A new, simple method for linking of antibodies to atomic force microscopy tips

Functionalization of atomic force microscope (AFM) tips with bioligands converts them into monomolecular biosensors which can detect complementary receptor molecules on the sample surface. Flexible PEG tethers are preferred because the bioligand can freely reorient and locally palpate the sample surface while the AFM tip is moved along. In a well-established coupling scheme [Hinterdorfer et al. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 3477-3481], a heterobifunctional PEG linker is used to tether thiol-containing bioligands to amino-functionalized AFM tips. Since antibodies contain no free thiol residues, prederivatization with N-succinimidyl 3-(acetylthio)propionate (SATP) is needed which causes a relatively high demand for antibody. The present study offers a convenient alternative with minimal protein consumption (e.g., 5 microg of protein in 50 microL of buffer) and no prederivatization, using a new heterobifunctional cross-linker that has two different amino-reactive functions. One end is an activated carboxyl (N-hydroxysuccinimide ester) which is much faster to react with the amino groups of the tips than the benzaldehyde function on its other end. The reactivity of the latter is sufficient, however, to covalently bind lysine residues of proteins via Schiff base formation. The method has been critically examined, using biotinylated IgG as bioligand on the tip and mica-bound avidin as complementary receptor. These experiments were well reproduced on amino-functionalized silicon nitride chips where the number of specifically bound IgG molecules (approximately 2000 per microm2) was estimated from the amount of specifically bound ExtrAvidin-peroxidase conjugate. For a bioscientific application, human rhinovirus particles were tethered to the tip, very-low-density lipoprotein receptor fragments were tethered to mica, and the specific interaction was studied by force microscopy.     

Synthesis and characterization of a photocleavable cross-linker and its application on tunable surface modification and protein photodelivery

A heterobifunctional photocleavable cross-linker based on an o-nitrobenzyl ester moiety was synthesized. The cross-linker has N-hydroxysuccinimidyl and disulfide groups attached at each end and thus can anchor a protein to a gold-coated substrate surface. Steady-state spectroscopic studies suggest that the cross-linker undergoes a clean C-O fragmentation upon irradiation with a quantum yield of 0.1. Consequently, immobilized proteins (such as avidin or antibodies) on a substrate surface can be released efficiently (>95%) under UV irradiation (lambda > 300 nm) without degrading the protein functionality. We also demonstrated protein delivery via bioconjugation of protein molecules to a gold-coated atomic-force microscope (AFM) tip. When the proteins are photoreleased from the AFM tip, they are delivered to the substrate surface as protein clusters of uniform size. This has been confirmed using both AFM and fluorescence microscopy. The application of bioconjugation in this study opens a new avenue for tunable surface modification and controllable protein delivery in studies of biological systems on the nanometer scale.     

Antibody linking to atomic force microscope tips via disulfide bond formation

Covalent binding of bioligands to atomic force microscope (AFM) tips converts them into monomolecular biosensors by which cognate receptors can be localized on the sample surface and fine details of ligand-receptor interaction can be studied. Tethering of the bioligand to the AFM tip via a approximately 6 nm long, flexible poly(ethylene glycol) linker (PEG) allows the bioligand to freely reorient and to rapidly "scan" a large surface area while the tip is at or near the sample surface. In the standard coupling scheme, amino groups are first generated on the AFM tip. In the second step, these amino groups react with the amino-reactive ends of heterobifunctional PEG linkers. In the third step, the 2-pyridyl-S-S groups on the free ends of the PEG chains react with protein thiol groups to give stable disulfide bonds. In the present study, this standard coupling scheme has been critically examined, using biotinylated IgG with free thiols as the bioligand. AFM tips with PEG-tethered biotin-IgG were specifically recognized by avidin molecules that had been adsorbed to mica surfaces. The unbinding force distribution showed three maxima that reflected simultaneous unbinding of 1, 2, or 3 IgG-linked biotin residues from the avidin monolayer. The coupling scheme was well-reproduced on amino-functionalized silicon nitride chips, and the number of covalently bound biotin-IgG per microm2 was estimated by the amount of specifically bound ExtrAvidin-peroxidase conjugate. Coupling was evidently via disulfide bonds, since only biotin-IgG with free thiol groups was bound to the chips. The mechanism of protein thiol coupling to 2-pyridyl-S-S-PEG linkers on AFM tips was further examined by staging the coupling step in bulk solution and monitoring turnover by release of 2-pyridyl-SH which tautomerizes to 2-thiopyridone and absorbs light at 343 nm. These experiments predicted 10(3)-fold slower rates for the disulfide coupling step than actually observed on AFM tips and silicon nitride chips. The discrepancy was reconciled by assuming 10(3)-fold enrichment of protein on AFM tips via preadsorption, as is known to occur on comparable inorganic surfaces.     

