Nanoarchitectonics with Porphyrin Functionalized DNA

Toward Automated DNA Nanoprinting: Advancing the Synthesis of Covalently Branched DNA

Covalently branched DNA molecules are hybrid structures where a small molecule core is covalently linked to different DNA strands. They merge the programmability of DNA nanotechnology with synthetic molecules' functionality, offering enhanced stability over their non-covalent counterparts like double-crossover tiles. They enable the efficient assembly of stable DNA nanostructures with new geometries and functionalities. These motifs can be prepared through "DNA printing", which uses a DNA nanostructure as a temporary template to covalently transfer specific DNA strands to a small molecule core. Here, the "printing" process is streamlined with DNA-immobilized polystyrene microspheres, laying the foundation for future automated DNA printing devices. First, the DNA template hybridizes with reactive complementary strands, which are then crosslinked using a small molecule. Second, beads with fully complementary molecules capture the "daughter" products by strand displacement. This ensures high product yields and high recovery of the "mother" template for reuse. This method allows the precise transfer of different DNA strands onto various small molecules, including aromatics and functional porphyrins. Notably, these branching motifs exhibit remarkable stability toward nucleases without any specialized modifications. Moreover, they can serve as robust building blocks for precise assembly of 3D structures, such as an addressable tetrahedron from only two components.

Nanoparticles of nucleotide-free analogue of vitamin B12 formed in protein nanocarriers and their neuroprotective activity in vivo

Recently, we have described the first supermolecular nanoentities of vitamin B12 derivative, viz. monocyano form of heptabutyl cobyrinate, unique nanoparticles with strong noncovalent intermolecular interactions, emerging optical and catalytic properties. Their nearest analogue, heptamethyl cobyrinate (ACCby), exhibits bioactivity. Here, we demonstrate the first example of the formation of nanoparticles of this nucleotide-free analogue of vitamin B12 in protein nanocarriers and neuroprotective activity in vivo of the own nanoform of the drug. The preparation and characterization of nanocarriers based on bovine serum albumin (BSA) loaded with vitamin B12 (viz. cyano- and aquacobalamins) and ACCby were performed. Nucleotide-free analogue of vitamin B12 is tightly retained by the protein structure and exists in an incorporated state in the form of nanoparticles. The effect of encapsulated drugs on the character and severity of primary generalized seizures in rats induced by the pharmacotoxicant thiosemicarbazide was studied. Cyanocobalamin and ACCby exhibited a neuroprotective effect. The best influence of the encapsulation on the effectiveness of the drugs was achieved in the case of AСCby, whose bioavailability as a neuroprotector did not change upon introduction in BSA particles, i.e., 33 % of surviving animals were observed upon ACCby administration in free form and in encapsulated state. No surviving rats were observed without the administration of drugs. Thus, BSA nanocarriers loaded by nanoparticles of nucleotide-free analogues of vitamin B12, including hydrophobic ones, can be recommended for neuroprotection and targeted delivery.

Revolutionizing DNA: advanced modification techniques for next-gen nanotechnology

The comprehensive advancement in DNA modification and coupling is driving DNA nanotechnology to new heights, paving the way for groundbreaking innovations in healthcare, materials science, and beyond. The ability to engineer DNA with tailored properties and functionalities underscores its immense potential in creating novel materials and devices. Utilizing a spectrum of techniques-such as amino handles, thiol groups, alkynes, azides, Diels-Alder reactions, hydrazides, and aminooxy functions-enables diverse coupling strategies, including Palladium-Catalyzed Couplings, to construct intricate DNA nanostructures. Further coupling modifications encompass hydrophobic alterations, redox-active moieties, chemical crosslinking agents, and Biotinylation. These modifications significantly broaden DNA's functional repertoire, offering precise control over interactions, structures, and features. By leveraging these advanced techniques, alongside next-generation sequencing (NGS)-based DNA modifications, researchers can design and implement DNA nanostructures with specific capabilities and applications, showcasing DNA's versatility as a programmable biomaterial. Through meticulous design and strategic implementation, DNA nanotechnology achieves unprecedented levels of precision and functionality, ushering in a new era of technological advancements and applications. These advanced DNA modification techniques hold great potential for transformative applications in nanotechnology, paving the way for innovations in drug delivery, diagnostics, and bioengineering.

Creation of Metal-Complex-Integrated Tensegrity Triangle DNA Crystals

Structural DNA nanotechnology is an emerging field and is expected to be used for various applications in materials science. In this study, we designed a DNA tensegrity triangle to accommodate the bipyridine complexes with metal ions (Ni2+ and Fe2+) at the center of the space within the triangle. A metal-bipyridine-incorporated DNA tensegrity triangle was crystalized, and the presence of metals within it was confirmed through X-ray crystal structure analysis. A signal of the anomalous dispersion effect derived from metal was observed in the center of the DNA triangle.

Supramolecular assembly of phenanthrene-DNA conjugates into light-harvesting nanospheres

The self-assembly of highly functionalized phenanthrene-DNA conjugates into supramolecular nanostructures is presented. DNA oligomers modified with phenanthrene residues at the 3'-end and internal positions self-assemble into spherical nanostructures. The nanospheres exhibit light-harvesting properties. Upon irradiation of phenanthrene, the excitation energy is transferred along phenanthrene units, resulting in phenanthrene-pyrene exciplex formation.

