Selectivity in the chiral self-assembly of nucleobase-arylazopyrazole photoswitches along DNA templates.

The control of supramolecular DNA assembly through external stimuli such as light represents a promising approach to control bioreactions, and modulate hybridization or delivery processes. Here, we report on the design of nucleobase-containing arylazopyrazole photoswitches that undergo chiral organization upon self-assembly along short DNA templates. Chiroptical spectroscopy shows that the specific nucleobases allow selectivity in the resulting supramolecular DNA complexes, and UV light irradiation triggers partial desorption of the arylazopyrazole photoswitches. Molecular modeling studies reveal the differences of binding modes between the two configurations in the templated assembly. Remarkably, our results show that the photoswitching behaviour controls the self-assembly process along DNA, opening the way to potential applications as nano- and biomaterials.

Modifying the Catalytic Activity of Lipopeptide Assemblies with Nucleobases.

Biohybrid catalysts that operate in aqueous media are intriguing for systems chemistry. In this paper, we investigate whether control over the self-assembly of biohybrid catalysts can tune their properties. As a model, we use the catalytic activity of functional hybrid molecules consisting of a catalytic H-dPro-Pro-Glu tripeptide, derivatized with fatty acid and nucleobase moieties. This combination of simple biological components merged the catalytic properties of the peptide with the self-assembly of the lipid, and the structural ordering of the nucleobases. The biomolecule hybrids self-assemble in aqueous media into fibrillar assemblies and catalyze the reaction between butanal and nitrostyrene. The interactions between the nucleobases enhanced the order of the supramolecular structures and affected their catalytic activity and stereoselectivity. The results point to the significant control and ordering that nucleobases can provide in the self-assembly of biologically inspired supramolecular catalysts.

The protometabolic nature of prebiotic chemistry.

The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.

Collective adaptability in a replication network of minimal nucleobase sequences.

A major challenge for understanding the origins of life is to explore how replication networks can engage in an evolutionary process. Herein, we shed light on this problem by implementing a network constituted by two different types of extremely simple biological components: the amino acid cysteine and the canonical nucleobases adenine and thymine, connected through amide bonds to the cysteine amino group and oxidation of its thiol into three possible disulfides. Supramolecular and kinetic analyses revealed that both self- and mutual interactions between such dinucleobase compounds drive their assembly and replication pathways. Those pathways involving sequence complementarity led to enhanced replication rates, suggesting a potential bias for selection. The interplay of synergistic dynamics and competition between replicators was then simulated, under conditions that are not easily accessible with experiments, in an open reactor parametrized and constrained with the unprecedentedly complete experimental kinetic data obtained for our replicative network. Interestingly, the simulations show bistability, as a selective amplification of different species depending on the initial mixture composition. Overall, this network configuration can favor a collective adaptability to changes in the availability of feedstock molecules, with disulfide exchange reactions serving as 'wires' that connect the different individual auto- and cross-catalytic pathways.

Tailored Multivalent Targeting of Siglecs with Photosensitizing Liposome Nanocarriers.

The modification of surfaces with multiple ligands allows the formation of platforms for the study of multivalency in diverse processes. Herein we use this approach for the implementation of a photosensitizer (PS)-nanocarrier system that binds efficiently to siglec-10, a member of the CD33 family of siglecs (sialic acid (SA)-binding immunoglobulin-like lectins). In particular, a zinc phthalocyanine derivative bearing three SA moieties (PcSA) has been incorporated in the membrane of small unilamellar vesicles (SUVs), retaining its photophysical properties upon insertion into the SUV's membrane. The interaction of these biohybrid systems with human siglec-10-displaying supported lipid bilayers (SLBs) has shown the occurrence of weakly multivalent, superselective interactions between vesicle and SLB. The SLB therefore acts as an excellent cell membrane mimic, while the binding with PS-loaded SUVs shows the potential for targeting siglec-expressing cells with photosensitizing nanocarriers.

A Janus-Type Phthalocyanine for the Assembly of Photoactive DNA Origami Coatings.

Design and synthesis of novel photosensitizer architectures is a key step toward new multifunctional molecular materials. Photoactive Janus-type molecules provide interesting building blocks for such systems by presenting two well-defined chemical functionalities that can be utilized orthogonally. Herein a multifunctional phthalocyanine is reported, bearing a bulky and positively charged moiety that hinders their aggregation while providing the ability to adhere on DNA origami nanostructures via reversible electrostatic interactions. On the other hand, triethylene glycol moieties render a water-soluble and chemically inert corona that can stabilize the structures. This approach provides insight into the molecular design and synthesis of Janus-type sensitizers that can be combined with biomolecules, rendering optically active biohybrids.

