Preparation of Multifunctional Silk-Based Microcapsules loaded with DNA Plasmids Encoding RNA Aptamers and Riboswitches

We introduce a protocol for the preparation of DNA-laden silk fibroin microcapsules via the Layer-by-Layer (LbL) assembly method on sacrificial spherical cores. Following adsorption of a prime layer and DNA plasmids, the formation of robust microcapsules was facilitated by inducing β-sheets in silk secondary structure during acute dehydration of a single silk layer. Hence, the layering occurred via multiple hydrogen bonding and hydrophobic interactions. Upon adsorption of multilayered shells, the core-shell structures can be further functionalized with gold nanoparticles (AuNPs) and/or antibodies (IgG) to be used for remote sensing and/or targeted delivery. Adjusting several key parameters during sequential deposition of key macromolecules on silica cores such as the presence of a polymer primer, the concentration of DNA and silk protein, as well as a number of adsorbed layers resulted in biocompatible, DNA-laden microcapsules with variable permeability and DNA loadings. Upon dissolution of silica cores, the protocol demonstrated the formation of hollow and robust microcapsules with DNA plasmids immobilized to the inner surface of the capsule membrane. Creating a selectively permeable biocompatible membrane between the DNA plasmids and the external environment preserved the DNA during long-term storage and played an important role in the improved output response from spatially confined plasmids. The activity of DNA templates and their accessibility were tested during in vitro transcription and translation reactions (cell-free systems). DNA plasmids encoding RNA light-up aptamers and riboswitches were successfully activated with corresponding analytes, as was visualized during localization of fluorescently labeled RNA transcripts or GFPa1 protein in the shell membranes.

Improving the Activity of DNA-Encoded Sensing Elements through Confinement in Silk Microcapsules

Assembling synthetic bioparts into simplified artificial cells holds tremendous promise for advancing studies into the synthesis, biosensing, and delivery of biomolecules. Currently, the most successful techniques for encapsulation of the transcription-translation machinery exploit compartmentalization in liposomal vesicles. However, improvements to these methods may increase permeability to polar molecules, functionalization of the membrane with biologically active elements, and encapsulation efficiency. Microcapsules prepared via templated layer-by-layer (LbL) assembly using natural polymers have the potential to resolve some of the hurdles associated with liposomes. Here, we introduce a design for immobilizing DNA templates encoding translationally activated riboswitches and RNA aptamers into microcapsules prepared from regenerated silk fibroin protein. Adjusting several key parameters such as the presence of a polymer primer, concentration of silk protein, and DNA loadings during LbL assembly resulted in biocompatible, semipermeable, DNA-laden microcapsules. To preserve bioactivity, DNA was immobilized inside of the capsule membrane, which not only promoted stability during long-term storage at ambient conditions but also improved output response from spatially confined DNA-encoded sensing elements (SEs). Multiple copies of mRNA and GFPa1 protein were synthesized upon activation with specific analytes during in vitro transcription/translation reactions, demonstrating that selective permeability of silk microcapsules was essential for the diffusion of components of the cell-free system inside of the capsules. Further functionalization of capsule shells with gold nanoparticles (AuNPs) and antibodies (IgG) demonstrated the applicability of microcompartmentalized colloidal objects carrying SEs for remote sensing and/or targeted delivery. In the future, multifunctional, biocompatible silk-based microcapsules loaded with different RNA sensors can help advance the design of multiplexed biosensors tracking multiple biomarkers in complex media.

Silk macromolecules with amino acid-poly(ethylene glycol) grafts for controlling layer-by-layer encapsulation and aggregation of recombinant bacterial cells

This study introduces double-brush designs of functionalized silk polyelectrolytes based upon regenerated silk fibroin (SF), which is modified with poly-L-lysine (SF-PLL), poly-L-glutamic acid (SF-PGA), and poly(ethylene glycol) (PEG) side chains with different grafting architecture and variable amino acid-PEG graft composition for cell encapsulation. The molecular weight of poly amino acids (length of side chains), molecular weight and degree of PEG grafting (D) were varied in order to assess the formation of cytocompatible and robust layer-by-layer (LbL) shells on two types of bacterial cells (Gram-negative and Gram-positive bacteria). We observed that shells assembled with charged polycationic amino acids adversely effected the properties of microbial cells while promoting the formation of large cell aggregates. In contrast, hydrogen-bonded shells with high PEG grafting density were the most cytocompatible, while promoting formation of stable colloidal suspensions of individual cell encapsulates. The stability to degradation of silk shells (under standard cell incubation procedure) was related to the intrinsic properties of thermodynamic bonding forces, with shells based on electrostatic interactions having stronger resistance to deterioration compared to pure hydrogen-bonded silk shells. By optimizing the charge density of silk polyelectrolytes brushes, as well as the length and the degree of PEG side grafts, robust and cytocompatible cell coatings were engineered that can control aggregation of cells for biosensor devices and other potential biomedical applications.

Cell surface engineering with edible protein nanoshells

Natural protein (silk fibroin) nanoshells are assembled on the surface of Saccharomyces cerevisiae yeast cells without compromising their viability. The nanoshells facilitate initial protection of the cells and allow them to function in encapsulated state for some time period, afterwards being completely biodegraded and consumed by the cells. In contrast to a traditional methanol treatment, the gentle ionic treatment suggested here stabilizes the shell silk fibroin structure but does not compromise the viability of the cells, as indicated by the fast response of the encapsulated cells, with an immediate activation by the inducer molecules. Extremely high viability rates (up to 97%) and preserved activity of encapsulated cells are facilitated by cytocompatibility of the natural proteins and the formation of highly porous shells in contrast to traditional polyelectrolyte-based materials. Moreover, in a high contrast to traditional synthetic shells, the silk proteins are biodegradable and can be consumed by cells at a later stage of growth, thus releasing the cells from their temporary protective capsules. These on-demand encapsulated cells can be considered a valuable platform for biocompatible and biodegradable cell encapsulation, controlled cell protection in a synthetic environment, transfer to a device environment, and cell implantation followed by biodegradation and consumption of protective protein shells.

