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The potential for liquid biopsy samples to be used in place of more invasive tissue biopsies has become increasingly revalent as it has been found that nucleic acids (NAs) present in the blood of cancer patients originate from tumors. Nanomagnetic extraction has proven to be a highly effective means to rapidly prepare NA from clinical samples for molecular diagnostics. In this article, the lysis reaction used to extract RNA from the human epithelial melanoma cells have been optimized using silica coated superparamagnetic nanoparticles (SPM NP). The lysis buffer (LB) is composed of several agents that denature cells

Magnetophoretic lab on a chip technologies are rapidly evolving into integrated systems for the identification of biomarkers and cells with ultra-high sensitivity. We demonstrate the highly efficient detection of the Human herpes simplex virus type 1 (HSV) UL27 gene through the programmed assembly of superparamagnetic (SPM) nanoparticles based on oligonucleotide hybridization. The state of assembly of the SPM nanoparticles was determined by optical signature of the synchronized motion on the beads on a micromagnetic array (MMA). This technique has been used to identify

Magnetically actuated lab-on-a-chip (LOC) technologies have enabled rapid, highly efficient separation of specific biomarkers and cells from complex biological samples. Nonlinear magnetophoresis (NLM) is a technique that uses a microfabricated magnet array (MMA) and a time varying external magnetic field to precisely control the transport of superparamagnetic (SPM) beads on the surface of a chip based on their size and magnetization. We analyze the transport and separation behavior of SPM monomers and dimers on four MMA geometries, i.e., circular, triangular, square and rectangular shaped micromagnets, across a range of external magnetic field rotation frequencies. The measured critical frequency of the SPM beads on an MMA, i.e., the velocity for which the hydrodynamic drag on a bead exceeds the magnetic force, is closely related to the local magnetic flux density landscape on a micromagnet in the presence of an external magnetic field. A set of design criteria has been established for the optimization of MMAs for NLM separation, with particular focus on the shape of the micromagnets forming the array. The square MMA was used to detect a model protein biomarker and gene fragment based on a magnetic bead assembly (MBA) assay. This assay uses ligand functionalized SPM beads to capture and directly detect an analyte through the formation of SPM bead aggregates. These beads aggregates were detected through NLM separation and microscopic analysis resulting in a highly sensitive assay that did not use carrier fluid.

Micromagnetic arrays (MMAs) have proven to be powerful tools for controlling the transport and separation of bioanalytes, i.e., they allow bioanalyte-superparamagnetic (SPM) bead complexes of specific size and magnetization to be moved in a synchronized manner that is precisely controlled with the orientation of an external magnetic field. This article presents a laser-photodetector system for the simple detection of individual SPM beads moving on a specific region of an MMA. This system detects the SPM beads through the change in intensity of reflective light as they move from the highly reflective micromagnetics to the supporting substrate. We demonstrate that this opti-MMA system allowed the size, number, and magnetic and optical properties of the SPM beads to be rapidly determined for regions > 49 µm2 in size. The response of the opti-MMA system was characterized in several optical configurations to develop a theoretical description of its sensitivity and dynamic range. The speed, low-cost, and sensitivity of this system promises to allow MMAs to be readily applied in in vitro diagnostics and biosensing.

There is a need for point of care diagnostic technologies that are rapid, sensitive, easy to use, and relatively inexpensive. In this article we describe an assay that uses an antibody functionalized nanoporous membrane and superparamagnetic beads to capture and detect human cardiac troponin I (cTnI), which is an important biomarker for acute myocardial infarction (AMI). The membrane assisted force differentiation assay (mFDA) is capable of detecting cTnI at a sensitivity of 0.1 pg ml-1 in 15% serum in less than 16 minutes, which is a significant improvement in performance over conventional lateral flow immuosorbant assays. The speed of this assay results from the rapid concentration of cTnI on the surface of the nanoporous membrane and the use of the magnetic beads to react with the analyte, which rapidly react with the immobilized cTnI. The increased sensitivity of assay results from the use of magnetically controlled forces that reduce the nonspecific background and modify both the on-rate and off-rate. We believe that the improved performance and ease of application of the mFDA will make it useful in the early identification of AMI as well as other diseases based on the detection of 1 pg ml-1 variations in the concentrations cTnI in blood.

