Enzymatic synthesis of ligand-bearing oligonucleotides for the development of metal-responsive DNA materials.

Metal-mediated artificial base pairs are some of the most promising building blocks for constructing DNA-based supramolecules and functional materials. These base pairs are formed by coordination bonds between ligand-type nucleobases and a bridging metal ion and have been exploited to develop metal-responsive DNA materials and DNA-templated metal arrays. In this review, we provide an overview of methods for the enzymatic synthesis of DNA strands containing ligand-type artificial nucleotides that form metal-mediated base pairs. Conventionally, ligand-bearing DNA oligomers have been synthesized via solid-phase synthesis using a DNA synthesizer. In recent years, there has been growing interest in enzymatic methods as an alternative approach to synthesize ligand-bearing DNA oligomers, because enzymatic reactions proceed under mild conditions and do not require protecting groups. DNA polymerases are used to incorporate ligand-bearing unnatural nucleotides into DNA, and DNA ligases are used to connect artificial DNA oligomers to natural DNA fragments. Template-independent polymerases are also utilized to post-synthetically append ligand-bearing nucleotides to DNA oligomers. In addition, enzymatic replication of DNA duplexes containing metal-mediated base pairs has been intensively studied. Enzymatic methods facilitate the synthesis of DNA strands containing ligand-bearing nucleotides at both internal and terminal positions. Enzymatically synthesized ligand-bearing DNAs have been applied to metal-dependent self-assembly of DNA structures and the allosteric control of DNAzyme activity through metal-mediated base pairing. Therefore, the enzymatic synthesis of ligand-bearing oligonucleotides holds great potential in advancing the development of various metal-responsive DNA materials, such as molecular sensors and machines, providing a versatile tool for DNA supramolecular chemistry and nanotechnology.

Oral microsphere formulation of M2 macrophage-mimetic Janus nanomotor for targeted therapy of ulcerative colitis.

Oral medication for ulcerative colitis (UC) is often hindered by challenges such as inadequate accumulation, limited penetration of mucus barriers, and the intricate task of mitigating excessive ROS and inflammatory cytokines. Here, we present a strategy involving sodium alginate microspheres (SAMs) incorporating M2 macrophage membrane (M2M)-coated Janus nanomotors (denominated as Motor@M2M) for targeted treatment of UC. SAM provides a protective barrier, ensuring that Motor@M2M withstands the harsh gastric milieu and exhibits controlled release. M2M enhances the targeting precision of nanomotors to inflammatory tissues and acts as a decoy for the neutralization of inflammatory cytokines. Catalytic decomposition of H2O2 by MnO2 in the oxidative microenvironment generates O2 bubbles, propelling Motor@M2M across the mucus barrier into inflamed colon tissues. Upon oral administration, Motor@M2M@SAM notably ameliorated UC severity, including inflammation mitigation, ROS scavenging, macrophage reprogramming, and restoration of the intestinal barrier and microbiota. Consequently, our investigation introduces a promising oral microsphere formulation of macrophage-biomimetic nanorobots, providing a promising approach for UC treatment.

Single-gold etching at the hypercarbon atom of C-centred hexagold(I) clusters protected by chiral N-heterocyclic carbenes.

Chemical etching of nano-sized metal clusters at the atomic level has a high potential for creating metal number-specific structures and functions that are difficult to achieve with bottom-up synthesis methods. In particular, precisely etching metal atoms one by one from nonmetallic element-centred metal clusters and elucidating the relationship between their well-defined structures, and chemical and physical properties will facilitate future materials design for metal clusters. Here we report the single-gold etching at a hypercarbon centre in gold(I) clusters. Specifically, C-centred hexagold(I) clusters protected by chiral N-heterocyclic carbenes are etched with bisphosphine to yield C-centred pentagold(I) (CAuI5) clusters. The CAuI5 clusters exhibit an unusually large bathochromic shift in luminescence, which is reproduced theoretically. The etching mechanism is experimentally and theoretically suggested to be a tandem dissociation-association-elimination pathway. Furthermore, the vacant site of the central carbon of the CAuI5 cluster can accommodate AuCl, allowing for post-functionalisation of the C-centred gold(I) clusters.

DNA three-way junction structures with amino acid side chains prepared via post-synthetic amide condensation.

