Helical Toroids Self‐Assembled from a Binary System of Polypeptide Homopolymer and its Block Copolymer

Toroids and helices are fundamental geometrical structures in nature. Polymers can self‐assemble into various nanostructures, including both toroids and helices; however, nanostructures combining toroidal and helical morphologies (that is, helical toroids) are rarely observed. A binary system is reported containing polypeptide homopolymer and its block copolymer, which can hierarchically self‐assemble into uniform helical nanotoroids in solution. The formation of the helical toroids is a successive two‐step process. First, the homopolymers aggregate into fibrils and convolve into toroids, thereby resembling the toroidal condensation of deoxyribonucleic acid (DNA) chains. Second, the block copolymers self‐assemble on the homopolymer toroids and result in helical surface patterns. Additionally, the chirality of the surface helical patterns can be varied by the chirality of the polypeptide block copolymers.     

A Sequence-specific Alkali-labile Photolesion Mapping to Adenine in Single-stranded DNA

Abstract— Following UV irradiation at 254 nm and treatment with hot piperidine, single-stranded 49-mer and 12-mer oligodeoxyribonucleotides have been shown by gel-sequencing experiments to contain a prominent alkali-labile cleavage site that maps to adenine in the sequence element 5'-TTGATC-3'. This behavior is abolished by single base substitutions within the photoreactive tract and does not occur with duplex DNA. The distinctive properties of the photolesion are consistent with the formation of an abasic site through initial loss of a photomodified adenine base of unknown structure. The presence of an abasic site is supported by the observations that the alkaline cleavage fragments are terminally phosphorylated and that strand scission can also be effected by spermidine and the tripeptide Lys-Trp-Lys.     

Critical behavior of megabase-size DNA toward the transition into a compact state

We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy (AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA. AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.     

Dual‐Input Regulation and Positional Control in Hybrid Oligonucleotide/Discotic Supramolecular Wires

The combination of oligonucleotides and synthetic supramolecular systems allows for novel and long‐needed modes of regulation of the self‐assembly of both molecular elements. Discotic molecules were conjugated with short oligonucleotides and their assembly into responsive supramolecular wires studied. The self‐assembly of the discotic molecules provides additional stability for DNA‐duplex formation owing to a cooperative effect. The appended oligonucleotides allow for positional control of the discotic elements within the supramolecular wire. The programmed assembly of these hybrid architectures can be modulated through the DNA, for example, by changing the number of base pairs or salt concentration, and through the discotic platform by the addition of discotic elements without oligonucleotide handles. These hybrid supramolecular‐DNA structures allow for advanced levels of control over 1D dynamic platforms with responsive regulatory elements at the interface with biological systems.     

Dynamic Expression of DNA Complexation with Self‐assembled Biomolecular Clusters

We report herein the implementation of a dynamic covalent chemistry approach to the generation of multivalent clusters for DNA recognition. We show that biomolecular clusters can be expressed in situ by a programmed self‐assembly process using chemoselective ligations. The cationic clusters are shown, by fluorescence displacement assay, gel electrophoresis and isothermal titration calorimetry, to effectively complex DNA through multivalent interactions. The reversibility of the ligation was exploited to demonstrate that template effects occur, whereby DNA imposes component selection in order to favor the most active DNA‐binding clusters. Furthermore, we show that a chemical effector can be used to trigger DNA release through component exchange reactions.     

Structural varieties of selectively mixed G‐ and C‐rich short DNA sequences studied with electrospray ionization mass spectrometry

Short guanine(G)‐repeat and cytosine(C)‐repeat DNA strands can self‐assemble to form four‐stranded G‐quadruplexes and i‐motifs, respectively. Herein, G‐rich and C‐rich strands with non‐G or non‐C terminal bases and different lengths of G‐ or C‐repeats are mixed selectively in pH 4.5 and 6.7 ammonium acetate buffer solutions and studied by electrospray ionization mass spectrometry (ESI‐MS). Various strand associations corresponding to bi‐, tri‐ and tetramolecular ions are observed in mass spectra, indicating that the formation of quadruplex structures is a random strand by strand association process. However, with increasing incubation time for the mixtures, initially associated hybrid tetramers will transform into self‐assembled conformations, which is mainly driven by the structural stability. The melting temperature values of self‐assembled quadruplexes suggest that the length of G‐repeats or C‐repeats shows more significant effect on the stability of quadruplex structures than that of terminal residues. Accordingly, we can obtain the self‐associated tetrameric species generated from the mixtures of various homologous G‐ or C‐strands efficiently by altering the length of G‐ or C‐repeats. Our studies demonstrate that ESI‐MS is a very direct, fast and sensitive tool to provide significant information on DNA strand associations and stoichiometric transitions, particularly for complex mixtures. Copyright © 2016 John Wiley & Sons, Ltd.     