Method for orienting DNA molecules on mica surfaces in one direction for atomic force microscopy imaging.

An efficient method was developed to stretch DNA molecules on an atomically flat surface for AFM imaging. This method involves anchoring DNA molecules from their 5' ends to amino silanized mica surfaces. N-Succinimidyl6-[3'-(2-pyridyldithio) propionamido]hexanoate (LC-SPDP), a heterobifunctional cross-linker with a flexible spacer arm was used for this purpose. Immobilization was carried out by introducing a thiol group to the 5' end of DNA by PCR. Thiolated molecules were then reacted with the cross linker to conjugate with its 2-pyridyl disulphide group via sulfhydryl exchange. The resulting complex was deposited on amino silanized mica where NHS-ester moiety of the cross linker reacted with the primary amino group on the surface. Samples were washed by a current of water and dried by an air jet in one direction parallel to the surface. DNA molecules were fully stretched in one direction on imaging them by AFM.     

Method for stretching DNA molecules on mica surface in one direction for AFM imaging.

An efficient method was developed to stretch DNA molecules on an atomically flat surface for AFM imaging. This method involves anchoring DNA molecules from their 5' ends to amino silanized mica surfaces. N-Succinimidyl6-[3'-(2-pyridyldithio) propionamido]hexanoate (LC-SPDP), a heterobifunctional cross-linker with a flexible spacer arm was used for this purpose. The immobilization process was carried out by introducing a thiol group to the 5' end of DNA by PCR. Thiolated molecules were then reacted with the cross linker to conjugate with its 2-pyridyl disulphide group via sulfhydryl exchange. The resulting complex was deposited on amino silanized mica where NHS-ester moiety of the cross linker reacted with the primary amino group on the surface. Samples were washed by a current of water and dried by an air jet in one direction parallel to the surface. DNA molecules were shown to be fully stretched in one direction on imaging them by AFM.     

Tobacco mosaic virus as an AFM tip calibrator

The study of high-resolution topographic surfaces of isolated single molecules is one of the applications of atomic force microscopy (AFM). Since tip-induced distortions are significant in topographic images the exact AFM tip shape must be known in order to correct dilated AFM height images using mathematical morphology operators. In this work, we present a protocol to estimate the AFM tip apex radius using tobacco mosaic virus (TMV) particles. Among the many advantages of TMV, are its non-abrasivity, thermal stability, bio-compatibility with other isolated single molecules and stability when deposited on divalent ion pretreated mica. Compared to previous calibration systems, the advantage of using TMV resides in our detailed knowledge of the atomic structure of the entire rod-shaped particle. This property makes it possible to interpret AFM height images in term of the three-dimensional structure of TMV. Results obtained in this study show that when a low imaging force is used, the tip is sensing viral protein loops whereas at higher imaging force the tip is sensing the TMV particle core. The known size of the TMV particle allowed us to develop a tip-size estimation protocol which permits the successful erosion of tip-convoluted AFM height images. Our data shows that the TMV particle is a well-adapted calibrator for AFM tips for imaging single isolated biomolecules. The procedure developed in this study is easily applicable to any other spherical viral particles.     

Atomic force microscopy: from cell imaging to molecular manipulation

The atomic force microscope (AFM) allows to explore the surface of biological samples bathed in physiological solutions, with vertical and horizontal resolutions ranging from nanometers to angstr?ms. Complex biological structures as well as single molecules can be observed and recent examples of the possibilities offered by the AFM in the imaging of intact cells, isolated membranes, membrane model systems and single molecules are discussed in this review. Applications where the AFM tip is used as a nanotool to manipulate biomolecules and to determine intra and intermolecular forces from single molecules are also presented.     

Attaching single biomolecules selectively to the apex of AFM tips for measuring specific interactions

We present a general approach for preparing well-defined AFM tips for probing single target molecules. We demonstrated that carboxylic acid groups could be generated by electrochemical oxidation selectively at the apex of an AFM tip that is coated with a monolayer of oligo(ethylene glycol) derivatives for resisting nonspecific interactions. These carboxylic acid groups were used as handles to tether only one ligand molecule, such as biotin, to the tip apex for measurement of specific interactions with biomolecules.     

