Magnetic tweezers-based force clamp reveals mechanically distinct apCAM domain interactions

Cell adhesion molecules of the immunoglobulin superfamily (IgCAMs) play a crucial role in cell-cell interactions during nervous system development and function. The Aplysia CAM (apCAM), an invertebrate IgCAM, shares structural and functional similarities with vertebrate NCAM and therefore has been considered as the Aplysia homolog of NCAM. Despite these similarities, the binding properties of apCAM have not been investigated thus far. Using magnetic tweezers, we applied physiologically relevant, constant forces to apCAM-coated magnetic particles interacting with apCAM-coated model surfaces and characterized the kinetics of bond rupture. The average bond lifetime decreased with increasing external force, as predicted by theoretical considerations. Mathematical simulations suggest that the apCAM homophilic interaction is mediated by two distinct bonds, one involving all five immunoglobulin (Ig)-like domains in an antiparallel alignment and the other involving only two Ig domains. In summary, this study provides biophysical evidence that apCAM undergoes homophilic interactions, and that magnetic tweezers-based, force-clamp measurements provide a rapid and reliable method for characterizing relatively weak CAM interactions.

Highly ordered Fe-Au heterostructured nanorod arrays and their exceptional near-infrared plasmonic signature

The potential of highly ordered array nanostructures in sensing applications is well recognized, particularly with the ability to define the structural composition and arrangement of the individual nanorods accurately. The use of heterogeneous nanostructures generates an additional degree of freedom, which can be used to tailor the optical response of such arrays. In this article, we report on the fabrication and characterization of well-defined Fe-Au bisegmented nanorod arrays in a repeating hexagonal arrangement. Through an asymmetric etching method, free-standing Fe-Au nanorod arrays on a gold-coated substrate were produced with an inter-rod spacing of 26 nm. This separation distance renders the array capable of sustaining resonant electromagnetic wave coupling between individual rods. Owing to this coupling, the subwavelength arrangement, and the structural heterogeneity, the nanorod arrays exhibit unique plasmonic responses in the near-infrared (NIR) range. Enhanced sensitivity in this spectral region has not been identified for gold-only nanorods of equivalent dimensions. The NIR response offers confirmation of the potential of these highly ordered, high-density arrays for biomedical relevant applications, such as subcutaneous spectroscopy and biosensing.

Isolation of Bowman-Birk-Inhibitor from soybean extracts using novel peptide probes and high gradient magnetic separation

Soybean proteins offer exceptional promise in the area of cancer prevention and treatment. Specifically, Bowman-Birk Inhibitor (BBI) has the ability to suppress carcinogenesis in vivo, which has been attributed to BBI's inhibition of serine protease (trypsin and chymotrypsin) activity. The lack of molecular probes for the isolation of this protein has made it difficult to work with, limiting its progress as a significant candidate in the treatment of cancer. This study has successfully identified a set of novel synthetic peptides targeting the BBI, and has demonstrated the ability to bind BBI in vitro. One of those probes has been covalently immobilised on superparamagnetic microbeads to allow the isolation of BBI from soy whey mixtures in a single step. Our ultimate goal is the use of the described synthetic probe to facilitate the isolation of this potentially therapeutic protein for low cost, scalable analysis and production of BBI.

M13 bacteriophage-activated superparamagnetic beads for affinity separation

The growth of the biopharmaceutical industry has created a demand for new technologies for the purification of genetically engineered proteins.The efficiency of large-scale, high-gradient magnetic fishing could be improved if magnetic particles offering higher binding capacity and magnetization were available. This article describes several strategies for synthesizing microbeads that are composed of a M13 bacteriophage layer assembled on a superparamagnetic core. Chemical cross-linking of the pVIII proteins to a carboxyl-functionalized bead produces highly responsive superparamagnetic particles (SPM) with a side-on oriented, adherent virus monolayer. Also, the genetic manipulation of the pIII proteins with a His(6) peptide sequence allows reversible assembly of the bacteriophage on a nitrilotriacetic-acid-functionalized core in an end-on configuration. These phage-magnetic particles are successfully used to separate antibodies from high-protein concentration solutions in a single step with a >90% purity. The dense magnetic core of these particles makes them five times more responsive to magnetic fields than commercial materials composed of polymer-(iron oxide) composites and a monolayer of phage could produce a 1000 fold higher antibody binding capacity. These new bionanomaterials appear to be well-suited to large-scale high-gradient magnetic fishing separation and promise to be cost effective as a result of the self-assembling and self-replicating properties of genetically engineered M13 bacteriophage.