Tuning the Nanoaggregates of Sialylated Biohybrid Photosensitizers for Intracellular Activation of the Photodynamic Response.

In the endeavor of extending the clinical use of photodynamic therapy (PDT) for the treatment of superficial cancers and other neoplastic diseases, deeper knowledge and control of the subcellular processes that determine the response of photosensitizers (PS) are needed. Recent strategies in this direction involve the use of activatable and nanostructured PS. Here, both capacities have been tuned in two dendritic zinc(II) phthalocyanine (ZnPc) derivatives, either asymmetrically or symmetrically substituted with 3 and 12 copies of the carbohydrate sialic acid (SA), respectively. Interestingly, the amphiphilic ZnPc-SA biohybrid (1) self-assembles into well-defined nanoaggregates in aqueous solution, facilitating cellular internalization and transport whereas the PS remains inactive. Within the cells, these nanostructured hybrids localize in the lysosomes, as usually happens for anionic and hydrophilic aggregated PS. Yet, in contrast to most of them (e. g., compound 2), hybrid 1 recovers the capacity for photoinduced ROS generation within the target organelles due to its amphiphilic character; this allows disruption of aggregation when the compound is inserted into the lysosomal membrane, with the concomitant highly efficient PDT response.

Peripherally Crowded Cationic Phthalocyanines as Efficient Photosensitizers for Photodynamic Therapy.

Photodynamic therapy is a treatment modality of cancer based on the production of cytotoxic species upon the light activation of photosensitizers. Zinc phthalocyanine photosensitizers bearing four or eight bulky 2,6-di(pyridin-3-yl)phenoxy substituents were synthesized, and pyridyl moieties were methylated. The quaternized derivatives did not aggregate at all in water and retained their good photophysical properties. High photodynamic activity of these phthalocyanines was demonstrated on HeLa, MCF-7, and EA.hy926 cells with a very low EC50 of 50 nM (for the MCF-7 cell line) upon light activation while maintaining low toxicity in the dark (TC50 ≈ 600 µM), giving thus good phototherapeutic indexes (TC50/EC50) above 1400. The compounds localized primarily in the lysosomes, leading to their rupture after light activation. This induced an apoptotic cell death pathway with secondary necrosis because of extensive and swift damage to the cells. This work demonstrates the importance of a bulky and rigid arrangement of peripheral substituents in the development of photosensitizers.

Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks.

Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.

Synergy of Electrostatic and π-π Interactions in the Realization of Nanoscale Artificial Photosynthetic Model Systems.

In the scientific race to build up photoactive electron donor-acceptor systems with increasing efficiencies, little is known about the interplay of their building blocks when integrated into supramolecular nanoscale arrays, particularly in aqueous environments. Here, we describe an aqueous donor-acceptor ensemble whose emergence as a nanoscale material renders it remarkably stable and efficient. We have focused on a tetracationic zinc phthalocyanine (ZnPc) featuring pyrenes, which shows an unprecedented mode of aggregation, driven by subtle cooperation between electrostatic and π-π interactions. Our studies demonstrate monocrystalline growth in solution and a symmetry-breaking intermolecular charge transfer between adjacent ZnPcs upon photoexcitation. Immobilizing a negatively charged fullerene (C60 ) as electron acceptor onto the monocrystalline ZnPc assemblies was found to enhance the overall stability, and to suppress the energy-wasting charge recombination found in the absence of C60 . Overall, the resulting artificial photosynthetic model system exhibits a high degree of preorganization, which facilitates efficient charge separation and subsequent charge transport.

Phthalocyanine-DNA origami complexes with enhanced stability and optical properties.

In this communication, electrostatically assembled phthalocyanine (Pc)-DNA origami (DO) complexes are formed and their optical properties are demonstrated. The formation of the complex prevents the Pc aggregation, thus yielding an enhanced optical response and photooxidative resilience towards aggregation in biologically relevant media. Simultaneously, the Pc protects the DO against enzymatic digestion. Both features solve previous drawbacks associated with phthalocyanine photosensitizers and DNA nanocarriers. The studied complexes may find use in technologies related to the photogeneration of singlet oxygen, e.g., photocatalysis, diagnositic arrays and photodynamic therapy.

