Lipid-based passivation in nanofluidics

Probing protein-DNA interactions and compaction in nanochannels

DNA confined to nanofluidic channels with a cross-section from tens to hundreds of nm wide and hundreds of microns long stretches in an equilibrium process free of flow or end tethering. Because DNA is free to move along the channel axis, its extension is exquisitely sensitive to DNA-DNA interactions and the DNA persistence length, as well as the contour length. We discuss how this sensitivity has been used to probe DNA-protein interactions at physiological concentrations of both DNA and proteins.

Lifting the Concentration Limit of Mass Photometry by PEG Nanopatterning

Mass photometry (MP) is a rapidly growing optical technique for label-free mass measurement of single biomolecules in solution. The underlying measurement principle provides numerous advantages over ensemble-based methods but has been limited to low analyte concentrations due to the need to uniquely and accurately quantify the binding of individual molecules to the measurement surface, which results in diffraction-limited spots. Here, we combine nanoparticle lithography with surface PEGylation to substantially lower surface binding, resulting in a 2 orders of magnitude improvement in the upper concentration limit associated with mass photometry. We demonstrate the facile tunability of degree of passivation, enabling measurements at increased analyte concentrations. These advances provide access to protein-protein interactions in the high nanomolar to low micromolar range, substantially expanding the application space of mass photometry.

Mammalian Cell Membrane Hybrid Polymersomes for mRNA Delivery

Cell membranes are structures essential to the cell function and adaptation. Recent studies have targeted cell membranes to identify their protective and interactive properties. Leveraging these attributes of cellular membranes and their application to vaccine delivery is gaining increasing prominence. This study aimed to fuse synthetic polymeric nanoparticles with cell membranes to develop cell membrane hybrid polymersomes (HyPSomes) for enhanced vaccine delivery. We designed a platform to hybridize cell membranes with methoxy-poly(ethylene glycol)-block-polylactic acid nanoparticles by using the properties of both components. The formed HyPSomes were optimized by using dynamic light scattering, transmission electron microscopy, and Förster resonance energy transfer, and their stability was confirmed. The synthesized HyPSomes replicated the antigenic surface of the source cells and possessed the stability and efficacy of synthetic nanoparticles. These HyPSomes demonstrated enhanced cellular uptake and translation efficiency and facilitated endosome escape. HyPSomes showed outstanding capabilities for the delivery of foreign mRNAs to antigen-presenting cells. HyPSomes may serve as vaccine delivery systems by bridging the gap between synthetic and natural systems. These systems could be used in other contexts, e.g., diagnostics and drug delivery.

Understanding the "Berg limit": the 65° contact angle as the universal adhesion threshold of biomatter

Surface phenomena in aqueous environments such as long-range hydrophobic attraction, macromolecular adhesion, and even biofouling are predominantly influenced by a fundamental parameter-the water contact angle. The minimal contact angle required for these and related phenomena to occur has been repeatedly reported to be around 65° and is commonly referred to as the "Berg limit." However, the universality of this specific threshold across diverse contexts has remained puzzling. In this perspective article, we aim to rationalize the reoccurrence of this enigmatic contact angle. We show that the relevant scenarios can be effectively conceptualized as three-phase problems involving the surface of interest, water, and a generic oil-like material that is representative of the nonpolar constituents within interacting entities. Our analysis reveals that attraction and adhesion emerge when substrates display an underwater oleophilic character, corresponding to a "hydrophobicity under oil", which occurs for contact angles above approximately 65°. This streamlined view provides valuable insights into macromolecular interactions and holds implications for technological applications.

Fluorescence Microscopy of Nanochannel-Confined DNA

Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level, and the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments, and analyze the data.

Probing physical properties of single amyloid fibrils using nanofluidic channels

Amyloid fibril formation is central to the pathology of many diseases, including neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Amyloid fibrils can also have functional and scaffolding roles, for example in bacterial biofilms, and have also been exploited as useful biomaterials. Despite being linear protein homopolymers, amyloid fibrils can exhibit significant structural and morphological polymorphism, making it relevant to study them on the single fibril level. We here introduce the concept of nanofluidic channel analysis to the study of single, fluorescently-labeled amyloid fibrils in solution, monitoring the extension and emission intensity of individual fibrils confined in nanochannels with a depth of 300 nm and a width that gradually increases from 300 to 3000 nm. The change in fibril extension with channel width permitted accurate determination of the persistence length of individual fibrils using Odijk's theory for strongly confined polymers. The technique was applied to amyloid fibrils prepared from the Alzheimer's related peptide amyloid-β(1-42) and the Parkinson's related protein α-synuclein, obtaining mean persistence lengths of 5.9 ± 4.5 μm and 3.0 ± 1.6 μm, respectively. The broad distributions of fibril persistence lengths indicate that amyloid fibril polymorphism can manifest in their physical properties. Interestingly, the α-synuclein fibrils had lower persistence lengths than the amyloid-β(1-42) fibrils, despite being thicker. Furthermore, there was no obvious within-sample correlation between the fluorescence emission intensity per unit length of the labelled fibrils and their persistence lengths, suggesting that stiffness may not be proportional to thickness. We foresee that the nanofluidics methodology established here will be a useful tool to study amyloid fibrils on the single fibril level to gain information on heterogeneity in their physical properties and interactions.