DNA three-way junction (3WJ) structures with three amino acid side chains in the core have been synthesized via post-synthetic DNA modification. Amide condensation reactions of oligonucleotides containing 2'-aminouridine with activated esters yielded DNA strands modified with His, Cys and Asp side chains to form modified 3WJs. Even a 3WJ with three negatively charged Asp side chains formed stably at room temperature. Furthermore, DNA hybridization alone placed two (His and Asp) and three (His, Cys, and Asp) side chains within the 3WJs, indicating that the DNA 3WJs are a useful platform for spatial arrangement of amino acid side chains.

Ligase-mediated synthesis of CuII-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases.

A CuII-responsive allosteric DNAzyme has been developed by introducing bifacial 5-carboxyuracil (caU) nucleobases, which form both hydrogen-bonded caU-A and metal-mediated caU-CuII-caU base pairs. The base sequence was logically designed based on a known RNA-cleaving DNAzyme so that the caU-modified DNAzyme (caU-DNAzyme) can form a catalytically inactive structure containing three caU-A base pairs and an active form with three caU-CuII-caU pairs. The caU-DNAzyme was synthesized by joining short caU-containing fragments with a standard DNA ligase. The activity of caU-DNAzyme was suppressed without CuII, but enhanced 21-fold with the addition of CuII. Furthermore, the DNAzyme activity was turned on and off during the reaction by the addition and removal of CuII ions. Both ligase-mediated synthesis and CuII-dependent allosteric regulation were achieved by the bifacial base pairing properties of caU. This study provides a new strategy for designing stimuli-responsive DNA molecular systems.

Metal-dependent activity control of a compact-sized 8-17 DNAzyme based on metal-mediated unnatural base pairing.

A compact 8-17 DNAzyme was modified with a CuII-meditated artificial base pair to develop a metal-responsive allosteric DNAzyme. The base sequence was rationally designed based on the reported three-dimensional structure. The activity of the modified DNAzyme was enhanced 5.1-fold by the addition of one equivalent of CuII ions, showing good metal responsiveness. Since it has been challenging to modify compactly folded DNAzymes without losing their activity, this study demonstrates the utility of the metal-mediated artificial base pairing to create stimuli-responsive functional DNAs.

Temperature-Dependent Spontaneous Resolution of a Tetrahedral Chiral-at-Nickel(II) Complex under Supramolecular Control.

Although stereochemical control of carbon centers is a well-established technique in modern synthetic chemistry, that of tetrahedral metal complexes with a stereogenic metal center remains difficult due to the dynamic nature of their coordination bonds. Here we report the synthesis of a tetrahedral d8 high-spin chiral-at-nickel(II) complex composed exclusively of achiral ligands and the supramolecular control of its temperature-dependent spontaneous resolution in crystals. Under certain conditions, complex molecules with the same absolute configuration of the nickel(II) center grow into conglomerate crystals with a helically arranged structure due to intermolecular hydrogen bonding. This process is highly spontaneous, does not require any chiral sources, and is closely related to the origin of homochirality in biological systems. The obtained enantiopure nickel(II) complex will be a new type of redox-active chiral source for asymmetric synthetic chemistry.

Selective synthesis of tightly- and loosely-twisted metallomacrocycle isomers towards precise control of helicity inversion motion.

Molecular twist is a characteristic component of molecular machines. Selectively synthesising isomers with different modes of twisting and controlling their motion such as helicity inversion is an essential challenge for achieving more advanced molecular systems. Here we report a strategy to control the inversion kinetics: the kinetically selective synthesis of tightly- and loosely-twisted isomers of a trinuclear PdII-macrocycle and their markedly different molecular behaviours. The loosely-twisted isomers smoothly invert between (P)- and (M)-helicity at a rate of 3.31 s-1, while the helicity inversion of the tightly-twisted isomers is undetectable but rather relaxes to the loosely-twisted isomers. This critical difference between these two isomers is explained by the presence or absence of an absolute configuration inversion of the nitrogen atoms of the macrocyclic amine ligand. Strategies to control the helicity inversion and structural loosening motions by the mode of twisting offer future possibilities for the design of molecular machines.

Effector-dependent structural transformation of a crystalline framework with allosteric effects on molecular recognition ability.