Formation study of toroidal condensation of DNA.

A detailed study of the formation of toroidal condensation produced from the 2700 base pair fragments of plasmid PUC13 DNA, induced by metal ions, is introduced. We have extracted several typical intermediate structures based on investigation by electron microscopy, and compared their size distributions. The observations suggest that the formation process of DNA condensation is the process of folding and arranging DNA chains and that of disorder-order transition. The result also indicates that the condensed particles are polymeric, but not randomly aggregative, further proving the toroidal structures are formed in certain regularities.     

Self‐Sorting Supramolecular Polymerization: Helical and Lamellar Aggregates of Tetra‐Bay‐Acyloxy Perylene Bisimide

A new perylene bisimide (PBI), with a fluorescence quantum yield up to unity, self‐assembles into two polymorphic supramolecular polymers. This PBI bears four solubilizing acyloxy substituents at the bay positions and is unsubstituted at the imide position, thereby allowing hydrogen‐bond‐directed self‐assembly in nonpolar solvents. The formation of the polymorphs is controlled by the cooling rate of hot monomer solutions. They show distinctive absorption profiles and morphologies and can be isolated in different polymorphic liquid‐crystalline states. The interchromophoric arrangement causing the spectral features was elucidated, revealing the formation of columnar and lamellar phases, which are formed by either homo‐ or heterochiral self‐assembly, respectively, of the atropoenantiomeric PBIs. Kinetic studies reveal a narcissistic self‐sorting process upon fast cooling, and that the transformation into the heterochiral (racemic) sheetlike self‐assemblies proceeds by dissociation via the monomeric state.     

Complex Formation of Crown Ethers with the Cucurbit[6]uril–Spermidine and Cucurbit[6]uril–Spermine Complex in Aqueous Solution

Alkyl amines are able to form complexes with either crown ethers or cyclodextrins or cucurbit[6]uril. The same is known for polyamines such as spermidine and spermine. However, the simultaneous formation of such polyamines with crown ethers and cucurbit[6]uril has not been studied. The ability of polyamines such as spermidine and spermine to form mixed complexes with different ligands, e.g. crown ethers and cucurbit[6]uril has been studied in aqueous solution using pH-metric and calorimetric titrations. The thermodynamic data of reaction between crown ethers with spermidine, spermine and their cucurbit[6]uril complexes have been determined. The presence of cucurbit[6]uril on the polyamines has no important influence upon the reaction of these amines with crown ethers. The reactions between polyamines, cucurbit[6]uril and crown ethers are simple examples for the self organization of molecules due to specific interactions. Received in final form: 26 January 2005     

pH‐Dependent Assembly of DNA–Gold Nanoparticles Based on the i‐Motif: A Switchable Device with the Potential of a Nanomachine

The pH‐dependent self‐assembling of gold nanoparticles is described. Oligonucleotides containing four or six consecutive dC residues are immobilized on 15‐nm gold nanoparticles. Their assembly is based on the formation of a DNA i‐motif as determined by the color change from red to blue between pH 5.5 and 6.5. The process occurs within a narrow pH range and is reversible. The i‐motif is formed by the antiparallel intercalation of two parallel duplexes provided by two different gold nanoparticles. This assembly process can be utilized to generate novel systems for colorimetric sensing, applications in medical imaging and therapy, and for the construction of a proton‐driven nanomachine.     

