Insights into Templated Supramolecular Polymerization: Binding of Naphthalene Derivatives to ssDNA Templates of Different Lengths

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.

Nucleic-Acid-Templated Synthesis of Smart Polymer Vectors for Gene Delivery

Nucleic acids are information-rich and readily available biomolecules, which can be used to template the polymerization of synthetic macromolecules. Here, we highlight the control over the size, composition, and sequence one can nowadays obtain by using this methodology. We also highlight how templated processes exploiting dynamic covalent polymerization can, in return, result in therapeutic nucleic acids fabricating their own dynamic delivery vector - a biomimicking concept that can provide original solutions for gene therapies.

Computer Aided Development of Nucleic Acid Applications in Nanotechnologies

Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.

A kinetic model for the impact of packaging signal mimics on genome encapsulation

Inspired by recent experiments on the spontaneous assembly of virus-like particles from a solution containing a synthetic coat protein and double-stranded DNA, we put forward a kinetic model that has as main ingredients a stochastic nucleation and a deterministic growth process. The efficiency and rate of DNA packaging strongly increase after tiling the DNA with CRISPR-Cas proteins at predesignated locations, mimicking assembly signals in viruses. Our model shows that treating these proteins as nucleation-inducing diffusion barriers is sufficient to explain the experimentally observed increase in encapsulation efficiency, but only if the nucleation rate is sufficiently high. We find an optimum in the encapsulation kinetics for conditions where the number of packaging signal mimics is equal to the number of nucleation events that can occur during the time required to fully encapsulate the DNA template, presuming that the nucleation events can only take place adjacent to a packaging signal. Our theory is in satisfactory agreement with the available experimental data.

Photoswitchable architecture transformation of a DNA-hybrid assembly at the microscopic and macroscopic scale

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks. Oligonucleotide-based nanotechnology and soft-materials benefit from the high information storage density, self-correction, and memory function of DNA. Here we control these beneficial properties with light in a photoresponsive biohybrid hydrogel, adding an extra level of function to the system. An ssDNA template was combined with a complementary photo-responsive unit to reversibly switch between various functional states of the supramolecular assembly using a combination of light and heat. We studied the structural response of the hydrogel at both the microscopic and macroscopic scale using a combination of UV-vis absorption and CD spectroscopy, as well as fluorescence, transmission electron, and atomic force microscopy. The hydrogels grown from these supramolecular self-assembly systems show remarkable shape-memory properties and imprinting shape-behavior while the macroscopic shape of the materials obtained can be further manipulated by irradiation.

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks.

DNA condensation and formation of ultrathin nanosheets via DNA assisted self-assembly of an amphiphilic fullerene derivative

DNA nanotechnology propose various assembly strategies to develop novel functional nanostructures utilizing unique interactions of DNA with small molecules, nanoparticles, polymers, and other biomolecules. Although, well defined nanostructures of DNA and amphiphilic small molecules were achieved through hybridization of covalently modified DNA, attaining precise organization of functional moieties through non-covalent interactions remain as a challenging task. Herein, we report mutually assisted assembly of an amphiphilic fullerene derivative and various DNA structures through non-covalent interactions, which leads to initial DNA condensation and subsequent assembly yielding ordered fullerene-DNA nanosheets. The molecular design of the cationic, amphiphilic fullerene derivative (FPy) ensures molecular solubility in the 10% DMSO-PBS buffer system and facile interactions with DNA through groove binding and electrostatic interactions of fullerene moiety and positively charged pyridinium moiety, respectively. The formation of FPy/DNA nanostructures were thoroughly investigated in the presence of λ-DNA, pBR322 plasmid DNA, and single and double stranded 20-mer oligonucleotides using UV-visible spectroscopy, AFM and TEM analysis. λ-DNA and pBR322 plasmid DNA readily condense in presence of FPy leading to micrometer sized few layer nanosheets with significant crystallinity due to ordered arrangement of fullerenes. Similarly, single and double stranded 20-mer oligonucleotides also interact efficiently with FPy and form highly crystalline nanosheets, signifying the role of electrostatic interaction and subsequent charge neutralization in the condensation triggered assembly. However, there is significant differences in the crystallinity and ordered arrangements of fullerenes between these two cases, where longer DNA form condensed structures and less ordered nanosheets while short oligonucleotides lead to more ordered and highly crystalline nanosheets, which could be attributed to the differential DNA condensation. Finally, we have demonstrated the addressability of the assembly using a cyanine modified single strand DNA, which also forms highly crystalline nanosheets and exhibit efficient quenching of the cyanine fluorescence upon self-assembly. These results open up new prospects in the development of functional DNA nanostructures through non-covalent interactions and hence have potential applications in the context of DNA nanotechnology.

