Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid

Gaseous Synergistic Self-Assembly and Arraying to Develop Bio-Organic Photocapacitors for Neural Photostimulation

Bioinspired supramolecular architectonics is attracting increasing interest due to their flexible organization and multifunctionality. However, state-of-the-art bioinspired architectonics generally take place in solvent-based circumstance, thus leading to achieving precise control over the self-assembly remains challenging. Moreover, the intrinsic difficulty of ordering the bio-organic self-assemblies into stable large-scale arrays in the liquid environment for engineering devices severely restricts their extensive applications. Herein, a gaseous organization strategy is proposed with the physical vapor deposition (PVD) technology, allowing the bio-organic monomers not only self-assemble into architectures well-established from the solvent-based approaches but morphologies distinct from those delivered from the liquid cases. Specifically, 9-fluorenylmethyloxycarbonyl-phenylalanine-phenylalanine (Fmoc-FF) self-assembles into spheres with tailored dimensions in the gaseous environment rather than conventional nanofibers, due to the distinct organization mechanisms. Arraying of the spherical architectures can integrate their behaviors, thus endorsing the bio-organic film the ability of programmable optoelectronic properties, which can be employed to design P-N heterojunction-based bio-photocapacitors for non-invasive and nongenetic neurostimulations. The findings demonstrate that the gaseous strategy may offer an alternative approach to achieve unprecedented bio-organic superstructures, and allow ordering into large-scale arrays for behavior integration, potentially paving the avenue of developing supramolecular devices and promoting the practical applications of bio-organic architectonics.

Morphology and Applications of Self-Assembled Peptide Nucleic Acids

Obtaining new materials by exploiting the self-assembly of biomolecules is a very challenging field. In recent years, short peptides and nucleic acids have been used as scaffolds to produce supramolecular structures for different applications in the biomedical and technological fields. In this review, we will focus on the self-assembly of peptide nucleic acids (PNAs), their conjugates with peptides, or other molecules. We will describe the physical properties of the assembled systems and, where described, the application they were designed for.

A Host-Guest Approach to Engineering Oxidase-Mimetic Assembly with Substrate Selectivity and Dynamic Catalysis

The creation of synthetic materials that emulate the complexity of natural systems, such as enzymes, remains a challenge in biomimicry. Here, we present a simple yet effective strategy to introduce substrate selectivity and dynamic responsiveness into an enzyme-mimetic supramolecular material. We achieved this by anchoring γ-cyclodextrin to a fluorene-modified Lys/Cu2+ assembly, which mimics copper-dependent oxidase. The binding affinity among the components was examined using 1H NMR, isothermal titration calorimetry (ITC), and theoretical simulation. The γ-cyclodextrin acts as a host, forming a complex with the fluorenyl moiety and aromatic substrates of specific sizes. This ensures the proximity of the substrate reactive groups to the copper center, leading to size-selective enhancement of aromatic substrate oxidation, particularly favoring biphenyl substrates. Notably, α- and β-cyclodextrins do not exhibit this effect, and the native oxidase lacks this selectivity. Additionally, the binding affinity of the aromatic substrate to the catalyst can be dynamically tuned by adding α-cyclodextrin or by irradiating with different wavelengths in the presence of competitive azo-guests, resulting in switched oxidative activities. This approach offers a new avenue for designing biomimetic materials with tailorable active site structures and catalytic properties.

Supramolecular polyplexes from Janus peptide nucleic acids (bm-PNA-G5): self-assembled bm-PNA G-quadruplex and its tetraduplex with DNA