Dynamic covalent bond from first principles: Diarylbibenzofuranone structural,electronic, and oxidation studies

A structure that can self‐heal under standard conditions is a challenge faced nowadays and is one of the most promising areas in smart materials science. This can be achieved by dynamic bonds, of which diarylbibenzofuranone (DABBF) dynamic covalent bond is an appealing solution. In this report, we studied the DABBF bond formation against arylbenzofuranone (ABF) and O₂ reaction (autoxidation). Our results show that the barrierless DABBF bond formation is preferred over autoxidation due to the charge transfer process that results in the weakly bonded superoxide. We calculated the electronic and structural properties using total energy density functional theory. © 2017 Wiley Periodicals, Inc.     

FORMATION STUDY OF TOROIDAL CONDENSATION OF DNA

A detailed study of the formation of toroidal condensation produced from the 2700 base pair fragments of plasmid PUCI3 DNA, induced by metal ions, is introduced. We have extracted several typical intermediate structures based on investigation by electron microscopy, and compared their size distributions. The observations suggest that the formation process of DNA condensation is the process of folding and arranging DNA chains and that of disorderorder transition. The result also indicates that the condensed particles are polymeric, but not randomly aggregative, further proving thetoroidal structures are formed in certain regularities.     

Enzymetically Regulating the Self‐Healing of Protein Hydrogels with High Healing Efficiency

Enzyme‐mediated self‐healing of dynamic covalent bond‐driven protein hydrogels was realized by the synergy of two enzymes, glucose oxidase (GOX) and catalase (CAT). The reversible covalent attachment of glutaraldehyde to lysine residues of GOX, CAT, and bovine serum albumin (BSA) led to the formation and functionalization of the self‐healing protein hydrogel system. The enzyme‐mediated protein hydrogels exhibit excellent self‐healing properties with 100 % recovery. The self‐healing process was reversible and effective with an external glucose stimulus at room temperature.     

Terminology Related to the Phenomenon ‘Self‐Disproportionation of Enantiomers’ (SDE)

Terms related to the phenomenon self‐disproportion of enantiomers (SDE) are discussed, particularly with respect to recently suggested alternative terms. Of the numerous terms proffered to describe this phenomenon, it is recommended that the acronym SDE be retained based on its qualities and the fact that its perceived shortcomings are invalid. The term can be readily applied to any process that exhibits the phenomenon of transforming a scalemic sample into fractions containing different enantiomeric compositions in comparison to the enantiomeric composition of the starting sample, and is not restricted solely to chromatographic occurrences. Chromatographic observations, though, can be specifically described by the term enantiomer self‐disproportionation over achiral chromatography (ESDAC). Use of the term homochiral in concert with its intended original meaning is also advocated.     

A Versatile Approach towards the Compaction,Decompaction, and Immobilization of DNA at Interfaces by Using Cyclodextrins

We investigate the temperature dependence of interactions of β‐cyclodextrin (CD)/hexadecyltrimethylammonium bromide (CTAB) self‐assemblies with DNA during the decompaction of DNA/CTAB complexes. By combining direct imaging techniques with density and sound‐velocity measurements, we can explain the decompaction process and suggest a suitable model. The DNA‐decompaction process by using CDs is accompanied by interactions with surfaces, such as glass or mica. The mechanism of β‐CD/CTAB self‐assembly is elucidated and the immobilization of DNA onto negatively charged surfaces is explained. Differences between the fractal dimensions of DNA that is adsorbed onto the surfaces are related to strong and weak binding, which permit the partial relaxation of DNA on the surfaces. The β‐CD/CTAB self‐assembled monolayers are demonstrated to be a facile and efficient route for surface functionalization, which allows for the immobilization of biomacromolecules in close proximity without any intermediate binding or deprotection steps. Moreover, this route is expected to show several advantages that might contribute to improving the performance of future biosensors as gentle immobilization‐limiting alteration of the protein structure, oriented immobilization, thereby allowing homogeneous accessibility, reversible immobilization, thereby allowing reutilizations, and high compatibility with various types of biomacromolecules.     