Amphiphilic phthalocyanines in polymeric micelles: a supramolecular approach toward efficient third-generation photosensitizers.

In this paper we describe a straightforward supramolecular strategy to encapsulate silicon phthalocyanine (SiPc) photosensitizers (PS) in polymeric micelles made of poly(ε-caprolactone)-b-methoxypoly(ethylene glycol) (PCL-PEG) block copolymers. While PCL-PEG micelles are promising nanocarriers based on their biocompatibility and biodegradability, the design of our new PS favors their encapsulation. In particular, they combine two axial benzoyl substituents, each of them carrying either three hydrophilic methoxy(triethylenoxy) chains (1), three hydrophobic dodecyloxy chains (3), or both kinds of chains (2). The SiPc derivatives 1 and 2 are therefore amphiphilic, with the SiPc unit contributing to the hydrophobic core, while lipophilicity increases along the series, making it possible to correlate the loading efficacy in PCL-PEG micelles with the hydrophobic/hydrophilic balance of the PS structure. This has led to a new kind of third-generation nano-PS that efficiently photogenerates 1O2, while preliminary in vitro experiments demonstrate an excellent cellular uptake and a promising PDT activity.

Programmed Recognition between Complementary Dinucleolipids To Control the Self-Assembly of Lipidic Amphiphiles.

One of the major goals in systems chemistry is to create molecular assemblies with emergent properties that are characteristic of life. An interesting approach toward this goal is based on merging different biological building blocks into synthetic systems with properties arising from the combination of their molecular components. The covalent linkage of nucleic acids (or their constituents: nucleotides, nucleosides and nucleobases) with lipids in the same hybrid molecule leads, for example, to the so-called nucleolipids. Herein, we describe nucleolipids with a very short sequence of two nucleobases per lipid, which, in combination with hydrophobic effects promoted by the lipophilic chain, allow control of the self-assembly of lipidic amphiphiles to be achieved. The present work describes a spectroscopic and microscopy study of the structural features and dynamic self-assembly of dinucleolipids that contain adenine or thymine moieties, either pure or in mixtures. This approach leads to different self-assembled nanostructures, which include spherical, rectangular and fibrillar assemblies, as a function of the sequence of nucleobases and chiral effects of the nucleolipids involved. We also show evidence that the resulting architectures can encapsulate hydrophobic molecules, revealing their potential as drug delivery vehicles or as compartments to host interesting chemistries in their interior.

Phthalocyanine-Virus Nanofibers as Heterogeneous Catalysts for Continuous-Flow Photo-Oxidation Processes.

The generation of highly reactive oxygen species (ROS) at room temperature for application in organic synthesis and wastewater treatment represents a great challenge of the current chemical industry. In fact, the development of biodegradable scaffolds to support ROS-generating active sites is an important prerequisite for the production of environmentally benign catalysts. Herein, the electrostatic cocrystallization of a cationic phthalocyanine (Pc) and negatively charged tobacco mosaic virus (TMV) is described, together with the capacity of the resulting crystals to photogenerate ROS. To this end, a novel peripherally crowded zinc Pc (1) is synthesized. With 16 positive charges, this photosensitizer shows no aqueous aggregation, and is able to act as a molecular glue in the unidimensional assembly of TMV. A step-wise decrease of ionic strength in mixtures of both components results in exceptionally long fibers, constituted by hexagonally bundled viruses thoroughly characterized by electron and confocal microscopy. The fibers are able to produce ROS in a proof-of-concept microfluidic device, where they are immobilized and irradiated in several cycles, showing a resilient performance. The bottom-up approach also enables the light-triggered disassembly of fibers after use. This work represents an important example of a biohybrid material with projected application in light-mediated heterogeneous catalysis.

The Informational Substrate of Chemical Evolution: Implications for Abiogenesis.

A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology indicates that information processing in cells occurs through a hierarchy of genes regulating the activity of other genes through complex metabolic networks. There is an implicit semiotic character in this way of dealing with information, based on functional molecules that act as signs to achieve self-regulation of the whole network. In contrast to cells, chemical systems are not thought of being able to process information, yet they must have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could somehow process information, in order to regulate their own constituent reactions and supramolecular organization processes. The purpose of this essay is then to reflect about the distinctive features of information in living and non-living matter, and on how the capacity of biological organisms for information processing was possibly rooted in a particular type of chemical systems (here referred to as autonomous chemical systems), which could self-sustain and reproduce through organizational closure of their molecular building blocks.