Nucleic acids (DNA and RNA) can form diverse secondary structures ranging from hairpins to duplex, triplex, G4-tetraplex and C4-i-motifs. Many of the DNA analogues designed as antisense oligonucleotides (ASO) are also adept at embracing such folded structures, although to different extents with altered stabilities. One such analogue, peptide nucleic acid (PNA), which is uncharged and achiral, forms hybrids with complementary DNA/RNA with greater stability and specificity than DNA:DNA/RNA hybrids. Like DNAs, these single-stranded PNAs can form PNA:DNA/RNA duplexes, PNA:DNA:PNA triplexes, PNA-G4 tetraplexes and PNA-C4-i-motifs. We have recently designed Janus-like bimodal PNAs endowed with two different nucleobase sequences on either side of a single aminoethylglycyl (aeg) PNA backbone and shown that these can simultaneously bind to two complementary DNA sequences from both faces of PNA. This leads to the formation of supramolecular polyplexes such as double duplexes, triple duplexes and triplexes of double duplexes with appropriate complementary DNA/RNA. Herein, we demonstrate that Janus/bimodal PNA with a poly G-sequence on the triazole side of the PNA backbone and mixed bases on the t-amide side, templates the initial formation of a (PNA-G5)4 tetraplex (triazole side), followed by the formation of a PNA:DNA duplex (t-amide side). Such a polyplex shows synergistic overall stabilisation compared to the isolated duplexes/quadruplex. The assembly of polyplexes with a shared backbone for duplexes and tetraplexes is programmable and may have potential applications in the self-assembly of nucleic acid nano- and origami structures. It is also shown that Janus PNAs enter the cells better than the standard aeg-PNA oligomers, and hence have implications for in vivo applications as well.

Metal Ion-Induced Unusual Stability of the Metastable Vesicle-like Intermediates Evolving during the Self-Assembly of Phenylalanine: Prominent Role of Surface Charge Inversion

The underlying mechanism and intermediate formation in the self-assembly of aromatic amino acids, peptides, and proteins remain elusive despite numerous reports. We, for the first time, report that one can stabilize the intermediates by tuning the metal ion-amino acid interaction. Microscopic and spectroscopic investigations of the self-assembly of carboxybenzyl (Z)-protected phenylalanine (ZF) reveal that the bivalent metal ions eventually lead to the formation of fibrillar networks similar to blank ZF whereas the trivalent ions develop vesicle-like intermediates that do not undergo fibrillation for a prolonged time. The time-lapse measurement of surface charge reveals that the surface charge of blank ZF and in the presence of bivalent metal ions changes from a negative value to zero, implying unstable intermediates leading to the fibril network. Strikingly, a prominent charge inversion from an initial negative value to a positive value in the presence of trivalent metal ions imparts unusual stability to the metastable intermediates.

Recent advancements in bionanomaterial applications of peptide nucleic acid assemblies

Peptide nucleic acid (PNA) is a unique combination of peptides and nucleic acids. PNA can exhibit hydrogen bonding interactions with complementary nucleobases like DNA/RNA. Also, its polyamide backbone allows easy incorporation of biomolecules like peptides and proteins to build hybrid molecular constructs. Because of chimeric structural properties, PNA has lots of potential to build diverse nanostructures. However, progress in the PNA material field is still immature compared with its massive applications in antisense oligonucleotide research. Examples of well-defined molecular assemblies have been reported with PNA amphiphiles, self-assembling guanine-PNA monomers/dimers, and PNA-decorated nucleic acids/ polymers/ peptides. All these works indicate the great potential of PNA to be used as bionanomaterials. The review summarizes the recent reports on PNA-based nanostructures and their versatile applications. Additionally, this review shares a perspective to promote a better understanding of controlling molecular assembly by the systematic structural modifications of PNA monomers.

The Design of a Participatory Peptide Nucleic Acid Duplex Crosslinker to Enhance the Stiffness of Self-Assembled Peptide Gels

Herein, peptide nucleic acids (PNAs) are employed in the design of a participatory duplex PNA-peptide crosslinking agent. Biophysical and mechanical studies show that crosslinkers present during peptide assembly leading to hydrogelation participate in the formation of fibrils while simultaneously installing crosslinks into the higher-order network that constitutes the peptide gel. The addition of 2 mol % crosslinker into the assembling system results in a ~100 % increase in mechanical stiffness without affecting the rate of peptide assembly or the local morphology of fibrils within the gel network. Stiffness enhancement is realized by only affecting change in the elastic component of the viscoelastic gel. A synthesis of the PNA-peptide duplex crosslinkers is provided that allows facile variation in peptide composition and addresses the notorious hydrophobic content of PNAs. This crosslinking system represents a new tool for modulating the mechanical properties of peptide-based hydrogels.

