Self-Assembly in Action

Piperazine-Derived Bisphosphonate-Based Ionizable Lipid Nanoparticles Enhance mRNA Delivery to the Bone Microenvironment

Nucleic acid delivery with mRNA lipid nanoparticles are being developed for targeting a wide array of tissues and cell types. However, targeted delivery to the bone microenvironment remains a significant challenge in the field, due in part to low local blood flow and poor interactions between drug carriers and bone material. Here we report bone-targeting ionizable lipids incorporating a piperazine backbone and bisphosphate moieties, which bind tightly with hydroxyapatite ([Ca5(PO4)3OH]), a key component of mineralized tissues. These lipids demonstrate biocompatibility and low toxicity in both vitro and in vivo studies. LNP formulated with these lipids facilitated efficient cellular transfection and improved binding to hydroxyapatite in vitro, and targeted delivery to the bone microenvironment in vivo following systemic administration. Overall, our findings demonstrate the critical role of the piperazine backbone in a novel ionizable lipid, which incorporates a bisphosphonate group to enable efficient bone-targeted delivery, highlighting the potential of rational design of ionizable lipids for next-generation bone-targeting delivery systems.

Cogwheel Mechanism of Helical Self-Organization is Thermodynamically Controlled, Self-Repairing, and Universal

The cogwheel mechanism of helical self-organization, reported by us, generates columns with the alkyl chains of their components parallel to the column axis. This mechanism disregards the enantiomeric purity of constituents and, under suitable design, provides the fastest rate of helical self-organization. Here, we investigate the supramolecular structure of a thermodynamically controlled helical self-organization system. Unexpectedly, we found that this system follows a cogwheel mechanism of helical self-organization that does not contain the two key parameters of the cogwheel mechanism: the length of the alkyl group of the self-assembling dendron identical to the helical half-pitch (hhp) of the column and the presence of chiral branches pointing toward the column center. Unpredictably, we uncovered that the presence of chiral branching points and strict alkyl chain lengths is not a requirement of the cogwheel mechanism. A self-repairing process provides access to a constant hhp via a shorter and longer alkyl chain length than the originally exact demanded value, which together with the lack of branching point(s) demonstrates the universality of the cogwheel mechanism of helical self-organization. Applications derived from this concept are envisioned.

From Frank-Kasper, Quasicrystals, and Biological Membrane Mimics to Reprogramming In Vivo the Living Factory to Target the Delivery of mRNA with One-Component Amphiphilic Janus Dendrimers

This Perspective is dedicated to the 25th Anniversary of Biomacromolecules. It provides a personal view on the developing field of the polymer and biology interface over the 25 years since the journal was launched by the American Chemical Society (ACS). This Perspective is meant to bridge an article published in the first issue of the journal and recent bioinspired developments in the laboratory of the corresponding author. The discovery of supramolecular spherical helices self-organizing into Frank-Kasper and quasicrystals as models of icosahedral viruses, as well as of columnar helical assemblies that mimic rodlike viruses by supramolecular dendrimers, is briefly presented. The transplant of these assemblies from supramolecular dendrimers to block copolymers, giant surfactants, and other self-organized soft matter follows. Amphiphilic self-assembling Janus dendrimers and glycodendrimers as mimics of biological membranes and their glycans are discussed. New concepts derived from them that evolved in the in vivo targeted delivery of mRNA with the simplest one-component synthetic vector systems are introduced. Some synthetic methodologies employed during the synthesis and self-assembly are explained. Unraveling bioinspired applications of novel materials concludes this brief 25th Anniversary Perspective of Biomacromolecules.