Resistive pulse sensing of analyte-induced multicomponent rod aggregation using tunable pores

Resistive pulse sensing is used to monitor individual and aggregated rod-shaped nanoparticles as they move through tunable pores in elastomeric membranes. By comparing particles of similar dimensions, it is demonstrated that the resistive pulse signal of a rod is fundamentally different from that of a sphere. Rods can be distinguished using two measurements: the blockade event magnitude (Δi(p) ), which reveals the particle's size, and the full width at half maximum (FWHM) duration, which relates to the particle's speed and length. While the observed Δi(p) values agree well with simulations, the measured FWHM times are much larger than expected. This increase in dwell time, caused by rods moving through the pore in various orientations, is not observed for spherical particles. These differences are exploited in a new agglutination assay using rod-shaped particles. By controlling the surface chemistry and location of the capture ligand, rods are made to form either long "end-on-end" or wide "side-on" aggregates upon the addition of an analyte. This observation will facilitate multiplexed detection in agglutination assays, as particles with a particular aspect ratio can be distinguished by two measurements. This is first demonstrated with a biotinylated target and avidin capture probe, followed by the detection of platelet-derived growth factor (PDGF-BB) using an aptamer capture probe, with limits of detection down to femtomolar levels.

Probing the soybean Bowman-Birk inhibitor using recombinant antibody fragments

The nutritional and health benefits of soy protein have been extensively studied over recent decades. The Bowman-Birk inhibitor (BBI), derived from soybeans, is a double-headed inhibitor of chymotrypsin and trypsin with anticarcinogenic and anti-inflammatory properties, which have been demonstrated in vitro and in vivo. However, the lack of analytical and purification methodologies complicates its potential for further functional and clinical investigations. This paper reports the construction of anti-BBI antibody fragments based on the principle of protein design. Recombinant antibody (scFv and diabody) molecules targeting soybean BBI were produced and characterized in vitro (K(D)~1.10(-9) M), and the antibody-binding site (epitope) was identified as part of the trypsin-specific reactive loop. Finally, an extremely fast purification strategy for BBI from soybean extracts, based on superparamagnetic particles coated with antibody fragments, was developed. To the best of the authors' knowledge, this is the first report on the design and characterization of recombinant anti-BBI antibodies and their potential application in soybean processing.

Magnetic-plasmonic dual modulated FePt-Au ternary heterostructured nanorods as a promising nano-bioprobe

Ternary FePt-Au nanorods are synthesized as magnetic-plasmonic 1D nanostructures. Besides their widely tunable magnetic properties, their unique plasmonic response to the illumination polarization provides a powerful tool to optically image these sub-wavelength single nanorods. These nanoparticles also show the potential as a novel nano-bioprobe based on the demonstration of simultaneous magnetic manipulation and optical imaging of single particles inside live cells.

Resistive pulse sensing of magnetic beads and supraparticle structures using tunable pores

Tunable pores (TPs) have been used for resistive pulse sensing of 1 μm superparamagnetic beads, both dispersed and within a magnetic field. Upon application of this field, magnetic supraparticle structures (SPSs) were observed. Onset of aggregation was most effectively indicated by an increase in the mean event magnitude, with data collected using an automated thresholding method. Simulations enabled discrimination between resistive pulses caused by dimers and individual particles. Distinct but time-correlated peaks were often observed, suggesting that SPSs became separated in pressure-driven flow focused at the pore constriction. The distinct properties of magnetophoretic and pressure-driven transport mechanisms can explain variations in the event rate when particles move through an asymmetric pore in either direction, with or without a magnetic field applied. Use of TPs for resistive pulse sensing holds potential for efficient, versatile analysis and measurement of nano- and microparticles, while magnetic beads and particle aggregation play important roles in many prospective biosensing applications.