Magnetic nanoparticles are promising new tools for therapeutic applications, such as magnetic nanoparticle hyperthermia therapy and targeted drug delivery. Recent in vitro studies have demonstrated that a force application with magnetic tweezers can also affect cell fate, suggesting a therapeutic potential for magnetically modulated mechanical stimulation. The magnetic properties of nanoparticles that induce physical responses and the subtle responses that result from mechanically induced membrane damage and/or intracellular signaling are evaluated. Magnetic particles with various physical, geometric, and magnetic properties and specific functionalization can now be used to apply mechanical force to specific regions of cells, which permit the modulation of cellular behavior through the use of spatially and time controlled magnetic fields. On one hand, mechanochemical stimulation has been used to direct the outgrowth on neuronal growth cones, indicating a therapeutic potential for neural repair. On the other hand, it has been used to kill cancer cells that preferentially express specific receptors. Advances made in the synthesis and characterization of magnetic nanomaterials and a better understanding of cellular mechanotransduction mechanisms may support the translation of mechanochemical stimulation into the clinic as an emerging therapeutic approach. European Commission - European Regional Development Fund Science Foundation Ireland Programme for Research in Third-Level Institutions Marie Curie Intra-European Fellowship

The downstream processing of proteins remains the most significant cost in protein production, and is largely attributed to rigorous chromatographic purification protocols, where the stringency of purity for biopharmaceutical products sometimes exceeds 99%. With an ever burgeoning biotechnology market, there is a constant demand for alternative purification methodologies, to ameliorate the dependence on chromatography, while still adhering to regulatory concerns over product purity and safety. In this article, we present an up-to-date view of bioseparation, with emphasis on magnetic separation and its potential application in the field. Additionally, we discuss the economic and performance benefits of synthetic ligands, in the form of peptides and miniaturized antibody fragments, compared to full-length antibodies. We propose that adoption of synthetic affinity ligands coupled with magnetic adsorbents, will play an important role in enabling sustainable bioprocessing in the future.

Due to their homophilic and heterophilic binding properties, cell adhesion molecules (CAMs) such as integrin, cadherin and the immunoglobulin superfamily CAMs are of primary importance in cell-cell and cell-substrate interactions, signalling pathways and other crucial biological processes. We study the molecular structures and conformational dynamics of the two fibronectin type III (Fn-III) extracellular domains of the Aplysia californica CAM (apCAM) protein, by constructing and probing an atomically-detailed structural model based on apCAM's homology with other CAMs. The stability and dynamic properties of the Fn-III domains, individually and in tandem, are probed and analysed using all-atom explicit-solvent molecular dynamics (MD) simulations and normal mode analysis of their corresponding elastic network models. The refined structural model of the Fn-III tandem of apCAM reveals a specific pattern of amino acid interactions that controls the stability of the β-sheet rich structure and could affect apCAM's response to physical or chemical changes of its environment. It also exposes the important role of several specific charged residues in modulating the structural properties of the linker segment connecting the two Fn-III domains, as well as of the inter-domain interface.

Candida albicans is the lead fungal pathogen of nosocomial bloodstream infections worldwide and has mortality rates of 43%. Nanoparticles have been identified as a means to improve medical outcomes for Candida infections, enabling sample concentration, serving as contrast agents for in vivo imaging, and delivering therapeutics. However, little is known about how nanoparticles interact with the fungal cell wall. In this report we used laser scanning confocal microscopy to examine the interaction of fluorescent polystyrene nanoparticles of specific surface chemistry and diameter with C. albicans and mutant strains deficient in various C. albicans surface proteins. Carboxylate-functionalized nanoparticles adsorbed mainly to the hyphae of wild-type C. albicans. The dissociative binding constant of the nanoparticles was ∼150, ∼30 and ∼2.5 pM for 40, 100 nm and 200 nm diameter particles, respectively. A significant reduction in particle binding was observed with a Δals3 strain compared to wild-type strains, identifying the Als3 adhesin as the main mediator of this nanoparticle adhesion. In the absence of Als3, nanoparticles bound to germ tubes and yeast cells in a pattern resembling the localization of Als1, indicating Als1 also plays a role. Nanoparticle surface charge was shown to influence binding – positively charged amine-functionalized nanoparticles failed to bind to the hyphal cell wall. Binding of carboxylate-functionalized nanoparticles was observed in the presence of serum, though interactions were reduced. These observations show that Als3 and Als1 are important targets for nanoparticle-mediated diagnostics and therapeutics, and provide direction for optimal diameter and surface characteristics of nanoparticles that bind to the fungal cell wall. Science Foundation Ireland Whitaker International Program of the IEE