Synthesis of C3-symmetric star shaped amphiphiles for drug delivery applications

C 3-symmetric star-shaped aromatic compounds are known to possess unique characteristics which facilitate their industrial and biomedical applications. Herein, we report the design, synthesis, self-assembly and drug/dye delivery capabilities of C3-symmetric, hexa-substituted benzene-based amphiphiles. The synthesis of the hexa-substituted C3-symmetric core involves C-acetylation of phloroglucinol to yield the corresponding tri-acetyl derivative. This was further subjected to O-propargylation, followed by the carbonyl reduction of acetyl groups to yield the central core. Various hydrophilic (mPEG) and lipophilic units were then incorporated into this core via click and esterification reactions, respectively, to produce a new type of star shaped amphiphiles. So the obtained amphiphilic architectures have a tendency to aggregate in an aqueous medium forming nanosized assemblies with an inner hydrophobic core, allowing the substituents to control the tension-active properties. The critical aggregation concentration of the amphiphiles was evaluated by fluorescence measurement using the dye Nile red as a fluorescent probe. The hydrodynamic diameter of self-assembled aggregates in aqueous solution was studied by dynamic light scattering, while the actual size and morphology were determined by cryo-transmission electron microscopy (cryo-TEM) analysis. The physicochemical properties of the amphiphiles suggested their suitability for exploring their drug delivery applications. In this endeavor, the amphiphiles were utilized for the encapsulation of model hydrophobic entities and studying their subsequent release from their hydrophobic core in a controlled manner. The transport potential of the synthesised amphiphiles was explored for transdermal drug delivery. Furthermore, cytotoxicity studies were conducted using MCF7 and HeLa cells, which indicated that the nanocarriers had no toxic effect on the cells.

Screening Libraries to Discover Molecular Design Principles for the Targeted Delivery of mRNA with One-Component Ionizable Amphiphilic Janus Dendrimers Derived from Plant Phenolic Acids

Viral and synthetic vectors to deliver nucleic acids were key to the rapid development of extraordinarily efficient COVID-19 vaccines. The four-component lipid nanoparticles (LNPs), containing phospholipids, PEG-conjugated lipids, cholesterol, and ionizable lipids, co-assembled with mRNA via a microfluidic technology, are the leading nonviral delivery vector used by BioNTech/Pfizer and Moderna to access COVID-19 mRNA vaccines. LNPs exhibit a statistical distribution of their four components when delivering mRNA. Here, we report a methodology that involves screening libraries to discover the molecular design principles required to realize organ-targeted mRNA delivery and mediate activity with a one-component ionizable multifunctional amphiphilic Janus dendrimer (IAJD) derived from plant phenolic acids. IAJDs co-assemble with mRNA into monodisperse dendrimersome nanoparticles (DNPs) with predictable dimensions, via the simple injection of their ethanol solution in a buffer. The precise location of the functional groups in one-component IAJDs demonstrated that the targeted organs, including the liver, spleen, lymph nodes, and lung, are selected based on the hydrophilic region, while activity is associated with the hydrophobic domain of IAJDs. These principles, and a mechanistic hypothesis to explain activity, simplify the synthesis of IAJDs, the assembly of DNPs, handling, and storage of vaccines, and reduce price, despite employing renewable plant starting materials. Using simple molecular design principles will lead to increased accessibility to a large diversity of mRNA-based vaccines and nanotherapeutics.

Stimuli-Responsive Principles of Supramolecular Organizations Emerging from Self-Assembling and Self-Organizable Dendrons, Dendrimers, and Dendronized Polymers

All activities of our daily life, of the nature surrounding us and of the entire society and its complex economic and political systems are affected by stimuli. Therefore, understanding stimuli-responsive principles in nature, biology, society, and in complex synthetic systems is fundamental to natural and life sciences. This invited Perspective attempts to organize, to the best of our knowledge, for the first time the stimuli-responsive principles of supramolecular organizations emerging from self-assembling and self-organizable dendrons, dendrimers, and dendronized polymers. Definitions of stimulus and stimuli from different fields of science are first discussed. Subsequently, we decided that supramolecular organizations of self-assembling and self-organizable dendrons, dendrimers, and dendronized polymers may fit best in the definition of stimuli from biology. After a brief historical introduction to the discovery and development of conventional and self-assembling and self-organizable dendrons, dendrimers, and dendronized polymers, a classification of stimuli-responsible principles as internal- and external-stimuli was made. Due to the enormous amount of literature on conventional dendrons, dendrimers, and dendronized polymers as well as on their self-assembling and self-organizable systems we decided to discuss stimuli-responsive principles only with examples from our laboratory. We apologize to all contributors to dendrimers and to the readers of this Perspective for this space-limited decision. Even after this decision, restrictions to a limited number of examples were required. In spite of this, we expect that this Perspective will provide a new way of thinking about stimuli in all fields of self-organized complex soft matter.

