Enzymatic Synthesis of Aptamer-Polynucleotide Nanoparticles with High Anticancer Drug Loading for Targeted Delivery.

We report a targeted prodrug delivery platform that can deliver a cytostatic nucleobase analog with high drug loading. We chose fluorouracil (5FU), a drug used to treat various cancers, whose active metabolite 5-fluorodeoxyuridine monophosphate (5-FdUMP) is the antineoplastic agent. We use terminal deoxynucleotidyl transferase (TdT) to polymerize 5-fluorodeoxyuridine triphosphate (5-FdUTP) onto the 3'-end of an aptamer. We find that (i) addition of hydrophobic, unnatural nucleotides at the 3'-end of the 5-FdU polynucleotide by TdT leads to their spontaneous self-assembly into nuclease resistant micelles, (ii) aptamers presented on the micelle corona retain specificity for their cognate receptor on tumor cells, and (iii) the micelles deliver 5FU to tumor cells and exhibit greater cytotoxicity than the free drug. The modular design of our platform, consisting of a targeting moiety, a polynucleotide drug, and a self-assembly domain, can be adapted to encompass a range of polymerizable therapeutic nucleotides and targeting units.

Controlling Silicification on DNA Origami with Polynucleotide Brushes.

DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However, the silicification reaction is sensitive to the reaction conditions and often results in uncontrolled DNA origami aggregation, especially when growth of thicker silica layers is desired. Here, we investigated how site-specifically placed polynucleotide brushes influence the silicification of DNA origami. Our experiments showed that long DNA brushes, in the form of single- or double-stranded DNA, significantly suppress the aggregation of DNA origami during the silicification process. Furthermore, we found that double-stranded DNA brushes selectively promote silica growth on DNA origami surfaces. These observations were supported and explained by coarse-grained molecular dynamics simulations. This work provides new insights into our understanding of the silicification process on DNA and provides a powerful toolset for the development of novel DNA-based organic-inorganic nanomaterials.

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures.

DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site-specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to "smart" functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.

The energetics of rapid cellular mechanotransduction.

Cells throughout the human body detect mechanical forces. While it is known that the rapid (millisecond) detection of mechanical forces is mediated by force-gated ion channels, a detailed quantitative understanding of cells as sensors of mechanical energy is still lacking. Here, we combine atomic force microscopy with patch-clamp electrophysiology to determine the physical limits of cells expressing the force-gated ion channels (FGICs) Piezo1, Piezo2, TREK1, and TRAAK. We find that, depending on the ion channel expressed, cells can function either as proportional or nonlinear transducers of mechanical energy and detect mechanical energies as little as ~100 fJ, with a resolution of up to ~1 fJ. These specific energetic values depend on cell size, channel density, and cytoskeletal architecture. We also make the surprising discovery that cells can transduce forces either nearly instantaneously (<1 ms) or with a substantial time delay (~10 ms). Using a chimeric experimental approach and simulations, we show how such delays can emerge from channel-intrinsic properties and the slow diffusion of tension in the membrane. Overall, our experiments reveal the capabilities and limits of cellular mechanosensing and provide insights into molecular mechanisms that different cell types may employ to specialize for their distinct physiological roles.

Self-Assembled Single-Stranded DNA Nano-Networks in Solution and at Surfaces.

We studied the directed self-assembly of two types of complementary single-stranded DNA (ssDNA) strands [i.e., poly(dA) and poly(dT)] into more complex, organized, and percolating networks in dilute solutions and at surfaces. Understanding ssDNA self-assembly into 2D networks on surfaces is important for the use of such networks in the fabrication of well-defined nanotechnological devices, as, for instance, required in nanoelectronics or for biosensing. To control the formation of 2D networks on surfaces, it is important to know whether DNA assemblies are formed already in dilute solutions or only during the drying/immobilization process at the surface, where the concentration automatically increases. Fluorescence cross-correlation spectroscopy clearly shows the presence of larger DNA complexes in mixed poly(dA) and poly(dT) solutions already at very low DNA concentrations (<1 nM), that is, well below the overlap concentration. Here, we describe for the first time such supramolecular complexes in solution and how their structure depends on the ssDNA length and concentration and ionic strength. Hence, future attempts to control such networks should also focus on network precursors in solution and not only on their immobilization on surfaces.

Self-Healing of Hyaluronic Acid to Improve In Vivo Retention and Function.

