Building a community to engineer synthetic cells and organelles from the bottom-up.

Employing concepts from physics, chemistry and bioengineering, 'learning-by-building' approaches are becoming increasingly popular in the life sciences, especially with researchers who are attempting to engineer cellular life from scratch. The SynCell2020/21 conference brought together researchers from different disciplines to highlight progress in this field, including areas where synthetic cells are having socioeconomic and technological impact. Conference participants also identified the challenges involved in designing, manipulating and creating synthetic cells with hierarchical organization and function. A key conclusion is the need to build an international and interdisciplinary research community through enhanced communication, resource-sharing, and educational initiatives.

Centrifugal Generation of Droplet-Based 3D Cell Cultures.

Quickly and easily producing uniform populations of microsphere-based 3D cell cultures using droplet-based templating methods has the potential to enable widespread use of such platforms in drug discovery or cancer research. Here, we advance the design of centrifuge-based droplet generation devices, describe the use of this platform for droplet generation with controlled cell occupancy, and demonstrate weeklong culture duration. Using simple-to-construct devices and easily implemented protocols, the initial concentration of encapsulated cells is adjustable up to hundreds of cells per microsphere. This work demonstrates the first instance of using centrifugal droplet-generating devices to produce large numbers of cell-encapsulating microspheres. Applications of this versatile methodology include the rapid formation of templated 3D cell culture populations suitable for suspension culture or large batch bioreactor studies that require uniform populations.

Single-Cell Response to the Rigidity of Semiconductor Nanomembranes on Compliant Substrates.

Single-crystalline semiconductor nanomembranes (NMs) bonded to compliant substrates are increasingly used for biomedical research and in health care. Nevertheless, there is a limited understanding of how individual cells sense the unique mechanical properties of these substrates and adjust their behavior in response to them. In this work, we performed proliferation assays, cytoskeleton analysis, and focal adhesion (FA) studies for NIH-3T3 fibroblasts on 220 and 20 nm single-crystalline Si on polydimethylsiloxane (PDMS) substrates with an elastic modulus of ∼31 kPa. We also characterized cell response on bulk Si as a reference. Our in vitro studies show that varying the thickness of the NM between 20 and 220 nm affects the proliferation rate of the cells, their cytoskeleton, fiber organization, spread area, and degree of FA. For example, cultured cells on 220 nm Si/PMDS exhibit the same response as on bulk Si, that is, they are well-spread with a pentagonal (or dendritic) shape and show a good organization of stress fibers and FAs. On the other hand, the cells on 20 nm Si/PDMS are spherical, with fiber organization and FAs in undetectable levels. We explained the results of our in vitro studies through a shear-lag mechanical model. The calculated FA-substrate contact stiffnesses for fibroblasts on bulk Si and 220 nm Si/PDMS closely match, and they are significantly higher than the stiffness of the integrin clutches and the plaque. Conversely, focal contacts with 20 nm Si/PDMS have comparable lateral compliance to adhesion-mediating intracellular organisms. In conclusion, our work relies on recent advances in NM technology to fill a critical knowledge gap about how individual cells sense and react to the mechanical properties of NM-based substrates. Our findings will have a major impact on the design of flexible electronic materials for applications in biomedical science and health care.

Oil-Free Acoustofluidic Droplet Generation for Multicellular Tumor Spheroid Culture.

We present an easy-to-assemble microfluidic system for synthesizing cell-loaded dextran/alginate (DEX/ALG) hydrogel spheres using an aqueous two-phase system (ATPS) for templated fabrication of multicellular tumor spheroids (MTSs). An audio speaker driven by an amplified output of a waveform generator or smartphone provides acoustic modulation to drive the breakup of an ATPS into MTS template droplets within microcapillary fluidic devices. We apply extensions of Plateau-Rayleigh theory to help define the flow and frequency parameter space necessary for acoustofluidic ATPS droplet formation in these devices. This method provides a simple droplet microfluidic approach using off-the-shelf acoustic components for quickly initiating MTSs and subsequent 3D cell culture.

Line-Focused Optical Excitation of Parallel Acoustic Focused Sample Streams for High Volumetric and Analytical Rate Flow Cytometry.