Conditions for the stable adsorption of lipid monolayers to solid surfaces

Lipid monolayers are ubiquitous in biological systems and have multiple roles in biotechnological applications, such as lipid coatings that enhance colloidal stability or prevent surface fouling. Despite the great technological importance of surface-adsorbed lipid monolayers, the connection between their formation and the chemical characteristics of the underlying surfaces has remained poorly understood. Here, we elucidate the conditions required for stable lipid monolayers nonspecifically adsorbed on solid surfaces in aqueous solutions and water/alcohol mixtures. We use a framework that combines the general thermodynamic principles of monolayer adsorption with fully atomistic molecular dynamics simulations. We find that, very universally, the chief descriptor of adsorption free energy is the wetting contact angle of the solvent on the surface. It turns out that monolayers can form and remain thermodynamically stable only on substrates with contact angles above the adsorption contact angle, θads. Our analysis establishes that θads falls into a narrow range of around 60∘-70∘ in aqueous media and is only weakly dependent on the surface chemistry. Moreover, to a good approximation, θads is roughly determined by the ratio between the surface tensions of hydrocarbons and the solvent. Adding small amounts of alcohol to the aqueous medium lowers θads and thereby facilitates monolayer formation on hydrophilic solid surfaces. At the same time, alcohol addition weakens the adsorption strength on hydrophobic surfaces and results in a slowdown of the adsorption kinetics, which can be useful for the preparation of defect-free monolayers.

Probing the coverage of nanoparticles by biomimetic membranes through nanoplasmonics

Although promising for biomedicine, the clinical translation of inorganic nanoparticles (NPs) is limited by low biocompatibility and stability in biological fluids. A common strategy to circumvent this drawback consists in disguising the active inorganic core with a lipid bilayer coating, reminiscent of the structure of the cell membrane to redefine the chemical and biological identity of NPs. While recent reports introduced membrane-coating procedures for NPs, a robust and accessible method to quantify the integrity of the bilayer coverage is not yet available. To fill this gap, we prepared SiO₂ nanoparticles (SiO₂NPs) with different membrane coverage degrees and monitored their interaction with AuNPs by combining microscopic, scattering, and optical techniques. The membrane-coating on SiO₂NPs induces spontaneous clustering of AuNPs, whose extent depends on the coating integrity. Remarkably, we discovered a linear correlation between the membrane coverage and a spectral descriptor for the AuNPs' plasmonic resonance, spanning a wide range of coating yields. These results provide a fast and cost-effective assay to monitor the compatibilization of NPs with biological environments, essential for bench tests and scale-up. In addition, we introduce a robust and scalable method to prepare SiO₂NPs/AuNPs hybrids through spontaneous self-assembly, with a high-fidelity structural control mediated by a lipid bilayer.

Polymer Brushes on Silica Nanostructures Prepared by Aminopropylsilatrane Click Chemistry: Superior Antifouling and Biofunctionality

In nanobiotechnology, the importance of controlling interactions between biological molecules and surfaces is paramount. In recent years, many devices based on nanostructured silicon materials have been presented, such as nanopores and nanochannels. However, there is still a clear lack of simple, reliable, and efficient protocols for preventing and controlling biomolecule adsorption in such structures. In this work, we show a simple method for passivation or selective biofunctionalization of silica, without the need for polymerization reactions or vapor-phase deposition. The surface is simply exposed stepwise to three different chemicals over the course of ∼1 h. First, the use of aminopropylsilatrane is used to create a monolayer of amines, yielding more uniform layers than conventional silanization protocols. Second, a cross-linker layer and click chemistry are used to make the surface reactive toward thiols. In the third step, thick and dense poly(ethylene glycol) brushes are prepared by a grafting-to approach. The modified surfaces are shown to be superior to existing options for silica modification, exhibiting ultralow fouling (a few ng/cm2) after exposure to crude serum. In addition, by including a fraction of biotinylated polymer end groups, the surface can be functionalized further. We show that avidin can be detected label-free from a serum solution with a selectivity (compared to nonspecific binding) of more than 98% without the need for a reference channel. Furthermore, we show that our method can passivate the interior of 150 nm × 100 nm nanochannels in silica, showing complete elimination of adsorption of a sticky fluorescent protein. Additionally, our method is shown to be compatible with modifications of solid-state nanopores in 20 nm thin silicon nitride membranes and reduces the noise in the ion current. We consider these findings highly important for the broad field of nanobiotechnology, and we believe that our method will be very useful for a great variety of surface-based sensors and analytical devices.

Single-Molecule Trapping and Measurement in a Nanostructured Lipid Bilayer System

The repulsive electrostatic force between a biomolecule and a like-charged surface can be geometrically tailored to create spatial traps for charged molecules in solution. Using a parallel-plate system composed of silicon dioxide surfaces, we recently demonstrated single-molecule trapping and high precision molecular charge measurements in a nanostructured free energy landscape. Here we show that surfaces coated with charged lipid bilayers provide a system with tunable surface properties for molecular electrometry experiments. Working with molecular species whose effective charge and geometry are well-defined, we demonstrate the ability to quantitatively probe the electrical charge density of a supported lipid bilayer. Our findings indicate that the fraction of charged lipids in nanoslit lipid bilayers can be significantly different from that in the precursor lipid mixtures used to generate them. We also explore the temporal stability of bilayer properties in nanofluidic systems. Beyond their relevance in molecular measurement, such experimental systems offer the opportunity to examine lipid bilayer formation and wetting dynamics on nanostructured surfaces.

