the hydrolysis of the ester group competes with the amidization process, potentially degrading the efficiency of the coupling chemistry. The work herein examines the efficiency of covalent protein immobilization in borate buffer (50 mM, pH 8.50) using the thiolate monolayer formed by the chemisorption of dithiobis (succinimidyl propionate) (DSP) on gold films. The structure and reactivity of these adlayers are assessed via infrared spectroscopy (IR), X-ray photoelectron spectroscopy (XPS), electrochemical reductive desorption, and contact angle measurements. The hydrolysis of the DSP-based monolayer is proposed to follow a reaction mechanism with an initial nucleation step, in contrast to a simple pseudo first-order reaction rate law for the entire reaction, indicating a strong dependence of the interfacial reaction on the packing and presence of defects in the adlayer. This interpretation is used in the subsequent analysis of IR-ERS kinetic plots which give a heterogeneous aminolysis rate constant, ka, that is over 3 orders of magnitude lower than that of the heterogeneous hydrolysis rate constant, kh. More importantly, a projection of these heterogeneous kinetic rates to protein immobilization suggests that under coupling conditions in which low protein concentrations and buffers of near physiological pH are used, proteins are more likely physically adsorbed rather than covalently linked. This result is paramount for biosensors that use NHS chemistry for protein immobilization due to effects that may arise from noncovalently linked proteins.

Direct label-free electrical immunodetection of transplant rejection protein biomarker in physiological buffer using floating gate AlGaN/GaN high electron mobility transistors

Monokine induced by interferon gamma (MIG/CXCL9) is used as an immune biomarker for early monitoring of transplant or allograft rejection. This paper demonstrates a direct electrical, label-free detection method of recombinant human MIG with anti-MIG IgG molecules in physiologically relevant buffer environment. The sensor platform used is a biologically modified GaN-based high electron mobility transistor (HEMT) device. Biomolecular recognition capability was provided by using high affinity anti-MIG monoclonal antibody to form molecular affinity interface receptors on short N-hydroxysuccinimide-ester functionalized disulphide (DSP) self-assembled monolayers (SAMs) on the gold sensing gate of the HEMT device. A floating gate configuration has been adopted to eliminate the influences of external gate voltage. Preliminary test results with the proposed chemically treated GaN HEMT biosensor show that MIG can be detected for a wide range of concentration varying from 5 ng/mL to 500 ng/mL.

Selective albumin-binding surfaces modified with a thrombin-inhibiting peptide

Blood-contacting medical devices have been associated with severe clinical complications, such as thrombus formation, triggered by the activation of the coagulation cascade due to the adsorption of certain plasma proteins on the surface of biomaterials. Hence, the coating of such surfaces with antithrombotic agents has been used to increase biomaterial haemocompatibility. Biomaterial-induced clotting may also be decreased by albumin adsorption from blood plasma in a selective and reversible way, since this protein is not involved in the coagulation cascade. In this context, this paper reports that the immobilization of the thrombin inhibitor D-Phe-Pro-D-Arg-D-Thr-CONH2 (fPrt) onto nanostructured surfaces induces selective and reversible adsorption of albumin, delaying the clotting time when compared to peptide-free surfaces. fPrt, synthesized with two glycine residues attached to the N-terminus (GGfPrt), was covalently immobilized onto self-assembled monolayers (SAMs) having different ratios of carboxylate-hexa(ethylene glycol)- and tri(ethylene glycol)-terminated thiols (EG6-COOH/EG3) that were specifically designed to control GGfPrt orientation, exposure and density at the molecular level. In solution, GGfPrt was able to inactivate the enzymatic activity of thrombin and to delay plasma clotting time in a concentration-dependent way. After surface immobilization, and independently of its concentration, GGfPrt lost its selectivity to thrombin and its capacity to inhibit thrombin enzymatic activity against the chromogenic substrate n-p-tosyl-Gly-Pro-Arg-p-nitroanilide. Nevertheless, surfaces with low concentrations of GGfPrt could delay the capacity of adsorbed thrombin to cleave fibrinogen. In contrast, GGfPrt immobilized in high concentrations was found to induce the procoagulant activity of the adsorbed thrombin. However, all surfaces containing GGfPrt have a plasma clotting time similar to the negative control (empty polystyrene wells), showing resistance to coagulation, which is explained by its capacity to adsorb albumin in a selective and reversible way. This work opens new perspectives to the improvement of the haemocompatibility of blood-contacting medical devices.