Magnetic manipulation and optical imaging of an active plasmonic single-particle Fe-Au nanorod

Superparamagnetic microbeads play an important role in a number of scientific and biotechnology applications including single-molecule force measurements, affinity separation, and in vivo and in vitro diagnostics. Magneto-optically active nanorods composed of single-crystalline Au and polycrystalline Fe segments were synthesized with diameters of 60 or 295 nm using templated electrodeposition. The Fe section was magnetically soft and had a saturation magnetization of approximately 200 emu/g, resulting in a 10-fold increase in magnetization relative to that iron oxide nanoparticles. The strong plasmonic response of the Au segment of the rod in both the longitudinal and transverse directions made it possible to detect the orientation of a single rod in a polarized light microscope with nanometer resolution. These nanorods provide significantly improved physical properties over iron oxide superparamagnetic beads, making it possible to simultaneously manipulate and monitor the orientation of biomolecules with well-defined forces at the nanometer scale.

Flow-enhanced nonlinear magnetophoresis for high-resolution bioseparation

A new mode of transport is described that was capable of high-resolution separation of superparamagnetic materials from complex mixtures based on their size. Laminar flow and a rotating external magnetic field were applied to superparamagnetic beads assembled on a semiperiodic micromagnet array. Beads at the edge of the micromagnet array oscillated in-phase with the external magnetic field with an amplitude that decreased with increasing frequency, ω, until they reached an immobilization frequency, ω(i), where the beads stopped moving. Laminar flow along the edge of the array could be tuned to sweep the beads for which ω < ω(i) downstream at a velocity that increased with size while leaving beads for which ω > ω(i) undisturbed. Flow-enhanced nonlinear magnetophoresis (F-NLM) promises to enable multiple superparamagnetc bead types to be used in the fractionation of cells and implementation of diagnostic assays.

Topography and nanomechanics of live neuronal growth cones analyzed by atomic force microscopy

Neuronal growth cones are motile structures located at the end of axons that translate extracellular guidance information into directional movements. Despite the important role of growth cones in neuronal development and regeneration, relatively little is known about the topography and mechanical properties of distinct subcellular growth cone regions under live conditions. In this study, we used the AFM to study the P domain, T zone, and C domain of live Aplysia growth cones. The average height of these regions was calculated from contact mode AFM images to be 183 +/- 33, 690 +/- 274, and 1322 +/- 164 nm, respectively. These findings are consistent with data derived from dynamic mode images of live and contact mode images of fixed growth cones. Nano-indentation measurements indicate that the elastic moduli of the C domain and T zone ruffling region ranged between 3-7 and 7-23 kPa, respectively. The range of the measured elastic modulus of the P domain was 10-40 kPa. High resolution images of the P domain suggest its relatively high elastic modulus results from a dense meshwork of actin filaments in lamellipodia and from actin bundles in the filopodia. The increased mechanical stiffness of the P and T domains is likely important to support and transduce tension that develops during growth cone steering.

Immunoassays in nanoliter volume reactors using fluorescent particle diffusometry

A model analyte, the M13 virus, was detected through the change in the Brownian motion of a population of microparticles. Epi-fluorescence microscopy was used to simultaneously track antibody-coated and bare microparticles to unambiguously measure the diffusion coefficient and demonstrate multiplexed detection. The sensitivity of the diffusometry assay was high enough that individual virus-to-particle binding ratios could be detected. Analysis of the experimental errors indicated that the primary limitation in the sensitivity of this technique was the variation in the size of the population of microparticles. Analysis of the diffusion measurement results indicated that the change in the drag coefficient of the virus-particle assembly was not a simple sum of the drag coefficients of the individual components and the rate of particle-particle reaction was slower than would be predicted from the uncoupled particle hydrodynamics. The possibility of using diffusometry for sensing and proteomics applications is examined.