Permeability and micromechanical properties of silk ionomer microcapsules

We studied the pH-responsive behavior of layer-by-layer (LbL) microcapsules fabricated from silk fibroin chemically modified with different poly amino acid side chains: cationic (silk-poly L-lysine, SF-PL) or anionic (silk-poly-L-glutamic acid, SF-PG). We observed that stable ultrathin shell microcapsules can be assembled with a dramatic increase in swelling, thickness, and microroughness at extremely acidic (pH < 2.5) and basic (pH > 11.0) conditions without noticeable disintegration. These changes are accompanied by dramatic changes in shell permeability with a 2 orders of magnitude increase in the diffusion coefficient. Moreover, the silk ionomer shells undergo remarkable softening with a drop in Young's modulus by more than 1 order of magnitude due to the swelling, stretching, and increase in material porosity. The ability to control permeability and mechanical properties over a wide range for the silk-based microcapsules, with distinguishing stability under harsh environmental conditions, provides an important system for controlled loading and release and applications in bioengineering.

pH-responsive layer-by-layer nanoshells for direct regulation of cell activity

Saccharomyces cerevisiae yeast cells encapsulated with pH-responsive synthetic nanoshells from lightly cross-linked polymethacrylic acid showed a high viability rate of around 90%, an indication of high biocompatibility of synthetic pH-responsive shells. We demonstrated that increasing pH above the isoelectric point of the polymer shell leads to a delay in growth rate; however, it does not affect the expression of enhanced green fluorescent protein. We suggest that progressive ionization and charge accumulation within the synthetic shells evoke a structural change in the outer shells which affect the membrane transport. This change facilitates the ability to manipulate growth kinetics and functionality of the cells with the surrounding environment. We observed that hollow layer-by layer nanoshells showed a remarkable degree of reversible swelling/deswelling over a narrow pH range (pH 5.0-6.0), but their assembly directly on the cell surface resulted in the suppression of large dimensional changes. We suggest that the variation in surface charges caused by deprotonation/protonation of carboxylic groups in the nanoshells controlled cell growth and cell function, which can be utilized for external chemical control of cell-based biosensors.

Robust and responsive silk ionomer microcapsules

We demonstrate the assembly of extremely robust and pH-responsive thin shell LbL microcapsules from silk fibroin counterparts modified with poly(lysine) and poly(glutamic) acid, which are based on biocompatible silk ionomer materials in contrast with usually exploited synthetic polyelectrolytes. The microcapsules are extremely stable in an unusually wide pH range from 1.5 to 12.0 and show a remarkable degree of reversible swelling/deswelling response in dimensions, as exposed to extreme acidic and basic conditions. These changes are accompanied by reversible variations in shell permeability that can be utilized for pH-controlled loading and unloading of large macromolecules. Finally, we confirmed that these shells can be utilized to encapsulate yeast cells with a viability rate much higher than that for traditional synthetic polyelectrolytes.

Direct probing of micromechanical properties of hydrogen-bonded layer-by-layer microcapsule shells with different chemical compositions

The mechanical properties of hydrogen-bonded layer-by-layer (LbL) microcapsule shells constructed from tannic acid (TA) and poly(vinylpyrrolidone) (PVPON) components have been studied in both the dry and swollen states. In the dry state, the value of the elastic modulus was measured to be within 0.6-0.7 GPa, which is lower than the typical elastic modulus for electrostatically assembled LbL shells. Threefold swelling of the LbL shells in water results in a significant reduction of the elastic modulus to values well below 1 MPa, which is typical value seen for highly compliant gel materials. The increase of the molecular weight of the PVPON component from 55 to 1300 kDa promotes chain entanglements and causes a stiffening of the LbL shells with a more than 2-fold increase in elastic modulus value. Moreover, adding a polyethylenimine prime layer to the LbL shell affects the growth of hydrogen-bonded multilayers which consequently results in dramatically stiffer, thicker, and rougher LbL shells with the elastic modulus increasing by more than an order of magnitude, up to 4.3 MPa. An alternation of the elastic properties of very compliant hydrogen-bonded shells by variation of molecular weight is a characteristic feature of weakly bonded LbL shells. Such an ability to alter the elastic modulus in a wide range is critically important for the design of highly compliant microcapsules with tunable mechanical stability, loading ability, and permeability.

Truly nonionic polymer shells for the encapsulation of living cells

Engineering surfaces of living cells with natural or synthetic compounds can mediate intercellular communication and provide a protective barrier from hostile agents. We report on truly nonionic hydrogen-bonded LbL coatings for cell surface engineering. These ultrathin, highly permeable polymer membranes are constructed on living cells without the cationic component typically employed to increase the stability of LbL coatings. Without the cytotoxic cationic PEI pre-layer, the viability of encapsulated cells drastically increases to 94%, in contrast to 20% viability in electrostatically-bonded LbL shells. Moreover, the long-term growth of encapsulated cells is not affected, thus facilitating efficient function of protected cells in hostile environment.