Flow cytometry provides highly sensitive multiparameter analysis of cells and particles but has been largely limited to the use of a single focused sample stream. This limits the analytical rate to ∼50K particles/s and the volumetric rate to ∼250 µL/min. Despite the analytical prowess of flow cytometry, there are applications where these rates are insufficient, such as rare cell analysis in high cellular backgrounds (e.g., circulating tumor cells and fetal cells in maternal blood), detection of cells/particles in large dilute samples (e.g., water quality, urine analysis), or high-throughput screening applications. Here we report a highly parallel acoustic flow cytometer that uses an acoustic standing wave to focus particles into 16 parallel analysis points across a 2.3 mm wide optical flow cell. A line-focused laser and wide-field collection optics are used to excite and collect the fluorescence emission of these parallel streams onto a high-speed camera for analysis. With this instrument format and fluorescent microsphere standards, we obtain analysis rates of 100K/s and flow rates of 10 mL/min, while maintaining optical performance comparable to that of a commercial flow cytometer. The results with our initial prototype instrument demonstrate that the integration of key parallelizable components, including the line-focused laser, particle focusing using multinode acoustic standing waves, and a spatially arrayed detector, can increase analytical and volumetric throughputs by orders of magnitude in a compact, simple, and cost-effective platform. Such instruments will be of great value to applications in need of high-throughput yet sensitive flow cytometry analysis.

A Microsphere-Supported Lipid Bilayer Platform for DNA Reactions on a Fluid Surface.

We report a versatile microsphere-supported lipid bilayer system that can serve as a general-purpose platform for implementing DNA nanotechnologies on a fluid surface. To demonstrate our platform, we implemented both toehold-mediated strand displacement (TMSD) and DNAzyme reactions, which are typically performed in solution and which are the cornerstone of DNA-based molecular logic and dynamic DNA nanotechnology, on the surface. We functionalized microspheres bearing supported lipid bilayers (µSLBs) with membrane-bound nucleic acid components. Using functionalized µSLBs, we developed TMSD and DNAzyme reactions by optimizing reaction conditions to reduce nonspecific interactions between DNA and phospholipids and to enhance bilayer stability. Additionally, the physical and optical properties of the bilayer were tuned via lipid composition and addition of fluorescently tagged lipids to create stable and multiplexable µSLBs that are easily read out by flow cytometry. Multiplexed TMSD reactions on µSLBs enabled the successful operation of a Dengue serotyping assay that correctly identified all 16 patterns of target sequences to demonstrate detection of DNA strands derived from the sequences of all four Dengue serotypes. The limit of detection for this assay was 3 nM. Furthermore, we demonstrated DNAzyme reactions on a fluid lipid surface, which benefit from free diffusion on the surface. This work provides the basis for expansion of both TMSD and DNAzyme based molecular reactions on supported lipid bilayers for use in molecular logic and DNA nanotechnology. As our system is multiplexable and results in fluid surfaces, it may be of use in compartmentalization and improved kinetics of molecular logic reactions and as a useful building block in a variety of DNA nanotechnology systems.

Multiplexed Lipid Bilayers on Silica Microspheres for Analytical Screening Applications.

Most druggable targets are membrane components, including membrane proteins and soluble proteins that interact with ligands or receptors embedded in membranes. Current target-based screening and intermolecular interaction assays generally do not include the lipid membrane environment in presenting these targets, possibly altering their native structure and leading to misleading or incorrect results. To address this issue, an ideal assay involving membrane components would (1) mimic the natural membrane environment, (2) be amenable to high-throughput implementation, and (3) be easily multiplexed. In a step toward developing such an ideal target-based analytical assay for membrane components, we present fluorescently indexed multiplexed biomimetic membrane assays amenable to high-throughput flow cytometric detection. We build fluorescently multiplexed biomimetic membrane assays by using varying amounts of a fluorescently labeled lipid, NBD-DOPE [1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl)], incorporated into a phospholipid membrane bilayer supported on 3 µm silica microspheres. Using flow cytometry, we demonstrate this multiplexed approach by measuring specific affinity of two well-characterized systems, the fluorescently labeled soluble proteins cholera toxin B subunit-Alexa 647 and streptavidin-PE/Cy5, to membranes containing different amounts of ligand targets of these proteins, GM1 and biotin-DOPE, respectively. This work will enable future efforts in developing highly efficient biomimetic assays for interaction analysis and drug screening involving membrane components.