Hierarchical cystine flower based electrochemical genosensor for detection of Escherichia coli O157:H7

Synthesis and self-assembly of cystine flowers on gold electrode for biosensing application.

Application of atomic force microscopy for characteristics of single intermolecular interactions

Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions.

Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays

BACKGROUND

Drop drying is a key factor in a wide range of technical applications, including spotted microarrays. The applied nL liquid volume provides specific reaction conditions for the immobilization of probe molecules to a chemically modified surface.

RESULTS

We investigated the influence of nL and μL liquid drop volumes on the process of probe immobilization and compare the results obtained to the situation in liquid solution. In our data, we observe a strong relationship between drop drying effects on immobilization and surface chemistry. In this work, we present results on the immobilization of dye labeled 20mer oligonucleotides with and without an activating 5'-aminoheptyl linker onto a 2D epoxysilane and a 3D NHS activated hydrogel surface.

CONCLUSIONS

Our experiments identified two basic processes determining immobilization. First, the rate of drop drying that depends on the drop volume and the ambient relative humidity. Oligonucleotides in a dried spot react unspecifically with the surface and long reaction times are needed. 3D hydrogel surfaces allow for immobilization in a liquid environment under diffusive conditions. Here, oligonucleotide immobilization is much faster and a specific reaction with the reactive linker group is observed. Second, the effect of increasing probe concentration as a result of drop drying. On a 3D hydrogel, the increasing concentration of probe molecules in nL spotting volumes accelerates immobilization dramatically. In case of μL volumes, immobilization depends on whether the drop is allowed to dry completely. At non-drying conditions, very limited immobilization is observed due to the low oligonucleotide concentration used in microarray spotting solutions. The results of our study provide a general guideline for microarray assay development. They allow for the initial definition and further optimization of reaction conditions for the immobilization of oligonucleotides and other probe molecule classes to different surfaces in dependence of the applied spotting and reaction volume.

Enhancement of immunoassay's fluorescence and detection sensitivity using three-dimensional plasmonic nano-antenna-dots array

Protein detection is universal and vital in biological study and medical diagnosis (e.g., cancer detection). Fluorescent immunoassay is one of the most widely used and most sensitive methods in protein detection (Giljohann, D. A.; Mirkin, C. A. Nature2009, 462, 461-464; Yager, P.; et al. Nature2006, 442, 412-418). Improvements of such assays have many significant implications. Here, we report the use of a new plasmonic structure and a molecular spacer to enhance the average fluorescence of an immunoassay of Protein A and human immunoglobulin G (IgG) by over 7400-fold and the immunoassay's detection sensitivity by 3,000,000-fold (the limit of detection is reduced from 0.9 × 10(-9) to 0.3 × 10(-15) molar (i.e., from 0.9 nM to 300 aM), compared to identical assays performed on glass plates). Furthermore, the average fluorescence enhancement has a dynamic range of 8 orders of magnitude and is uniform over the entire large sample area with a spatial variation ±9%. Additionally, we observed that, when a single molecule fluorophore is placed at a "hot spot" of the plasmonic structure, its fluorescence is enhanced by 4 × 10(6)-fold, thus indicating the potential to further significantly increase the average fluorescence enhancement and the detection sensitivity. Together with good spatial uniformity, wide dynamic range, and ease to manufacture, the giant enhancement in immunoassay's fluorescence and detection sensitivity (orders of magnitude higher than previously reported) should open up broad applications in biology study, medical diagnosis, and others.