Ligand functionalization of titanium nanopattern enables the analysis of cell-ligand interactions by super-resolution microscopy

The spatiotemporal aspects of early signaling events during interactions between cells and their environment dictate multiple downstream outcomes. While advances in nanopatterning techniques have allowed the isolation of these signaling events, a major limitation of conventional nanopatterning methods is its dependence on gold (Au) or related materials that plasmonically quench fluorescence and, thus, are incompatible with super-resolution fluorescence microscopy. Here we describe a novel method that integrates nanopatterning with single-molecule resolution fluorescence imaging, thus enabling mechanistic dissection of molecular-scale signaling events in conjunction with nanoscale geometry manipulation. Our method exploits nanofabricated titanium (Ti) whose oxide (TiO₂) is a dielectric material with no plasmonic effects. We describe the surface chemistry for decorating specific ligands such as cyclo-RGD (arginine, glycine and aspartate: a ligand for fibronectin-binding integrins) on TiO₂ nanoline and nanodot substrates, and demonstrate the ability to perform dual-color super-resolution imaging on these patterns. Ti nanofabrication is similar to other metallic materials like Au, while the functionalization of TiO₂ is relatively fast, safe, economical, easy to set up with commonly available reagents, and robust against environmental parameters such as humidity. Fabrication of nanopatterns takes ~2-3 d, preparation for functionalization ~1.5-2 d, and functionalization 3 h, after which cell culture and imaging experiments can be performed. We suggest that this method may facilitate the interrogation of nanoscale geometry and force at single-molecule resolution, and should find ready applications in early detection and interpretation of physiochemical signaling events at the cell membrane in the fields of cell biology, immunology, regenerative medicine, and related fields.

Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles

Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes.

Nanofluidic scattering microscopy enables label-free, quantitative measurements of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles freely diffusing inside a nanofluidic channel.

A biomimetic anti-biofouling coating in nanofluidic channels

A biomimetic coating using a tailored phosphorylcholine-containing monomer enables to suppress non-specific protein adsorption in nanofluidic channels, paving a way to explore a new anti-biofouling strategy using monomer-based materials for nanodevices.

Cell membrane coating integrity affects the internalization mechanism of biomimetic nanoparticles

Cell membrane coated nanoparticles (NPs) have recently been recognized as attractive nanomedical tools because of their unique properties such as immune escape, long blood circulation time, specific molecular recognition and cell targeting. However, the integrity of the cell membrane coating on NPs, a key metrics related to the quality of these biomimetic-systems and their resulting biomedical function, has remained largely unexplored. Here, we report a fluorescence quenching assay to probe the integrity of cell membrane coating. In contradiction to the common assumption of perfect coating, we uncover that up to 90% of the biomimetic NPs are only partially coated. Using in vitro homologous targeting studies, we demonstrate that partially coated NPs could still be internalized by the target cells. By combining molecular simulations with experimental analysis, we further identify an endocytic entry mechanism for these NPs. We unravel that NPs with a high coating degree (≥50%) enter the cells individually, whereas the NPs with a low coating degree (<50%) need to aggregate together before internalization. This quantitative method and the fundamental understanding of how cell membrane coated NPs enter the cells will enhance the rational designing of biomimetic nanosystems and pave the way for more effective cancer nanomedicine.

Lipid bilayer coatings for rapid enzyme-linked immunosorbent assay

The enzyme-linked immunosorbent assay (ELISA) is a widely used method for protein detection and relies on the specific capture of target proteins while minimizing the nonspecific binding of other interfering proteins and biomolecules. To prevent nonspecific binding events, blocking agents such as bovine serum albumin (BSA) protein, mixtures of proteins in media such as milk or serum, and/or surfactants are typically added to ELISA plates after probe attachment and before analyte capture. Herein, we developed a streamlined ELISA strategy in which readily prepared lipid nanoparticles are utilized as the blocking agent and are added together with the probe molecule to the ELISA plate, resulting in fewer processing steps, quicker protocol time, and superior detection performance compared to conventional BSA blocking. These measurement capabilities were established for coronavirus disease-2019 (COVID-19) antibody detection in saline and human serum conditions and are broadly applicable for developing rapid ELISA diagnostics.

A High-Throughput Nanofluidic Device for Exosome Nanoporation to Develop Cargo Delivery Vehicles

Efficient loading of various exogenous cargos into exosomes while not affecting their integrity and functionalities remains a major challenge. Here, a nanofluidic device named "exosome nanoporator (ENP)" is presented for high-throughput loading of various cargos into exosomes. By transporting exosomes through nanochannels with height comparable to their dimension, exosome membranes are permeabilized by mechanical compression and fluid shear, allowing the influx of cargo molecules into the exosomes from the surrounding solution while maintaining exosome integrity. The ENP consisting of an array of 30 000 nanochannels demonstrates a high sample throughput, and the working mechanism of the device is elucidated through experimental and numerical study. Further, the exosomes treated by the ENP can deliver their drug cargos to human non-small cell lung cancer cells and induce cell death, indicating the potential opportunities of the device for developing new exosome-based delivery vehicles for medical and biological applications.

C-terminal truncation of α-synuclein alters DNA structure from extension to compaction

Parkinson's disease (PD) is linked to aggregation of the protein α-synuclein (aS) into amyloid fibers. aS is proposed to regulate synaptic activity and may also play a role in gene regulation via interaction with DNA in the cell nucleus. Here, we address the role of the negatively-charged C-terminus in the interaction between aS and DNA using single-molecule techniques. Using nanofluidic channels, we demonstrate that truncation of the C-terminus of aS induces differential effects on DNA depending on the extent of the truncation. The DNA extension increases for full-length aS and the (1-119)aS variant, but decreases about 25% upon binding to the (1-97)aS variant. Atomic force microscopy imaging showed full protein coverage of the DNA at high aS concentration. The characterization of biophysical properties of DNA when in complex with aS variants may provide important insights into the role of such interactions in PD, especially since C-terminal aS truncations have been found in clinical samples from PD patients.