Method for measuring the unbinding energy of strongly-bound membrane-associated proteins.

We describe a new method to measure the activation energy for unbinding (enthalpy ΔH*u and free energy ΔG*u) of a strongly-bound membrane-associated protein from a lipid membrane. It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method is used to determine ΔH*u and ΔG*u for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH5.5. ΔH*u is determined from the Arrhenius equation whereas ΔG*u is determined by fitting the data to a model based on mean first passage time for escape from a potential well. The binding free energy ΔGb of sE was also measured at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipid bilayer. The unbinding free energy (20±3kcal/mol, 20% PG) was found to be roughly three times the binding energy per monomer, (7.8±0.3kcal/mol for 30% PG, or est. 7.0kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH5.5, but assembles into trimers after associating with membranes. This new method to determine unbinding energies should be useful to understand better the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.

Self-Assembled Light-Harvesting System from Chromophores in Lipid Vesicles.

Lipid vesicles are used as the organizational structure of self-assembled light-harvesting systems. Following analysis of 17 chromophores, six were selected for inclusion in vesicle-based antennas. The complementary absorption features of the chromophores span the near-ultraviolet, visible, and near-infrared region. Although the overall concentration of the pigments is low (~1 µM for quantitative spectroscopic studies) in a cuvette, the lipid-vesicle system affords high concentration (≥10 mM) in the bilayer for efficient energy flow from donor to acceptor. Energy transfer was characterized in 13 representative binary mixtures using static techniques (fluorescence-excitation versus absorptance spectra, quenching of donor fluorescence, modeling emission spectra of a mixture versus components) and time-resolved spectroscopy (fluorescence, ultrafast absorption). Binary donor-acceptor systems that employ a boron-dipyrrin donor (S0 ↔ S1 absorption/emission in the blue-green) and a chlorin or bacteriochlorin acceptor (S0 ↔ S1 absorption/emission in the red or near-infrared) have an average excitation-energy-transfer efficiency (ΦEET) of ~50%. Binary systems with a chlorin donor and a chlorin or bacteriochlorin acceptor have ΦEET ∼ 85%. The differences in ΦEET generally track the donor-fluorescence/acceptor-absorption spectral overlap within a dipole-dipole coupling (Förster) mechanism. Substantial deviation from single-exponential decay of the excited donor (due to the dispersion of donor-acceptor distances) is expected and observed. The time profiles and resulting ΦEET are modeled on the basis of (Förster) energy transfer between chromophores relatively densely packed in a two-dimensional compartment. Initial studies of two ternary and one quaternary combination of chromophores show the enhanced spectral coverage and energy-transfer efficacy expected on the basis of the binary systems. Collectively, this approach may provide one of the simplest designs for self-assembled light-harvesting systems that afford broad solar collection and efficient energy transfer.

DNA-assisted photoinduced charge transfer between a cationic poly(phenylene vinylene) and a cationic fullerene.

Water-soluble cationic conjugated poly(phenylene vinylene) (PPV) and cationic fullerene were complexed with negatively charged single stranded DNA and double stranded DNA via electrostatic interactions to achieve photoinduced charge transfer with efficiencies as high as those observed from oppositely charged, cationic PPV and anionic fullerene but with distinctly different quenching mechanisms.

Diblock copolymer micelles and supported films with noncovalently incorporated chromophores: a modular platform for efficient energy transfer.

We report generation of modular, artificial light-harvesting assemblies where an amphiphilic diblock copolymer, poly(ethylene oxide)-block-poly(butadiene), serves as the framework for noncovalent organization of BODIPY-based energy donor and bacteriochlorin-based energy acceptor chromophores. The assemblies are adaptive and form well-defined micelles in aqueous solution and high-quality monolayer and bilayer films on solid supports, with the latter showing greater than 90% energy transfer efficiency. This study lays the groundwork for further development of modular, polymer-based materials for light harvesting and other photonic applications.

Lipid membrane domains for the selective adsorption and surface patterning of conjugated polyelectrolytes.