Molecular Chromophore-DNA Architectures With Fullerenes: Optical Properties and Solar Cells

Supramolecular chemistry allows the construction of complex molecular architectures and the design of collective photophysical properties. DNA is an attractive template to build such supramolecular architectures due to its helical structure, the defined distances between the bases and the canonical base pairing that results in precise control of the chromophore position. The tailored properties of DNA-templated supramolecules eventually allow their implementation into optoelectronic applications. For the generation of free charge carriers from photo-generated excitons, fullerenes can be utilized. We synthesized two fullerene derivates, one of which binds by electrostatic interactions to single-stranded DNA, while the other contains two 2'-deoxyuridine moieties and assembles specifically along oligo-2'-deoxyadenosines (dA20) as DNA template. The DNA-directed assembly of both fullerenes in aqueous solution was investigated by UV/Vis absorbance and circular dichroism (CD) spectroscopy. The specific interactions with DNA make fullerenes with the 2'-deoxyuridine moieties a significantly better component for supramolecular DNA architectures. We studied the fluorescence quenching of both fullerenes with a DNA chromophore assembly. To investigate one of the key properties for optoelectronic applications, that is the supramolecular structure of the DNA-based assemblies in the solid phase, we characterized the CD of supramolecular chromophore-DNA architectures in thin films. Remarkably, the helical chirality of the chromophore assemblies that is induced by the DNA template is conserved even in the solid state. Upon implementation into organic solar cells, the external quantum efficiency measurements showed charge carrier generation on all three chromophore components of the DNA assemblies. The fullerenes with the 2'-deoxyuridine moieties enhance the quantum efficiency of the conversion process significantly, demonstrating the potential of DNA as structural element for ordering chromophores into functional π-systems, which may be employed in future organic solar cells.

Molecular recognition mechanisms directing the self-assembly of biological structures

Self-assembling may be defined as the spontaneous association of material units into structures that are often capable of cyclic reorganization and functional behavior. Various molecular recognition processes stabilize assemblies of polymers and biological structures. The present article analyzes cases in which chemical, shape and other recognition mechanisms are individually or cooperatively operative. Simpler self-assembling theories reported in the literature are highlighted. Detailed processes for which chemical recognition is the prevailing, enthalpy-driven, process include the non-ideal component of miscibility, supramolecular polymerization, host-guest complexes and template polymerization. Also discussed are systems such as liquid crystalline closed polymers, ternary mesogenic systems and rigid crystalline polymers for which shape recognition is the prevailing entropy-driven process. Other recognition mechanisms include ion condensation effects, hydrophobic bonding and growth-coupled-to-orientation. Combinations of various recognition mechanisms are particularly evident in biological structures. Self-assembling mechanisms involved in the genesis of some biological systems can be scientifically identified, but much more needs to be known to describe the "engineered" assembling modes that support complex functional organs.

Templated Polymerization of Nucleobase Complexes via Molecular Recognition

Macromolecules have a strong tendency to interact with each other in solution to form a supramolecular structure through various secondary binding forces. In this study, nucleobase-containing templates poly(9-(4-vinylbenzyl)adenine) (P_S AH) and poly(1-(4-vinylbenzyl)cytosine) (P_S CH) are prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization. Vinylbenzyl thymine (M_S T) is polymerized in the presence of these two nucleobase-containing templates. M_S T shows higher affinities toward the template P_S AH compared with the template P_S CH. In accordance with the Watson-Crick pairing principle, thymine forms hydrogen bonding (H-bonding) with adenine, but not between thymine and cytosine. A complex is formed when P_S AH is used as template which indicates that there is a template polymerization of nucleobase complexes via molecular recognition.