Histidine-Based Supramolecular Nanoassembly Exhibiting Dual Enzyme-Mimetic Functions: Altering the Tautomeric Preference of Histidine to Tailor Oxidative/Hydrolytic Catalysis

Challenges persist in replicating enzyme-like active sites with functional group arrangements in supramolecular catalysis. In this study, we present a supramolecular material comprising Fmoc-modified histidine and copper. We also investigated the impact of noncanonical amino acids (δmH and εmH), isomers of histidine, on the catalytic process. The Fmoc-δmH-based nanoassembly exhibits an approximately 15-fold increase in oxidative activity and an ∼50-fold increase in hydrolytic activity compared to Fmoc-εmH (kcat/Km). This distinction arises from differences in basicity and ligation properties between the ε- and δ-nitrogen of histidine. The addition of guanosine monophosphate further enhances the oxidative activity of the histidine- and methylated histidine-based catalysts. The Fmoc-δmH/Cu2+-based nanoassembly catalyzes the oxidation/hydrolysis cascade of 2',7'-dichlorofluorescein diacetate, benefiting from the synergistic effect between the copper center and the nonligating ε-nitrogen of histidine. These findings advance the biomimetic catalyst design and provide insights into the mechanistic role of essential residues in natural systems.

Frontiers of molecular crystal structure prediction for pharmaceuticals and functional organic materials

The reliability of organic molecular crystal structure prediction has improved tremendously in recent years. Crystal structure predictions for small, mostly rigid molecules are quickly becoming routine. Structure predictions for larger, highly flexible molecules are more challenging, but their crystal structures can also now be predicted with increasing rates of success. These advances are ushering in a new era where crystal structure prediction drives the experimental discovery of new solid forms. After briefly discussing the computational methods that enable successful crystal structure prediction, this perspective presents case studies from the literature that demonstrate how state-of-the-art crystal structure prediction can transform how scientists approach problems involving the organic solid state. Applications to pharmaceuticals, porous organic materials, photomechanical crystals, organic semi-conductors, and nuclear magnetic resonance crystallography are included. Finally, efforts to improve our understanding of which predicted crystal structures can actually be produced experimentally and other outstanding challenges are discussed.

Colorimetric Sensor Based on the Oxidase-Mimic Supramolecular Catalyst for Selective and Sensitive Biomolecular Detection

We have engineered a colorimetric sensor capable of selective and sensitive detection of amino acids. This sensor employs a supramolecular copper-dependent oxidase mimic as the probe, stemming from our prior research. The oxidase mimic is constructed through the self-assembly of commercially available guanosine monophosphate (GMP), Fmoc-lysine, and Cu2+. It catalyzes the formation of a red product with a maximum absorbance at 510 nm. The changes in color and absorbance are responsive to both the concentrations and types of amino acids present. This effect is most pronounced in the presence of histidine, with a detection limit (LOD) of 6.4 nM. Furthermore, the catalytic probe can distinguish histidine from histamine and imidazole propionate, as well as 1-methyl-histidine from 3-methyl-histidine, based on their distinct coordination capacities with copper. This underscores the high selectivity of the sensing platform. Both theoretical simulations and experimental results (including UV-vis spectra, fluorescence, and EPR) indicate that the amino acids may engage in copper center coordination, thereby impeding O2 access to copper─a pivotal aspect of the oxidase catalysis. This sensing platform, characteristic of its swift response, simple fabrication, and exceptional sensitivity and selectivity, can also be applied to detect other biological analytes such as nucleotides. It holds potential for use in environmental and biochemical analyses.

Specific interaction based drug loading strategies

Drug carriers have been commonly used for drug control release, enhancing drug efficacy and/or minimizing side-effects. However, it is still difficult to get a high loading efficiency when encapsulating super hydrophilic drugs with a narrow therapeutic index, such as many neurotoxins. Increasing the carrier proportion can improve drug loading to a certain degree, while the burst released drug when the formulation enters the body may cause overdose side-effects. Moreover, high-dose carriers themselves may increase the metabolic burden of the body. Hence, new drug carriers and/or loading strategies are urgently needed to promote the applications of these drugs. This minireview will introduce drug loading strategies based on specific interactions (between drugs and carriers) and will discuss the challenges and perspectives of these strategies. This work is expected to provide alternative inspiration for the delivery of hydrophilic drugs.