TMPyP binding evokes a complex, tunable nanomechanical response in DNA

TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, TMPyP's effect on DNA nanomechanics is unknown. Here we investigated, by manipulating λ-phage DNA with optical tweezers combined with microfluidics in equilibrium and perturbation kinetic experiments, how TMPyP influences DNA nanomechanics across wide ranges of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 μm/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding, which is a highly dynamic process, leads to dsDNA lengthening and softening. dsDNA stability increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. Overstretch cooperativity decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA's contour length. The addition of NaCl at high (1 M) concentration competed with the TMPyP-evoked nanomechanical changes. Because the largest amplitude of the changes is induced by the pharmacologically relevant TMPyP concentration range, this porphyrin derivative may be used to tune DNA's structure and properties, hence control the wide array of biomolecular DNA-dependent processes including replication, transcription, condensation and repair.

Correlative Super-resolution Optical and Electron Microscopic Imaging of Intracellular Ribosomal RNA by a Terpyridine Iridium(III) Complex

Ribosomal RNA (rRNA) plays a vital role in binding amino acids together, which dictates the primary structure of a protein. Visualization of its intracellular distribution and dynamics during protein synthesis enables a better understanding of the correlated biological essence. However, appropriate tools targeting live cell rRNA that are capable of multimodal imaging at the nanoscale are still lacking. Here, we rationally designed a series of terpyridine ammonium iridium(III) complexes, one of which is capable of selectively labeling rRNA in living cells. Its metal core and photostable nature allow further super-resolution STED imaging of rRNA found on the rough endoplasmic reticulum at a ∼40 nm resolution that is well correlated under correlative light and electron microscopy (CLEM). Interestingly, the Ir(III) complex demonstrated rRNA dynamics in living cells while boosting protein synthesis at the nanoscale. Our work offers a versatile tool to visualize rRNA synchronously under optical and electron microscopy, which provides a better understanding of rRNA evolution in living systems.

Highly Efficient Carbon Dioxide Electroreduction via DNA-Directed Catalyst Immobilization

Electrochemical reduction of carbon dioxide (CO2) is a promising route to up-convert this industrial byproduct. However, to perform this reaction with a small-molecule catalyst, the catalyst must be proximal to an electrode surface. Efforts to immobilize molecular catalysts on electrodes have been stymied by the need to optimize the immobilization chemistries on a case-by-case basis. Taking inspiration from nature, we applied DNA as a molecular-scale "Velcro" to investigate the tethering of three porphyrin-based catalysts to electrodes. This tethering strategy improved both the stability of the catalysts and their Faradaic efficiencies (FEs). DNA-catalyst conjugates were immobilized on screen-printed carbon and carbon paper electrodes via DNA hybridization with nearly 100% efficiency. Following immobilization, a higher catalyst stability at relevant potentials is observed. Additionally, lower overpotentials are required for the generation of carbon monoxide (CO). Finally, high FE for CO generation was observed with the DNA-immobilized catalysts as compared to the unmodified small-molecule systems, as high as 79.1% FE for CO at -0.95 V vs SHE using a DNA-tethered catalyst. This work demonstrates the potential of DNA "Velcro" as a powerful strategy for catalyst immobilization. Here, we demonstrated improved catalytic characteristics of molecular catalysts for CO2 valorization, but this strategy is anticipated to be generalizable to any reaction that proceeds in aqueous solutions.

2D Materials Nanoarchitectonics for 3D Structures/Functions

It has become clear that superior material functions are derived from precisely controlled nanostructures. This has been greatly accelerated by the development of nanotechnology. The next step is to assemble materials with knowledge of their nano-level structures. This task is assigned to the post-nanotechnology concept of nanoarchitectonics. However, nanoarchitectonics, which creates intricate three-dimensional functional structures, is not always easy. Two-dimensional nanoarchitectonics based on reactions and arrangements at the surface may be an easier target to tackle. A better methodology would be to define a two-dimensional structure and then develop it into a three-dimensional structure and function. According to these backgrounds, this review paper is organized as follows. The introduction is followed by a summary of the three issues; (i) 2D to 3D dynamic structure control: liquid crystal commanded by the surface, (ii) 2D to 3D rational construction: a metal-organic framework (MOF) and a covalent organic framework (COF); (iii) 2D to 3D functional amplification: cells regulated by the surface. In addition, this review summarizes the important aspects of the ultimate three-dimensional nanoarchitectonics as a perspective. The goal of this paper is to establish an integrated concept of functional material creation by reconsidering various reported cases from the viewpoint of nanoarchitectonics, where nanoarchitectonics can be regarded as a method for everything in materials science.