Investigating Fundamental Principles of Nonequilibrium Assembly Using Temperature-Sensitive Copolymers

Both natural biomaterials and synthetic materials benefit from complex energy landscapes that provide the foundation for structure-function relationships and environmental sensitivity. Understanding these nonequilibrium dynamics is important for the development of design principles to harness this behavior. Using a model system of poly(ethylene glycol) methacrylate-based thermoresponsive lower critical solution temperature (LCST) copolymers, we explored the impact of composition and stimulus path on nonequilibrium thermal hysteretic behavior. Through turbidimetry analysis of nonsuperimposable heat-cool cycles, we observe that LCST copolymers show clear hysteresis that varies as a function of pendent side chain length and hydrophobicity. Hysteresis is further impacted by the temperature ramp rate, as insoluble states can be kinetically trapped under optimized temperature protocols. This systematic study brings to light fundamental principles that can enable the harnessing of out-of-equilibrium effects in synthetic soft materials.

An Accelerated Modular-Orthogonal Ni-Catalyzed Methodology to Symmetric and Nonsymmetric Constitutional Isomeric AB2 to AB9 Dendrons Exhibiting Unprecedented Self-Organizing Principles

Five libraries of natural and synthetic phenolic acids containing five AB₃, ten constitutional isomeric AB₂, one AB₄, and one AB₅ were previously synthesized and reported by our laboratory in 5 to 11 steps. They were employed to construct seven libraries of self-assembling dendrons, by divergent generational, deconstruction, and combined approaches, enabling the discovery of a diversity of supramolecular assemblies including Frank-Kasper phases, soft quasicrystals, and complex helical organizations, some undergoing deracemization in the crystal state. However, higher substitution patterns within a single dendron were not accessible. Here we report three libraries consisting of 30 symmetric and nonsymmetric constitutional isomeric phenolic acids with unprecedented sequenced patterns, including two AB₂, three AB₃, eight AB₄, five AB₅, six AB₆, three AB₇, two AB₈, and one AB₉ synthesized by accelerated modular-orthogonal Ni-catalyzed borylation and cross-coupling. A single etherification step with 4-(n-dodecyloxy)benzyl chloride transformed all these phenolic acids, of interest also for other applications, into self-assembling dendrons. Despite this synthetic simplicity, they led to a diversity of unprecedented self-organizing principles: lamellar structures of interest for biological membrane mimics, helical columnar assemblies from rigid-solid angle dendrons forming Tobacco Mosaic Virus-like assemblies, columnar organizations from adaptable-solid angle dendrons forming disordered micellar-like nonhelical columns, columns from supramolecular spheres, five body-centered cubic phases displaying supramolecular orientational memory, rarely encountered in previous libraries forming predominantly Frank-Kasper phases, and two Frank-Kasper phases. Lessons from these self-organizing principles, discovered within a single generation of self-assembling dendrons, may help elaborate design principles for complex helical and nonhelical organizations of synthetic and biological matter.

Emergence of cationic polyamine dendrimersomes: design, stimuli sensitivity and potential biomedical applications

For decades, self-assembled lipid vesicles have been widely used in clinics as nanoscale delivery systems for various biomedical applications, including treatment of various diseases. Due to their core-shell architecture and versatile nature, they have been successfully used as carriers for the delivery of a wide range of therapeutic cargos, including drugs and nucleic acids, in cancer treatment. Recently, surface-modified polyamine dendrimer-based vesicles, or dendrimersomes, have emerged as promising alternatives to lipid vesicles for various biomedical applications, due to their ease of synthesis, non-immunogenicity, stability in circulation and lower size polydispersity. This mini-review provides an overview of the recent advances resulting from the use of biomimetic hydrophobically-modified polyamine-based dendrimersomes towards biomedical applications, focusing mainly on the two most widely used polyamine dendrimers, namely polyamidoamine (PAMAM) and poly(propylene imine) (PPI) dendrimers.