From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies

DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.

Allosteric pathway selection in templated assembly

Assembling large numbers of molecular building blocks into functional nanostructures is no trivial task. It relies on guiding building blocks through complex energy landscapes shaped by synergistic and antagonistic supramolecular interactions. In nature, the use of molecular templates is a potent strategy to navigate the process to the desired structure with high fidelity. Yet, nature's templating strategy remains to be fully exploited in man-made nanomaterials. Designing effective template-guided self-assembling systems can only be realized through precise insight into how the chemical design of building blocks and the resulting balance of repulsive and attractive forces give rise to pathway selection and suppression of trapped states. We develop a minimal model to unravel the kinetic pathways and pathway selection of the templated assembly of molecular building blocks on a template. We show how allosteric activation of the associative interactions can suppress undesired solution-aggregation pathways and gives rise to a true template-assembly path.

A DNA-mimic contact-active functional group for antifouling ultrafiltration membranes

Despite advanced materials and techniques to reduce the fouling issue of membranes, 10-30% of the cost of ultrafiltration (UF) processes have been spent on membrane cleaning. Particularly in water treatment, the traditional heavy metal-based method is challenged due to its environmental pollution risk and increasing public health awareness. Here, we report the synthesis of a metal-free contact-active antifouling and antimicrobial membrane by covalently functionalizing a commercial polyacrylonitrile (PAN) UF membrane with 2,4-diamino-1,3,5-triazine (DAT) via a one-step catalyst-free hydrothermal [4 + 2] cyclization of dicyandiamide reaction. The proposed mechanism of the antimicrobial activity of the DAT-functionalized membrane is through strong attraction between the DAT groups and the microbial membrane protein via strong hydrogen bonding, leading to microbial membrane disruption and thus microbe death. A high water flux and good reusability of the membrane against protein in a UF experiment were achieved. The low cost, easy availability of the compounds, as well as the facile reaction offer a high potential of the membrane for real applications in ultrafiltration.

Self-Assembled Porphyrazine Nucleosides on DNA Templates: Highly Fluorescent Chromophore Arrays and Sizing Forensic Tandem Repeat Sequences

The formation of chromophore arrays using a DNA templating approach leads to the creation of supramolecular assemblies, where the optical properties of the overall system can be fine-tuned to a large extent. In particular, porphyrin derivatives have been shown to be versatile building blocks; mostly covalent chemistry was used for embedding the units into DNA strands. Self-assembly of porphyrin modified nucleosides, on the other hand, has not been investigated as a simplified approach. We report on the synthesis of a magnesium(II) tetraaza porphine (MgTAP) coupled to deoxyuridine, and array formation on DNA templates which contain well-defined oligo(dA) segments showing strong fluorescence enhancement which is significantly larger than that with a Zn-porphyrin. The use of the deep-eutectic solvent glycholine is essential for successful assembly formation. The system allows for sizing of short tandem repeat markers with multiple adenosines, thus the concept could be adaptable to in vitro forensic DNA profiling with a suitable set of different chromophores on all nucleosides.

Soluble Polymers with Intrinsic Porosity for Flue Gas Purification and Natural Gas Upgrading

A soluble polymer with intrinsic microporosity, 2,4-diamino-1,3,5-triazine-functionalized organic polymer, is used for the first time as a solid adsorbent, providing an easy solution to overcome the fouling issue. Promising adsorption performances including good CO₂ adsorption capacity, excellent CO₂ /N₂ and CO₂ /CH₄ selectivities, high chemical and thermal stabilities, and easiness of preparation and regeneration are shown.