Multifunctional nanoparticles that actively target specific cells are promising tools for cancer diagnosis and therapy. In this article we review the synthesis and surface chemistry of Fe–Au nanorods and their characterization using microscopy. The diameter of the rods used in this study was selected to be 150–200 nm so that they did not enter the cells. The 80 nm-long Au tips of the nanorods were functionalized with heregulin (HRG), and the micron-long Fe portion was coated with a poly(ethylene glycol) monolayer to minimize non-specific interactions. Nanorods functionalized with HRG were found to preferentially bind to MCF7 cells that express high levels of the receptor tyrosine-protein kinase ErbB2/3. Magnetic tweezers measurements were used to characterize the kinetic properties of the bond between the HRG on the rods and ErbB2/3 on the surface of the cells. The strong magnetization of Fe–Au nanorods makes them excellent candidates for in-vitro and in-vivo imaging, and magnetic therapeutic applications targeting cancer cells in circulation. Science Foundation Ireland Erasmus Mundus Gulf Countries Postdoctoral Fellowship Marie Curie Intra-European Fellowship

Superparamagnetic microparticles are extensively used in the purification of biomolecules due to the speed and ease of magnetic separation. It is desirable that the microparticles used in biological affinity separations have both high surface area and high magnetic mobility to facilitate a high binding capacity of target biomolecules and their rapid removal from solution, respectively. Scaling laws for conventional spherical superparamagnetic microparticles are such that increasing the microparticle specific surface area results in a significant decrease in the magnetic mobility. More favorable combinations of these key parameters can be found if alternative microparticle morphologies are developed for use in affinity separations. Emulsion-templated self-assembly of iron oxide nanoparticles into microparticles using oil-in-water emulsions was carried out using a modified Couette shear mixer with separate inlet ports for the oil and aqueous phases, enabling high throughput microparticle synthesis. By controlling the dissolved nanoparticle concentration and nanoparticle surface activity at the droplet interfaces, the resulting microparticles were tuned to spherical, dimpled, or crumpled morphologies. The specific binding capacity and magnetic mobility of each type of microparticle were measured by a peroxidase-based colorimetric assay and by their magnetic field-induced motion in a viscous fluid, respectively. Superparamagnetic microparticles with dimpled and crumpled morphologies were found to have higher specific binding capacities compared to spherical microparticles, while maintaining high magnetic field velocities due to their high iron oxide content. Superparamagnetic microparticles with these novel morphologies would make excellent tools for affinity-based bioseparations where binding capacity and magnetic mobility are key factors.

In this article, we review lab on a chip (LOC) devices that have been developed for processing magnetically labelled biological analytes, e.g., proteins, nucleic acids, viruses and cells, based on micromagnetic structures and a time-varying magnetic field. We describe the methods that have been developed for fabricating micromagnetic arrays and the bioprocessing operations that have been demonstrated using superparamagnetic (SPM) beads, i.e., programmed transport, switching, separation of specific analytes, and pumping and mixing of fluids in microchannels. The primary advantage of micromagnet devices is that they make it possible to develop systems that control individual SPM beads, enabling high-efficiency separation and analysis. These devices do not require hydrodynamic control and lend themselves to parallel processing of large arrays of SPM beads with modest levels of power consumption. Micromagnet devices are well suited for bioanalytical applications that require high-resolution separation, e.g., detection of rare cell types such as circulating tumour cells, or biosensor applications that require multiple magnetic bioprocessing operations on a single chip.

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. European Commission Science Foundation Ireland National Institutes of Health

Aplysia californica neurons comprise a powerful model system for quantitative analysis of cellular and biophysical properties that are essential for neuronal development and function. The Aplysia cell adhesion molecule (apCAM), a member of the immunoglobulin superfamily of cell adhesion molecules, is present in the growth cone plasma membrane and involved in neurite growth, synapse formation, and synaptic plasticity. apCAM has been considered to be the Aplysia homolog of the vertebrate neural cell adhesion molecule (NCAM); however, whether apCAM exhibits similar binding properties and neuronal functions has not been fully established because of the lack of detailed binding data for the extracellular portion of apCAM. In this work, we used the atomic force microscope to perform single-molecule force spectroscopy of the extracellular region of apCAM and show for the first time (to our knowledge) that apCAM, like NCAM, is indeed a homophilic cell adhesion molecule. Furthermore, like NCAM, apCAM exhibits two distinct bonds in the trans configuration, although the kinetic and structural parameters of the apCAM bonds are quite different from those of NCAM. In summary, these single-molecule analyses further indicate that apCAM and NCAM are species homologs likely performing similar functions.

