Detection of the Enzymatic Cleavage of DNA through Supramolecular Chiral Induction to a Cationic Polythiophene

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.

Fluorescent Dynamic Covalent Polymers for DNA Complexation and Templated Assembly

Dynamic covalent polymers (DCPs) offer opportunities as adaptive materials of particular interest for targeting, sensing and delivery of biological molecules. In this view, combining cationic units and fluorescent units along DCP chains is attractive for achieving optical probes for the recognition and delivery of nucleic acids. Here, we report on the design of acylhydrazone-based DCPs combining cationic arginine units with π-conjugated fluorescent moieties based on thiophene-ethynyl-fluorene cores. Two types of fluorescent building blocks bearing neutral or cationic side groups on the fluorene moiety are considered in order to assess the role of the number of cationic units on complexation with DNA. The (chir)optical properties of the building blocks, the DCPs, and their complexes with several types of DNA are explored, providing details on the formation of supramolecular complexes and on their stability in aqueous solutions. The DNA-templated formation of DCPs is demonstrated, which provides new perspectives on the assembly of fluorescent DCP based on the nucleic acid structure.

Ionic Push–Pull Polythiophenes: A Further Step towards Eco-Friendly BHJ Organic Solar Cells

Four new conjugated polymers alternating benzothiadiazole units and thiophene moieties functionalized with ionic phosphonium or sulfonic acid salts in the side chains were synthesized by a postfunctionalization approach of polymeric precursors. The introduction of ionic groups makes the conjugated polymers soluble in water and/or polar solvents, allowing for the fabrication of bulk heterojunction (BHJ) solar cells using environmentally friendly conditions. All polymers were fully characterized by spectroscopic, thermal, electrochemical, X-ray diffraction, scanning electron, and atomic force techniques. BHJ solar cells were obtained from halogen-free solvents (i.e., ethanol and/or anisole) by blending the synthesized ionic push–pull polymers with a serinol-fullerene derivative or an ionic homopolymer acting as electron-acceptor (EA) or electron-donor (ED) counterparts, respectively. The device with the highest optical density and the smoothest surface of the active layer was the best-performing, showing a 4.76% photoconversion efficiency.

Binding Mode Multiplicity and Multiscale Chirality in the Supramolecular Assembly of DNA and a π-Conjugated Polymer

Water-soluble π-conjugated polymers are increasingly considered for DNA biosensing. However, the conformational rearrangement, supramolecular organization and dynamics upon interaction with DNA have been overlooked, which prevents the rational design of such detection tools. To elucidate the binding of a cationic polythiophene (CPT) to DNA with atomistic resolution, we performed molecular simulations of their supramolecular assembly. Comparison of replicated simulations show a multiplicity of CPT binding geometries that contribute to the wrapping of CPT around DNA. The different binding geometries are stabilized by both electrostatic interactions between CPT lateral cations and DNA phosphodiesters and van der Waals interactions between the CPT backbone and the DNA grooves. Simulated circular dichroism (CD) spectra show that the induced CD signal stems from a conserved geometrical feature across the replicated simulations, i. e. the presence of segments of syn configurations between thiophene units along the CPT chain. At the macromolecular scale, we inspected the different shapes related to the CPT binding modes around the DNA through symmetry metrics. Altogether, molecular dynamics (MD) simulations, model Hamiltonian calculations of the CD spectra, and symmetry indices provide insights into the origin of induced chirality from the atomic to the macromolecular scale. Our multidisciplinary approach points out the hierarchical aspect of CPT chiral organization induced by DNA.

Organic Semiconductor-DNA Hybrid Assemblies

Organic semiconductors are photonic and electronic materials with high luminescence, quantum efficiency, color tunability, and size-dependent optoelectronic properties. The self-assembly of organic molecules enables the establishment of a fabrication technique for organic micro- and nano-architectures with well-defined shapes, tunable sizes, and defect-free structures. DNAs, a class of biomacromolecules, have recently been used as an engineering material capable of intricate nanoscale structuring while simultaneously storing biological genetic information. Here, the up-to-date research on hybrid materials made from organic semiconductors and DNAs is presented. The trends in photonic and electronic phenomena discovered in DNA-functionalized and DNA-driven organic semiconductor hybrids, comprising small molecules and polymers, are observed. Various hybrid forms of solutions, arrayed chips, nanowires, and crystalline particles are discussed, focusing on the role of DNA in the hybrids. Furthermore, the recent technical advances achieved in the integration of DNAs in light-emitting devices, transistors, waveguides, sensors, and biological assays are presented. DNAs not only serve as a recognizing element in organic-semiconductor-based sensors, but also as an active charge-control material in high-performance optoelectronic devices.

Structural and Photophysical Templating of Conjugated Polyelectrolytes with Single-Stranded DNA

A promising approach to influence and control the photophysical properties of conjugated polymers is directing their molecular conformation by templating. We explore here the templating effect of single-stranded DNA oligomers (ssDNAs) on cationic polythiophenes with the goal to uncover the intermolecular interactions that direct the polymer backbone conformation. We have comprehensively characterized the optical behavior and structure of the polythiophenes in conformationally distinct complexes depending on the sequence of nucleic bases and addressed the effect on the ultrafast excited-state relaxation. This, in combination with molecular dynamics simulations, allowed us a detailed atomistic-level understanding of the structure-property correlations. We find that electrostatic and other noncovalent interactions direct the assembly with the polymer, and we identify that optimal templating is achieved with (ideally 10-20) consecutive cytosine bases through numerous π-stacking interactions with the thiophene rings and side groups of the polymer, leading to a rigid assembly with ssDNA, with highly ordered chains and unique optical signatures. Our insights are an important step forward in an effective approach to structural templating and optoelectronic control of conjugated polymers and organic materials in general.

Supramolecular Chirality in Azobenzene-Containing Polymer System: Traditional Postpolymerization Self-Assembly Versus In Situ Supramolecular Self-Assembly Strategy

Recently, the design of novel supramolecular chiral materials has received a great deal of attention due to rapid developments in the fields of supramolecular chemistry and molecular self-assembly. Supramolecular chirality has been widely introduced to polymers containing photoresponsive azobenzene groups. On the one hand, supramolecular chiral structures of azobenzene-containing polymers (Azo-polymers) can be produced by nonsymmetric arrangement of Azo units through noncovalent interactions. On the other hand, the reversibility of the photoisomerization also allows for the control of the supramolecular organization of the Azo moieties within polymer structures. The construction of supramolecular chirality in Azo-polymeric self-assembled system is highly important for further developments in this field from both academic and practical points of view. The postpolymerization self-assembly strategy is one of the traditional strategies for mainly constructing supramolecular chirality in Azo-polymers. The in situ supramolecular self-assembly mediated by polymerization-induced self-assembly (PISA) is a facile one-pot approach for the construction of well-defined supramolecular chirality during polymerization process. In this review, we focus on a discussion of supramolecular chirality of Azo-polymer systems constructed by traditional postpolymerization self-assembly and PISA-mediated in situ supramolecular self-assembly. Furthermore, we will also summarize the basic concepts, seminal studies, recent trends, and perspectives in the constructions and applications of supramolecular chirality based on Azo-polymers with the hope to advance the development of supramolecular chirality in chemistry.

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.