Traveling wave magnetophoresis for high resolution chip based separations

A new mode of magnetophoresis is described that is capable of separating micron-sized superparamagnetic beads from complex mixtures with high sensitivity to their size and magnetic moment. This separation technique employs a translating periodic potential energy landscape to transport magnetic beads horizontally across a substrate. The potential energy landscape is created by superimposing an external, rotating magnetic field on top of the local fixed magnetic field distribution near a periodic arrangement of micro-magnets. At low driving frequencies of the external field rotation, the beads become locked into the potential energy landscape and move at the same velocity as the traveling magnetic field wave. At frequencies above a critical threshold, defined by the bead's hydrodynamic drag and magnetic moment, the motion of a specific population of magnetic beads becomes uncoupled from the potential energy landscape and its magnetophoretic mobility is dramatically reduced. By exploiting this frequency dependence, highly efficient separation of magnetic beads has been achieved, based on fractional differences in bead diameter and/or their specific attachment to two microorganisms, i.e., B. globigii and S. cerevisiae.

Specific adsorption of histidine-tagged proteins on silica surfaces modified with Ni2+/NTA-derivatized poly(ethylene glycol)

Silica surfaces modified with nitrilotriacetic acid (NTA)-polyethylene glycol (PEG) derivatives were used to immobilize hexahistidine-tagged green fluorescent protein (His6-GFP), biotin/streptavidin-AlexaFluor555 (His6-biotin/SA-AF), and gramicidin A-containing vesicles (His6-gA). Three types of surface-reactive PEG derivatives-NTA-PEG3400-Si(OMe)3, NTA-PEG3400-vinylsulfone, and mPEG5000-Si(OMe)3 (control)-were grafted onto silica and tested for their ability to capture His6-tag species via His6/Ni2+/NTA chelation. The composition and thicknesses of the PEG-modified surfaces were characterized using X-ray photoelectron spectroscopy, contact angle, and ellipsometry. Protein capture efficiencies of the NTA-PEG-grafted surfaces were evaluated by measuring fluorescence intensities of these surfaces after exposure to His6-tag species. XPS and ellipsometry data indicate that surface adsorption occurs via specific interactions between the His6-tag and the Ni2+/NTA-PEG-grafted surface. Protein immobilization was most effective for NTA-PEG3400-Si(OMe)3-modified surfaces, with maximal areal densities achieved at 45 pmol/cm2 for His6-GFP and 95 fmol/cm2 for His6-biotin/SA-AF. Lipid vesicles containing His6-gA in a 1:375 gA/lipid ratio could also be immobilized on Ni2+/NTA-PEG3400-Si(OMe)3-modified surfaces at 0.5 mM total lipid. Our results suggest that NTA-PEG-Si(OMe)3 conjugates may be useful tools for immobilizing His6-tag proteins on solid surfaces to produce protein-functionalized surfaces.

Magnetic Tweezers Measurement of the Bond Lifetime−Force Behavior of the IgG−Protein A Specific Molecular Interaction

The bond lifetime-force behavior of the immunoglobulin G (IgG)-protein A interaction has been studied with magnetic tweezers to characterize the physical properties of the bond under nonequilibrium conditions. Super-paramagnetic microparticles were developed that have a high and uniform magnetization to simultaneously apply a piconewton-scale tensile force to many thousands of IgG-protein A bonds. A strong and a weak slip bond were detected with an effective bond length that is characteristic of short-range, stiff intermolecular interactions. These bonds are attributed to the interaction of protein A with the constant region (Fc) and heavy chain variable domain (VH) of IgG, respectively. The IgG-VH interaction appears to be one of the weakest specific molecular interactions that has been identified with a single molecule force measurement technique. This study demonstrates that magnetic tweezers can be used to rapidly characterize very weak biomolecular interactions as well as strong biomolecular interactions with a high degree of accuracy.