Convergent advances in the field of soft matter, macromolecular chemistry, and engineering have led to the development of biomaterials that possess autonomous, adaptive, and self-healing characteristics similar to living systems. These rationally designed biomaterials can surpass the capabilities of their parent material. Herein, the modification of hyaluronic acid (HA) to exhibit self-healing properties is described, and its physical and biological function both in vitro and in vivo is studied. The in vitro findings showed that self-healing HA designed to undergo self-repair improves lubrication, enhances free radical scavenging, and attenuates enzymatic degradation compared to unmodified HA. Longitudinal imaging following intraarticular injection of self-healing HA shows improved in vivo retention despite its low molecular weight. Concomitant with these functions, intraarticular injection of self-healing HA mitigates anterior cruciate ligament injury-mediated cartilage degeneration in rodents. This proof-of-concept study shows how incorporation of functional properties such as self-healing can be used to surpass the existing capabilities of biolubricants.

Microphase Separation of Resilin-like and Elastin-like Diblock Copolypeptides in Concentrated Solutions.

Diblock copolymers are valued for their ability to form thin films with nanoscale features that typically reflect those of their microphase-separated structures in concentrated solution. Here, we show that such self-assembled structures can be easily formed with diblock copolymers composed of thermally responsive polypeptides, such as resilin-like polypeptides (RLP) and elastin-like polypeptides (ELP), by exploiting the inverse temperature transition behavior of ELPs in aqueous media. Specifically, we examine the self-assembly of a series of RLP-b-ELP diblock copolypeptides in concentrated aqueous solution (30 and 50 wt %) by small-angle X-ray scattering (SAXS). By systematically varying RLP block length and temperature (10-45 °C), we observed microphase separation into hexagonally packed cylinders and lamellae. By analyzing the observed order-order transitions (OOT) and order-disorder transitions (ODT), we determined that self-assembly in this system is primarily driven by polymer-solvent interactions. While these thermally responsive polymers showed clear ODTs and OOTs at certain temperatures, temperature only had a weak effect on the spacing of the resulting nanostructures. In contrast, we found that nanostructure spacing was far more sensitive to RLP block length. Finally, we used atomic force microscopy (AFM) to demonstrate that spin casting RLP-b-ELP diblock copolypeptides also produce nanostructured thin films with spacings that correlate with those in concentrated solution.

Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes.

Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush-functionalized DNA nanostructures. We demonstrate that SI-TcEP can site-specifically pattern DONs with brushes containing both natural and non-natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse-grained simulations predict the conformation of the brush-functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush-functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site-specific growth of polynucleotide brushes. The ability to site-specifically decorate DONs with brushes of natural and non-natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.

Controlled Lengthwise Assembly of Helical Peptide Nanofibers to Modulate CD8+ T-Cell Responses.

Peptide nanofibers are useful for many biological applications, including immunotherapy, tissue engineering, and drug delivery. The robust lengthwise assembly of these peptides into nanofibers is typically difficult to control, resulting in polydisperse fiber lengths and an incomplete understanding of how nanofiber length affects biological responses. Here, rationally designed capping peptides control the length of helical peptide nanofibers with unique precision. These designed peptides bind the tips of elongated nanofibers to shorten and narrow their length distributions. Demonstrating their use as immunotherapies, capped nanofibers are preferentially cross-presented by dendritic cells compared to uncapped nanofibers. Due to increased cross-presentation, these capped nanofibers trigger stronger CD8+ T-cell responses in mice than uncapped nanofibers. This strategy illustrates a means for controlling the length of supramolecular peptide nanofibers to modulate their immunogenicity in the context of immunotherapies.

Understanding and Mapping Sensitivity in MoS2 Field-Effect-Transistor-Based Sensors.

Sensors based on two-dimensional (2D) field-effect transistors (FETs) are extremely sensitive and can detect charged analytes with attomolar limits of detection (LOD). Despite some impressive LODs, the operating mechanisms and factors that determine the signal-to-noise ratio in 2D FET-based sensors remain poorly understood. These uncertainties, coupled with an expansive design space for sensor layout and analyte positioning, result in a field with many reported highlights but limited collective progress. Here, we provide insight into sensing mechanisms of 2D molybdenum disulfide (MoS2) FETs by realizing precise control over the position and charge of an analyte using a customized atomic force microscope (AFM), with the AFM tip acting as an analyte. The sensitivity of the MoS2 FET channel is revealed to be nonuniform, manifesting sensitive hotspots with locations that are stable over time. When the charge of the analyte is varied, an asymmetry is observed in the device drain-current response, with analytes acting to turn the device off leading to a 2.5× increase in the signal-to-noise ratio (SNR). We developed a numerical model, applicable to all FET-based charge-detection sensors, that confirms our experimental observation and suggests an underlying mechanism. Further, extensive characterization of a set of different MoS2 FETs under various analyte conditions, coupled with the numerical model, led to the identification of three distinct SNRs that peak with dependence on the layout and operating conditions used for a sensor. These findings reveal the important role of analyte position and coverage in determining the optimal operating bias conditions for maximal sensitivity in 2D FET-based sensors, which provides key insights for future sensor design and control.