Computer simulations as an effective way to distinguish supramolecular nanostructure in cyclic and phenyl alcohols

Molecular dynamics simulations supported by x-ray-diffraction experimental data were utilized to demonstrate how replacing the cyclic ring with the phenyl one in molecules of alcohols significantly differentiates their nanostructure by reducing the number of H-bonded clusters. Besides, molecules in the phenyl alcohols associate themselves in clusters via phenyl ring organization which likely is the result of OH⋯π and π⋯π interactions. Thus, at room temperature, the supramolecular structure of phenyl alcohols is more heterogeneous and governed by the formation of various clusters arising due to three types of interactions, while in cyclic alcohols, the H bonding controls the association of molecules. We believe that our methodology could be applied to better understand the fundamental process of association via H bonding and the competitive aggregation caused by phenyl rings.

A supramolecular metalloenzyme possessing robust oxidase-mimetic catalytic function

Enzymes fold into unique three-dimensional structures to distribute their reactive amino acid residues, but environmental changes can disrupt their essential folding and lead to irreversible activity loss. The de novo synthesis of enzyme-like active sites is challenging due to the difficulty of replicating the spatial arrangement of functional groups. Here, we present a supramolecular mimetic enzyme formed by self-assembling nucleotides with fluorenylmethyloxycarbonyl (Fmoc)-modified amino acids and copper. This catalyst exhibits catalytic functions akin those of copper cluster-dependent oxidases, and catalytic performance surpasses to date-reported artificial complexes. Our experimental and theoretical results reveal the crucial role of periodic arrangement of amino acid components, enabled by fluorenyl stacking, in forming oxidase-mimetic copper clusters. Nucleotides provide coordination atoms that enhance copper activity by facilitating the formation of a copper-peroxide intermediate. The catalyst shows thermophilic behavior, remaining active up to 95 °C in an aqueous environment. These findings may aid the design of advanced biomimetic catalysts and offer insights into primordial redox enzymes.

Boosting the Piezoelectric Sensitivity of Amino Acid Crystals by Mechanical Annealing for the Engineering of Fully Degradable Force Sensors

Biodegradable piezoelectric force sensors can be used as implantable medical devices for monitoring physiological pressures of impaired organs or providing essential stimuli for drug delivery and tissue regeneration without the need of additional invasive removal surgery or battery power. However, traditional piezoelectric materials, such as inorganic ceramics and organic polymers, show unsatisfactory degradability, and cytotoxicity. Amino acid crystals are biocompatible and exhibit outstanding piezoelectric properties, but their small crystal size makes it difficult to align the crystals for practical applications. Here, a mechanical-annealing strategy is reported for engineering all-organic biodegradable piezoelectric force sensors using natural amino acid crystals as piezoelectric materials. It is shown that the piezoelectric constant of the mechanical-annealed crystals can reach 12 times that of the single crystal powders. Moreover, mechanical annealing results in flat and smooth surfaces, thus improving the contact of the crystal films with the electrodes and leading to high output voltages of the devices. The packaged force sensors can be used to monitor dynamic motions, including muscle contraction and lung respiration, in vivo for 4 weeks and then gradually degrade without causing obvious inflammation or systemic toxicity. This work provides a way to engineer all-organic and biodegradable force sensors for potential clinical applications.

Tuning dynamic DNA- and peptide-driven self-assembly in DNA-peptide conjugates

DNA-peptide conjugates offer an opportunity to marry the benefits of both biomolecular classes, combining the high level of programmability found with DNA, with the chemical diversity of peptides. These hybrid systems offer potential in fields such as therapeutics, nanotechnology, and robotics. Using the first DNA-β-turn peptide conjugate, we present three studies investigating the self-assembly of DNA-peptide conjugates over a period of 28 days. Time-course studies, such as these have not been previously conducted for DNA-peptide conjugates, although they are common in pure peptide assembly, for example in amyloid research. By using aging studies to assess the structures produced, we gain insights into the dynamic nature of these systems. The first study explores the influence varying amounts of DNA-peptide conjugates have on the self-assembly of our parent peptide. Study 2 explores how DNA and peptide can work together to change the structures observed during aging. Study 3 investigates the presence of orthogonality within our system by switching the DNA and peptide control on and off independently. These results show that two orthogonal self-assemblies can be combined and operated independently or in tandem within a single macromolecule, with both spatial and temporal effects upon the resultant nanostructures.