High-resolution analysis of neuronal growth cone morphology by comparative atomic force and optical microscopy

Neuronal growth cones are motile sensory structures at the tip of axons, transducing guidance information into directional movements towards target cells. The morphology and dynamics of neuronal growth cones have been well characterized with optical techniques; however, very little quantitative information is available on the three-dimensional structure and mechanical properties of distinct subregions. In the present study, we imaged the large Aplysia growth cones after chemical fixation with the atomic force microscope (AFM) and directly compared our data with images acquired by light microscopy methods. Constant force imaging in contact mode in combination with force-distant measurements revealed an average height of 200 nm for the peripheral (P) domain, 800 nm for the transition (T) zone, and 1200 nm for the central (C) domain, respectively. The AFM images show that the filopodial F-actin bundles are stiffer than surrounding F-actin networks. Enlarged filopodia tips are 60 nm higher than the corresponding shafts. Measurements of the mechanical properties of the specific growth cone regions with the AFM revealed that the T zone is stiffer than the P and the C domain. Direct comparison of AFM and optical data acquired by differential interference contrast and fluorescence microscopy revealed a good correlation between these imaging methods. However, the AFM provides height and volume information at higher resolution than fluorescence methods frequently used to estimate the volume of cellular compartments. These findings suggest that AFM measurements on live growth cones will provide a quantitative understanding of how proteins can move between different growth cone regions.

Nanoliter-scale reactor arrays for biochemical sensing

A general approach is described for array-based biochemical sensing that uses contact-free dispersal of compounds into addressable microfabricated reactors. The arrays are composed of 1 to 100 nL volume open reactors that have been microfabricated on quartz substrates using lithography. The open architecture of these reactors allows them to be addressed in parallel or individually with an ink-jet arrayer that is capable of distributing 0.004 to 1 nL volumes of reagents. A seven-step biochemical assay has been conducted on a small array of reactors to demonstrate how they can be integrated with an ink-jet arrayer and optical detector. This nanoreactor assay format appears to overcome several limitations that chip-based microarray technology currently imposes on protein assays: the arrays can be created in a manner that does not expose the biochemical reagents to osmotic stress, independent reactions can be conducted in individual reactors, and the conditions in all of the reactors (e.g., concentration and pH) can be rapidly scanned. We believe that these nanoreactor arrays will be useful for biochemical sensing that involves delicate proteins and protein assemblies.

Properties of mixed lipid monolayers assembled on hydrophobic surfaces through vesicle adsorption

Supported lipid films are becoming increasingly important tools for the study of membrane protein function because of the availability of high-sensitivity surface analytical and patterning techniques. In this study, we have characterized the physical chemical properties of lipid films assembled on hydrophobic surfaces through the spontaneous adsorption of large unilamellar lipid vesicles composed of dioleoylphosphatidylglycerol (DOPG) and dioleoylphosphatidylcholine (DOPC). The density of the lipid films was measured with surface plasmon resonance spectroscopy as the lipid composition of the vesicles and ionic concentration were varied. As expected, monolayer films were formed, but the density of the monolayers was found to be weakly dependent on the lipid composition of the vesicles and strongly dependent on the ionic concentration of the solution in contact with the monolayer. Atomic force microscopy (AFM) images of the lipid films indicate that they are composed of a homogeneous monolayer. Surface force measurements were used to determine the surface charge and DOPG density of the monolayers. The DOPG content of the films was found to be weakly dependent on the DOPG composition of the vesicles and strongly dependent on the salt concentration of the environment. A model has been developed to describe the behavior of the lipid composition of the films in terms of the hydrophobic, electrostatic, and steric forces acting on the lipid monolayer on the hydrophobic surface.