Investigation of Supramolecular Nanofibers Formed from Multicomponent Nucleotide-Appended Bolaamphiphiles and Heteropolymeric DNA as a Template

A novel DNA-templated multicomponent self-assembly of well-defined, molecular-level-controlled nanostructures in aqueous solution is demonstrated by using a thermal cycling procedure. The strategy uses four building blocks comprising 1,18-nucleotide-appended bolaamphiphiles (3'-phosphorylated adenosine, thymidine, guanosine, or cytidine connected to each end of an oligomethylene chain) and a heteropolymeric 58-mer containing a palindromic sequence as the template DNA. Atomic force microscopic observations, circular dichroism, and temperature-dependent absorption spectra revealed that the multicomponent self-assembly of the four nucleotide bolaamphiphiles and template DNA formed right-handed helical nanofibers with complementary base pairs during thermal cycling. Nanofibers were not formed if one of the four nucleotide bolaamphiphiles was missing, suggesting that construction of the helical nanofiber resulted from self-assembly of all four bolaamphiphiles to form matched base pairs sorted according to the sequence of the template DNA.

From nucleobase to DNA templates for precision supramolecular assemblies and synthetic polymers

In this minireview, we report on the recent advances of utilization of nucleobases and DNA as templates to achieve well-defined supramolecular polymers, synthetic polymers, and sequence-controlled polymers.

One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting

Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.

Dynamic Landau theory for supramolecular self-assembly

Although pathway-specific kinetic theories are fundamentally important to describe and understand reversible polymerisation kinetics, they come in principle at a cost of having a large number of system-specific parameters. Here, we construct a dynamical Landau theory to describe the kinetics of activated linear supramolecular self-assembly, which drastically reduces the number of parameters and still describes most of the interesting and generic behavior of the system in hand. This phenomenological approach hinges on the fact that if nucleated, the polymerisation transition resembles a phase transition. We are able to describe hysteresis, overshooting, undershooting and the existence of a lag time before polymerisation takes off, and pinpoint the conditions required for observing these types of phenomenon in the assembly and disassembly kinetics. We argue that the phenomenological kinetic parameter in our theory is a pathway controller, i.e., it controls the relative weights of the molecular pathways through which self-assembly takes place.

Synthesis, crystal structures, photoluminescence properties and DNA binding of triazine-nickel(II) complexes for DNA detection

We report here the synthesis of three new nickel(II) complexes: [Ni(PzTA)2CO3]·5H2O (PzTA=2,4-diamino-6-(2'-pyrazin)-1,3,5-triazine) in 1, [NiQ(PyTA)(H2O)2]Cl·H2O (HQ=8-hydroxyquinoline, PyTA=2,4-diamino-6-(2'-pyridyl)-1,3,5-triazine) in 2, [NiQ(PzTA)(H2O)2]Cl·H2O in 3, and they were characterized by UV spectroscopy, elemental analysis, molar conductivity and X-ray single crystal diffraction. Binding of the complexes to ct-DNA was investigated with electronic spectroscopy, ethidium bromide displacement from DNA, viscometry and cyclic voltammetry. The results depicted the DNA binding mode of the three complexes was intercalation, and complex 1 together with external static-electricity. Moreover, the three complexes also presented potential anti-oxidant activity. Interestingly, we found 1 was sensitive to oxygen and to the polarity of nonaqueous solvents in fluorescence spectroscopy. Fluorescence of 2 and 3 is weak in neutral aqueous solvents, but is greatly enhanced by addition of ct-DNA. Thus, 2 and 3 can be used to DNA detection as DNA fluorescence probes with a LOD of 1.61 ng mL(-1), 4.90 ng mL(-1) for the relative wide linear range of 0.01-20 μg mL(-1), 0.02-30 μg mL(-1), respectively. These findings indicate that 1 may be a potential optical probe for oxygen-free environments in nonaqueous form, while 2 and 3 were DNA-targeted probes.