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.

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 a90% 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.

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.

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, omega, until they reached an immobilization frequency, omega(nu) where the beads stopped moving. Laminar flow along the edge of the array could be tuned to sweep the beads for which omega < omega(i) downstream at a velocity that increased with size while leaving beads for which omega > omega(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.

Nanoparticles (NPs) are now used in numerous technologies and serve as carriers for several new classes of therapeutics. Studies of the distribution of NPs in vivo demonstrate that they can be transported through biological barriers and are concentrated in specific tissues. Here, transport behavior, and final destination of polystyrene NPs are reported in primary mouse cortical neurons and SH-SY5Y cells, cultured in two-compartmental microfluidic devices. In both cell types, negative polystyrene NPs (PS(-)) smaller than 100 nm are taken up by the axons, undergo axonal retrograde transport, and accumulate in the somata. Examination of NP transport reveals different transport mechanisms depending on the cell type, particle charge, and particle internalization by the lysosomes. In cortical neurons, PS(-) inside lysosomes and 40 nm positive polystyrene NPs undergo slow axonal transport, whereas PS(-) outside lysosomes undergo fast axonal transport. Inhibition of dynein in cortical neurons decreases the transport velocity and cause a dose-dependent reduction in the number of accumulated PS(-), suggesting that the fast axonal transport is dynein mediated. These results show that the axonal retrograde transport of NPs depends on the endosomal pathway taken and establishes a means for screening nanoparticle-based therapeutics for diseases that involve neurons.

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.

A magnetophoretic fluorescence sensor (MFS) has been developed to rapidly detect dengue virus in serum at a sensitivity that was approximately three orders of magnitude higher than conventional solid phase immunoassays. UV inactivated type 2 dengue virus was first reacted with a mixture of superparamagnetic and fluorescent microparticles functionalised with an anti-type 2 dengue virus monoclonal antibody in 10% fetal calf serum. The magnetic particles were separated from the serum based on their magnetophoretic mobility, and dengue virus was detected by the co-localization of magnetic and fluorescent particles at a specific point in the flow chamber. The MFS was capable of detecting dengue-2 virus at 10 PFU ml(-1) with a reaction time of 15 min. The MFS demonstrated a high specificity in the presence of yellow fever virus, a closely related flavivirus, which also did not produce any detectable increase in background signal. The improved performance of this technique appears to result from the rapid kinetics of the microparticle reaction, improved signal-to-noise ratio resulting from magnetophoretic separation, and rapid fluorescent particle detection. These results suggest that the MFS may be useful in early stage diagnosis of dengue infections, as well as other diseases.

The guidance of axons to their proper targets is not only a crucial event in neurodevelopment, but also a potential therapeutic target for neural repair. Axon guidance is mediated by various chemo- and haptotactic cues, as well as the mechanical interactions between the cytoskeleton and the extracellular matrix (ECM). Axonal growth cones, dynamic ends of growing axons, convert external stimuli to biochemical signals, which, in turn, are translated into behavior, e.g., turning or retraction, via cytoskeleton–matrix linkages. Despite the inherent mechanical nature of the problem, the role of mechanics in axon guidance is poorly understood. Recent years has witnessed the application of a range of microtechnologies in neurobiology, from microfluidic circuits to single molecule force spectroscopy. In this mini-review, we describe microtechnologies geared towards dissecting the mechanical aspects of axon guidance, divided into three categories: controlling the growth cone microenvironment, stimulating growth cones with externally applied forces, and measuring forces exerted by the growth cones. A particular emphasis is given to those studies that combine multiple techniques, as dictated by the complexity of the problem.