Materials Nanoarchitectonics at Dynamic Interfaces: Structure Formation and Functional Manipulation

The next step in nanotechnology is to establish a methodology to assemble new functional materials based on the knowledge of nanotechnology. This task is undertaken by nanoarchitectonics. In nanoarchitectonics, we architect functional material systems from nanounits such as atoms, molecules, and nanomaterials. In terms of the hierarchy of the structure and the harmonization of the function, the material created by nanoarchitectonics has similar characteristics to the organization of the functional structure in biosystems. Looking at actual biofunctional systems, dynamic properties and interfacial environments are key. In other words, nanoarchitectonics at dynamic interfaces is important for the production of bio-like highly functional materials systems. In this review paper, nanoarchitectonics at dynamic interfaces will be discussed, looking at recent typical examples. In particular, the basic topics of "molecular manipulation, arrangement, and assembly" and "material production" will be discussed in the first two sections. Then, in the following section, "fullerene assembly: from zero-dimensional unit to advanced materials", we will discuss how various functional structures can be created from the very basic nanounit, the fullerene. The above examples demonstrate the versatile possibilities of architectonics at dynamic interfaces. In the last section, these tendencies will be summarized, and future directions will be discussed.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

Supramolecular assembly of pyrene-DNA conjugates: influence of pyrene substitution pattern and implications for artificial LHCs

The supramolecular self-assembly of pyrene-DNA conjugates into nanostructures is presented. DNA functionalized with different types of pyrene isomers at the 3'-end self-assemble into nano-objects. The shape of the nanostructures is influenced by the type of pyrene isomer appended to the DNA. Multilamellar vesicles are observed with the 1,6- and 1,8-isomers, whereas conjugates of the 2,7-isomer exclusively assemble into spherical nanoparticles. Self-assembled nano-spheres obtained with the 2,7-dialkynyl pyrene isomer were used for the construction of an artificial light-harvesting complex (LHC) in combination with Cy3 as the energy acceptor.

Photogeneration of Spin Quintet Triplet-Triplet Excitations in DNA-Assembled Pentacene Stacks

Singlet fission (SF), an exciton-doubling process observed in certain molecular semiconductors where two triplet excitons are generated from one singlet exciton, requires correctly tuned intermolecular coupling to allow separation of the two triplets to different molecular units. We explore this using DNA-encoded assembly of SF-capable pentacenes into discrete π-stacked constructs of defined size and geometry. Precise structural control is achieved via a combination of the DNA duplex formation between complementary single-stranded DNA and the local molecular geometry that directs the SF chromophores into a stable and predictable slip-stacked configuration, as confirmed by molecular dynamics (MD) modeling. Transient electron spin resonance spectroscopy revealed that within these DNA-assembled pentacene stacks, SF evolves via a bound triplet pair quintet state, which subsequently converts into free triplets. SF evolution via a long-lived quintet state sets specific requirements on intermolecular coupling, rendering the quintet spectrum and its zero-field-splitting parameters highly sensitive to intermolecular geometry. We have found that the experimental spectra and zero-field-splitting parameters are consistent with a slight systematic strain relative to the MD-optimized geometry. Thus, the transient electron spin resonance analysis is a powerful tool to test and refine the MD-derived structure models. DNA-encoded assembly of coupled semiconductor molecules allows controlled construction of electronically functional structures, but brings with it significant dynamic and polar disorders. Our findings here of efficient SF through quintet states demonstrate that these conditions still allow efficient and controlled semiconductor operation and point toward future opportunities for constructing functional optoelectronic systems.

Supermolecular Nanoentities of Vitamin B12 Derivative as a Link in the Evolution of the Parent Molecules During Self-Assembly at the Air-Water Interface

Nanoarchitectures with promising properties have now been formed from many important biomolecules. However, the preparation of nanoparticles of vitamin B₁₂ and its derivatives remains an ongoing research challenge. This paper describes the formation of supermolecular nanoentities (SMEs) of vitamin B₁₂ derivatives, unique nanoparticles with strong noncovalent intermolecular interactions, emerging properties, and activity. These were created by a nanoarchitectonic approach using directed assembly of layers at the air-water interface as a link in the chain of evolution of the parent molecules under specially created conditions. Such layers can be represented as a nanocosm, where, at a critical density, the assemblies act as nanoreactors in which the transformation of the original material occurs. The discovered SMEs not only replicate the functioning of vitamin B₁₂ assemblies with proteins in living organisms and act as vitamin B₁₂-depended enzymes but also demonstrate important advantages over vitamin B₁₂. They are more efficient in oxygen reduction/evolution reactions and in transformation into other forms. These SMEs, in performing advanced tasks, are an alternative to widely used materials based on noble metals for catalysis, medicine, and environment protection. Our findings open new perspectives both for the fabrication of novel SMEs of biomolecules and for a better understanding of the evolution of biomolecules in nature.

Two birds one stone: β-fluoropyrrolyl-cysteine SNAr chemistry enabling functional porphyrin bioconjugation

Bioconjugation, a synthetic tool that endows small molecules with biocompatibility and target specificity through covalent attachment of a biomolecule, holds promise for next-generation diagnosis or therapy. Besides the establishment of chemical bonding, such chemical modification concurrently allows alteration of the physicochemical properties of small molecules, but this has been paid less attention in designing novel bioconjugates. Here, we report a "two birds one stone" methodology for irreversible porphyrin bioconjugation based on β-fluoropyrrolyl-cysteine S_NAr chemistry, in which the β-fluorine of porphyrin is selectively replaced by a cysteine in either peptides or proteins to generate novel β-peptidyl/proteic porphyrins. Notably, due to the distinct electronic nature between fluorine and sulfur, such replacement makes the Q band red-shift to the near-infrared region (NIR, >700 nm). This facilitates intersystem crossing (ISC) to enhance the triplet population and thus singlet oxygen production. This new methodology features water tolerance, a fast reaction time (15 min), good chemo-selectivity, and broad substrate scope, including various peptides and proteins under mild conditions. To demonstrate its potential, we applied porphyrin β-bioconjugates in several scenarios, including (1) cytosolic delivery of functional proteins, (2) metabolic glycan labeling, (3) caspase-3 detection, and (4) tumor-targeting phototheranostics.