Atomic force microscopy: from cellular imaging to molecular manipulation

Using a sharp tip attached at the end of a soft cantilever as a probe, the atomic force microscope (AFM) explores the surface topography of biological samples bathed in physiological solutions. In the last few years, the AFM has gained popularity among biologists. This has been obtained through the improvement of the equipment and imaging techniques as well as through the development of new non-imaging applications. Biological imaging has to face a main difficulty that is the softness and the dynamics of most biological materials. Progress in understanding the AFM tip-biological samples interactions provided spectacular results in different biological fields. Recent examples of the possibilities offered by the AFM in the imaging of intact cells, isolated membranes, membrane model systems and single molecules at work are discussed in this review. Applications where the AFM tip is used as a nanotool to manipulate biomolecules and to determine intra- and intermolecular forces from single molecules are also presented.     

Atomic force microscopy: a powerful tool to observe biomolecules at work

Atomic force microscopes (AFMs) move a sharp tip attached to a soft cantilever in a TV-raster-like pattern over a surface and record deflections of the tip that correspond to the surface topography. When operated in physiological solutions, an AFM allows biomolecules to be observed in their native environment. Progress in instrumentation, sample-preparation methods and recording conditions has provided images of biomolecules and their assemblies that reveal submolecular details. In addition, the AFM allows conformational changes to be observed directly. This article discusses these points and illustrates them with some pertinent examples.     

Extraction of membrane proteins from a living cell surface using the atomic force microscope and covalent crosslinkers

The force curve mode of the atomic force microscope (AFM) was applied to extract intrinsic membrane proteins from the surface of live cells using AFM tips modified by amino reactive bifunctional covalent crosslinkers. The modified AFM tips were individually brought into brief contact with the living cell surface to form covalent bonds with cell surface molecules. The force curves recorded during the detachment process from the cell surface were often characterized by an extension of a few hundred nanometers followed mostly by a single step jump to the zero force level. Collection and analysis of the final rupture force revealed that the most frequent force values (of the force) were in the range of 0.4–0.6 nN. The observed rupture force most likely represented extraction events of intrinsic membrane proteins from the cell membrane because the rupture force of a covalent crosslinking system was expected to be significantly larger than 1.0 nN, and the separation force of noncovalent ligand-receptor pairs to be less than 0.2 nN, under similar experimental conditions. The transfer of cell surface proteins to the AFM tip was verified by recording characteristic force curves of protein stretching between the AFM tips used on the cell surface and a silicon surface modified with amino reactive bifunctional crosslinkers. This method will be a useful addition to bionanotechnological research for the application of AFM.     

Atomic force bio-analytics

The atomic force microscope (AFM) allows biomolecules to be observed and manipulated under native conditions. It operates in buffer solution, produces molecular images with outstanding signal-to-noise ratio, and addresses single molecules. Progress in sample preparation and instrumentation has led to topographs that reveal sub-nanometer details and surface dynamics of biomolecules. Antibodies or oligonucleotides immobilized on cantilevers induce bending upon binding of the cognate biomolecule, allowing sub-picomolar concentrations to be measured. Biomolecules tethered between support and retracting AFM-tip produce force extension curves that reflect the mechanical stability of secondary structure elements. Furthermore, multifunctional tips may activate single molecules to observe them at work. In all cases, the cantilever is critical: its mechanical properties dictate the force-sensitivity and the scanning speed.     

MAPPING CELL WALL POLYSACCHARIDES OF LIVING MICROBIAL CELLS USING ATOMIC FORCE MICROSCOPY

Functionalized atomic force microscope tips were used to sense specific forces of interaction between ligand—receptor pairs and to map the positions of polysaccharides on a living microbial cell surface. Gold-coated tips were functionalized with concanavalin A using a cross-linker with a spacer arm of 15.6Å. It was possible to measure the binding force between concanavalin A and mannan polymers on the yeast (Saccharomyces cerevisiae) cell surface. This force ranged from 75 to 200pN. The shape of the force curve indicated that the polymers were pulled away from the cell surface for a fairly long distance that sometimes reached several hundred nanometres. The distribution of mannan on the cell surface was mapped by carrying out the force measurement in the force volume mode of atomic force microscopy (AFM). During the measurement, the maximum cantilever deflection after contact between the tip and the sample was kept constant at 10nm using trigger mode to keep the pressing force on the sample surface as gently as possible at a force of 180pN. This regime was used to minimize the non-specific adhesion between the tip and the cell surface. Specific molecular recognition events took place on specific areas of the cell surface that could be interpreted as reflecting a non-uniform distribution of mannan on the cell surface.     