The HIV-1 nucleocapsid chaperone protein forms locally compacted globules on long double-stranded DNA

The nucleocapsid (NC) protein plays key roles in Human Immunodeficiency Virus 1 (HIV-1) replication, notably by condensing and protecting the viral RNA genome and by chaperoning its reverse transcription into double-stranded DNA (dsDNA). Recent findings suggest that integration of viral dsDNA into the host genome, and hence productive infection, is linked to a small subpopulation of viral complexes where reverse transcription was completed within the intact capsid. Therefore, the synthesized dsDNA has to be tightly compacted, most likely by NC, to prevent breaking of the capsid in these complexes. To investigate NC’s ability to compact viral dsDNA, we here characterize the compaction of single dsDNA molecules under unsaturated NC binding conditions using nanofluidic channels. Compaction is shown to result from accumulation of NC at one or few compaction sites, which leads to small dsDNA condensates. NC preferentially initiates compaction at flexible regions along the dsDNA, such as AT-rich regions and DNA ends. Upon further NC binding, these condensates develop into a globular state containing the whole dsDNA molecule. These findings support NC’s role in viral dsDNA compaction within the mature HIV-1 capsid and suggest a possible scenario for the gradual dsDNA decondensation upon capsid uncoating and NC loss.

Lipid-Bicelle-Coated Microfluidics for Intracellular Delivery with Reduced Fouling

Innovative technologies for intracellular delivery are ushering in a new era for gene editing, enabling the utilization of a patient's own cells for stem cell and immunotherapies. In particular, cell-squeezing platforms provide unconventional forms of intracellular delivery, deforming cells through microfluidic constrictions to generate transient pores and to enable effective diffusion of biomolecular cargo. While these devices are promising gene-editing platforms, they require frequent maintenance due to the accumulation of cellular debris, limiting their potential for reaching the throughputs necessary for scalable cellular therapies. As these cell-squeezing technologies are improved, there is a need to develop next-generation platforms with higher throughput and longer lifespan, importantly, avoiding the buildup of cell debris and thus channel clogging. Here, we report a versatile strategy to coat the channels of microfluidic devices with lipid bilayers based on noncovalent lipid bicelle technology, which led to substantial improvements in reducing cell adhesion and protein adsorption. The antifouling properties of the lipid bilayer coating were evaluated, including membrane uniformity, passivation against nonspecific protein adsorption, and inhibition of cell attachment against multiple cell types. This surface functionalization approach was applied to coat constricted microfluidic channels for the intracellular delivery of fluorescently labeled dextran and plasmid DNA, demonstrating significant reductions in the accumulation of cell debris. Taken together, our work demonstrates that lipid bicelles are a useful tool to fabricate antifouling lipid bilayer coatings in cell-squeezing devices, resulting in reduced nonspecific fouling and cell clogging to improve performance.

Real-time compaction of nanoconfined DNA by an intrinsically disordered macromolecular counterion

We demonstrate how a recently developed nanofluidic device can be used to study protein-induced compaction of genome-length DNA freely suspended in solution. The protein we use in this study is the hepatitis C virus core protein (HCVcp), which is a positively charged, intrinsically disordered protein. Using nanofluidic devices in combination with fluorescence microscopy, we observe that protein-induced compaction preferentially begins at the ends of linear DNA. This observation would be difficult to make with many other single-molecule techniques, which generally require the DNA ends to be anchored to a substrate. We also demonstrate that this protein-induced compaction is reversible and can be dynamically modulated by exposing the confined DNA molecules to solutions containing either HCVcp (to promote compaction) or Proteinase K (to disassemble the compact nucleo-protein complex). Although the natural binding partner for HCVcp is genomic viral RNA, the general biophysical principles governing protein-induced compaction of DNA are likely relevant for a broad range of nucleic acid-binding proteins and their targets.

Sensing Ability and Formation Criterion of Fluid Supported Lipid Bilayer Coated Graphene Field-Effect Transistors

Supported lipid bilayers (SLBs) have been widely used to provide native environments for membrane protein studies. In this study, we utilized graphene field-effect transistors (GFETs) coated with a fluid SLB to perform label-free detection of membrane-associated ligand-receptor interactions in their native lipid bilayer environment. It is known that the analyte-binding event needs to occur within the Debye length for it to be significantly sensed by an FET sensor. However, the thickness of a lipid bilayer is around 4-5-nm-thick, which is larger than the Debye length of a solution with physiologically relevant ionic strength. There is thus a question of whether an FET sensor can detect the binding event above the bilayer. In this study, we show how the existence of an SLB can influence the effective detection distance and the formation criterion of a fluid and continuous SLB on a graphene surface. We discovered that the water intercalation between the graphene and the underlying silica substrate hinders the SLB formation but is required for the stable electrical recording by a GFET. To verify the existence of a fluid SLB on graphene, which was previously complicated by the graphene fluorescence quenching effect, we developed a modified fluorescence recovery after photobleaching method. In addition, our results showed that SLB coated GFETs can quantitatively detect ligand binding onto the receptors embedded in the SLBs. The comparison of our experimental data with a theoretical model shows that the contribution of the SLB acyl chain hydrophobic region to the screening effect can be negligible and, therefore, that the effective detection region can extend beyond the SLB.