Structure-switchable aptamer-arranged reconfigurable DNA nanonetworks for targeted cancer therapy

The structural DNA nanotechnology holds great potential application in bioimaging, drug delivery and cancer therapy. Herein, an intelligent aptamer-incorporated DNA nanonetwork (Apt-Nnes) is demonstrated for cancer cell imaging and targeted drug delivery, which essentially is a micron-scale pattern with the thickness of double-stranded monolayer. Cancer cell-surface receptors can make it perform magical transformation into small size of nanosheet intermediates and specifically enter target cells. The binding affinity of Apt-Nnes is increased by 3-fold due to multivalent binding effect of aptamers and it can maintain the structural integrity in fetal bovine serum (FBS) for 8 h. More interestingly, target cancer cells can cause the structural disassembly, and each resulting unit transports 4963 doxorubicin (Dox) into target cells, causing the specific cellular cytotoxicity. The cell surface receptor-mediated disassembly of large size of DNA nanostructures into small size of fractions provides a valuable insight into developing intelligent DNA nanostructure suitable for biomedical applications.

Deoxyribonucleic Acid Encoded and Size-Defined π-Stacking of Perylene Diimides

Natural photosystems use protein scaffolds to control intermolecular interactions that enable exciton flow, charge generation, and long-range charge separation. In contrast, there is limited structural control in current organic electronic devices such as OLEDs and solar cells. We report here the DNA-encoded assembly of π-conjugated perylene diimides (PDIs) with deterministic control over the number of electronically coupled molecules. The PDIs are integrated within DNA chains using phosphoramidite coupling chemistry, allowing selection of the DNA sequence to either side, and specification of intermolecular DNA hybridization. In this way, we have developed a "toolbox" for construction of any stacking sequence of these semiconducting molecules. We have discovered that we need to use a full hierarchy of interactions: DNA guides the semiconductors into specified close proximity, hydrophobic-hydrophilic differentiation drives aggregation of the semiconductor moieties, and local geometry and electrostatic interactions define intermolecular positioning. As a result, the PDIs pack to give substantial intermolecular π wave function overlap, leading to an evolution of singlet excited states from localized excitons in the PDI monomer to excimers with wave functions delocalized over all five PDIs in the pentamer. This is accompanied by a change in the dominant triplet forming mechanism from localized spin-orbit charge transfer mediated intersystem crossing for the monomer toward a delocalized excimer process for the pentamer. Our modular DNA-based assembly reveals real opportunities for the rapid development of bespoke semiconductor architectures with molecule-by-molecule precision.

Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure

DNA nanotechnology has emerged as a promising method for designing spontaneously inserting and fully controllable synthetic ion channels. However, both insertion efficiency and stability of existing DNA-based membrane channels leave much room for improvement. Here, we demonstrate an approach to overcoming the unfavorable DNA-lipid interactions that hinder the formation of a stable transmembrane pore. Our all-atom MD simulations and experiments show that the insertion-driving cholesterol modifications can cause fraying of terminal base pairs of nicked DNA constructs, distorting them when embedded in a lipid bilayer. Importantly, we show that DNA nanostructures with no backbone discontinuities form more stable conductive pores and insert into membranes with a higher efficiency than the equivalent nicked constructs. Moreover, lack of nicks allows design and maintenance of membrane-spanning helices in a tilted orientation within the lipid bilayer. Thus, reducing the conformational degrees of freedom of the DNA nanostructures enables better control over their function as synthetic ion channels.

Nanoarchitectonics for Hierarchical Fullerene Nanomaterials

Nanoarchitectonics is a universal concept to fabricate functional materials from nanoscale building units. Based on this concept, fabrications of functional materials with hierarchical structural motifs from simple nano units of fullerenes (C60 and C70 molecules) are described in this review article. Because fullerenes can be regarded as simple and fundamental building blocks with mono-elemental and zero-dimensional natures, these demonstrations for hierarchical functional structures impress the high capability of the nanoarchitectonics approaches. In fact, various hierarchical structures such as cubes with nanorods, hole-in-cube assemblies, face-selectively etched assemblies, and microstructures with mesoporous frameworks are fabricated by easy fabrication protocols. The fabricated fullerene assemblies have been used for various applications including volatile organic compound sensing, microparticle catching, supercapacitors, and photoluminescence systems.