A crosslinked colloidal network of peptide/nucleic base amphiphiles for targeted cancer cell encapsulation

The use of peptide amphiphiles (PAs) is becoming increasingly popular, not only because of their unique self-assembly properties but also due to the versatility of designs, allowing biological responsiveness, biocompatibility, and easy synthesis, which could potentially contribute to new drug design and disease treatment concepts. Oligonucleotides, another major functional bio-macromolecule class, have been introduced recently as new functional building blocks into PAs, further enriching the tools available for the fabrication of bio-functional PAs. Taking advantage of this, in the present work, two nucleic base-linked (adenine, A and thymine, T) RGD-rich peptide amphiphiles (NPAs) containing the fluorophores naphthalimide and rhodamine (Nph-A and Rh-T) were designed and synthesized. The two NPAs exhibit distinctive assembly behaviours with spherical (Rh-T) and fibrous (Nph-A) morphologies, and mixing Nph-A with Rh-T leads to a densely crosslinked colloidal network (Nph-A/Rh-T) via mutually promoted supramolecular polymerization via nucleation-growth assembly. Because of the RGD-rich sequences in the crosslinked network, further research on in situ targeted cancer cell (MDA-MB-231) encapsulation via RGD-integrin recognition was performed, and the modulation of cell behaviours (e.g., cell viability and migration) was demonstrated using both confocal laser scanning microscopy (CLSM) imaging and a scratch wound healing assay.

Soft-Matter Nanotubes: A Platform for Diverse Functions and Applications

Self-assembled organic nanotubes made of single or multiple molecular components can be classified into soft-matter nanotubes (SMNTs) by contrast with hard-matter nanotubes, such as carbon and other inorganic nanotubes. To date, diverse self-assembly processes and elaborate template procedures using rationally designed organic molecules have produced suitable tubular architectures with definite dimensions, structural complexity, and hierarchy for expected functions and applications. Herein, we comprehensively discuss every functions and possible applications of a wide range of SMNTs as bulk materials or single components. This Review highlights valuable contributions mainly in the past decade. Fifteen different families of SMNTs are discussed from the viewpoints of chemical, physical, biological, and medical applications, as well as action fields (e.g., interior, wall, exterior, whole structure, and ensemble of nanotubes). Chemical applications of the SMNTs are associated with encapsulating materials and sensors. SMNTs also behave, while sometimes undergoing morphological transformation, as a catalyst, template, liquid crystal, hydro-/organogel, superhydrophobic surface, and micron size engine. Physical functions pertain to ferro-/piezoelectricity and energy migration/storage, leading to the applications to electrodes or supercapacitors, and mechanical reinforcement. Biological functions involve artificial chaperone, transmembrane transport, nanochannels, and channel reactors. Finally, medical functions range over drug delivery, nonviral gene transfer vector, and virus trap.

Valence, loop formation and universality in self-assembling patchy particles

Patchy particles have emerged as an attractive model to mimic phase separation and self-assembly of globular proteins solutions, colloidal patchy particles, and molecular fluids where directional interactions are operative. In our previous work, we extensively explored the coupling of directional and isotropic interactions on both the phase separation and self-assembly in a system of patchy particles with five spots. Here, we extend this work to consider different patch valences and isotropic interaction strengths with an emphasis on self-assembly. Although the location of self-assembly transition lines in the temperature-density plane depend on a number of parameters, we find universal behavior of cluster size that is dependent only on the probability of a spot being bound, the patch valence, and the density. Using these principles, we quantify both the mass distribution and the shape for all clusters, as well as clusters containing loops. Following the logical implications of these results, combined with a simplified version of a mean-field theory that incorporates Flory-Stockmayer theory, we find a universal curve for the temperature dependence of cluster mass and a universal curve for the fraction of clusters that contain loops. As the curves are dependent on the particle valence, such results provide a method for parameterizing patchy particle models using experimental data.