Annealing of ssDNA and compaction of dsDNA by the HIV-1 nucleocapsid and Gag proteins visualized using nanofluidic channels

The nucleocapsid protein NC is a crucial component in the human immunodeficiency virus type 1 life cycle. It functions both in its processed mature form and as part of the polyprotein Gag that plays a key role in the formation of new viruses. NC can protect nucleic acids (NAs) from degradation by compacting them to a dense coil. Moreover, through its NA chaperone activity, NC can also promote the most stable conformation of NAs. Here, we explore the balance between these activities for NC and Gag by confining DNA–protein complexes in nanochannels. The chaperone activity is visualized as concatemerization and circularization of long DNA via annealing of short single-stranded DNA overhangs. The first ten amino acids of NC are important for the chaperone activity that is almost completely absent for Gag. Gag condenses DNA more efficiently than mature NC, suggesting that additional residues of Gag are involved. Importantly, this is the first single DNA molecule study of full-length Gag and we reveal important differences to the truncated Δ-p6 Gag that has been used before. In addition, the study also highlights how nanochannels can be used to study reactions on ends of long single DNA molecules, which is not trivial with competing single DNA molecule techniques.

Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis

Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.

A nanofluidic device for real-time visualization of DNA-protein interactions on the single DNA molecule level

Single DNA molecule techniques have revolutionized our understanding of DNA-protein interactions. Traditional techniques for such studies have the major drawback that the DNA molecule studied is attached to a bead or a surface. Stretching of DNA molecules in nanofluidic channels has enabled single-molecule studies of DNA-protein interactions without the need of tethering the molecule to a foreign entity. This in turn allows for studying reactions along the whole extension of the molecule, including the free DNA ends. However, existing studies either rely on measurements where all components are mixed before introduction into the nanochannels or where passive diffusion brings the reagents to the confined DNA molecule. We here present a new generation of nanofluidic devices, where active exchange of the local environment within the nanofluidic channel is possible, while keeping the DNA molecule stretched and in confinement. To demonstrate the functionality of this novel device we added different analytes, such as SDS, spermidine and DNase I, to YOYO-1 stained DNA and studied the response in real time. We also performed a FRET-based reaction, where two different analytes were added sequentially to the same DNA molecule. We believe that this design will enable in situ mapping of complex biochemical processes, involving multiple proteins and cofactors, on single DNA molecules as well as other biomacromolecules.

Alpha-Synuclein Modulates the Physical Properties of DNA

Fundamental research on Parkinson's disease (PD) most often focuses on the ability of α-synuclein (aS) to form oligomers and amyloids, and how such species promote brain cell death. However, there are indications that aS also plays a gene-regulatory role in the cell nucleus. Here, the interaction between monomeric aS and DNA in vitro has been investigated with single-molecule techniques. Using a nanofluidic channel system, it was discovered that aS binds to DNA and by studying the DNA-protein complexes at different confinements we determined that aS binding increases the persistence length of DNA from 70 to 90 nm at high coverage. By atomic force microscopy it was revealed that at low protein-to-DNA ratio, the aS binding occurs as small protein clusters scattered along the DNA; at high protein-to-DNA ratio, the DNA is fully covered by protein. As DNA-aS interactions may play roles in PD, it is of importance to characterize biophysical properties of such complexes in detail.

PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction

Gram-positive bacteria deploy type IV secretion systems (T4SSs) to facilitate horizontal gene transfer. The T4SSs of Gram-positive bacteria rely on surface adhesins as opposed to conjugative pili to facilitate mating. Enterococcus faecalis PrgB is a surface adhesin that promotes mating pair formation and robust biofilm development in an extracellular DNA (eDNA) dependent manner. Here, we report the structure of the adhesin domain of PrgB. The adhesin domain binds and compacts DNA in vitro. In vivo PrgB deleted of its adhesin domain does not support cellular aggregation, biofilm development and conjugative DNA transfer. PrgB also binds lipoteichoic acid (LTA), which competes with DNA binding. We propose that PrgB binding and compaction of eDNA facilitates cell aggregation and plays an important role in establishment of early biofilms in mono- or polyspecies settings. Within these biofilms, PrgB mediates formation and stabilization of direct cell-cell contacts through alternative binding of cell-bound LTA, which in turn promotes establishment of productive mating junctions and efficient intra- or inter-species T4SS-mediated gene transfer.

Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement

We report that long double-stranded DNA confined to quasi-1D nanochannels undergoes superdiffusive motion under the action of the enzyme T4 DNA ligase in the presence of necessary co-factors. Inside the confined environment of the nanochannel, double-stranded DNA molecules stretch out due to self-avoiding interactions. In absence of a catalytically active enzyme, we see classical diffusion of the center of mass. However, cooperative interactions of proteins with the DNA can lead to directed motion of DNA molecules inside the nanochannel. Here we show directed motion in this configuration for three different proteins (T4 DNA ligase, MutS, E. coli DNA ligase) in the presence of their energetic co-factors (ATP, NAD⁺).