Zero-to-Two Nanoarchitectonics: Fabrication of Two-Dimensional Materials from Zero-Dimensional Fullerene

Nanoarchitectonics of two-dimensional materials from zero-dimensional fullerenes is mainly introduced in this short review. Fullerenes are simple objects with mono-elemental (carbon) composition and zero-dimensional structure. However, fullerenes and their derivatives can create various types of two-dimensional materials. The exemplified approaches demonstrated fabrications of various two-dimensional materials including size-tunable hexagonal fullerene nanosheet, two-dimensional fullerene nano-mesh, van der Waals two-dimensional fullerene solid, fullerene/ferrocene hybrid hexagonal nanosheet, fullerene/cobalt porphyrin hybrid nanosheet, two-dimensional fullerene array in the supramolecular template, two-dimensional van der Waals supramolecular framework, supramolecular fullerene liquid crystal, frustrated layered self-assembly from two-dimensional nanosheet, and hierarchical zero-to-one-to-two dimensional fullerene assembly for cell culture.

Layered assembly of cationic and anionic supramolecular polymers

The chemical synthesis and the supramolecular assembly of an aromatic oligoamine are described. The self-assembly of the cationic oligomers in aqueous solution leads to the formation of vesicular objects. The assembly process of the oligomers is monitored by absorption and fluorescence spectroscopy and the formed vesicles are characterized by atomic force and transmission electron microscopy. The electrostatic complementarity of anionic supramolecular polymers sheets and the cationic vesicles is used for a layered assembly process.

Nanoarchitectonics on living cells

In this review article, the recent examples of nanoarchitectonics on living cells are briefly explained. Not limited to conventional polymers, functional polymers, biomaterials, nanotubes, nanoparticles (conventional and magnetic ones), various inorganic substances, metal-organic frameworks (MOFs), and other advanced materials have been used as components for nanoarchitectonic decorations for living cells. Despite these artificial processes, the cells can remain active or remain in hibernation without being killed. In most cases, basic functions of the cells are preserved and their resistances against external assaults are much enhanced. The possibilities of nanoarchitectonics on living cells would be high, equal to functional modifications with conventional materials. Living cells can be regarded as highly functionalized objects and have indispensable contributions to future materials nanoarchitectonics.

Interactions of porphyrins with DNA: A review focusing recent advances in chemical modifications on porphyrins as artificial nucleases

The advance of porphyrins as artificial nucleases along the years have developed a class of compounds having potential therapeutic applications. Being an extrovert of chemistry, a variety of chemical modifications have been done on porphyrin macrocycle in order to improve the spectroscopic properties and to adapt as artificial receptors that can recognize molecules. The last twenty years has witnessed broad research in the arena of porphyrin- DNA interactions and their evolution from simple to more complex entities. In this review, we summarize the recent advances in the porphyrin-based structural modifications, with a specific emphasis on various effects of porphyrin on DNA cleavage potency. We particularly detailed the nuclease activity of cationic and anionic porphyrins, porphyrin dimers and conjugates as well as heme proteins till the third generation porphyrins as artificial nucleases.

Progress in Molecular Nanoarchitectonics and Materials Nanoarchitectonics

Although various synthetic methodologies including organic synthesis, polymer chemistry, and materials science are the main contributors to the production of functional materials, the importance of regulation of nanoscale structures for better performance has become clear with recent science and technology developments. Therefore, a new research paradigm to produce functional material systems from nanoscale units has to be created as an advancement of nanoscale science. This task is assigned to an emerging concept, nanoarchitectonics, which aims to produce functional materials and functional structures from nanoscale unit components. This can be done through combining nanotechnology with the other research fields such as organic chemistry, supramolecular chemistry, materials science, and bio-related science. In this review article, the basic-level of nanoarchitectonics is first presented with atom/molecular-level structure formations and conversions from molecular units to functional materials. Then, two typical application-oriented nanoarchitectonics efforts in energy-oriented applications and bio-related applications are discussed. Finally, future directions of the molecular and materials nanoarchitectonics concepts for advancement of functional nanomaterials are briefly discussed.

Threading Intercalator-Induced Nanocondensates and Role of Endogenous Metal Ions in Decondensation for DNA Delivery

The interplay of condensation and decondensation of DNA plays a crucial role in chromosome maintenance and gene expression. The molecular architectonics governing the chromatin condensation-decondensation cycle are worth studying, as DNA performs unique and distinct roles in each state and switches between two states without the loss of structural and functional integrity. This phenomenon has been adapted and implemented in transfection studies. Effective gene delivery into the cells to achieve respectable transfection efficiency has remained a challenge and emphasizes the need for understanding the steps involved in DNA delivery and transfection. Especially, recognizing the factors that effectively regulate DNA decondensation can provide logical solutions to the hurdles affecting the transfection efficiency. We designed a set of small molecule-based threading intercalation ligands as model condensing agents to study various factors influencing the DNA condensation and decondensation process. This study revealed condensation of DNA into nanocondensate by the threading intercalator and endogenous stimuli induced effective decondensation. Further, DNA nanocondensates are tracked using the intrinsic fluorescence in the lower pH of endocytic pathway and were evaluated as nonviral vectors for in cellulo delivery of plasmids. The correlation of decondensation of DNA nanocondensate with endogenous metal ions at their physiological concentrations provided valuable insights and implications for intracellular DNA delivery.