Formation of toroids by self-assembly of an α-α corner mimetic: supramolecular cyclization

An α-α corner mimetic self-assembles to form a rod-like supramolecular structure which bends and closes end-to-end like a cyclization reaction to form uniform toroids. Each peptide fragment containing l-leucine, α-aminoisobutyric acid (Aib) and l-tyrosine forms rigid 3₁₀ helical structures stabilized by multiple intramolecular N-HO hydrogen bonds. Two 3₁₀ helices are connected by the spacer 3-aminomethyl-benzylamine and maintain an angular distance of 120° and therefore mimic the α-α corner motif of a protein super secondary structure. The individual α-α corner subunits are themselves regularly interlinked through multiple water mediated intermolecular hydrogen-bonding interactions to form the rod-like supramolecular structure and toroids. The formation of the supramolecular structure has been proven with X-ray crystallography and other spectroscopic techniques. The cyclization of the supramolecular structure and toroid formation were studied by optical microscope, AFM and FE-SEM experiments. Despite other assignments such as exfoliation of graphene from graphite, the compound exhibits significant memory to finally produce the toroids.

Preparation of avermectin microcapsules with anti-photodegradation and slow-release by the assembly of lignin derivatives

A facile, environmentally friendly, and low-cost strategy for affording stability and the slow-release of avermectin based on self-assembly of lignin derivatives is described.

Precision polymers containing main-chain-amino acids: ADMET polymerization and crystallization

New PE-type precision oligomers displaying different amino acids (chiral/achiral, polar/non-polar) placed at every 19th carbon atom are presented.

Chemo-Enzymatic Synthesis of Perfluoroalkyl-Functionalized Dendronized Polymers as Cyto-Compatible Nanocarriers for Drug Delivery Applications

Among amphiphilic polymers with diverse skeletons, fluorinated architectures have attracted significant attention due to their unique property of segregation and self-assembly into discrete supramolecular entities. Herein, we have synthesized amphiphilic copolymers by grafting hydrophobic alkyl/perfluoroalkyl chains and hydrophilic polyglycerol [G2.0] dendrons onto a co-polymer scaffold, which itself was prepared by enzymatic polymerization of poly[ethylene glycol bis(carboxymethyl) ether]diethylester and 2-azidopropan-1,3-diol. The resulting fluorinated polymers and their alkyl chain analogs were then compared in terms of their supramolecular aggregation behavior, solubilization capacity, transport potential, and release profile using curcumin and dexamethasone drugs. The study of the release profile of encapsulated curcumin incubated with/without a hydrolase enzyme Candida antarctica lipase (CAL-B) suggested that the drug is better stabilized in perfluoroalkyl chain grafted polymeric nanostructures in the absence of enzyme for up to 12 days as compared to its alkyl chain analogs. Although both the fluorinated as well as non-fluorinated systems showed up to 90% release of curcumin in 12 days when incubated with lipase, a comparatively faster release was observed in the fluorinated polymers. Cell viability of HeLa cells up to 95% in aqueous solution of fluorinated polymers (100 μg/mL) demonstrated their excellent cyto-compatibility.

Coupling of isotropic and directional interactions and its effect on phase separation and self-assembly