Water-soluble DNA minor groove binders as potential chemotherapeutic agents: synthesis, characterization, DNA binding and cleavage, antioxidation, cytotoxicity and HSA interactions

Two new water-soluble copper(ii)-dipeptide complexes: [Cu(glygly)(PyTA)]ClO4·1.5H2O (1) and [Cu(glygly)(PzTA)]ClO4·1.5H2O (2) (glygly = glycylglycine anion, PyTA = 2,4-diamino-6-(2'-pyridyl)-1,3,5-triazine and PzTA = 2,4-diamino-6-(2'-pyrazino)-1,3,5-triazine), utilizing two interrelated DNA base-like ligands (PyTA and PzTA), have been synthesized and characterized. The structure elucidation for 1 performed by single crystal X-ray diffraction showed a one dimensional chain conformation in which the central copper ions arrange in a five-coordinate distorted square-pyramidal geometry. Spectroscopic titration, viscosity and electrophoresis measurements revealed that the complexes bound to DNA via an outside groove binding mode, and cleaved pBR322 DNA efficiently in the presence of ascorbate, probably via an oxidative mechanism with the involvement of ˙OH and ˙O2(-). Notably, the complexes exhibited considerable in vitro cytotoxicity against four human carcinoma cell lines (HepG2, HeLa, A549 and U87) with IC50 values ranging from 41.68 to 159.17 μM, in addition to their excellent SOD mimics (IC50 ~ 0.091 and 0.114 μM). Besides, multispectroscopic evidence suggested their HSA-binding at the cavity containing Trp-214 in subdomain IIA with moderate affinity, mainly via hydrophobic interaction. Further, the molecular docking technique utilized for ascertaining the mechanism and mode of action towards DNA and HSA theoretically verified the experimental results.

A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies

DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.

Synthesis and complementary self-association of novel lipophilic π-conjugated nucleoside oligomers

A series of lipophilic nucleosides comprising natural and non-natural bases that are π-conjugated to a short oligophenylene–ethynylene fragment has been synthesized and their respective association constants measured.

Mixed non-covalent assemblies of ethynyl nile red and ethynyl pyrene along oligonucleotide templates

Ethynyl pyrene and ethynyl nile red as modifications at the 5-position of 2'-deoxyuridines self-assemble non-covalently and specifically along oligo-2'-deoxyadenosines as templates. Oligo-2'-deoxyadenosines of the lengths (dA)10-(dA)20 are able to retain nearly exactly as many ethynyl nile red units in solution as binding sites are available on these templates. In contrast, in the presence of oligo-2'-thymidines the ethynyl nile red moieties are similarly insoluble to those in the absence of any oligonucleotide and yield an aggregate. The mixed assemblies of both chromophores are highly ordered, show left-handed chirality and yield dual fluorescence. The strong excitonic coupling indicates assemblies with a high degree of order. These results show that DNA represents an important supramolecular scaffold for the templated, helical and non-covalent arrangement not only for one type of chromophore but also for mixtures of two different chromophores.

Progressive macromolecular self-assembly: from biomimetic chemistry to bio-inspired materials

Macromolecular self-assembly (MSA) has been an active and fruitful research field since the 1980s, especially in this new century, which is promoted by the remarkable developments in controlled radical polymerization in polymer chemistry, etc. and driven by the demands in bio-related investigations and applications. In this review, we try to summarize the trends and recent progress in MSA in relation to biomimetic chemistry and bio-inspired materials. Our paper covers representative achievements in the fabrication of artificial building blocks for life, cell-inspired biomimetic materials, and macromolecular assemblies mimicking the functions of natural materials and their applications. It is true that the current status of the deliberately designed and obtained nano-objects based on MSA including a variety of micelles, multicompartment vesicles, and some hybrid and complex nano-objects is at their very first stage to mimic nature, but significant and encouraging progress has been made in achieving a certain similarity in morphologies or properties to that of natural ones. Such achievements also demonstrate that MSA has played an important and irreplaceable role in the grand and long-standing research of biomimetic and bio-inspired materials, the future success of which depends on mutual and persistent efforts in polymer science, material science, supramolecular chemistry, and biology.