Supramolecular Chiral Nanoarchitectonics

Exploration of molecular functions and material properties based on the control of chirality would be a scientifically elegant approach. Here, the fabrication and function of chiral-featured materials from both chiral and achiral components using a supramolecular nanoarchitectonics concept are discussed. The contents are classified in to three topics: i) chiral nanoarchitectonics of rather general molecular assemblies; ii) chiral nanoarchitectonics of metal-organic frameworks (MOFs); iii) chiral nanoarchitectonics in liquid crystals. MOF structures are based on nanoscopically well-defined coordinations, while mesoscopic orientations of liquid-crystalline phases are often flexibly altered. Discussion on the effects and features in these representative materials systems with totally different natures reveals the universal importance of supramolecular chiral nanoarchitectonics. Amplification of chiral molecular information from molecules to materials-level structures and the creation of chirality from achiral components upon temporal statistic fluctuations are universal, regardless of the nature of the assemblies. These features are thus surely advantageous characteristics for a wide range of applications.

DNA-organized artificial LHCs - testing the limits of chromophore segmentation

DNA-organized multi-chromophoric systems containing phenanthrene and pyrene derivatives exhibit a highly efficient excitation energy transfer from phenanthrene (donor) to pyrene (acceptor). The energy transfer also occurs if the phenanthrene antenna is interrupted by intervening DNA base pairs. Artificial light-harvesting complexes composed of up to five phenanthrene-DNA alternations with fluorescence quantum yields as high as 68% are described.

Synthesis, photoinduced amination and topological indices of novel porphyrin dyads

Transition-metal-catalyzed homo and hetero coupling is a rapidly growing area of research. This work refers to the nickel-catalyzed photoinduced amination study of [Formula: see text]-bromotetraarylporphyrin and its Ni(II), Zn(II) and Cu(II) complexes. The selective mono [Formula: see text]-bromination of 5,10,15,20-tetrakis(4[Formula: see text]-isopropylphenyl)porphyrin was achieved with [Formula: see text]-bromosuccinimide. Under similar conditions, [Formula: see text]-bromination of Ni(II), Zn(II) and Cu(II) complexes of 5,10,15,20-tetrakis(4[Formula: see text]-isopropylphenyl)porphyrin successfully afforded the corresponding 2-bromometalloporphyrins. The [Formula: see text]-bromoporphyrin/metalloporphyrins were coupled with three different amines through the creation of the C–N bond by using an economical and air-tolerant photoactive catalyst (NiBr[Formula: see text] · 3H2O) at room temperature under 365 nm radiations. Nickel-catalyzed amination yields are compared with the traditional Buchwald–Hartwig amination yields. Due to the low operational cost, photoinduced nickel-catalyzed C–N couplings were found to be more economical than the Buchwald–Hartwig amination procedure, although the latter afforded higher yields. The nickel-catalyzed photoamination reaction was also extended for the one-pot synthesis of pyridine-3,5-diamine bridged porphyrin dyad. The intramolecular cyclization of the pyridine-3,5-diamine-bridged porphyrin dyad afforded a novel quinolino-fused porphyrin dyad. Degree- and distance-based topological indices of the newly synthesized porphyrins were calculated and correlated with their molar refractivity. All newly synthesized porphyrins are characterized by UV-vis, FTIR, 1H NMR, elemental analysis and mass spectrometry.

Nanoarchitectonics beyond Self-Assembly: Challenges to Create Bio-Like Hierarchic Organization

Incorporation of non-equilibrium actions in the sequence of self-assembly processes would be an effective means to establish bio-like high functionality hierarchical assemblies. As a novel methodology beyond self-assembly, nanoarchitectonics, which has as its aim the fabrication of functional materials systems from nanoscopic units through the methodological fusion of nanotechnology with other scientific disciplines including organic synthesis, supramolecular chemistry, microfabrication, and bio-process, has been applied to this strategy. The application of non-equilibrium factors to conventional self-assembly processes is discussed on the basis of examples of directed assembly, Langmuir-Blodgett assembly, and layer-by-layer assembly. In particular, examples of the fabrication of hierarchical functional structures using bio-active components such as proteins or by the combination of bio-components and two-dimensional nanomaterials, are described. Methodologies described in this review article highlight possible approaches using the nanoarchitectonics concept beyond self-assembly for creation of bio-like higher functionalities and hierarchical structural organization.

2D Nanoarchitectonics: Soft Interfacial Media as Playgrounds for Microobjects, Molecular Machines, and Living Cells

Soft and flexible two-dimensional (2D) systems, such as liquid interfaces, would have much more potentials in dynamic regulation on nano-macro connected functions. In this Minireview article, we focus especially on dynamic motional functions at liquid dynamic interfaces as 2D material systems. Several recent examples are selected to be explained for overviewing features and importance of dynamic soft interfaces in a wide range of action systems. The exemplified research systems are mainly classified into three categories: (i) control of microobjects with motional regulations; (ii) control of molecular machines with functions of target discrimination and optical outputs; (iii) control of living cells including molecular machine functions at cell membranes and cell/biomolecular behaviors at liquid interface. Sciences on soft 2D media with motional freedom and their nanoarchitectonics constructions will have increased importance in future technology in addition to popular rigid solid 2D materials.

