Localized Photoactuation of Polymer Pens for Nanolithography.

Localized actuation is an important goal of nanotechnology broadly impacting applications such as programmable materials, soft robotics, and nanolithography. Despite significant recent advances, actuation with high temporal and spatial resolution remains challenging to achieve. Herein, we demonstrate strongly localized photoactuation of polymer pens made of polydimethylsiloxane (PDMS) and surface-functionalized short carbon nanotubes based on a fundamental understanding of the nanocomposite chemistry and device innovations in directing intense light with digital micromirrors to microscale domains. We show that local illumination can drive a small group of pens (3 × 3 over 170 µm × 170 µm) within a massively two-dimensional array to attain an out-of-plane motion by more than 7 µm for active molecular printing. The observed effect marks a striking three-order-of-magnitude improvement over the state of the art and suggests new opportunities for active actuation.

Photopolymerized Features via Beam Pen Lithography as a Novel Tool for the Generation of Large Area Protein Micropatterns.

A cantilever-free scanning probe lithography (CF-SPL)-based method for the rapid polymerization of nanoscale features on a surface via crosslinking and thiol-acrylate photoreactions is described, wherein the nanoscale position, height, and diameter of each feature can be finely and independently tuned. With precise spatiotemporal control over the illumination pattern, beam pen lithography (BPL) allows for the photo-crosslinking of polymers into ultrahigh resolution features over centimeter-scale areas using massively parallel >160 000 pen arrays of individually addressable pens that guide and focus light onto the surface with sub-diffraction resolution. The photoinduced crosslinking reaction of the ink material, which is composed of photoinitiator, diphenyl(2,4,6-trimethylbenzoyl) phosphine oxide, poly(ethylene glycol) diacrylate, and thiol-modified functional binding molecules (i.e., thiol-PEG-biotin or 16-mercaptohexanoic acid), proceeds to ≈80% conversion with UV exposure (72 mW cm-2 ) for short time periods (0.5 s). Such polymer patterns are further reacted with proteins (streptavidin and fibronectin) to yield protein arrays with feature arrangements at high resolution and densities controlled by local UV exposure. This platform, which combines polymer photochemistry and massive arrays of scanning probes, constitutes a new approach to making biomolecular microarrays in a high-throughput and high-yielding manner, opening new routes for biochip synthesis, bioscreening, and cell biology research.

Cyclization Improves Membrane Permeation by Antimicrobial Peptoids.

The peptidomimetic approach has emerged as a powerful tool for overcoming the inherent limitations of natural antimicrobial peptides, where the therapeutic potential can be improved by increasing the selectivity and bioavailability. Restraining the conformational flexibility of a molecule may reduce the entropy loss upon its binding to the membrane. Experimental findings demonstrate that the cyclization of linear antimicrobial peptoids increases their bactericidal activity against Staphylococcus aureus while maintaining high hemolytic concentrations. Surface X-ray scattering shows that macrocyclic peptoids intercalate into Langmuir monolayers of anionic lipids with greater efficacy than for their linear analogues. It is suggested that cyclization may increase peptoid activity by allowing the macrocycle to better penetrate the bacterial cell membrane.

Nanopores suggest a negligible influence of CpG methylation on nucleosome packaging and stability.

Nucleosomes are the fundamental repeating units of chromatin, and dynamic regulation of their positioning along DNA governs gene accessibility in eukaryotes. Although epigenetic factors have been shown to influence nucleosome structure and dynamics, the impact of DNA methylation on nucleosome packaging remains controversial. Further, all measurements to date have been carried out under zero-force conditions. In this paper, we present the first automated force measurements that probe the impact of CpG DNA methylation on nucleosome stability. In solid-state nanopore force spectroscopy, a nucleosomal DNA tail is captured into a pore and pulled on with a time-varying electrophoretic force until unraveling is detected. This is automatically repeated for hundreds of nucleosomes, yielding statistics of nucleosome lifetime vs electrophoretic force. The force geometry, which is similar to displacement forces exerted by DNA polymerases and helicases, reveals that nucleosome stability is sensitive to DNA sequence yet insensitive to CpG methylation. Our label-free method provides high-throughput data that favorably compares with other force spectroscopy experiments and is suitable for studying a variety of DNA-protein complexes.

Mechanism of membrane perturbation by the HIV-1 gp41 membrane-proximal external region and its modulation by cholesterol.

Membrane-activity of the glycoprotein 41 membrane-proximal external region (MPER) is required for HIV-1 membrane fusion. Consequently, its inhibition results in viral neutralization by the antibody 4E10. Previous studies suggested that MPER might act during fusion by locally perturbing the viral membrane, i.e., following a mechanism similar to that proposed for certain antimicrobial peptides. Here, we explore the molecular mechanism of how MPER permeates lipid monolayers containing cholesterol, a main component of the viral envelope, using grazing incidence X-ray diffraction and X-ray reflectivity. Our studies reveal that helical MPER forms lytic pores under conditions not affecting the lateral packing order of lipids. Moreover, we observe an increment of the surface area occupied by MPER helices in cholesterol-enriched membranes, which correlates with an enhancement of the 4E10 epitope accessibility in lipid vesicles. Thus, our data support the view that curvature generation by MPER hydrophobic insertion into the viral membrane is functionally more relevant than lipid packing disruption.