Stepwise motion of a microcantilever driven by the hydrolysis of viral ATPases

The biomolecular machines involved in DNA packaging by viruses generate one of the highest mechanical powers observed in nature. One component of the DNA packaging machinery, called the terminase, has been proposed as the molecular motor that converts chemical energy from ATP hydrolysis into mechanical movement of DNA during bacteriophage morphogenesis. However, the conformational changes involved in this energy conversion have never been observed. Here we report a real-time measurement of ATP-induced conformational changes in the terminase of bacteriophage T7 (gp19). The recording of the cantilever bending during its functionalization shows the existence of a gp19 monolayer arrangement confirmed by atomic force microscopy of the immobilized proteins. The ATP hydrolysis of the gp19 terminase generates a stepped motion of the cantilever and points to a mechanical cooperative effect among gp19 oligomers. Furthermore, the effect of ATP can be counteracted by non-hydrolyzable nucleotide analogs.

Imaging of nucleic acids with atomic force microscopy

Atomic force microscopy (AFM) is a key tool of nanotechnology with great importance in applications to DNA nanotechnology and to the recently emerging field of RNA nanotechnology. Advances in the methodology of AFM now enable reliable and reproducible imaging of DNA of various structures, topologies, and DNA and RNA nanostructures. These advances are reviewed here with emphasis on methods utilizing modification of mica to prepare the surfaces enabling reliable and reproducible imaging of DNA and RNA nanostructures. Since the AFM technology for DNA is more mature, AFM imaging of DNA is introduced in this review to provide experience and background for the improvement of AFM imaging of RNA. Examples of imaging different structures of RNA and DNA are discussed and illustrated. Special attention is given to the potential use of AFM to image the dynamics of nucleic acids at the nanometer scale. As such, we review recent advances with the use of time-lapse AFM.

Immobilization of an antithrombin-heparin complex on gold: anticoagulant properties and platelet interactions

The anticoagulant properties and platelet interactions of gold surfaces modified with an antithrombin-heparin (ATH) complex are reported. ATH was attached to gold through either a short disulfide (linker) or a thiol-terminated polyethylene oxide (PEO) (linker, spacer). Analogous surfaces were prepared with uncomplexed heparin. Antithrombin (AT) uptake was measured before and after selectively destroying the active pentasaccharide sequence of the heparin moiety, and was found to be predominantly through the active sequence on all of the surfaces. AT binding was higher on the ATH surfaces than on the corresponding heparin surfaces. Heparin activity was assessed by an anti-factor Xa assay. The ratio of active heparin density (from the anti-FXa assay) to total heparin density was taken as a measure of heparin bioactivity. The ratio was greater on the ATH- than on the heparin-modified surfaces, i.e. the PEO-ATH surfaces showed the greater proportion of active heparin. Platelet adhesion from flowing whole blood was found to be reduced on PEO- and ATH-modified surfaces compared to bare gold. The PEO-ATH modified surfaces, but not the heparinized surfaces, were shown to prolong the clotting time of recalcified plasma.

Impedimetric biosensor for the assessment of the clotting activity of rennet

Cheese production is relied upon the action of rennet (a mixture of chymosin and pepsin) onto casein micelles of milk. For the first time, the monitoring of this interaction with electrochemical impedance spectroscopy (EIS) was used to develop a faradic impedimetric biosensor for the assessment of the clotting activity of rennet, using hexacyanoferrate(II)/(III) couple as a redox probe. Gold electrodes were modified with self-assembled monolayers of different thiols (thioctic acid, dithiobis-N-succinimidyl propionate, and cysteamine), and (artificial) casein micelles were immobilized on the modified gold surfaces. The proposed method is based on the measurement of charge-transfer resistance (R(ct)) changes attributed to the degradation of the negatively charged immobilized casein micelles by rennet to neutral biostructures. This action results in the increase of the flux of the redox probe, which exists in the bulk solution, to the surface of the electrode and, consequently, in the decrease of R(ct). Experimental parameters such as the micelle loading, the reaction time, the concentration of rennet, and the working pH, were optimized. Besides EIS measurements, cyclic voltammetry, FT-IR, and atomic force microscopy (AFM) experiments were also performed before and after the interaction of the immobilized micelles with rennet. Finally, the proposed biosensors were successfully tried for various commercial samples.