The interactions of molecules and particles in solution often involve an interplay between isotropic and highly directional interactions that lead to a mutual coupling of phase separation and self-assembly. This situation arises, for example, in proteins interacting through hydrophobic and charged patch regions on their surface and in nanoparticles with grafted polymer chains, such as DNA. As a minimal model of complex fluids exhibiting this interaction coupling, we investigate spherical particles having an isotropic interaction and a constellation of five attractive patches on the particle's surface. Monte Carlo simulations and mean-field calculations of the phase boundaries of this model depend strongly on the relative strength of the isotropic and patch potentials, where we surprisingly find that analytic mean-field predictions become increasingly accurate as the directional interactions become increasingly predominant. We quantitatively account for this effect by noting that the effective interaction range increases with increasing relative directional to isotropic interaction strength. We also identify thermodynamic transition lines associated with self-assembly, extract the entropy and energy of association, and characterize the resulting cluster properties obtained from simulations using percolation scaling theory and Flory-Stockmayer mean-field theory. We find that the fractal dimension and cluster size distribution are consistent with those of lattice animals, i.e., randomly branched polymers swollen by excluded volume interactions. We also identify a universal functional form for the average molecular weight and a nearly universal functional form for a scaling parameter characterizing the cluster size distribution. Since the formation of branched clusters at equilibrium is a common phenomenon in nature, we detail how our analysis can be used in experimental characterization of such associating fluids.

Supramolecular Architectures of Dendritic Amphiphiles in Water

Dendritic molecules are an exciting research topic because of their highly branched architecture, multiple functional groups on the periphery, and very pertinent features for various applications. Self-assembling dendritic amphiphiles have produced different nanostructures with unique morphologies and properties. Since their self-assembly in water is greatly relevant for biomedical applications, researchers have been looking for a way to rationally design dendritic amphiphiles for the last few decades. We review here some recent developments from investigations on the self-assembly of dendritic amphiphiles into various nanostructures in water on the molecular level. The main content of the review is divided into sections according to the different nanostructure morphologies resulting from the dendritic amphiphiles' self-assembly. Finally, we conclude with some remarks that highlight the self-assembling features of these dendritic amphiphiles.

Mechanism of self-assembly process and seeded supramolecular polymerization of perylene bisimide organogelator

The mechanism of supramolecular polymerization has been elucidated for an archetype organogelator molecule composed of a perylene bisimide aromatic scaffold and two amide substituents. This molecule self-assembles into elongated one-dimensional nanofibers through a cooperative nucleation-growth process. Thermodynamic and kinetic analyses have been applied to discover conditions (temperature, solvent, concentration) where the spontaneous nucleation can be retarded by trapping of the monomers in an inactive conformation, leading to lag times up to more than 1 h. The unique kinetics in the nucleation process was confirmed as a thermal hysteresis in a cycle of assembly and disassembly processes. Under appropriate conditions within the hysteresis loop, addition of preassembled nanofiber seeds leads to seeded polymerization from the termini of the seeds in a living supramolecular polymerization process. These results demonstrate that seeded polymerizations are not limited to special situations where off-pathway aggregates sequester the monomeric reactant species but may be applicable to a large number of known and to be developed molecules from the large family of molecules that self-assemble into one-dimensional nanofibrous structures. Generalizing from the mechanistic insight into our seeded polymerization, we assert that a cooperative nucleation-growth supramolecular polymerization accompanied by thermal hysteresis can be controlled in a living manner.

Homochiral columns constructed by chiral self-sorting during supramolecular helical organization of hat-shaped molecules

A library of dendronized cyclotriveratrylene (CTV) crowns substituted with chiral, racemic, or achiral peripheral alkyl chains, including enantiopure R and S branched alkyls, "racemic by mixture", "racemic by synthesis", n-octyl, and n-dodecyl groups was synthesized. In solvophobic solvents and in bulk they self-assemble in helical columns. Their solution and bulk shape-persistent supramolecular structures were determined by a complementary combination of circular dichroism (CD) and UV in solution and thin film, microspot CD in thin film, differential scanning calorimetry combined with fiber X-ray diffraction, computer simulation, and molecular models. In solution, self-assembly via a cooperative mechanism generates single-handed columns from enantiopure CTVs and mixtures of right- and left-handed columns from racemic by mixture, racemic by synthesis, other combinations of R and S, and even from achiral compounds. In bulk state all supramolecular columns form a 3D hexagonal crystalline phase, Φ(h)(k) (P6₃ symmetry), that can be obtained only from single-handed columns and a columnar hexagonal 2D liquid crystal, Φ(h). The highest order Φ(h)(k) consists of enantiopure single-handed columns that are slightly distorted 12-fold triple helices. The "hat-shaped" dendronized CTV assembles in bent-branch pine-tree columns that allow interdigitation of alkyl groups in adjacent columns regardless of their direction. Enantiomerically rich, racemic, and achiral compositions undergo deracemization in the crystal state by transfer of the transient disc-like conformer of dendronized CTV from column to column during crown inversion. Solid state NMR experiments identified motional processes that allow such transfer. This unprecedented supramolecular chiral self-sorting will impact the creation of functions in complex systems.