Controlling the Structure and Length of Self‐Synthesizing Supramolecular Polymers through Nucleated Growth and Disassembly

Directing self‐assembly processes out‐of‐equilibrium to yield kinetically trapped materials with well‐defined dimensions remains a considerable challenge. Kinetically controlled assembly of self‐synthesizing peptide‐functionalized macrocycles through a nucleation–growth mechanism is reported. Spontaneous fiber formation in this system is effectively shut down as most of the material is diverted into metastable non‐assembling trimeric and tetrameric macrocycles. However, upon adding seeds to this mixture, well‐defined fibers with controllable lengths and narrow polydispersities are obtained. This seeded growth strategy also allows access to supramolecular triblock copolymers. The resulting noncovalent assemblies can be further stabilized through covalent capture. Taken together, these results show that self‐synthesizing materials, through their interplay between dynamic covalent bonds and noncovalent interactions, are uniquely suited for out‐of‐equilibrium self‐assembly.     

Directed Self‐Assembly of DNA Tiles into Complex Nanocages

Tile‐based self‐assembly is a powerful method in DNA nanotechnology and has produced a wide range of well‐defined nanostructures. But the resulting structures are relatively simple. Increasing the structural complexity and the scope of the accessible structures is an outstanding challenge in molecular self‐assembly. A strategy to partially address this problem by introducing flexibility into assembling DNA tiles and employing directing agents to control the self‐assembly process is presented. To demonstrate this strategy, a range of DNA nanocages have been rationally designed and constructed. Many of them can not be assembled otherwise. All of the resulting structures have been thoroughly characterized by gel electrophoresis and cryogenic electron microscopy. This strategy greatly expands the scope of accessible DNA nanostructures and would facilitate technological applications such as nanoguest encapsulation, drug delivery, and nanoparticle organization.     

Synthesis of Responsive Two‐Dimensional Polymers via Self‐Assembled DNA Networks

Despite a growing interest in two‐dimensional polymers, their rational synthesis remains a challenge. The solution‐phase synthesis of a two‐dimensional polymer is reported. A DNA‐based monomer self‐assembles into a supramolecular network, which is further converted into the covalently linked two‐dimensional polymer by anthracene dimerization. The polymers appear as uniform monolayers, as shown by AFM and TEM imaging. Furthermore, they exhibit a pronounced solvent responsivity. The results demonstrate the value of DNA‐controlled self‐assembly for the formation of two‐dimensional polymers in solution.     

Regulating Higher‐Order Organization through the Synergy of Two Self‐Sorted Assemblies

The extracellular matrix (ECM) is the natural fibrous scaffold that regulates cell behavior in a hierarchical manner. By mimicking the dynamic and reciprocal interactions between ECM and cells, higher‐order molecular self‐assembly (SA), mediated through the dynamic growth of scaffold‐like nanostructures assembled by different molecular components, was developed. Designed and synthesized were two self‐sorted coumarin‐based gelators, a peptide molecule and a benzoate molecule, which self‐assemble into nanofibers and nanobelts, respectively, with different dynamic profiles. Upon the dynamic growth of the fibrous scaffold assembled from peptide gelators, nanobelts assembled from benzoate gelators transform into a layer‐by‐layer nanosheet, reaching ninefold increase in height. By using light and an enzyme, the spatial–temporal growth of the scaffold can be modified, leading to in situ height regulation of the higher‐order architecture.     

Multicomponent Supramolecular Systems: Self‐Organization in Coordination‐Driven Self‐Assembly

The self‐organization of multicomponent supramolecular systems involving a variety of two‐dimensional (2 D) polygons and three‐dimensional (3 D) cages is presented. Nine self‐organizing systems, SS₁ – SS₉ , have been studied. Each involves the simultaneous mixing of organoplatinum acceptors and pyridyl donors of varying geometry and their selective self‐assembly into three to four specific 2 D (rectangular, triangular, and rhomboid) and/or 3 D (triangular prism and distorted and nondistorted trigonal bipyramidal) supramolecules. The formation of these discrete structures is characterized using NMR spectroscopy and electrospray ionization mass spectrometry (ESI‐MS). In all cases, the self‐organization process is directed by: 1) the geometric information encoded within the molecular subunits and 2) a thermodynamically driven dynamic self‐correction process. The result is the selective self‐assembly of multiple discrete products from a randomly formed complex. The influence of key experimental variables ‐ temperature and solvent ‐ on the self‐correction process and the fidelity of the resulting self‐organization systems is also described.