Single-Molecule Mechanics in Ligand Concentration Gradient

Single-molecule experiments provide unique insights into the mechanisms of biomolecular phenomena. However, because varying the concentration of a solute usually requires the exchange of the entire solution around the molecule, ligand-concentration-dependent measurements on the same molecule pose a challenge. In the present work we exploited the fact that a diffusion-dependent concentration gradient arises in a laminar-flow microfluidic device, which may be utilized for controlling the concentration of the ligand that the mechanically manipulated single molecule is exposed to. We tested this experimental approach by exposing a λ-phage dsDNA molecule, held with a double-trap optical tweezers instrument, to diffusionally-controlled concentrations of SYTOX Orange (SxO) and tetrakis(4-N-methyl)pyridyl-porphyrin (TMPYP). We demonstrate that the experimental design allows access to transient-kinetic, equilibrium and ligand-concentration-dependent mechanical experiments on the very same single molecule.

Molecular architectonics of DNA for functional nanoarchitectures

DNA is the key biomolecule central to almost all processes in living organisms. The eccentric idea of utilizing DNA as a material building block in molecular and structural engineering led to the creation of numerous molecular-assembly systems and materials at the nanoscale. The molecular structure of DNA is believed to have evolved over billions of years, with structure and stability optimizations that allow life forms to sustain through the storage and transmission of genetic information with fidelity. The nanoscale structural characteristics of DNA (2 nm thickness and ca. 40-50 nm persistence length) have inspired the creation of numerous functional patterns and architectures through noncovalent conventional and unconventional base pairings as well as through mutual templating-interactions with small organic molecules and metal ions. The recent advancements in structural DNA nanotechnology allowed researchers to design new DNA-based functional materials with chemical and biological properties distinct from their parent components. The modulation of structural and functional properties of hybrid DNA ensembles of small functional molecules (SFMs) and short oligonucleotides by adapting the principles of molecular architectonics enabled the creation of novel DNA nanoarchitectures with potential applications, which has been termed as templated DNA nanotechnology or functional DNA nanoarchitectonics. This review highlights the molecular architectonics-guided design principles and applications of the derived DNA nanoarchitectures. The advantages and ability of functional DNA nanoarchitectonics to overcome the trivial drawbacks of classical DNA nanotechnology to fulfill realistic and practical applications are highlighted, and an outlook on future developments is presented.

Bright G-Quadruplex Nanostructures Functionalized with Porphyrin Lanterns

The intricate arrangement of numerous and closely placed chromophores on nanoscale scaffolds can lead to key photonic applications ranging from optical waveguides and antennas to signal-enhanced fluorescent sensors. In this regard, the self-assembly of dye-appended DNA sequences into programmed photonic architectures is promising. However, the dense packing of dyes can result in not only compromised DNA assembly (leading to ill-defined structures and precipitates) but also to essentially nonfluorescent systems (due to π-π aggregation). Here, we introduce a two-step "tether and mask" strategy wherein large porphyrin dyes are first attached to short G-quadruplex-forming sequences and then reacted with per-O-methylated β-cyclodextrin (PMβCD) caps, to form supramolecular synthons featuring the porphyrin fluor fixed into a masked porphyrin lantern (PL) state, due to intramolecular host-guest interactions in water. The PL-DNA sequences can then be self-assembled into cyclic architectures or unprecedented G-wires tethered with hundreds of porphyrin dyes. Importantly, despite the closely arrayed PL units (∼2 nm), the dyes behave as bright chromophores (up to 180-fold brighter than the analogues lacking the PMβCD masks). Since other self-assembling scaffolds, dyes, and host molecules can be used in this modular approach, this work lays out a general strategy for the bottom-up aqueous self-assembly of bright nanomaterials containing densely packed dyes.

Meso-tetra(4-carboxyphenyl)porphine-Enhanced DNA Methylation Sensing Interface on a Light-Addressable Potentiometric Sensor

DNA methylation (DNAm) sensors are an emerging branch in the discipline of sensors. It is believed to be able to promote the next generation of epigenetics-based diagnostic technology. Differing from the traditional biochemical sensors that aimed at individual molecules, the challenge in DNAm sensors is how to determine the amount of 5-methylcytosine (5mC) in a continuous nucleotide sequence. Here, we report a comparative study about meso-tetra(4-carboxyphenyl)porphine (TCPP)-based DNAm sensing interfaces on a light-addressable potentiometric sensor (LAPS), depending on TCPP's postures that are flat in the π-conjugated TCPP layer on reduced-graphene-oxide-decorated LAPS (#1) and stand-up in the covalently anchored TCPP on glutaraldehyde (GA)-treated LAPS (#2), along with the blank one (only GA-treated LAPS, #3). These DNAm sensing interfaces are also distinct from the traditional biosensing interface on LAPS, that is: it is not functionalized by the sensing indicator (5mC antibody, in this case) but by the target nucleotide sequence. The surface characterization techniques such as Raman spectra, scanning electron microscopy, and X-ray photoelectron spectroscopy are conducted to prove the decorations, as well as the anchored nucleotides. It is found that, though all of them can detect as low as one 5mC in the target sequence, the enhanced DNAm sensitivity is obtained by #2, which is evidenced by the higher output-voltage changing ratio for the 5mC site of #2 than those of #1 and #3. Furthermore, the underlying causes for the improved sensitivity in #2 are proposed, according to the conformational and electronic properties of TCPP molecules. Conclusively, TCPP's synergetic function, including the molecular configuration and the activate (carboxyl) groups on its peripheral substituents, to improve the DNAm sensing interface on LAPS is investigated and demonstrated. This can shed light on a new approach for DNA methylation detection, with the merits of low cost, independence on bisulfite conversion, and polymerase chain reaction.