Fast, label-free force spectroscopy of histone-DNA interactions in individual nucleosomes using nanopores.

Herein we report a novel approach for fast, label-free probing of DNA-histone interactions in individual nucleosomes. We use solid-state nanopores to unravel individual DNA/histone complexes for the first time and find that the unraveling time depends on the applied electrophoretic force, and our results are in line with previous studies that employ optical tweezers. Our approach for studying nucleosomal interactions can greatly accelerate the understanding of fundamental mechanisms by which transcription, replication, and repair processes in a cell are modulated through DNA-histone interactions, as well as in diagnosis of diseases with abnormal patterns of DNA and histone modifications.

Cholesterol mediates membrane curvature during fusion events.

Biomembranes undergo extensive shape changes as they perform vital cellular functions. The mechanisms by which lipids and proteins control membrane curvature remain unclear. We use x-ray reflectivity, grazing incidence x-ray diffraction, and epifluorescence microscopy to study binding of HIV-1 glycoprotein gp41's membrane-bending domain to DPPC/cholesterol monolayers of various compositions at the air-liquid interface. The results offer a new insight into how membrane curvature could be regulated by cholesterol during fusion of the viral lipid envelope and the host cell membranes.

Membrane-proximal external HIV-1 gp41 motif adapted for destabilizing the highly rigid viral envelope.

Electron microscopy structural determinations suggest that the membrane-proximal external region (MPER) of glycoprotein 41 (gp41) may associate with the HIV-1 membrane interface. It is further proposed that MPER-induced disruption and/or deformation of the lipid bilayer ensue during viral fusion. However, it is predicted that the cholesterol content of this membrane (∼45 mol %) will act against MPER binding and restructuring activity, in agreement with alternative structural models proposing that the MPER constitutes a gp41 ectodomain component that does not insert into the viral membrane. Here, using MPER-based peptides, we test the hypothesis that cholesterol impedes the membrane association and destabilizing activities of this gp41 domain. To that end, partitioning and leakage assays carried out in lipid vesicles were combined with x-ray reflectivity and grazing-incidence diffraction studies of monolayers. CpreTM, a peptide combining the carboxyterminal MPER sequence with aminoterminal residues of the transmembrane domain, bound and destabilized effectively cholesterol-enriched membranes. Accordingly, virion incubation with this peptide inhibited cell infection potently but nonspecifically. Thus, CpreTM seems to mimic the envelope-perturbing function of the MPER domain and displays antiviral activity. As such, we infer that CpreTM bound to cholesterol-enriched membranes would represent a relevant target for anti-HIV-1 immunogen and inhibitor development.

A comparative study on the interactions of SMAP-29 with lipid monolayers.

This work investigates the discrimination of lipid monolayers by the ovine antimicrobial peptide SMAP-29 and compares it to that of the human LL-37 peptide. Fluid phospholipid monolayers were formed in a Langmuir trough and subsequently studied with the X-ray scattering techniques of X-ray reflectivity and grazing incidence X-ray diffraction. Any changes in the phospholipid structure after injection of peptide under the monolayer were considered to be due to interactions between the peptides and lipids. The data show that SMAP-29 discriminates against negatively charged phospholipids in a similar way to LL-37. However, it is even more interesting to note that despite a higher concentration of SMAP-29 near the monolayer, ensured by its greater charge as compared to LL-37, the amount of SMAP-29 needed to observe monolayer disruption was around three and a half times the number of molecules of LL-37 used to see similar changes with the same system. This result suggests that the structure, amino acid sequence or size of the peptide may well be as important as electrical charge and therefore gives many implications for the further study of antimicrobial peptides with regards to novel drug design and development.

A miniature mimic of host defense peptides with systemic antibacterial efficacy.

Oligomers of acylated lysines (OAKs) are synthetic mimics of host defense peptides (HDPs) with promising antimicrobial properties. Here we challenged the OAK concept for its ability to generate both systemically efficient and economically viable lead compounds for fighting multidrug-resistant bacteria. We describe the design and characterization of a miniature OAK composed of only 3 lysyls and 2 acyls (designated C(12(omega7))K-beta(12)) that preferentially targets gram-positive species by a bacteriostatic mode of action. To gain insight into the mechanism of action, we examined the interaction of OAK with various potential targets, including phospholipid bilayers, using surface plasmon resonance, and Langmuir monolayers, using insertion assays, epifluorescence microscopy, and grazing incidence X-ray diffraction, in a complementary manner. Collectively, the data support the notion that C(12(omega7))K-beta(12) damages the plasma-membrane architecture similarly to HDPs, that is, following a near-classic 2-step interaction including high-affinity electrostatic adhesion and a subsequent shallow insertion that was limited to the phospholipid head group region. Notably, preliminary acute toxicity and efficacy studies performed with mouse models of infection have consolidated the potential of OAK for treating bacterial infections, including systemic treatments of methicillin-resistant Staphylococcus aureus. Such simple yet robust chemicals might be useful for various antibacterial applications while circumventing potential adverse effects associated with cytolytic compounds.

Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides.

Antimicrobial peptides (AMPs) and their mimics are emerging as promising antibiotic agents. We present a library of "ampetoids" (antimicrobial peptoid oligomers) with helical structures and biomimetic sequences, several members of which have low-micromolar antimicrobial activities, similar to cationic AMPs like pexiganan. Broad-spectrum activity against six clinically relevant BSL2 pathogens is also shown. This comprehensive structure-activity relationship study, including circular dichroism spectroscopy, minimum inhibitory concentration assays, hemolysis and mammalian cell toxicity studies, and specular x-ray reflectivity measurements shows that the in vitro activities of ampetoids are strikingly similar to those of AMPs themselves, suggesting a strong mechanistic analogy. The ampetoids' antibacterial activity, coupled with their low cytotoxicity against mammalian cells, make them a promising class of antimicrobials for biomedical applications. Peptoids are biostable, with a protease-resistant N-substituted glycine backbone, and their sequences are highly tunable, because an extensive diversity of side chains can be incorporated via facile solid-phase synthesis. Our findings add to the growing evidence that nonnatural foldamers will emerge as an important class of therapeutics.

Cholesterol-phospholipid interactions: new insights from surface x-ray scattering data.

We report a structural study of cholesterol-DPPC (1,2-dipalmitoyl-sn-glycero-3-phophocholine) monolayers using x-ray reflectivity and grazing incidence x-ray diffraction. Reflectivity reveals that the vertical position of cholesterol relative to phospholipids strongly depends on its mole fraction (chi(CHOL)). Moreover, we find that at a broad range of chi(CHOL) cholesterol and DPPC form alloylike mixed domains of short-range order and the same stoichiometry as that of the film. Based on the data presented, we propose a new model of cholesterol-phospholipid organization in mixed monolayers.

Antibacterial properties and mode of action of a short acyl-lysyl oligomer.

We investigated the potency, selectivity, and mode of action of the oligo-acyl-lysine (OAK) NC(12)-2 beta(12), which was recently suggested to represent the shortest OAK sequence that retains nonhemolytic antibacterial properties. A growth inhibition assay against a panel of 48 bacterial strains confirmed that NC(12)-2 beta(12) exerted potent activity against gram-positive bacteria while exhibiting negligible hemolysis up to at least 100 times the MIC. Interestingly, NC(12)-2 beta(12) demonstrated a bacteriostatic mode of action, unlike previously described OAKs that were bactericidal and essentially active against gram-negative bacteria only. The results of various experiments with binding to model phospholipid membranes correlated well with those of the cytotoxicity experiments and provided a plausible explanation for the observed activity profile. Thus, surface plasmon resonance experiments performed with model bilayers revealed high binding affinity to a membrane composition that mimicked the plasma membrane of staphylococci (global affinity constant [K(app)], 3.7 x 10(6) M(-1)) and significantly lower affinities to mimics of Escherichia coli or red blood cell cytoplasmic membranes. Additional insertion isotherms and epifluorescence microscopy experiments performed with model Langmuir monolayers mimicking the outer leaflet of plasma membranes demonstrated the preferential insertion of NC(12)-2 beta(12) into highly anionic membranes. Finally, we provide mechanistic studies in support of the view that the bacteriostatic effect resulted from a relatively slow process of plasma membrane permeabilization involving discrete leakage of small solutes, such as intracellular ATP. Collectively, the data point to short OAKs as a potential source for new antibacterial compounds that can selectively affect the growth of gram-positive bacteria while circumventing potential adverse effects linked to lytic compounds.

Label-free optical detection of biomolecular translocation through nanopore arrays.

In recent years, nanopores have emerged as exceptionally promising single-molecule sensors due to their ability to detect biomolecules at subfemtomole levels in a label-free manner. Development of a high-throughput nanopore-based biosensor requires multiplexing of nanopore measurements. Electrical detection, however, poses a challenge, as each nanopore circuit must be electrically independent, which requires complex nanofluidics and embedded electrodes. Here, we present an optical method for simultaneous measurements of the ionic current across an array of solid-state nanopores, requiring no additional fabrication steps. Proof-of-principle experiments are conducted that show simultaneous optical detection and characterization of ssDNA and dsDNA using an array of pores. Through a comparison with electrical measurements, we show that optical measurements are capable of accessing equivalent transmembrane current information.