Conjugated polyelectrolytes (CPEs) are promising materials for generating optoelectronics devices under environmentally friendly processing conditions, but challenges remain to develop methods to define lateral features for improved junction interfaces and direct optoelectronic pathways. We describe here the potential to use a bottom-up approach that employs self-assembly in lipid membranes to form structures to template the selective adsorption of CPEs. Phase separation of gel phase anionic lipids and fluid phase phosphocholine lipids allowed the formation of negatively charged domain assemblies that selectively adsorb a cationic conjugated polyelectrolyte (P2). Spectroscopic studies found the adsorption of P2 to negatively charged membranes resulted in minimal structural change of the solution phase polymer but yielded an enhancement in fluorescence intensity (~50%) due to loss of quenching pathways. Fluorescence microscopy, dynamic light scattering, and AFM imaging were used to characterize the polymer-membrane interaction and the polymer-bound domain structures of the biphasic membranes. In addition to randomly formed circular gel phase domains, we also show that predefined features, such as straight lines, can be directed to form upon etched patterns on the substrate, thus providing potential routes toward the self-organization of optoelectronic architectures.

A DNA-templated fluorescent silver nanocluster with enhanced stability.

We report the discovery of a DNA sequence that templates a highly stable fluorescent silver nanocluster. In contrast to other DNA templated silver nanoclusters that have a relatively short shelf-life, the fluorescent species templated in this new DNA sequence retains significant fluorescence for at least a year. Moreover, this new silver nanocluster possesses low cellular toxicity and enhanced thermal, oxidative, and chemical stability.

Bright two-photon emission and ultra-fast relaxation dynamics in a DNA-templated nanocluster investigated by ultra-fast spectroscopy.

Metal nanoclusters have interesting steady state fluorescence emission, two-photon excited emission and ultrafast dynamics. A new subclass of fluorescent silver nanoclusters (Ag NCs) are NanoCluster Beacons. NanoCluster Beacons consist of a weakly emissive Ag NC templated on a single stranded DNA ("Ag NC on ssDNA") that becomes highly fluorescent when a DNA enhancer sequence is brought in proximity to the Ag NC by DNA base pairing ("Ag NC on dsDNA"). Steady state fluorescence was observed at 540 nm for both Ag NC on ssDNA and dsDNA; emission at 650 nm is observed for Ag NC on dsDNA. The emission at 550 nm is eight times weaker than that at 650 nm. Fluorescence up-conversion was used to study the dynamics of the emission. Bi-exponential fluorescence decay was recorded at 550 nm with lifetimes of 1 ps and 17 ps. The emission at 650 nm was not observed at the time scale investigated but has been reported to have a lifetime of 3.48 ns. Two-photon excited fluorescence was detected for Ag NC on dsDNA at 630 nm when excited at 800 nm. The two-photon absorption cross-section was calculated to be ∼3000 GM. Femtosecond transient absorption experiments were performed to investigate the excited state dynamics of DNA-Ag NC. An excited state unique to Ag NC on dsDNA was identified at ∼580 nm as an excited state bleach that related directly to the emission at 650 nm based on the excitation spectrum. Based on the optical results, a simple four level system is used to describe the emission mechanism for Ag NC on dsDNA.

Effects of solvent properties on the spectroscopy and dynamics of alkoxy-substituted PPV oligomer aggregates.

Conjugated systems are frequently studied in their nanoaggregate form to probe the effects of solvent and of film formation on their spectral and dynamical properties. This article focuses on the emission spectra and dynamics of nanoaggregates of alkoxy-substituted PPV oligomers with the goal of interpreting the vibronic emission envelopes observed in these systems (J. Phys. Chem. C2009, 113, 18851-18862). The aggregates are formed by adding a nonsolvent such as methanol (MeOH) or water to a solution of the oligomers in a good solvent such as methyl tetrahydrofuran (MeTHF) or tetrahydrofuran (THF). The emission spectra of aggregates formed using either of these combinations exhibit a vibronic pattern in which the ratio of the intensity of highest-energy band to that of the lower energy peaks depends strongly on the ratio of good to poor solvent. In aggregates formed from MeTHF:MeOH, this was shown to be due to the presence of both aggregate-like and monomer-like emitters forming a "core" and surrounding "shell"-like structure, respectively, within a single aggregate (J. Phys. Chem. C2011, 115, 15607-15616). In support of this model, the monomer-like emission is shown here to be significantly decreased by changing the solvent pair to the more polar THF:water. This suggests that nanoaggregates formed in THF:water contain a much smaller proportion of monomer-like chains than those formed in MeTHF/MeOH, as would be expected from using a more highly polar nonsolvent. Results from bulk steady-state and time-resolved emission measurements as well as fluorescence lifetime imaging microscopy (FLIM) of the aggregates are shown to be consistent with this interpretation.