Probing membrane proteins using atomic force microscopy

To gain insights into how biological molecules function, advanced technologies enabling imaging, sensing, and actuating single molecules are required. The atomic force microscope (AFM) would be one of novel potential tools for these tasks. In this study, techniques and efforts using AFM to probe biomolecules are introduced and reviewed. The state-of-art techniques for characterizing specific single receptor using the functionalized AFM tip are discussed. An example of studying the angiotensin II type 1 (AT1) receptors expressed in sensory neuronal cells by AFM with a functionalized tip is given. Perspectives for identifying and characterizing specific individual membrane proteins using AFM in living cells are provided. Given that many diseases have their roots at the molecular scale and are best understood as a malfunctioning biological nanomachines, the prospects of these unique techniques in basic biomedical research or in clinical practice are beyond our imagination.     

Tip size of ion-exchanger based K+-selective microelectrodes. I. Effects on selectivity

Double-barreled ion-exchanger based K+-selective microelectrodes (K+ ISMs) of a variety of tip diameters were used to study the dependency of ion selectivity upon tip size. The selectivity of K+ ISMs depended on tip size and barrel configuration. Within the range of tip diameters tested (approximately 0.5-6 micron) all K+ ISMs constructed of two barrels glued side by side ("figure-eight glass") exhibited sensitivity to K+ and NH4+. Figure-eight K+ ISMs with tip diameters less than 1.5 micron were not sensitive to tetramethylammonium, tetraethylammonium, or choline, whereas K+ ISMs with tip diameters greater than or equal to 1.5 micron sensed all of the quaternary amines. Tip size dependent selectivity was not present in K+ ISMs made from thick septum theta glass. The explanation for tip size dependent changes in ion selectivity is unknown but a discussion of theoretical possibilities is given.     

Nanomechanical recognition of sphingomyelin-rich membrane domains by atomic force microscopy

Sphingomyelin (SM) is a reservoir of signaling lipids and forms specific lipid domains in biomembranes together with cholesterol. In this study, atomic force microscopy (AFM) and force measurement were applied to investigate the interaction of SM-binding protein toxin, lysenin, with N-palmitoyl-D-erythro-sphingosylphosphorylcholine (palmitoyl sphingomyelin, PSM) bilayer spread over a mica substrate, in an aqueous buffer solution. Lysenin molecules were grafted on a silicon nitride tip for AFM by siloxane-thiol-amide coupling. The bilayers were prepared by the Langmuir-Blodgett (LB)/Langmuir-Schaefer (LS) method. By repeating cycles of tip approach/retraction motion, single-molecular adhesion motions were observed on the force curve, characterized as "fishing curves". The addition of cholesterol and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) did not alter the peak force but increased the peak extension. Mixtures of PSM/DOPC/cholesterol exhibited 2-dimensional two-phase domain separation. The characteristic fishing curves were observed exclusively in one of the phases, indicating the selective interaction of the lysenin tip to PSM-rich membrane domains. Our results indicate that the AFM tips conjugated with lysenin are useful to detect the surface distribution of SM-rich membrane domains as well as the nanomechanical properties of the domains.     

Hydration force in the atomic force microscope: A computational study.

Using a hard sphere model and numerical calculations, the effect of the hydration force between a conical tip and a flat surface in the atomic force microscope (AFM) is examined. The numerical results show that the hydration force remains oscillatory, even down to a tip apex of a single water molecule, but its lateral extent is limited to a size of a few water molecules. In general, the contribution of the hydration force is relatively small, but, given the small imaging force ( approximately 0.1 nN) typically used for biological specimens, a layer of water molecules is likely to remain "bound" to the specimen surface. This water layer, between the tip and specimen, could act as a "lubricant" to reduce lateral force, and thus could be one of the reasons for the remarkably high resolution achieved with contact-mode AFM. To disrupt this layer, and to have a true tip-sample contact, a probe force of several nanonewtons would be required. The numerical results also show that the ultimate apex of the tip will determine the magnitude of the hydration force, but that the averaged hydration pressure is independent of the radius of curvature. This latter conclusion suggests that there should be no penalty for the use of sharper tips if hydration force is the dominant interaction between the tip and the specimen, which might be realizable under certain conditions. Furthermore, the calculated hydration energy near the specimen surface compares well with experimentally determined values with an atomic force microscope, providing further support to the validity of these calculations.     