From DNA Nanotechnology to Material Systems Engineering

In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.

Directed Energy Transfer through DNA-Templated J-Aggregates

Strongly coupled molecular dye aggregates have unique optoelectronic properties that often resemble those of light harvesting complexes found in Nature. The exciton dynamics in coupled dye aggregates could enhance the long-range transfer of optical excitation energy with high efficiency. In principle, dye aggregates could serve as important components in molecular-scale photonic devices; however, rational design of these coupled dye aggregates with precise control over their organization, interactions, and dynamics remains a challenge. DNA nanotechnology has recently been used to build an excitonic circuit by organizing pseudoisocyanine (PIC) dyes forming J-aggregates on the templates of poly(dA)-poly(dT) DNA duplexes. Here, the excitonic properties of the PIC J-aggregates on DNA are characterized spectroscopically in detail using poly(dA)-poly(dT) tract lengths of 24 and 48 base pairs. The excitonic properties of these DNA templated dye assemblies depend on the length and sequence of the DNA template. The incorporation of a gap of two GC base pairs between two segments of poly(dA)-poly(dT) DNA markedly reduces the delocalization of excitation in the J-aggregates. With a quantum dot (QD) as the light absorber and energy donor and using Alexa Fluor 647 (AF647) as the energy acceptor, with a DNA-templated J-aggregate in between, significant energy transfer from QD to AF647 is observed over a distance far longer than possible without the aggregate bridge. By comparing the efficiency of energy transfer through a continuous J-aggregate with the efficiency when the aggregate has a discontinuity in the middle, the effects of energy transfer within the aggregate bridge between the donor and acceptor are evaluated.

Langmuir Nanoarchitectonics from Basic to Frontier

Methodology to combine nanotechnology and these organization processes has been proposed as a novel concept of nanoarchitectonics, which can fabricate functional materials with nanolevel units. As an instant nanoarchitectonics approach, confining systems within a two-dimensional plane to drastically reduce translational motion freedom can be regarded as one of the rational approaches. Supramolecular chemistry and nanofabrication and their related functions at the air-water interface with the concept of nanoarchitectonics would lead to the creation of a novel methodology of Langmuir nanoarchitectonics. In this feature article, we briefly summarize research efforts related to Langmuir nanoarchitectonics including the basics for anomalies in molecular interactions such as highly enhanced molecular recognition capabilities. It is also extended to frontiers including the fabrication of supramolecular receptors and two-dimensional patterns with subnanometer-scale structural regulation, manual control of molecular machines and receptors by hand-motion-like macroscopic actions, and the regulation of cell fates at nanoarchitected arrays of nanocarbon assemblies and at direct liquid interfaces.

Effect of the Number of Anchoring and Electron-Donating Groups on the Efficiency of Free-Base- and Zn-Porphyrin-Sensitized Solar Cells

A series of porphyrin compounds, free base (H₂P) and their Zn (II) metallated analogues (ZnP), bearing one, two or three carboxylic acid groups, have been synthesized, characterized, and used as sensitizers in dye sensitized solar cells (DSSCs). The performance of these devices has been analyzed, showing higher efficiencies of those sensitized with ZnP compounds. These results have been explained, on one hand, taking into account the electronic character of the metal ion, which acts as mediator in the injection step, and, on the other, considering the number of anchoring groups, which determines both the stereoelectronic character of the dye and the way it binds to TiO₂ surface.

Helix-Sense-Selective Polymerization of Phenylacetylenes Having a Porphyrin and a Zinc-Porphyrin Group: One-Handed Helical Arrangement of Porphyrin Pendants

Newly synthesized two kinds of achiral phenylacetylenes having a free-base- or a zinc-porphyrin (1 and Zn1, respectively) were polymerized by using a chiral rhodium catalyst system, Rh⁺(nbd)[(η⁶-C₆H₅)B⁻(C₆H₅)₃] catalyst and (R)-(+)- or (S)-(⁻)-1-phenylethylamine ((R)- or (S)-PEA, respectively) cocatalyst. Poly(1) and poly(Zn1) in THF showed a Cotton signal at the absorption region of the porphyrin and the main chain in the circular dichroism (CD) spectra. This result suggests that poly(1) and poly(Zn1) exist in a conformation with an excess of one-handed helix sense and the porphyrin moiety arranged in chiral helical fashion. The one-handed helical structure of poly(1) could be sustained in a mixture of THF/HMPA (10/2, v/v) due to stabilizing by stacking effect of porphyrin moieties along the main chain. This is the first example about helix-sense-selective polymerization by using Rh⁺(nbd)[(η⁶-C₆H₅)B⁻(C₆H₅)₃] catalyst. Additionally, poly(Zn1) showed about 10 times larger CD intensity in comparison with poly(1). This result suggests the regularity of arrangement of the porphyrin in poly(Zn1) is higher compared with poly(1). Spatial arrangement of porphyrins was achieved by utilizing a one-handed helical poly(phenylacetylenes) as a template.