Porphyrinoid biohybrid materials as an emerging toolbox for biomedical light management.

The development of photoactive and biocompatible nanomaterials is a current major challenge of materials science and nanotechnology, as they will contribute to promoting current and future biomedical applications. A growing strategy in this direction consists of using biologically inspired hybrid materials to maintain or even enhance the optical properties of chromophores and fluorophores in biological media. Within this area, porphyrinoids constitute the most important family of organic photosensitizers. The following extensive review will cover their incorporation into different kinds of photosensitizing biohybrid materials, as a fundamental research effort toward the management of light for biomedical use, including technologies such as photochemical internalization (PCI), photoimmunotherapy (PIT), and theranostic combinations of fluorescence imaging and photodynamic therapy (PDT) or photodynamic inactivation (PDI) of microorganisms.

Macrophage selective photodynamic therapy by meta-tetra(hydroxyphenyl)chlorin loaded polymeric micelles: A possible treatment for cardiovascular diseases.

Selective elimination of macrophages by photodynamic therapy (PDT) is a new and promising therapeutic modality for the reduction of atherosclerotic plaques. m-Tetra(hydroxyphenyl)chlorin (mTHPC, or Temoporfin) may be suitable as photosensitizer for this application, as it is currently used in the clinic for cancer PDT. In the present study, mTHPC was encapsulated in polymeric micelles based on benzyl-poly(ε-caprolactone)-b-methoxy poly(ethylene glycol) (Ben-PCL-mPEG) using a film hydration method, with loading capacity of 17%. Because of higher lipase activity in RAW264.7 macrophages than in C166 endothelial cells, the former cells degraded the polymers faster, resulting in faster photosensitizer release and higher in vitro photocytotoxicity of mTHPC-loaded micelles in those macrophages. However, we observed release of mTHPC from the micelles in 30min in blood plasma in vitro which explains the observed similar in vivo pharmacokinetics of the mTHPC micellar formulation and free mTHPC. Therefore, we could not translate the beneficial macrophage selectivity from in vitro to in vivo. Nevertheless, we observed accumulation of mTHPC in atherosclerotic lesions of mice aorta's which is probably the result of binding to lipoproteins upon release from the micelles. Therefore, future experiments will be dedicated to increase the stability and thus allow accumulation of intact mTHPC-loaded Ben-PCL-mPEG micelles to macrophages of atherosclerotic lesions.

Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems.

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided.

Photoantimicrobial Biohybrids by Supramolecular Immobilization of Cationic Phthalocyanines onto Cellulose Nanocrystals.

The development of photoactive and biocompatible nanostructures is a highly desirable goal to address the current threat of antibiotic resistance. Here, we describe a novel supramolecular biohybrid nanostructure based on the non-covalent immobilization of cationic zinc phthalocyanine (ZnPc) derivatives onto unmodified cellulose nanocrystals (CNC), following an easy and straightforward protocol, in which binding is driven by electrostatic interactions. These non-covalent biohybrids show strong photodynamic activity against S. aureus and E. coli, representative examples of Gram-positive and Gram-negative bacteria, respectively, and C. albicans, a representative opportunistic fungal pathogen, outperforming the free ZnPc counterparts and related nanosystems in which the photosensitizer is covalently linked to the CNC surface.

The systems perspective at the crossroads between chemistry and biology.

During the last century a number of authors pointed to the inherently systemic and dynamic nature of the living, yet their message was largely ignored by the mainstream of the scientific community. Tibor Ganti was one of those early pioneers, proposing a theoretical framework to understand the living principles in terms of chemical transformation cycles and their coupling. The turn of the century then brought with it a novel 'systems' paradigm, which shined light on all that previous work and carried many implications for the way we conceive of chemical and biological complexity today. In this article tribute is paid to some of those seminal contributions, highlighting the importance of adopting a systems view in present chemistry, particularly if plausible mechanisms of chemical evolution toward the first living entities want to be unraveled. We examine and put in perspective recent discoveries in the emerging subfield of 'prebiotic systems chemistry', reaching the conclusion that the functional coupling of protocellular subsystems (i.e., protometabolism, protogenome and membrane compartment) is the most challenging target to make qualitative advances in the problem of the origins of life. For the long-awaited goal of assembling an autonomous protocell from its most basic molecular building blocks, we further suggest that a systems integrative strategy should be considered from the earliest synthetic steps, already at the level of monomer precursors, opening the way to biogenesis.