Complex microparticle architectures from stimuli-responsive intrinsically disordered proteins.

The controllable production of microparticles with complex geometries is useful for a variety of applications in materials science and bioengineering. The formation of intricate microarchitectures typically requires sophisticated fabrication techniques such as flow lithography or multiple-emulsion microfluidics. By harnessing the molecular interactions of a set of artificial intrinsically disordered proteins (IDPs), we have created complex microparticle geometries, including porous particles, core-shell and hollow shell structures, and a unique 'fruits-on-a-vine' arrangement, by exploiting the metastable region of the phase diagram of thermally responsive IDPs within microdroplets. Through multi-site unnatural amino acid (UAA) incorporation, these protein microparticles can also be photo-crosslinked and stably extracted to an all-aqueous environment. This work expands the functional utility of artificial IDPs as well as the available microarchitectures of this class of biocompatible IDPs, with potential applications in drug delivery and tissue engineering.

Grafting To of Bottlebrush Polymers: Conformation and Kinetics.

Specifically adsorbed bottlebrush coatings are found in nature as brush-like glycoproteins that decorate biointerfaces and provide antifouling, lubrication, or wear-protection. Although various synthetic strategies have been developed to mimic glycoprotein structure and function, the use of these mimics is still limited because of the current lack of understanding of their adsorption behavior and surface conformation. In this paper, we examine the adsorption behavior of PEG-based, biotinylated bottlebrushes with different backbone and bristle lengths to streptavidin model surfaces in phosphate-buffered saline. By using quartz crystal microbalance, localized surface plasmon resonance, and atomic force microscopy, we learn how bottlebrush dimensions impact their adsorption kinetics, surface conformation, mechanical properties, and antifouling properties. Our bottlebrushes qualitatively mirror the adsorption behavior of linear polymers and exhibit three kinetic regimes of adsorption: (I) a transport-limited regime, (II) a pause, and (III) a penetration-limited regime. Furthermore, we find that the bristle length more dramatically affects brush properties than the backbone length. Generally, larger bottlebrush dimensions lead to reduced molar adsorption, retarded kinetics, weaker antifouling, and softer brush coatings. Longer bristles also lead to less mass adsorption, while the opposite trend is observed for increasing backbone length. In summary, our findings aid the rational design of new bottlebrush coatings by elucidating how their dimensions impact adsorption, surface conformation, and the properties of the final coating.

Ti3C2Tx MXene-Reduced Graphene Oxide Composite Electrodes for Stretchable Supercapacitors.

The development of stretchable electronics requires the invention of compatible high-performance power sources, such as stretchable supercapacitors and batteries. In this work, two-dimensional (2D) titanium carbide (Ti3C2Tx) MXene is being explored for flexible and printed energy storage devices by fabrication of a robust, stretchable high-performance supercapacitor with reduced graphene oxide (RGO) to create a composite electrode. The Ti3C2Tx/RGO composite electrode combines the superior electrochemical and mechanical properties of Ti3C2Tx and the mechanical robustness of RGO resulting from strong nanosheet interactions, larger nanoflake size, and mechanical flexibility. It is found that the Ti3C2Tx/RGO composite electrodes with 50 wt % RGO incorporated prove to mitigate cracks generated under large strains. The composite electrodes exhibit a large capacitance of 49 mF/cm2 (∼490 F/cm3 and ∼140 F/g) and good electrochemical and mechanical stability when subjected to cyclic uniaxial (300%) or biaxial (200% × 200%) strains. The as-assembled symmetric supercapacitor demonstrates a specific capacitance of 18.6 mF/cm2 (∼90 F/cm3 and ∼29 F/g) and a stretchability of up to 300%. The developed approach offers an alternative strategy to fabricate stretchable MXene-based energy storage devices and can be extended to other members of the large MXene family.

Effect of Octadecylamine Surfactant on DNA Interactions with Graphene Surfaces.