The downstream processing of proteins remains the most significant cost in protein production, and is largely attributed to rigorous chromatographic purification protocols, where the stringency of purity for biopharmaceutical products sometimes exceeds 99%. With an ever burgeoning biotechnology market, there is a constant demand for alternative purification methodologies, to ameliorate the dependence on chromatography, while still adhering to regulatory concerns over product purity and safety. In this article, we present an up-to-date view of bioseparation, with emphasis on magnetic separation and its potential application in the field. Additionally, we discuss the economic and performance benefits of synthetic ligands, in the form of peptides and miniaturized antibody fragments, compared to full-length antibodies. We propose that adoption of synthetic affinity ligands coupled with magnetic adsorbents, will play an important role in enabling sustainable bioprocessing in the future.

A means for synthesizing paramagnetic nanoparticles composed of an Au–Fe alloy is described using pulsed laser deposition (PLD) of the alloy into a mesoporous alumina membrane template. Nanoparticles 46 ± 13 nm in diameter and composed of a 17% Fe alloy have been created by depositing a 35% Fe alloy into a template with 65 nm diameter pores. These paramagnetic nanoparticles had a saturation magnetization of 11. 5e mu g −1 at 2000 G, and their UV–visible extinction spectrum was dominated by strong absorption similar to that of Fe 3O4 nanoparticles. The surfaces of these nanoparticles were readily functionalized with a dense monolayer of DNA oligonucleotides that had a 5 � thiol group. The Au–Fe nanoparticles appear to be well suited for biotechnological applications and single molecule measurements as they can be synthesized in a specific size range, are strongly paramagnetic, and may be easily functionalized with biological macromolecules. (Some figures in this article are in colour only in the electronic version)

Highly porous films of titania composed of nanoparticle aggregates were synthesized via gas-to-particle conversion and particle-precipitated chemical vapor deposition. The films were annealed in air for 12 h at temperatures ranging from 400 to 1000 °C. Atomic force microscopy was used to determine the Young's modulus and hardness of both the as-synthesized and annealed films. The Young's modulus and hardness of the as-synthesized films were 4.0 ± 0.4 MPa and 0.026 ± 0.003 MPa, respectively. There was no significant change in either modulus or hardness upon annealing until the films were annealed at a temperature of 1000 °C. The Young's modulus and hardness of these films were 56 ± 6 MPa and 0.10 ± 0.01 MPa, respectively. Results from dynamic light scattering measurements of aggregate size and surface area measurements suggest that annealing at 1000 °C leads to increased networking between distinct nanometer-scale titania aggregates, which strengthens the film.

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.

A new method has been developed for measuring the binding affinity of phage displayed peptides and a target protein using magnetic particles. The specific interaction between the phage displayed peptides and the target protein was subject to a force generated by the magnetic particle. The binding affinity was obtained by analyzing the force–bond lifetime.

Using the atomic force microscope (AFM), surface-forces measurements are made in water between chemically modified AFM probes and model membranes created by Langmuir−Blodgett (LB) deposition. A series of four different lipid monolayers with varying headgroups and monolayer properties were transferred onto monolayers on mica for analysis. Using a hydrophilic probe, the bilayers are elastically deformed at low load and punctured at a repeatable, material-dependent breakthrough force. Using hydrophobic probes, the bilayers are punctured on contact, at loads near zero, in all cases. This effect is also manifest when imaging mixed LB monolayers, which show a large topography contrast at low load when using hydrophilic tips but none when using hydrophobic tips. These results provide evidence that the forces required to deform lipid bilayers are dramatically changed in the vicinity of nonpolar surfaces, which is central to the understanding of membrane fusion processes and the function of membrane-associated pro...

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.

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.

Growth cones, dynamic structures at axon tips, integrate chemical and physical stimuli and translate them into coordinated axon behaviour, e.g., elongation or turning. External force application to growth cones directs and enhances axon elongation in vitro; however, direct mechanical stimulation is rarely combined with chemotactic stimulation. We describe a microfluidic device that exposes isolated cortical axons to gradients of diffusing and substrate-bound molecules, and permits the simultaneous application of piconewton (pN) forces to multiple individual growth cones via magnetic tweezers. Axons treated with Y-27632, a RhoA kinase inhibitor, were successfully towed against Semaphorin 3A gradients, which repel untreated axons, with less than 12 pN acting on a small number of neural cell adhesion molecules. Treatment with Y-27632 or monastrol, a kinesin-5 inhibitor, promoted axon towing on substrates coated with chondroitin sulfate proteoglycans, potent axon repellents. Thus, modulating key molecular pathways that regulate contractile stress generation in axons counteracts the effects of repellent molecules and promotes tension-induced growth. The demonstration of parallel towing of axons towards inhibitory environments with minute forces suggests that mechanochemical stimulation may be a promising therapeutic approach for the repair of the damaged central nervous system, where regenerating axons face repellent factors over-expressed in the glial scar.