Identification of recombinant AtPYL2, an abscisic acid receptor,in E. coli using a substrate-derived bioactive small molecule,a biotin linker with alkyne and amino groups,and a protein cross-linker

Target protein identification of bioactive small molecules is one of the most important research in forward chemical genetics. The affinity chromatography technique to use a resin bound with a small molecule is often used for identification of a target protein of a bioactive small molecule. Here we report a new method to isolate a protein targeted with a bioactive small molecule using a biotin linker with alkyne and amino groups, protein cross-linker containing disulfide bond, and a bioactive small molecule with an azido group (azido probe). After an azido probe is associated with a target protein, the complex of a target protein and azido probe is covalently bound through the biotin linker by azide-alkyne Huisgen cycloaddition and protein cross-linker containing disulfide bond. This ternary complex is immobilized on an affinity matrix with streptavidin, and then the target protein is selectively eluted with a buffer containing a reducing agent for cleavage of disulfide bonds. This method uses a probe having an azido group, which a small functional group, and has the possibility to be a solution strategy to overcome the hindrance of a functional group introduced into the probe that reduces association a target protein. The effectiveness of the method in this study was shown using linker 1, 3′-azidoabscisic acid 3, and protein cross-linker containing a disulfide bond (DTSSP 5).     

Compressive nanomechanics of opposing aggrecan macromolecules

In this study, we have measured the nanoscale compressive interactions between opposing aggrecan macromolecules in near-physiological conditions, in order to elucidate the molecular origins of tissue-level cartilage biomechanical behavior. Aggrecan molecules from fetal bovine epiphyseal cartilage were chemically end-grafted to planar substrates, standard nanosized atomic force microscopy (AFM) probe tips (R(tip) approximately 50 nm), and larger colloidal probe tips (R(tip) approximately 2.5 microm). To assess normal nanomechanical interaction forces between opposing aggrecan layers, substrates with microcontact printed aggrecan were imaged using contact mode AFM, and aggrecan layer height (and hence deformation) was measured as a function of solution ionic strength (IS) and applied normal load. Then, using high-resolution force spectroscopy, nanoscale compressive forces between opposing aggrecan on the tip and substrate were measured versus tip-substrate separation distance in 0.001-1M NaCl. Nanosized tips enabled measurement of the molecular stiffness of 2-4 aggrecan while colloidal tips probed the nanomechanical properties of larger assemblies (approximately 10(4) molecules). The compressive stiffness of aggrecan was much higher when using a densely packed colloidal tip than the stiffness measured for using the nanosized tip with a few aggrecan, demonstrating the importance of lateral interactions to the normal nanomechanical properties. The measured stress at 0.1M NaCl (near-physiological ionic strength) increased sharply at aggrecan densities under the tip of approximately 40 mg/ml (physiological densities are approximately 20-80 mg/ml), corresponding to an average inter-GAG spacing of 4-5 Debye lengths (4-5 nm); this characteristic spacing is consistent with the onset of significant electrostatic interactions between GAG chains of opposing aggrecan molecules. Comparison of nanomechanical data to the predictions of Poisson-Boltzmann-based models further elucidated the regimes over which electrostatic and nonelectrostatic interactions affect aggrecan stiffness in compression. The most important aspects of this study include: the incorporation of experiments at two different length scales, the use of microcontact printing to enable quantification of aggrecan deformation and the corresponding nanoscale compressive stress vs. strain curve, the use of tips of differing functionality to provide insights into the molecular mechanisms of deformation, and the comparison of experimental data to the predictions of three increasingly refined Poisson-Boltzmann (P-B)-based theoretical models for the electrostatic double layer component of the interaction.     

Electropolymerization molecularly imprinted polymer (E-MIP) SPR sensing of drug molecules: pre-polymerization complexed terthiophene and carbazole electroactive monomers

A novel chemosensitive ultrathin film with high selectivity was developed for the detection of naproxen, paracetamol, and theophylline using non-covalent electropolymerized molecular imprinted polymers (E-MIP). A series of monofunctional and bifunctional H-bonding terthiophene and carbazole monomers were compared for imprinting these drugs without the use of a separate cross-linker. A key step is the fast and efficient potentiostatic method of washing the template, which facilitated enhanced real-time sensing by surface plasmon resonance (SPR) spectroscopy. Various surface characterizations (contact angle, ellipsometry, XPS, AFM) of the E-MIP film verified the templating and release of the drug from the cross-linked conducting polymer film.