Organic Composomes as Supramolecular Aptamers

Lipid-Based Catalysis Demonstrated by Bilayer-Enabled Ester Hydrolysis

Lipids have not traditionally been considered likely candidates for catalyzing reactions in biological systems. However, there is significant evidence that aggregates of amphiphilic compounds are capable of catalyzing reactions in synthetic organic chemistry. Here, we demonstrate the potential for the hydrophobic region of a lipid bilayer to provide an environment suitable for catalysis by means of a lipid aggregate capable of speeding up a chemical reaction. By bringing organic molecules into the nonpolar or hydrophobic region of a lipid bilayer, reactions can be catalyzed by individual or collections of small, nonpolar, or amphiphilic molecules. We demonstrate this concept by the ester hydrolysis of calcein-AM to produce a fluorescent product, which is a widely used assay for esterase activity in cells. The reaction was first carried out in a two-phase octanol-water system, with the organic phase containing the cationic amphiphiles cetyltrimethylammonium bromide (CTAB) or octadecylamine. The octanol phase was then replaced with phospholipid vesicles in water, where the reaction was also found to be carried out. The reaction was monitored using quantitative fluorescence, which revealed catalytic turnover numbers on a scale of 10-7 to 10-8 s-1 for each system, which is much slower than enzymatic catalysis. The reaction product was characterized by 1H-NMR measurements, which were consistent with ester hydrolysis. The implications of thinking about lipids and lipid aggregates as catalytic entities are discussed in the context of biochemistry, pharmacology, and synthetic biology.

Kinetic Mechanism of Surfactant-Based Molecular Recognition: Selective Permeability across an Oil-Water Interface Regulated by Supramolecular Aggregates

Lipids are known to play a vital role in the molecular organization of all cellular life. Molecular recognition is another fundamental biological process that is generally attributed to biological polymers, such as proteins and nucleic acids. However, there is evidence that aggregates of lipids and lipid-like molecules are also capable of selectively binding to or regulating the partitioning of other molecules. We previously demonstrated that a model two-phase octanol/water system can selectively partition Red 40 and Blue 1 dyes added to an aqueous phase, with the selectivity depending on the surfactant (e.g., cetyltrimethylammonium bromide) dissolved in the organic phase. Here, we elucidate the mechanism of molecular recognition in this system by using quantitative partitioning experiments and molecular dynamics (MD) simulations. Our results indicate that the selectivity for the red dye is thermodynamically favored at all surfactant concentrations, while selectivity for the blue dye is kinetically favored at high surfactant concentrations. The kinetic selectivity for the blue dye correlates with the presence of molecular aggregation at the oil-water interface. Coarse-grained MD simulations elucidate nanoscale supramolecular structures that can preferentially bind one small molecule rather than another at an interface, providing a selectively permeable barrier in the absence of proteins. The results suggest a new supramolecular mechanism for molecular recognition with potential applications in drug delivery, drug discovery, and biosensing.

From autocatalysis to survival of the fittest in self-reproducing lipid systems

Studying autocatalysis - in which molecules catalyse their own formation - might help to explain the emergence of chemical systems that exhibit traits normally associated with biology. When coupled to other processes, autocatalysis can lead to complex systems-level behaviour in apparently simple mixtures. Lipids are an important class of chemicals that appear simple in isolation, but collectively show complex supramolecular and mesoscale dynamics. Here we discuss autocatalytic lipids as a source of extraordinary behaviour such as primitive chemical evolution, chemotaxis, temporally controllable materials and even as supramolecular catalysts for continuous synthesis. We survey the literature since the first examples of lipid autocatalysis and highlight state-of-the-art synthetic systems that emulate life, displaying behaviour such as metabolism and homeostasis, with special consideration for generating structural complexity and out-of-equilibrium models of life. Autocatalytic lipid systems have enormous potential for building complexity from simple components, and connections between physical effects and molecular reactivity are only just beginning to be discovered.

Combinatorial mixtures of organic solutes for improved liquid/liquid extraction of ions

Biological systems routinely extract and organize ions in complex yet highly ordered and active systems. Much of this function is attributed to proteins, although recent evidence indicates aggregates of lipids are also capable of molecular recognition. Here we tested the hypothesis that combinatorial mixtures of organic solutes might lead to enhanced liquid/liquid extraction. We started with liquid oleic acid as an organic phase extracting copper ions from water and added a library of additives. By using Bayesian optimization to autonomously direct the combinatorial formulation, we discovered mixtures that enhanced the extraction performance. The main additive that improved the system was octylphosphonic acid. Interestingly, the optimal mixture has a significant improvement compared to this additive alone. This suggests that the combinations of organic solutes are better than using pure components in liquid/liquid extraction. Furthermore, we found that precipitation occurs in the samples showing better extraction efficiency, which has interesting material properties and potential for new types of supramolecular biosensors.

Odor Discrimination by Lipid Membranes

Odor detection and discrimination in mammals is known to be initiated by membrane-bound G-protein-coupled receptors (GPCRs). The role that the lipid membrane may play in odor discrimination, however, is less well understood. Here, we used model membrane systems to test the hypothesis that phospholipid bilayer membranes may be capable of odor discrimination. The effect of S-carvone, R-carvone, and racemic lilial on the model membrane systems was investigated. The odorants were found to affect the fluidity of supported lipid bilayers as measured by fluorescence recovery after photobleaching (FRAP). The effect of odorants on surface-supported lipid multilayer microarrays of different dimensions was also investigated. The lipid multilayer micro- and nanostructure was highly sensitive to exposure to these odorants. Fluorescently-labeled lipid multilayer droplets of 5-micron diameter were more responsive to these odorants than ethanol controls. Arrays of lipid multilayer diffraction gratings distinguished S-carvone from R-carvone in an artificial nose assay. Our results suggest that lipid bilayer membranes may play a role in odorant discrimination and molecular recognition in general.