A technique has been developed to apply force to the antibody-antigen complex in a solid-phase immunoassay. Force was applied to the immunochemical complex by labeling the secondary antibody with a magnetically susceptible, micrometer-size particle and placing the assay chamber in a magnetic field of defined magnitude and orientation. The force was strong enough to displace weakly bound particles but was not strong enough to rupture the immunochemical complex. The number of particles bound to the surface after applying the differentiation force was related to the analyte concentration, thus an optical detection scheme was developed for counting the number of particles on the surface. The sensitivity of the force differentiation assay was demonstrated to be one to two orders of magnitude higher than conventional solid-phase immunoassay techniques for model protein, virus, and bacterial analytes, with 99% specificity. The enhanced sensitivity of this assay appears to result from lowering the assay background through the identification of weakly adhesive, nonspecific interactions. (C) 2000 Academic Press.

A processable polyimide having azo-chromophore functionalized with cyanosulfonyl group (PI-SOT) was prepared for nonlinear optics applications. To introduce a highly nonlinear optical active chromophore on the polyimide matrix, we first synthesized monomers 4-[N,N-bis(hydroxyethyl)amino]-4′-(2,5-dioxolane)azobenzene (AZO-OH2) and 4,4′-(hexafluoroisopropylidene)diphthalimide (6F-DI). After the polymerization reaction between AZO-OH2 and 6F-DI by using the Mitsunobu reaction, the dioxolane group of the resulting polymer PI-PRO was deprotected from the polymer PI-DEP having aldehyde group, and this polymer was further reacted with methanesulfonylacetonitrile to produce the final polymer PI-SOT. The molecular weight of PI-SOT was determined to be Mn=5650 (Mw/Mn=1.4). From DSC and TGA thermograms a glass transition temperature of ca. 186°C and an initial decomposition temperature of ca. 201°C were observed. PI-SOT dissolved in cyclohexanone could be easily processed into high optical quality films. The optical nonlinearity was determined to be d 31 =50 pm V −1 and d 33 ≅150 pm V −1 (nonresonant d33(∞) value: 47 pm V−1) by the second harmonic generation method in in-situ condition at a fundamental wavelength of 1064 nm and its value showed good thermal stability up to 150°C. By using the simple reflection measurement technique, a large electro-optic coefficient of r 33 =28 pm V −1 at 633 nm wavelength was obtained.

Interactions between molecules and at interfaces are vital to many scientific and technological fields. Techniques such as atomic force microscopy (AFM) have been used to measure forces and force gradients associated with interactions between individual molecules as well as interactions between interfaces. A recent alteration of the AFM configuration combined a tipless cantilever with an array of substrate supported tips. Herein, we present a further extension of AFM force measurement capabilities, by chemically patterning both the cantilever and the tip array. In a proof-of-concept experiment a gold-coated cantilever and tip array were patterning with alkylthiolate monolayers, and the interfacial forces were measured for the various combinations. This patterning allows many different interactions to be rapidly measured in situ, under identical conditions, thereby improving reliability and opening the door to combinatorial applications. Future developments are discussed including the means to measure hund...

The high cost and harsh processing conditions associated with microfabricated biosensors demand a new approach to receptor immobilization. We have grafted biotin labeled, 3400 molecular weight poly(ethylene glycol) (PEG) to silicon surfaces to produce a dense PEG monolayer with functionally active biotin. These surfaces have been activated with antibodies through the strong streptavidin-biotin interaction by simply incubating the surfaces with antibody-streptavidin conjugates. The stability of the biotinylated PEG monolayers produces a sensing element that can be regenerated by removal of the streptavidin conjugate and stored in a dry state for extended periods of time.