Non-lithographic nanofluidic channels with precisely controlled circular cross sections

Nanofluidic channels have received growing interest due to their potential for applications in the manipulation of nanometric objects, such as DNA, proteins, viruses, exosomes, and nanoparticles. Although significant advances in nanolithography-based fabrication techniques over the past few decades have allowed us to explore novel nanofluidic transport phenomena and unique applications, the development of new technologies enabling the low-cost preparation of nanochannels with controllable and reproducible shapes and dimensions is still lacking. Thus, we herein report the application of a nanofiber printed using a near-field electrospinning method as a sacrificial mold for the preparation of polydimethylsiloxane nanochannels with circular cross sections. Control of the size and shape of these nanochannels allowed the preparation of nanochannels with channel widths ranging from 70-368 nm and height-to-width ratios of 0.19-1.00. Capillary filling tests confirmed the excellent uniformity and reproducibility of the nanochannels. These results therefore are expected to inspire novel nanofluidic studies due to the simple and low-cost nature of this fabrication process, which allows precise control of the shape and dimensions of the circular cross section.

Nanoplasmonic sensors for biointerfacial science

In recent years, nanoplasmonic sensors have become widely used for the label-free detection of biomolecules across medical, biotechnology, and environmental science applications. To date, many nanoplasmonic sensing strategies have been developed with outstanding measurement capabilities, enabling detection down to the single-molecule level. One of the most promising directions has been surface-based nanoplasmonic sensors, and the potential of such technologies is still emerging. Going beyond detection, surface-based nanoplasmonic sensors open the door to enhanced, quantitative measurement capabilities across the biointerfacial sciences by taking advantage of high surface sensitivity that pairs well with the size of medically important biomacromolecules and biological particulates such as viruses and exosomes. The goal of this review is to introduce the latest advances in nanoplasmonic sensors for the biointerfacial sciences, including ongoing development of nanoparticle and nanohole arrays for exploring different classes of biomacromolecules interacting at solid-liquid interfaces. The measurement principles for nanoplasmonic sensors based on utilizing the localized surface plasmon resonance (LSPR) and extraordinary optical transmission (EOT) phenomena are first introduced. The following sections are then categorized around different themes within the biointerfacial sciences, specifically protein binding and conformational changes, lipid membrane fabrication, membrane-protein interactions, exosome and virus detection and analysis, and probing nucleic acid conformations and binding interactions. Across these themes, we discuss the growing trend to utilize nanoplasmonic sensors for advanced measurement capabilities, including positional sensing, biomacromolecular conformation analysis, and real-time kinetic monitoring of complex biological interactions. Altogether, these advances highlight the rich potential of nanoplasmonic sensors and the future growth prospects of the community as a whole. With ongoing development of commercial nanoplasmonic sensors and analytical models to interpret corresponding measurement data in the context of biologically relevant interactions, there is significant opportunity to utilize nanoplasmonic sensing strategies for not only fundamental biointerfacial science, but also translational science applications related to clinical medicine and pharmaceutical drug development among countless possibilities.

Hairpins in the conformations of a confined polymer

If a semiflexible polymer confined to a narrow channel bends around by 180°, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here, we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte-Carlo simulations of confined discrete wormlike chains. We develop a simple model that qualitatively explains the form of the extension distribution. The model shows that the tail of the distribution at short extensions is determined by conformations with one hairpin.

Concentrating and labeling genomic DNA in a nanofluidic array

Nucleotide incorporation by DNA polymerase forms the basis of DNA sequencing-by-synthesis. In current platforms, either the single-stranded DNA or the enzyme is immobilized on a solid surface to locate the incorporation of individual nucleotides in space and/or time. Solid-phase reactions may, however, hinder the polymerase activity. We demonstrate a device and a protocol for the enzymatic labeling of genomic DNA arranged in a dense array of single molecules without attaching the enzyme or the DNA to a surface. DNA molecules accumulate in a dense array of pits embedded within a nanoslit due to entropic trapping. We then perform ϕ29 polymerase extension from single-strand nicks created on the trapped molecules to incorporate fluorescent nucleotides into the DNA. The array of entropic traps can be loaded with λ-DNA molecules to more than 90% of capacity at a flow rate of 10 pL min^-1. The final concentration can reach up to 100 μg mL^-1, and the DNA is eluted from the array by increasing the flow rate. The device may be an important preparative module for carrying out enzymatic processing on DNA extracted from single-cells in a microfluidic chip.

Nanofluidics: A New Arena for Materials Science

A significant growth of research in nanofluidics is achieved over the past decade, but the field is still facing considerable challenges toward the transition from the current physics-centered stage to the next application-oriented stage. Many of these challenges are associated with materials science, so the field of nanofluidics offers great opportunities for materials scientists to exploit. In addition, the use of unusual effects and ultrasmall confined spaces of well-defined nanofluidic environments would offer new mechanisms and technologies to manipulate nanoscale objects as well as to synthesize novel nanomaterials in the liquid phase. Therefore, nanofluidics will be a new arena for materials science. In the past few years, burgeoning progress has been made toward this trend, as overviewed in this article, including materials and methods for fabricating nanofluidic devices, nanofluidics with functionalized surfaces and functional material components, as well as nanofluidics for manipulating nanoscale materials and fabricating new nanomaterials. Many critical challenges as well as fantastic opportunities in this arena lie ahead. Some of those, which are of particular interest, are also discussed.

Fluorescence Microscopy of Nanochannel-Confined DNA

Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.