Micellar Composition Affects Lipid Accretion Kinetics in Molecular Dynamics Simulations: Support for Lipid Network Reproduction

Mixed lipid micelles were proposed to facilitate life through their documented growth dynamics and catalytic properties. Our previous research predicted that micellar self-reproduction involves catalyzed accretion of lipid molecules by the residing lipids, leading to compositional homeostasis. Here, we employ atomistic Molecular Dynamics simulations, beginning with 54 lipid monomers, tracking an entire course of micellar accretion. This was done to examine the self-assembly of variegated lipid clusters, allowing us to measure entry and exit rates of monomeric lipids into pre-micelles with different compositions and sizes. We observe considerable rate-modifications that depend on the assembly composition and scrutinize the underlying mechanisms as well as the energy contributions. Lastly, we describe the measured potential for compositional homeostasis in our simulated mixed micelles. This affirms the basis for micellar self-reproduction, with implications for the study of the origin of life.

Overview and emerging trends in optical fiber aptasensing

Optical fiber biosensors have attracted growing interest over the last decade and quickly became a key enabling technology, especially for the detection of biomarkers at extremely low concentrations and in small volumes. Among the many and recent fiber-optic sensing amenities, aptamers-based sensors have shown unequalled performances in terms of ease of production, specificity, and sensitivity. The immobilization of small and highly stable bioreceptors such as DNA has bolstered their use for the most varied applications e.g., medical diagnosis, food safety and environmental monitoring. This review highlights the recent advances in aptamer-based optical fiber biosensors. An in-depth analysis of the literature summarizes different fiber-optic structures and biochemical strategies for molecular detection and immobilization of receptors over diverse surfaces. In this review, we analyze the features offered by those sensors and discuss about the next challenges to be addressed. This overview investigates both biochemical and optical parameters, drawing the guiding lines for forthcoming innovations and prospects in this ever-growing field of research.

Dynamic lipid aptamers: non-polymeric chemical path to early life

A widespread dogma asserts that life could not have emerged without biopolymers - RNA and proteins. However, the widely acknowledged implausibility of a spontaneous appearance and proliferation of these complex molecules in primordial messy chemistry casts doubt on this scenario. A proposed alternative is "Lipid-First", based on the evidence that lipid assemblies may spontaneously emerge in heterogeneous environments, and are shown to undergo growth and fission, and to portray autocatalytic self-copying. What seems undecided is whether lipid assemblies have protein-like capacities for stereospecific interactions, a sine qua non of life processes. This Viewpoint aims to alleviate such doubts, pointing to growing experimental evidence that lipid aggregates possess dynamic surface configurations capable of stereospecific molecular recognition. Such findings help support a possible key role of lipids in seeding life's origin.

Self-reproducing catalytic micelles as nanoscopic protocell precursors

Protocells at life's origin are often conceived as bilayer-enclosed precursors of life, whose self-reproduction rests on the early advent of replicating catalytic biopolymers. This Perspective describes an alternative scenario, wherein reproducing nanoscopic lipid micelles with catalytic capabilities were forerunners of biopolymer-containing protocells. This postulate gains considerable support from experiments describing micellar catalysis and autocatalytic proliferation, and, more recently, from reports on cross-catalysis in mixed micelles that lead to life-like steady-state dynamics. Such results, along with evidence for micellar prebiotic compatibility, synergize with predictions of our chemically stringent computer-simulated model, illustrating how mutually catalytic lipid networks may enable micellar compositional reproduction that could underlie primal selection and evolution. Finally, we highlight studies on how endogenously catalysed lipid modifications could guide further protocellular complexification, including micelle to vesicle transition and monomer to biopolymer progression. These portrayals substantiate the possibility that protocellular evolution could have been seeded by pre-RNA lipid assemblies.

Aptamer Functionalized Lipid Multilayer Gratings for Label-Free Analyte Detection

Lipid multilayer gratings are promising optical biosensor elements that are capable of transducing analyte binding events into changes in an optical signal. Unlike solid state transducers, reagents related to molecular recognition and signal amplification can be incorporated into the lipid grating ink volume prior to fabrication. Here we describe a strategy for functionalizing lipid multilayer gratings with a DNA aptamer for the protein thrombin that allows label-free analyte detection. A double cholesterol-tagged, double-stranded DNA linker was used to attach the aptamer to the lipid gratings. This approach was found to be sufficient for binding fluorescently labeled thrombin to lipid multilayers with micrometer-scale thickness. In order to achieve label-free detection with the sub-100 nm-thick lipid multilayer grating lines, the binding affinity was improved by varying the lipid composition. A colorimetric image analysis of the light diffracted from the gratings using a color camera was then used to identify the grating nanostructures that lead to an optimal signal. Lipid composition and multilayer thickness were found to be critical parameters for the signal transduction from the aptamer functionalized lipid multilayer gratings.