Chiral Fibers Formation Upon Assembly of Tetraphenylalanine Peptide Conjugated to a PNA Dimer

Self‐assembly of biomolecules such as peptides, nucleic acids or their analogues affords supramolecular objects, exhibiting structures and physical properties dependent on the amino‐acid or nucleobase composition. Conjugation of the peptide diphenylalanine (FF) to peptide nucleic acids triggers formation of self‐assembled structures, mainly stabilized by interactions between FF. In this work we report formation of homogeneous chiral fibers upon self‐assembly of the hybrid composed of the tetraphenylalanine peptide (4F) conjugated to the PNA dimer adenine‐thymine (at). In this case nucleobases seem to play a key role in determining the morphology and chirality of the fibers. When the PNA “at” is replaced by guanine‐cytosine dimer “gc”, disordered structures are observed. Spectroscopic characterization of the self‐assembled hybrids, along with AFM and SEM studies is reported. Finally, a structural model consistent with the experimental evidence has also been obtained, showing how the building blocks of 4Fat arrange to give helical fibers.

Stable and momentary psychosocial correlates of everyday smoking: An application of Temporal Self-Regulation Theory

Smoking is one of the leading causes of non-communicable disease mortality and morbidity. Smoking behaviour is determined by both stable, person-level (e.g., motivation, nicotine dependence) and variable, situation-level factors (e.g., urges, cues). However, most theoretical approaches to understanding health behaviours so far have not integrated these two spheres of influence. Temporal Self-Regulation Theory (TST) integrates these person-level and situation-level factors, but has not yet been comprehensively applied to predicting smoking behaviour. We use Ecological Momentary Assessment to examine the utility of TST in predicting daily smoking. 46 smokers reported individual and environmental cues right after smoking and at random time points during the day. Cognitions, self-control, past behaviour, and nicotine dependence were assessed at baseline. Multi-level logistic regressions show that smoking is largely guided by momentary cues, but individual motivation can buffer their influence. This suggests that TST is a useful integrative approach to understand modifiable determinants of smoking and thus intervention targets.

Diphenylalanine Motif Drives Self-Assembling in Hybrid PNA-Peptide Conjugates

Peptides and nucleic acids can self-assemble to give supramolecular structures that find application in different fields, ranging from the delivery of drugs to the obtainment of materials endowed with optical properties. Forces that stabilize the "suprastructures" typically are hydrogen bonds or aromatic interactions; in case of nucleic acids, Watson-Crick pairing drives self-assembly while, in case of peptides, backbone hydrogen bonds and interactions between aromatic side chains trigger the formation of structures, such as nanotubes or ribbons. Molecules containing both aromatic peptides and nucleic acids could in principle exploit different forces to self-assemble. In this work we meant to investigate the self-assembly of mixed systems, with the aim to understand which forces play a major role and determine formation/structure of aggregates. We therefore synthesized conjugates of the peptide FF to the peptide nucleic acid dimer "gc" and characterized their aggregates by different spectroscopic techniques, including NMR, CD and fluorescence.

From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides

Peptides and their synthetic analogs are a class of molecules with enormous relevance as therapeutics for their ability to interact with biomacromolecules like nucleic acids and proteins, potentially interfering with biological pathways often involved in the onset and progression of pathologies of high social impact. Nucleobase-bearing peptides (nucleopeptides) and pseudopeptides (PNAs) offer further interesting possibilities related to their nucleobase-decorated nature for diagnostic and therapeutic applications, thanks to their reported ability to target complementary DNA and RNA strands. In addition, these chimeric compounds are endowed with intriguing self-assembling properties, which are at the heart of their investigation as self-replicating materials in prebiotic chemistry, as well as their application as constituents of innovative drug delivery systems and, more generally, as novel nanomaterials to be employed in biomedicine. Herein we describe the properties of nucleopeptides, PNAs and related supramolecular systems, and summarize some of the most relevant applications of these systems.

Supramolecular Architectures of Nucleic Acid/Peptide Hybrids

Supramolecular architectures that are built artificially from biomolecules, such as nucleic acids or peptides, with structural hierarchical orders ranging from the molecular to nano-scales have attracted increased attention in molecular science research fields. The engineering of nanostructures with such biomolecule-based supramolecular architectures could offer an opportunity for the development of biocompatible supramolecular (nano)materials. In this review, we highlighted a variety of supramolecular architectures that were assembled from both nucleic acids and peptides through the non-covalent interactions between them or the covalently conjugated molecular hybrids between them.