The end-to-end stretching of a duplex DNA oligonucleotide has been studied using potential of mean force (PMF) calculations based on molecular dynamics (MD) simulations and atomic force microscopy (AFM) experiments. Near quantitative agreement between the calculations and experiments was obtained for both the extension length and forces associated with strand separation. The PMF calculations show that the oligonucleotide extends without a significant energetic barrier from a length shorter than A-DNA to a length 2.4 times the contour length of B-DNA at which the barrier to strand separation is encountered. Calculated forces associated with the barrier are 0.09 +/- 0.03 nN, based on assumptions concerning tip and thermal-activated barrier crossing contributions to the forces. Direct AFM measurements show the oligonucleotide strands separating at 2.6 +/- 0.8 contour lengths with a force of 0.13 +/- 0.05 nN. Analysis of the energies from the MD simulations during extension reveals compensation between increases in the DNA-self energy and decreases in the DNA-solvent interaction energy, allowing for the barrierless extension of DNA beyond the canonical B form. The barrier to strand separation occurs when unfavorable DNA interstrand repulsion cannot be compensated for by favorable DNA-solvent interactions. The present combination of single molecule theoretical and experimental approaches produces a comprehensive picture of the free energy surface of biological macromolecular structural transitions.

Interaction forces and topography of mixed phospholipid–glycolipid bilayers were investigated by atomic force microscopy (AFM) in aqueous conditions with probes functionalized with self-assembled monolayers terminating in hydroxy groups. Short-range repulsive forces were measured between the hydroxy-terminated probe and the surface of the two-dimensional (2-D) solid-like domains of distearoyl-phosphatidylethanolamine (DSPE) and digalactosyldiglyceride (DGDG). The form and range of the short-range repulsive force indicated that repulsive hydration/steric forces dominate the interaction at separation distances of 0.3–1.0 nm after which the probe makes mechanical contact with the bilayers. At loads

Several developing technologies rely upon the activity of surface-bound biomolecules to control the functionality of an interface. The specificity of these biomolecules can be compromised by mechanical stresses present during their preparation or use. Moreover, many new biomechanical devices are also sensitive to mechanical stress. This paper is concerned with the direct assessment of the mechanical limits beyond which biomolecules are rendered inactive. These mechanical limits are evaluated by a combined approach involving an atomic force microscope (AFM), an optical microscope, and standard colorimetric techniques. The AFM is used to systematically stress micrometer-sized domains of biomolecule-laden surfaces; the results of which can be directly observed with an optical microscope following histochemical staining of the surface with biologically specific dyes. Using this method, we examined the limiting conditions of two benchmark systems, i.e., streptavidin and DNA. Because of the breadth of histochem...

Mixed distearoylphosphatidylethanolamine (DSPE) and dioleoylphosphatidylethanolamine (DOPE) monolayers and bilayers have been deposited on mica using the Langmuir-Blodgett (LB) technique, as a model system for biomembranes. Investigation with atomic force microscopy revealed phase-separation for both monolayers in air and bilayers in water in the form of microscopic DSPE domains embedded in a DOPE matrix. For the monolayers in air, the step height measured between the higher DSPE phase and the lower DOPE phase was larger than expected from the molecular lengths, and a significant contrast in adhesion and friction was observed despite identical lipid end groups. This unexpected behavior resulted primarily from a difference in the film mechanical properties, the DOPE phase being inelastically deformed by the probe. For the bilayers in water, similar trends were found in terms of height, adhesion, and friction, but an additional short-range repulsive hydration/steric force over the DSPE phase contributed to the observed differences.

Cell-cell adhesion is a fundamental requirement for all multicellular organisms. The calcium-independent cell adhesion molecules of the immunoglobulin superfamily (IgSF-CAMs) represent a major subgroup. They consist of immunoglobulin folds alone or in combination with other protein modules, often fibronectin type-III folds. More than 100 IgSF-CAMs have been identified in vertebrates and invertebrates. Most of the IgSF-CAMs are cell surface molecules that are membrane-anchored either by a single transmembrane segment or by a glycosylphosphatidylinositol (GPI) anchor. Some of the IgSF-CAMs also occur in soluble form, e.g., in the cerebrospinal fluid or in the vitreous fluid of the eye, due to naturally occurring cleavage of the GPI anchor or the membrane-proximal peptide segment. Some IgSF-CAMs, such as NCAM, occur in various forms that are generated by alternative splicing. This unit contains a series of protocols that have been used to study the function of IgSF-CAMs in vitro and in vivo. Curr. Protoc. Cell Biol. 61:9.5.1-9.5.85. © 2013 by John Wiley & Sons, Inc. Keywords: neural development; adhesive strength; cell-cell adhesion; primary cell culture; axon; protein-protein interaction