Synthesis and characterization of paramagnetic microparticles through emulsion-templated free radical polymerization

A novel method is described for the preparation of high-magnetization paramagnetic microparticles functionalized with a controlled density of poly(ethylene glycol) (PEG) and carboxyl groups. These microparticles were synthesized using four steps: (1) creation of an oil-in-water emulsion in which hydrophobic iron oxide nanoparticles and a UV-activated initiator were distributed in hexane; (2) formation of uniform microparticles through emulsion homogenization and evaporation of hexane; (3) functionalization of the microparticle with a PEG-functionalized surfactant and acrylic acid; and (4) polymerization of the microparticles. Characterization of the microparticles with electron microscopy and light scattering revealed that they were composed of densely packed iron oxide nanoparticles and that the size of the microparticles may be controlled through the pore size of the membrane used to homogenize the emulsion. The concentration of surfactant and acrylic acid used in the third processing step was found to determine the surface chemistry, iron content, and magnetization of the microparticles. Increasing the PEG surfactant to acrylic acid ratio resulted in higher PEG surface densities, lower iron content, and lower magnetization. The resulting microparticles were readily functionalized with antibodies and showed a low propensity for nonspecific protein adsorption. We believe that these microparticles will be useful for magnetic tweezers measurements and bioanalytical devices that require microparticles with a high magnetization.

Mesoporous membrane device for asymmetric biosensing

An array of micron size reactors has been designed and fabricated on a mesoporous membrane to create a platform for asymmetric biochemical sensing. Fabrication of this device required that a technique be developed to integrate the mesoporous alumina membrane with a polymeric layer that maintains the integrity of the membrane surface and permeability. This device was used to control an enzyme reaction at the surface of the membrane through the diffusion of the substrates from the opposite sides of the membrane. Asymmetric reactions promise new modes of sensing, enhanced stability of delicate biomolecular systems, and enhanced sensitivity and speed in sensing.

Dissociation of multiple protein ion charge states following a single gas-phase purification and concentration procedure

The formation of a range of precursor ion charge states from a single concentrated and purified charge state, followed by activation of each charge state, is introduced as a means to obtain more protein structural information than is available from dissociation of a single charge state alone. This approach is illustrated using off-resonance collisional activation of the [M + 8H]8+ to [M + 6H]6+ precursor ions of the bacteriophage MS2 viral coat protein following concentration and purification of the [M + 8H]8+ charge state. This range of charge states was selected on the basis of an ion trap collisional activation study of the effects of precursor ion charge state on the dissociation of the [M + 12H]12+ to [M + 5H]5+ ions. Gas-phase ion/ion proton-transfer reactions and the ion parking technique were applied to purify and concentrate selected precursor ion charge states as well as to simplify the product ion spectra. The high-charge-state ions fragment preferentially at the N-terminal side of proline residues while the product ion spectra of the lowest charge states investigated are dominated by C-terminal aspartic acid cleavages. Maximum structural information is obtained by fragmentation of the intermediate-charge states.

Gas-phase concentration, purification, and identification of whole proteins from complex mixtures

Five proteins present in a relatively complex mixture derived from a whole cell lysate fraction of E. coli have been concentrated, purified, and dissociated in the gas phase, using a quadrupole ion trap mass spectrometer. Concentration of intact protein ions was effected using gas-phase ion/ion proton-transfer reactions in conjunction with mass-to-charge dependent ion "parking" to accumulate protein ions initially dispersed over a range of charge states into a single lower charge state. Sequential ion isolation events interspersed with additional ion parking ion/ion reaction periods were used to "charge-state purify" the protein ion of interest. Five of the most abundant protein components present in the mixture were subjected to this concentration/purification procedure and then dissociated by collisional activation of their intact multiply charged precursor ions. Four of the five proteins were subsequently identified by matching the uninterpreted product ion spectra against a partially annotated protein sequence database, coupled with a novel scoring scheme weighted for the relative abundances of the experimentally observed product ions and the frequency of fragmentations occurring at preferential cleavage sites. The identification of these proteins illustrates the potential of this "top-down" protein identification approach to reduce the reliance on condensed-phase chemistries and extensive separations for complex protein mixture analysis.