Optimizing the Performance of Supported Lipid Bilayers as Cell Culture Platforms Based on Extracellular Matrix Functionalization

Strategies to fabricate biofunctionalized surfaces are essential for many biotechnological applications. Zwitterionic lipid bilayer coatings doped with lipids with chemically selective headgroups provide a robust platform for immobilization of biomolecules in an antifouling, protein resistant background. Herein, we assess the biological activity of two important components of the extracellular matrix (ECM), collagen type I (Col I) and fibronectin (FN), which are covalently attached to a supported lipid bilayer (SLB), and compare their activity with the same proteins, nonspecifically adsorbed onto a SiO₂ surface. The characterization of protein coatings by quartz crystal microbalance with dissipation revealed that Col I and FN attached to SLB are less dense and have higher structural flexibility than when adsorbed onto SiO₂. Cell adhesion, proliferation, and function, as well as Col I-FN interactions, were more efficient on the ECM-functionalized SLB, making it a promising platform for cell-based diagnostics, tissue engineering, medical implants, and biosensor development.

A nano flow cytometer for single lipid vesicle analysis

We present a nanofluidic device for fluorescence-based detection and characterization of small lipid vesicles on a single particle basis. The device works like a nano flow cytometer where individual vesicles are visualized by fluorescence microscopy while passing through parallel nanochannels in a pressure-driven flow. An experiment requires less than 20 μl sample volume to quantify both the vesicle content and the fluorescence signals emitted by individual vesicles. We show that the device can be used to accurately count the number of fluorescent synthetic lipid vesicles down to a vesicle concentration of 170 fM. We also show that the size-distribution of the vesicles can be resolved from their fluorescence intensity distribution after calibration. We demonstrate the applicability of the assay in two different examples. In the first, we use the nanofluidic device to determine the particle concentration in a sample containing cell-derived extracellular vesicles labelled with a lipophilic dye. In the second, we demonstrate that dual-color detection can be used to probe peptide binding to synthetic lipid vesicles; we identify a positive membrane-curvature sensing behavior of an arginine enriched version of the Antennapedia homeodomain peptide penetratin. Altogether, these results illustrate the potential of this nanofluidic-based methodology for characterization and quantification of small biological vesicles and their interactors without ensemble averaging. The device is therefore likely to find use as a quantitative analytical tool in a variety of fields ranging from diagnostics to fundamental biology research. Moreover, our results have potential to facilitate further development of automated lab-on-a-chip devices for vesicle analysis.

Exploring DNA–protein interactions on the single DNA molecule level using nanofluidic tools

This review highlights the use of nanofluidic channels for studying DNA–protein interactions on the single DNA molecule level.

Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels

RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.

Platelet Immobilization on Supported Phospholipid Bilayers for Single Platelet Studies

The worldwide cardiovascular disease (CVD) epidemic is of grave concern. A major role in the etiology of CVDs is played by the platelets (thrombocytes). Platelets are anuclear cell fragments circulating in the blood. Their primary function is to catalyze clot formation, limiting traumatic blood loss in the case of injury. The same process leads to thrombosis in the case of CVDs, which are commonly managed with antiplatelet therapy. Platelets also have other, nonhemostatic functions in wound healing, inflammation, and tissue regeneration. They play a role in the early stages of atherosclerosis and the spread of cancer through metastases. Much remains to be learned about the regulation of these diverse platelet functions under physiological and pathological conditions. Breakthroughs in this regard are expected to come from single platelet studies and systems approaches. The immobilization of platelets at surfaces is advantageous for developing such approaches, but platelets are activated when they come in contact with foreign surfaces. In this work, we develop and validate a protocol for immobilizing platelets on supported lipid bilayers without activation due to immobilization. Our protocol can therefore be used for studying platelets with a wide variety of surface-sensitive techniques.

Nanometric Gap Structure with a Fluid Lipid Bilayer for the Selective Transport and Detection of Biological Molecules

The biological membrane is a natural biosensing platform that can detect specific molecules with extremely high sensitivity. We developed a biosensing methodology by combining a model biological membrane and a nanometer-sized gap structure on a glass substrate. The model membrane comprised lithographically patterned polymeric and fluid lipid bilayers. The polymeric bilayer was bonded to a poly(dimethylsiloxane) (PDMS) sheet by using an adhesion layer with a defined thickness (lipid vesicles). Extruded lipid vesicles having a biotin moiety on the surface were used as the adhesion layer in conjunction with the biotin-streptavidin linkage. A gap structure was formed between the fluid bilayer and PDMS (nanogap junction). The thickness of the gap structure was several tens of nanometers, as determined by the thickness of the adhesion layer. The nanogap junction acted as a sensitive biosensing platform. From a mixture of proteins (cholera toxin and albumin), the target protein (cholera toxin) was selectively transported into the gap by the specific binding to a glycolipid (GM1) in the fluid bilayer and lateral diffusion. The target protein molecules were then detected with an elevated signal-to-noise ratio due to the reduced background noise in the nanometric gap. The combination of selective transport and reduced background noise drastically enhanced the sensitivity toward the target protein. The nanogap junction should have broad biomedical applications by realizing highly selective and sensitive biosensing in samples having diverse coexisting molecules.