Understanding of how to integrate DNA molecules with graphene materials is important for the development of biosensors and biomolecular logic circuits. For some of these applications, controlling DNA structural conformation on the graphene substrate is critically important and can be achieved through the use of self-assembled monolayers. Here, we performed all-atom molecular dynamics simulations to understand how various 1-octadecylamine (ODA) coatings of the graphene surface affect the conformation of double-stranded DNA (dsDNA) on the surface. The simulation results demonstrated that dsDNA structures become more stable as ODA concentration increases due to the formation of DNA-ODA hydrogen bonds and reduction of DNA-surface interactions, which aid in retaining internal DNA interactions. Specifically, the interaction of ODA molecules with DNA prevents nucleobases from forming π-π stacking interactions with the surface. Some dsDNA conformations, such as sharp kinks or unwinding, can occur more frequently in DNA with A-T sequences due to weaker pairing interactions than with G-C sequences. Furthermore, our results conclude that both DNA sequence and ODA concentration play an essential role in experimentally observed conformational changes of DNA on the graphene surface.

Interaction of Proteins with a Planar Poly(acrylic acid) Brush: Analysis by Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D).

We describe the preparation of a poly(acrylic acid) (PAA) brush, polymerized by atom transfer radical polymerization (ATRP) of tert-butyl acrylate (tBA) and subsequent acid hydrolysis, on the flat gold surfaces of quartz-crystal microbalance (QCM) crystals. The PAA brushes were characterized by Fourier transform infrared (FT-IR) spectroscopy, ellipsometry and water contact angle analysis. The interaction of the PAA brushes with human serum albumin (HSA) was studied for a range of ionic strengths and pH conditions by quartz-crystal microbalance with dissipation monitoring (QCM-D). The quantitative analysis showed a strong adsorption of protein molecules onto the PAA brush. By increasing the ionic strength, we were able to release a fraction of the initially bound HSA molecules. This finding highlights the importance of counterions in the polyelectrolyte-mediated protein adsorption/desorption. A comparison with recent calorimetric studies related to the binding of HSA to polyelectrolytes allowed us to fully analyze the QCM data based on the results of the thermodynamic analysis of the binding process.

Thermodynamic Analysis of the Uptake of a Protein in a Spherical Polyelectrolyte Brush.

A thermodynamic study of the adsorption of Human Serum Albumin (HSA) onto spherical polyelectrolyte brushes (SPBs) by isothermal titration calorimetry (ITC) is presented. The SPBs are composed of a solid polystyrene core bearing long chains of poly(acrylic acid). ITC measurements done at different temperatures and ionic strengths lead to a full set of thermodynamicbinding constants together with the enthalpies and entropies of binding. The adsorption of HSA onto SPBs is described with a two-step model. The free energy of binding ΔGb depends only weakly on temperature because of a marked compensation of enthalpy by entropy. Studies of the adsorbed HSA by Fourier transform infrared spectroscopy (FT-IR) demonstrate no significant disturbance in the secondary structure of the protein. The quantitative analysis demonstrates that counterion release is the major driving force for adsorption in a process where proteins become multivalent counterions of the polyelectrolyte chains upon adsorption. A comparison with the analysis of other sets of data related to the binding of HSA to polyelectrolytes demonstrates that the cancellation of enthalpy and entropy is a general phenomenon that always accompanies the binding of proteins to polyelectrolytes dominated by counterion release.

Enzymatic synthesis and modification of high molecular weight DNA using terminal deoxynucleotidyl transferase.

The recognition that nucleic acids can be used as polymeric materials led to the blossoming of the field of DNA nanotechnology, with a broad range of applications in biotechnology, biosensors, diagnostics, and drug delivery. These applications require efficient methods to synthesize and chemically modify high molecular weight DNA. Here, we discuss terminal deoxynucleotidyl transferase (TdT)-catalyzed enzymatic polymerization (TcEP) as an alternative to conventional enzymatic and solid-phase DNA synthesis. We describe biochemical requirements for TcEP and provide step-by-step protocols to carry out TcEP in solution and from surfaces.

Shear Modulus Measurement by Quantitative Phase Imaging and Correlation with Atomic Force Microscopy.