Cooperative supramolecular polymerization: comparison of different models applied on the self-assembly of bis(merocyanine) dyes

Three new molecular building blocks 1 a-c for supramolecular polymerization are described that feature two dipolar merocyanine dyes tethered by p-xylylene spacers. Concentration- and temperature-dependent UV/Vis spectroscopy in chloroform combined with dynamic light scattering, capillary viscosimetry and atomic force microscopy investigations were applied to elucidate the mechanistic features of the self-assembly of these strongly dipolar dyes. Our detailed studies reveal that the self-assembly is very pronounced for bis(merocyanines) 1 a,b bearing linear alkyl chains, but completely absent for bis(merocyanine) 1 c bearing sterically more bulky ethylhexyl substituents. Both temperature- and concentration-dependent UV/Vis data provide unambiguous evidence for a cooperative self-assembly process for bis(merocyanines) 1 a,b, which was analyzed in detail by the Meijer-Schenning-Van-der-Schoot model (applicable to temperature-dependent data) and by the Goldstein-Stryer model (applicable to concentration-dependent data). By combining both methods all parameters of interest to understand the self-assembly process could be derived, including in particular the nucleus size (8-10 monomeric units), the cooperativity factor (ca. 0.006), and the nucleation and elongation constants of about 10(3) and 10(6)  M(-1) in chloroform at room temperature, respectively.

DNA and nuclear aggregates of polyamines

Polyamines (PAs) are linear polycations that are involved in many biological functions. Putrescine, spermidine and spermine are highly represented in the nucleus of eukaryotic cells and have been the subject of decades of extensive research. Nevertheless, their capability to modulate the structure and functions of DNA has not been fully elucidated. We found that polyamines self-assemble with phosphate ions in the cell nucleus and generate three forms of compounds referred to as Nuclear Aggregates of Polyamines (NAPs), which interact with genomic DNA. In an in vitro setting that mimics the nuclear environment, the assembly of PAs occurs within well-defined ratios, independent of the presence of the DNA template. Strict structural and functional analogies exist between the in vitro NAPs (ivNAPs) and their cellular homologues. Atomic force microscopy showed that ivNAPs, as theoretically predicted, have a cyclic structure, and in the presence of DNA, they form a tube-like arrangement around the double helix. Features of the interaction between ivNAPs and genomic DNA provide evidence for the decisive role of "natural" NAPs in regulating important aspects of DNA physiology, such as conformation, protection and packaging, thus suggesting a new vision of the functions that PAs accomplish in the cell nucleus.

Self-assembly of dendritic dipeptides as a model of chiral selection in primitive biological systems

Biological macromolecules are homochiral, composed of sequences of stereocenters possessing the same repeated absolute configuration. This chapter addresses the mechanism of homochiral selection in polypeptides. In particular, the relationship between the stereochemistry (L or D) of structurally distinct α-amino acids is explored. Through functionalization of Tyr-Xaa dipeptides with self-assembling dendrons, the effect of stereochemical sequence of the dipeptide on the thermodynamics of self-assembly and the resulting structural features can be quantified. The dendritic dipeptide approach effectively isolates the stereochemical information of the shortest sequence of stereochemical information possible in polypeptide, while simultaneously allowing for dendron driven tertiary and quaternary structure formation and subsequent transfer of chiral information from the dipeptide to the dendritic sheath. This approach elucidates a mechanism of selecting a homochiral relationship between dissimilar but neighboring α-amino acids through thermodynamic preference for homochirality in solution-phase and bulk supramolecular helical polymerization.