Quantum interference between the third and fourth exciton states in semiconducting carbon nanotubes using resonance Raman spectroscopy.

We exploit an energy level crossover effect [Haroz et al., Phys. Rev. B 77, 125405 (2008)] to probe quantum interference in the resonance Raman response from carbon nanotube samples highly enriched in the single semiconducting chiralities of (8,6), (9,4), and (10,5). UV Raman excitation profiles of G-band spectra reveal unambiguous signatures of interference between the third and fourth excitonic states (E(33) and E(44)). Both constructive and destructive responses are observed and lead to anomalous intensity ratios in the LO and TO modes. Especially large anomalies for the (10,5) structure result from nearly identical energies found for the two E(ii) transitions. The interference patterns demonstrate that the sign of the exciton-phonon coupling matrix elements changes for the LO mode between the two electronic states, and remains the same for the TO mode. Significant non-Condon contributions to the Raman response are also found.

Ion specific influences on the stability and unfolding transitions of a naturally aggregating protein; RecA.

The Escherichia coli RecA protein is a naturally aggregated protein complex that is affected by the presence of salts. In order to gain further insight into the nature of the ion-interactions on a naturally aggregating protein we used circular dichroism (CD), fluorescence and dynamic light scattering (DLS) to study the effects of different concentrations of MgCl2, CaCl2, NaCl, Na2SO4, and MgSO4 on RecA structure and thermal unfolding. The results show unique ion influences on RecA structure, aggregation, unfolding transitions and stability and the anion effects correlate with the reverse Hofmeister series. The mechanisms of the ion-induced changes most likely result from specific ion binding, changes in the interfacial tension and altered protein-solvent interactions that may be especially important for protein-protein interactions in naturally aggregating proteins. The presence of some ions leads to the formation of RecA complexes that are resistant to complete denaturation and nonspecific aggregation.

Ag K-edge EXAFS analysis of DNA-templated fluorescent silver nanoclusters: insight into the structural origins of emission tuning by DNA sequence variations.

DNA-templated silver nanoclusters are promising biological fluorescence probes due to their useful fluorescence properties, including tunability of emission wavelength through DNA template sequence variations. Ag K-edge EXAFS analysis of DNA-templated silver nanoclusters has been used to obtain insight into silver nanocluster bonding, size, and structural correlations to fluorescence. The results indicate the presence of small silver nanoclusters (<30 silver atoms) containing Ag-Ag bonds and Ag-N/O ligations to DNA. The DNA sequence used leads to differences in silver-DNA ligation as well as silver nanocluster size. The results support a model in which cooperative effects of both Ag-DNA ligation and variations in cluster size lead to the tuning of the fluorescence emission of DNA-templated silver nanoclusters.

Violation of the condon approximation in semiconducting carbon nanotubes.

The Condon approximation is widely applied in molecular and condensed matter spectroscopy and states that electronic transition dipoles are independent of nuclear positions. This approximation is related to the Franck-Condon principle, which in its simplest form holds that electronic transitions are instantaneous on the time scale of nuclear motion. The Condon approximation leads to a long-held assumption in Raman spectroscopy of carbon nanotubes: intensities arising from resonance with incident and scattered photons are equal. Direct testing of this assumption has not been possible due to the lack of homogeneous populations of specific carbon nanotube chiralities. Here, we present the first complete Raman excitation profiles (REPs) for the nanotube G band for 10 pure semiconducting chiralities. In contrast to expectations, a strong asymmetry is observed in the REPs for all chiralities, with the scattered resonance always appearing weaker than the incident resonance. The observed behavior results from violation of the Condon approximation and originates in changes in the electronic transition dipole due to nuclear motion (non-Condon effect), as confirmed by our quantum chemical calculations. The agreement of our calculations with the experimental REP asymmetries and observed trends in family dependence indicates the behavior is intrinsic.