Many approaches have been developed to characterize cell elasticity. Among these, atomic force microscopy (AFM) combined with modeling has been widely used to characterize cellular compliance. However, such approaches are often limited by the difficulties associated with using a specific instrument and by the complexity of analyzing the measured data. More recently, quantitative phase imaging (QPI) has been applied to characterize cellular stiffness by using an effective spring constant. This metric was further correlated to mass distribution (disorder strength) within the cell. However, these measurements are difficult to compare to AFM-derived measurements of Young's modulus. Here, we describe, to our knowledge, a new way of analyzing QPI data to directly retrieve the shear modulus. Our approach enables label-free measurement of cellular mechanical properties that can be directly compared to values obtained from other rheological methods. To demonstrate the technique, we measured shear modulus and phase disorder strength using QPI, as well as Young's modulus using AFM, across two breast cancer cell-line populations dosed with three different concentrations of cytochalasin D, an actin-depolymerizing toxin. Comparison of QPI-derived and AFM moduli shows good agreement between the two measures and further agrees with theory. Our results suggest that QPI is a powerful tool for cellular biophysics because it allows for optical quantitative measurements of cell mechanical properties.

Enzymatically Degassed Surface-Initiated Atom Transfer Radical Polymerization with Real-Time Monitoring.

Polymer brush coatings are frequently prepared by radical polymerization, a notoriously oxygen sensitive process. Glucose oxidase (GOx) can inexpensively enable radical polymerization in solution by enzymatically consuming oxygen as it oxidizes glucose. Here, we report the growth of polymeric brushes using GOx-assisted atom transfer radical polymerization (ATRP) from a surface while open to air. Specifically, we grew a set of biomedically relevant polymer brushes, including poly(oligo(ethylene glycol) methacrylate) (POEGMA), poly(2-dimethylaminoethyl methacrylate) (PDMAEMA), poly(sulfobetaine methacrylate) (PSBMA), and poly(2-(methylsulfinyl)ethyl acrylate (PMSEA). For each of these polymers, we monitored GOx-assisted and GOx-free ATRP reaction kinetics in real time using quartz crystal microbalance (QCM) and verified findings with localized surface plasmon resonance (LSPR). We modeled brush growth kinetics considering bimolecular termination. This model fit our data well ( r2 > 0.987 for all samples) and shows the addition of GOx increased effective kinetic chain lengths, propagation rates, and reproducibility. We tested the antifouling properties of the polymer brush coatings against human blood plasma and were surprised to find that coatings prepared with GOx repelled more plasma proteins in all cases than their GOx-free counterparts.

Doxorubicin-loaded protease-activated near-infrared fluorescent polymeric nanoparticles for imaging and therapy of cancer.

INTRODUCTION: Despite significant progress in the field of oncology, cancer remains one of the leading causes of death. Chemotherapy is one of the most common treatment options for cancer patients but is well known to result in off-target toxicity. Theranostic nanomedicines that integrate diagnostic and therapeutic functions within an all-in-one platform can increase tumor selectivity for more effective chemotherapy and aid in diagnosis and monitoring of therapeutic responses. MATERIAL AND METHODS: In this work, theranostic nanoparticles were synthesized with commonly used biocompatible and biodegradable polymers and used as cancer contrast and therapeutic agents for optical imaging and treatment of breast cancer. These core-shell nanoparticles were prepared by nanoprecipitation of blends of the biodegradable and biocompatible amphiphilic copolymers poly(lactic-co-glycolic acid)-b-poly-l-lysine and poly(lactic acid)-b-poly(ethylene glycol). Poly-l-lysine in the first copolymer was covalently decorated with near-infrared fluorescent Alexa Fluor 750 molecules. RESULTS: The spherical nanoparticles had an average size of 60-80 nm. The chemotherapeutic drug doxorubicin was encapsulated in the core of nanoparticles at a loading of 3% (w:w) and controllably released over a period of 30 days. A 33-fold increase in near-infrared fluorescence, mediated by protease-mediated cleavage of the Alexa Fluor 750-labeled poly-l-lysine on the surface of the nanoparticles, was observed upon interaction with the model protease trypsin. The cytocompatibility of drug-free nanoparticles and growth inhibition of drug-loaded nanoparticles on MDA-MB-231 breast cancer cells were investigated with a luminescence cell-viability assay. Drug-free nanoparticles were found to cause minimal toxicity, even at high concentrations (0.2-2,000 µg/mL), while doxorubicin-loaded nanoparticles significantly reduced cell viability at drug concentrations >10 µM. Finally, the interaction of the nanoparticles with breast cancer cells was studied utilizing fluorescence microscopy, demonstrating the potential of the nanoparticles to act as near-infrared fluorescence optical imaging agents and drug-delivery carriers. CONCLUSION: Doxorubicin-loaded, enzymatically activatable nanoparticles of less than 100 nm were prepared successfully by nanoprecipitation of copolymer blends. These nanoparticles were found to be suitable as controlled drug delivery systems and contrast agents for imaging of cancer cells.