Force spectroscopy of an elastic peptide: effect of D₂O and temperature on persistence length

This study explores the mechanical unfolding of elastic protein analogues as a function of temperature, in both H₂O and D₂O, using atomic force microscopy (AFM) force spectroscopy in a specially constructed AFM liquid cell. This represents the first time that the effect of D₂O on protein flexibility has been investigated at the single molecule level by this technique. Model elastic peptides, R6, were encoded from synthetic genes expressed in Escherichia coli. The peptides possess short N- and C-terminal domains with central repetitive domains containing 13 repeats of the motif PGQGQQ-plus-GYYPTSLQQ. These sequences mimic those in native high molecular weight subunit glutenin proteins which confer elasticity to bread dough. Fitting single molecule stretching events to the worm-like chain model, allows determination of the molecular persistence length under various experimental conditions. The effect of increasing the temperature is to increase the persistence length of the peptide in both H₂O and D₂O, consistent with the expected "thermal softening" effect. However, the effect is significantly enhanced in D₂O, in which the persistence length at 45°C is ∼25% greater than the value measured in H₂O at the same temperature. Stronger intrapeptide H-bonding due to isotopic substitution of hydrogen for deuterium is the most likely cause of the enhanced backbone rigidity.

Single molecule atomic force microscopy and force spectroscopy of chitosan

Atomic force microscopy (AFM) and AFM-based force spectroscopy was used to study the desorption of individual chitosan polymer chains from substrates with varying chemical composition. AFM images of chitosan adsorbed onto a flat mica substrate show elongated single strands or aggregated bundles. The aggregated state of the polymer is consistent with the high level of flexibility and mobility expected for a highly positively charged polymer strand. Conversely, the visualization of elongated strands indicated the presence of stabilizing interactions with the substrate. Surfaces with varying chemical composition (glass, self-assembled monolayer of mercaptoundecanoic acid/decanethiol and polytetrafluoroethylene (PTFE)) were probed with chitosan modified AFM tips and the corresponding desorption energies, calculated from plateau-like features, were attributed to the desorption of individual polymer strands. Desorption energies of 2.0±0.3×10(-20)J, 1.8±0.3×10(-20)J and 3.5±0.3×10(-20)J were obtained for glass, SAM of mercaptoundecanoic/dodecanethiol and PTFE, respectively. These single molecule level results can be used as a basis for investigating chitosan and chitosan-based materials for biomaterial 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.

Streptavidin 2D crystal substrates for visualizing biomolecular processes by atomic force microscopy

Flat substrate surfaces are a key to successful imaging of biological macromolecules by atomic force microscopy (AFM). Although usable substrate surfaces have been prepared for still imaging of immobilized molecules, surfaces that are more suitable have recently been required for dynamic imaging to accompany the progress of the scan speed of AFM. In fact, the state-of-the-art high-speed AFM has achieved temporal resolution of 30 ms, a capacity allowing us to trace molecular processes played by biological macromolecules. Here, we characterize three types of streptavidin two-dimensional crystals as substrates, concerning their qualities of surface roughness, uniformity, stability, and resistance to nonspecific protein adsorption. These crystal surfaces are commonly resistant to nonspecific protein adsorption, but exhibit differences in other properties to some extent. These differences must be taken into consideration, but these crystal surfaces are still useful for dynamic AFM imaging, as demonstrated by observation of calcium-induced changes in calmodulin, GroES binding to GroEL, and actin polymerization on the surfaces.