Magnetic tweezers (MTW) enable highly accurate forces to be transduced to molecules to study mechanotransduction at the molecular or cellular level. We review recent MTW studies in single molecule and cell biophysics that demonstrate the flexibility of this technique. We also discuss technical advances in the method on several fronts, i.e., from novel approaches for the measurement of torque to multiplexed biophysical assays. Finally, we describe multi-component nanorods with enhanced optical and magnetic properties and discuss their potential as future MTW probes. European Commission - European Regional Development Fund Higher Education Authority Science Foundation Ireland Marie Curie Intra-European Fellowship

The atomic force microscope (AFM) measures force and displacement with high sensitivity and submillisecond temporal resolution. By functionalizing the AFM probe with specific chemical groups or macromolecules, it is possible to characterize the chemical and physical properties of single molecules on the nanometer scale. In this paper we discuss the key issues that must be addressed when designing and characterizing a successful immobilization chemistry, and describe the chemistry we developed to covalently immobilize oligonucleotides in a specific orientation.

We present the design and calibration of a scanning force microscope which can be used to study friction, adhesion, and contact potential differences between the cantilever tip and surface. The microscope uses a modular design where the laser, cantilever/sample holder, reflecting mirror, and detector are mounted directly on an optical table. The laser, reflecting mirror, and detector are mounted on translation and rotation stages. With this design the components can be rearranged to calibrate the Z piezo motion as a function of applied voltage. Using the detector micrometers, the detector response (voltage‐to‐distance relationship) can be determined after each series of measurements. The cantilever/sample holder is constructed such that the components are material matched and thermally compensated from a common reference point. This design feature minimizes thermal drift of the instrument. The instrument can be used in a contact scanning mode where both normal and lateral deflections of the cantilever are...

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.

Molecular recognition forms the basis for assembly and regulation in living organisms. We have used the atomic force microscope (AFM) to study the interaction of a model receptor streptavidin with its ligand biotin under physiological conditions. Surfaces functionalized with biotin and streptavidin exhibited adhesive forces 3-8 times greater than the nonspecific interactions observed between blocked streptavidin and biotinylated surfaces. The magnitude and distribution of the observed adhesive forces suggest they result from individual streptavidin-biotin interactions. This technique provides a means to directly study molecular recognition interactions at the molecular level. Nature has developed the unique ability for molecular recognition through the use of multiple noncovalent bonds (Le., van der Waals, hydrogen, ionic, and hydrophobic interactions) which possess a high degree of spatial and orientational specificity. Molecular recognition plays a central role in cellular behavior1 and the immunological response,2 and has also become the basis for a wide range of bioanalytical technique^.^ Although the structure and binding properties of molecular recognition systems can be measured, the forces involved in intermolecular interactions remain largely unknown. Molecular recognition interactions have been characterized through observations of the behavior of cells on which ligands and receptors naturally occur or have been atta~hed.~?~ Although these studies have largely been qualitative, the application of micropipet techniques to the study of cellular interactions5 has provided the meansfor micromanipulation with a force sensitivity of N. The surface force apparatus has also recently been used to characterize quantitatively the surface forces between model molecular recognition systems.6 The control of surface properties and the very small forces and distances involved in intermolecular interactions continue to limit the characterization of discrete molecular recognition interactions. The AFM has several properties that make it an ideal tool for measuring intermolecular forces: theoretical force sensitivity on the order of N, displacement sensitivity of 0.01 nm, contact areas as small as 10 nm2, and ability to operate under physiological condition^.^ In fact, the measurement of interactions as small as asingle hydrogen bond has recently been reported.8 The bond energies for specific molecular interactions fall between those typical * To whom correspondence should be addressed.

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.

Variability in the coverage or usable lifetime of active molecules at the apex of an atomic force microscope (AFM) tip is a key limitation to biomolecular force measurements with AFM. Microfabricated tip arrays make it possible to measure molecular forces between large arrays of biological molecules with AFM. The forces are measured between a probeless microfabricated cantilever and a microfabricated array containing approximately 105 addressable probes with variable radii. We measure intermolecular forces between the model ligand–receptor pair streptavidin–biotin, to demonstrate that these tip arrays can circumvent these coverage and lifetime obstacles. Further development of these arrays promises to provide a means for measuring millions of different intermolecular interactions, paving the way for AFM to be realistically applied to screen combinatorial libraries.