A kinetic Zipper model and the assembly of tobacco mosaic virus

We put forward a modified Zipper model inspired by the statics and dynamics of the spontaneous reconstitution of rodlike tobacco mosaic virus particles in solutions containing the coat protein and the single-stranded RNA of the virus. An important ingredient of our model is an allosteric switch associated with the binding of the first protein unit to the origin-of-assembly domain of the viral RNA. The subsequent addition and conformational switching of coat proteins to the growing capsid we believe is catalyzed by the presence of the helical arrangement of bound proteins to the RNA. The model explains why the formation of complete viruses is favored over incomplete ones, even though the process is quasi-one-dimensional in character. We numerically solve the relevant kinetic equations and show that time evolution is different for the assembly and disassembly of the virus, the former exhibiting a time lag even if all forward rate constants are equal. We find the late-stage assembly kinetics in the presence of excess protein to be governed by a single-exponential relaxation, which agrees with available experimental data on TMV reconstruction.

Positive cooperativity in the template-directed synthesis of monodisperse macromolecules

Two series of oligorotaxanes R and R' that contain -CH(2)NH(2)(+)CH(2)- recognition sites in their dumbbell components have been synthesized employing template-directed protocols. [24]Crown-8 rings self-assemble by a clipping strategy around each and every recognition site using equimolar amounts of 2,6-pyridinedicarboxaldehyde and tetraethyleneglycol bis(2-aminophenyl) ether to efficiently provide up to a [20]rotaxane. In the R series, the -NH(2)(+)- recognition sites are separated by trismethylene bridges, whereas in the R' series the spacers are p-phenylene linkers. The underpinning idea here is that in the former series, the recognition sites are strategically positioned 3.5 Å apart from one another so as to facilitate efficient [π···π] stacking between the aromatic residues in contiguous rings in the rotaxanes and consequently, a discrete rigid and rod-like conformation is realized; these noncovalent interactions are absent in the latter series rendering them conformationally flexible/nondiscrete. Although in the R' series, the [3]-, [4]-, [8]-, and [12]rotaxanes were isolated after reaction times of <5-30 min in yields of 72-85%, in the R series, the [3]-, [4]-, [5]-, [8]-, [12]-, [16]-, and [20]rotaxanes were isolated in <5 min to 14 h in 88-98% yields. It follows that while in the R' series the higher order oligorotaxanes are formed in lower yields more rapidly, in the R series, the higher order oligorotaxanes are formed in higher yields more slowly. In the R series, the high percentage yields are sustained throughout, despite the fact that up to 39 components are participating in the template-directed self-assembly process. Simple arithmetic reveals that the conversion efficiency for each imine bond formation peaks at 99.9% in the R series and 99.3% in the R' series. This maintenance of reaction efficiency in the R series can be ascribed to positive cooperativity, that is, when one ring is formed it aids and abets the formation of subsequent rings presumably because of stabilizing extended [π···π] stacking interactions between the arene units. Experiments have been performed wherein the dumbbell is starved of the macrocyclic components, and up to five times more of the fully saturated rotaxane is formed than is predicted based on a purely statistical outcome, providing a clear indication that positive cooperativity is operative. Moreover, it would appear that as the R series is traversed from the [3]- to the [4]- to the [5]rotaxane, the cooperativity becomes increasingly positive. This kind of cooperative behavior is not observed for the analogous oligorotaxanes in the R' series. The conventional bevy of analytical techniques (e.g., HR-MS (ESI) and both (1)H and (13)C NMR spectroscopy) help establish the fact that all the oligorotaxanes are pure and monodisperse. Evidence of efficient [π···π] stacking between contiguous arene units in the rings in the R series is revealed by (1)H NMR spectroscopy. Ion-mobility mass spectrometry performed on the R and R' series yielded the collisional cross sections (CCSs), confirming the rigidity of the R oligorotaxanes and the flexibility of the R' ones. The extended [π···π] stacking interactions are found to be present in the solid-state structures of the [3]- and [4]rotaxanes in the R series and also on the basis of molecular mechanics calculations performed on the entire series of oligomers. The collective data presented herein supports our original design in that the extended [π···π] stacking between contiguous arene units in the rings of the R series of oligorotaxanes facilitate an essentially rigid rod-like conformation with evidence that positive cooperativity improves the efficiency of their formation. This situation stands in sharp contrast to the conformationally flexible R' series where the oligorotaxanes form with no cooperativity.