Mixed-scale channel networks including Kingfisher-beak-shaped 3D microfunnels for efficient single particle entrapment

Reproducible research results for nanofluidics and their applications require viable fabrication technologies to produce nanochannels integrated with microchannels that can guide fluid flow and analytes into/out of the nanochannels. We present the simple fabrication of mixed-scale polydimethylsiloxane (PDMS) channel networks consisting of nanochannels and microchannels via a single molding process using a monolithic mixed-scale carbon mold. The monolithic carbon mold is fabricated by pyrolyzing a polymer mold patterned by photolithography. During pyrolysis, the polymer mold shrinks by ∼90%, which enables nanosized carbon molds to be produced without a complex nanofabrication process. Because of the good adhesion between the polymer mold and the Si substrate, non-uniform volume reduction occurs during pyrolysis resulting in the formation of curved carbon mold side walls. These curved side walls and the relatively low surface energy of the mold provide efficient demolding of the PDMS channel networks. In addition, the trigonal prismatic shape of the polymer is converted into to a Kingfisher-beak-shaped carbon structure due to the non-uniform volume reduction. The transformation of this mold architecture produces a PDMS Kingfisher-beak-shaped 3D microfunnel that connects the microchannel and the nanochannel smoothly. The smooth reduction in the cross-sectional area of the 3D microfunnels enables efficient single microparticle trapping at the nanochannel entrance; this is beneficial for studies of cell transfection.

DNA compaction by the bacteriophage protein Cox studied on the single DNA molecule level using nanofluidic channels

The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA–Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 and WΦ affect DNA. By measuring the extension of nanoconfined DNA in absence and presence of Cox we show that the protein compacts DNA and that the binding is highly cooperative, in agreement with the model of a Cox filament around which DNA is wrapped. Furthermore, comparing microscopy images for the wild-type P2 Cox protein and two mutants allows us to discriminate between compaction due to filament formation and compaction by monomeric Cox. P2 and WΦ Cox have similar effects on the physical properties of DNA and the subtle, but significant, differences in DNA binding are due to differences in binding affinity rather than binding mode. The presented work highlights the use of single DNA molecule studies to confirm structural predictions from X-ray crystallography. It also shows how a small protein by oligomerization can have great impact on the organization of DNA and thereby fulfill multiple regulatory functions.

Preservation of Supported Lipid Membrane Integrity from Thermal Disruption: Osmotic Effect

Preservation of structural integrity under various environmental conditions is one major concern in the development of the supported lipid membrane (SLM)-based devices. It is common for SLMs to experience temperature shifts from manufacture, processing, storage, and transport to operation. In this work, we studied the thermal adaption of the supported membranes on silica substrates. Homogenous SLMs with little defects were formed through the vesicle fusion method. The mass and fluidity of the bilayers were found to deteriorate from a heating process but not a cooling process. Fluorescence characterizations showed that the membranes initially budded as a result of heating-induced lipid lateral area expansion, followed by the possible fates including maintenance, retraction, and fission, among which the last contributes to the irreversible compromise of the SLM integrity and spontaneous release of the interlipid stress accumulated. Based on the mechanism, we developed a strategy to protect SLMs from thermal disruption by increasing the solute concentration in medium. An improved preservation of the membrane mass and fluidity against the heating process was observed, accompanied by a decrease in the retraction and fission of the buds. Theoretical analysis revealed a high osmotic energy penalty for the fission, which accounts for the depressed disruption. This osmotic-based protection strategy is facile, solute nonspecific, and long-term efficient and has little impact on the original SLM properties. The results may help broaden SLM applications and sustain the robustness of SLM-based devices under multiple thermal conditions.

Ultrafast immunoassays by coupling dielectrophoretic biomarker enrichment in nanoslit channel with electrochemical detection on graphene

Heterogeneous immunoassays usually require long incubation times to promote specific target binding and several wash steps to eliminate non-specific binding. Hence, signal saturation is rarely achieved at detection limit levels of analyte, leading to significant errors in analyte quantification due to extreme sensitivity of the signals to incubation time and methodology. The poor binding kinetics of immunoassays at detection limit levels can be alleviated through creating an enriched analyte plug in the vicinity of immobilized capture probes to enable signal saturation at higher levels and at earlier times, due to higher analyte association and its faster replenishment at the binding surface. Herein, we achieve this by coupling frequency-selective dielectrophoretic molecular dam enrichment of the target biomarker in physiological media to capture probes immobilized on graphene-modified surfaces in a nanoslit to enable ultrafast immunoassays with near-instantaneous (<2 minutes) signal saturation at dilute biomarker levels (picomolar) within ultra-low sample volumes (picoliters). This methodology is applied to the detection of Prostate Specific Antigen (PSA) diluted in serum samples, followed by validation against a standard two-step immunoassay using three de-identified patient samples. Based on the ability of dielectrophoretic molecular dam analyte enrichment methods to enable the detection of PSA at 1-5 pg mL(-1) levels within a minute, and the relative insensitivity of the signals to incubation time after the first two minutes, we envision its application for improving the sensitivity of immunoassays and their accuracy at detection limit levels.

Surface nanostructures for fluorescence probing of supported lipid bilayers on reflective substrates

The fluorescence interference contrast (FLIC) effect prevents the use of fluorescence techniques to probe the continuity and fluidity of supported lipid bilayers on reflective materials due to a lack of detectable fluorescence. Here we show that adding nanostructures onto reflective surfaces to locally confer a certain distance between the deposited fluorophores and the reflecting surface enables fluorescence detection on the nanostuctures. The nanostructures consist of either deposited nanoparticles or epitaxial nanowires directly grown on the substrate and are designed such that they can support a lipid bilayer. This simple method increases the fluorescence signal sufficiently to enable bilayer fluorescence detection and to observe the recovery of fluorescence after photobleaching in order to assess lipid bilayer formation on any reflective surface.

New technologies for DNA analysis--a review of the READNA Project

The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.