Quantitative time-resolved measurement of membrane protein-ligand interactions using microcantilever array sensors

Membrane proteins are central to many biological processes, and the interactions between transmembrane protein receptors and their ligands are of fundamental importance in medical research. However, measuring and characterizing these interactions is challenging. Here we report that sensors based on arrays of resonating microcantilevers can measure such interactions under physiological conditions. A protein receptor--the FhuA receptor of Escherichia coli--is crystallized in liposomes, and the proteoliposomes then immobilized on the chemically activated gold-coated surface of the sensor by ink-jet spotting in a humid environment, thus keeping the receptors functional. Quantitative mass-binding measurements of the bacterial virus T5 at subpicomolar concentrations are performed. These experiments demonstrate the potential of resonating microcantilevers for the specific, label-free and time-resolved detection of membrane protein-ligand interactions in a micro-array format.

3-Mercapto-1-propanesulfonic acid and Bis(3-sulfopropyl) disulfide adsorbed on Au(111): in situ scanning tunneling microscopy and electrochemical studies

3-Mercapto-1-propanesulfonic acid (MPS) and bis(3-sulfopropyl) disulfide (SPS) adsorbed on a Au(111) electrode were studied by using in situ scanning tunneling microscopy (STM). Although the adsorptions of MPS and SPS are known to be oxidative and reductive, respectively, on an Au(111) electrode, these two admolecules behave similarly in terms of phase evolution, surface coverage, potential for stripping, and characteristics of cyclic voltammetry. However, different adsorption mechanisms of these molecules result in different structures. Raising electrode potential causes more MPS and SPS molecules to adsorb, yielding ordered adlattices between 0.67 and 0.8 V (vs reversible hydrogen electrode). The ordered adlattices of MPS and SPS appear as striped and netlike structures with molecules adsorbed parallel to the Au(111) surface. Switching potential to 0.9 V or more positive still does not result in upright molecular orientation, possibly inhibited by electrostatic interaction between the end group of -SO(3)(-) and the Au(111) electrode. Lowering the potential to 0.4 V disrupted the ordered adlayer. Stripping voltammetric experiments show that MPS and SPS admolecules are desorbed from Au(111) at the same potential, suggesting that these molecules are both adsorbed via their sulfur headgroups. The S-S bond in SPS is likely broken upon its adsorption on Au(111).

Chemical strategies for generating protein biochips

Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.

Mapping the positions of beads on a string: dethreading rotaxanes by molecular force spectroscopy

The direct manipulation by atomic force microscopy (AFM) of individual macrocycles within a rotaxane offers a potential route to a new sequencing tool for complex macromolecules such as polysaccharides, glycoproteins and nucleic acids. In this paper we demonstrate for the first time that a sliding contact made between a macrocycle, α-cyclodextrin, and its polymer axle by an AFM tip can be used to map the positions of specific groups along the polymer as if they were beads along a string, thereby generating sequence information. We find very good agreement (linear fit with slope = 1.03, R(2) = 0.968) between the calculated and measured positions of phenylenediamine and benzenetricarboxylic acid groups within polymers of polyethylene oxide (PEO). The rupture force profiles attributable to the dethreading interactions of phenylenediamine and benzenetricarboxylic acid differ observably from each other and, in the latter case, from the rupture of the corresponding host-guest complex. As well as opening the way to a macromolecular sequencing technique, the ability demonstrated by this method to manipulate the dethreading of a rotaxane offers a new tool for investigating the process energetics in a wide array of spontaneously forming and forced rotaxane systems.

Evaluation of interaction forces between profilin and designed peptide probes by atomic force microscopy

We evaluated the binding affinity of peptide probes for profilin (protein) using force curve measurement techniques and atomic force microscopy (AFM). The peptide probes designed and synthesized for this investigation were H-A3GP5GP5GP5G-OH (1), H-A3GP5G-OH (2), H-A3G7-OH (3), and H-A3G-OH (4). Each peptide probe was immobilized on a cantilever tip, and the interaction force to profilin, immobilized on a mica substrate, was examined by force curve measurements. The retraction forces obtained showed a sequence-dependent affinity of the peptide probe for profilin. The retraction force for peptide probe 1 was the largest of the four probes examined, and it confirmed that peptide probe 1 has high affinity for profilin. The single molecular retraction force between peptide probe 1 and profilin was estimated to be 96 pN, as determined by Gaussian fitting to the histogram of the retraction forces.