Structurally flexible porous crystals that combine high regularity and stimuli responsiveness have received attracted attention in connection with natural allostery found in regulatory systems of activity and function in biological systems. Porous crystals with molecular recognition sites in the inner pores are particularly promising for achieving elaborate functional control, where the local binding of effectors triggers their distortion to propagate throughout the structure. Here we report that the structure of a porous molecular crystal can be allosterically controlled by local adsorption of effectors within low-symmetry nanochannels with multiple molecular recognition sites. The exchange of effectors at the allosteric site triggers diverse conversion of the framework structure in an effector-dependent manner. In conjunction with the structural conversion, it is also possible to switch the molecular affinity at different recognition sites. These results may provide a guideline for the development of supramolecular materials with flexible and highly-ordered three-dimensional structures for biological applications.

Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases.

Rational design of self-assembled DNA nanostructures has become one of the fastest-growing research areas in molecular science. Particular attention is focused on the development of dynamic DNA nanodevices whose configuration and function are regulated by specific chemical inputs. Herein, we demonstrate the concept of metal-mediated base-pair switching to induce inter- and intramolecular DNA strand displacement in a metal-responsive manner. The 5-hydroxyuracil (UOH) nucleobase is employed as a metal-responsive unit, forming both a hydrogen-bonded UOH-A base pair and a metal-mediated UOH-GdIII-UOH base pair. Metal-mediated strand displacement reactions are demonstrated under isothermal conditions based on the base-pair switching between UOH-A and UOH-GdIII-UOH. Furthermore, metal-responsive DNA tweezers and allosteric DNAzymes are developed as typical models for DNA nanodevices simply by incorporating UOH bases into the sequence. The metal-mediated base-pair switching will become a versatile strategy for constructing stimuli-responsive DNA nanostructures, expanding the scope of dynamic DNA nanotechnology.

Photoluminescence control by atomically precise surface metallization of C-centered hexagold(i) clusters using N-heterocyclic carbenes.

The properties of metal clusters are highly dependent on their molecular surface structure. The aim of this study is to precisely metallize and rationally control the photoluminescence properties of a carbon(C)-centered hexagold(i) cluster (CAuI6) using N-heterocyclic carbene (NHC) ligands with one pyridyl, or one or two picolyl pendants and a specific number of silver(i) ions at the cluster surface. The results suggest that the photoluminescence of the clusters depends highly on both the rigidity and coverage of the surface structure. In other words, the loss of structural rigidity significantly reduces the quantum yield (QY). The QY in CH2Cl2 is 0.04 for [(C)(AuI-BIPc)6AgI3(CH3CN)3](BF4)5 (BIPc = N-isopropyl-N'-2-picolylbenzimidazolylidene), a significant decrease from 0.86 for [(C)(AuI-BIPy)6AgI2](BF4)4 (BIPy = N-isopropyl-N'-2-pyridylbenzimidazolylidene). This is due to the lower structural rigidity of the ligand BIPc because it contains a methylene linker. Increasing the number of capping AgI ions, i.e., the coverage of the surface structure, increases the phosphorescence efficiency. The QY for [(C)(AuI-BIPc2)6AgI4(CH3CN)2](BF4)6 (BIPc2 = N,N'-di(2-pyridyl)benzimidazolylidene) recovers to 0.40, 10-times that of the cluster with BIPc. Further theoretical calculations confirm the roles of AgI and NHC in the electronic structures. This study reveals the atomic-level surface structure-property relationships of heterometallic clusters.

Phenanthroline-modified DNA three-way junction structures stabilized by interstrand 3 : 1 metal complexation.

Incorporation of interstrand metal complexes into DNA is a versatile strategy for metal-dependent stabilization and structural induction of DNA supramolecular structures. In this study, we have synthesized DNA three-way junction (3WJ) structures modified with phenanthroline (phen) ligands. The phen-modified 3WJ was found to be thermally stabilized (ΔTm = +16.9 °C) by the formation of an interstrand NiII(phen)3 complex. Furthermore, NiII-mediated structure induction of 3WJs was demonstrated with the phen-modified strands and their unmodified counterparts. This study suggests that ligand-modified 3WJs would be useful structural motifs for the construction of metal-responsive DNA molecular systems.

Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner.

Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and functional transformation of DNA assemblies. In this study, N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleoside with an iminodiacetic acid (IDA) ligand at the 5-position of the uracil base has been developed as a bifacial nucleoside that can form both hydrogen-bonded and metal-mediated base pairs. Metal complexation study of dcaU nucleosides revealed their ability to form a 2:1 complex with a GdIII ion at the monomeric level. The characteristics of base pairing of dcaU nucleosides were then examined inside DNA duplexes. The results revealed that the formation of the metal-mediated dcaU-GdIII-dcaU pair significantly stabilized the DNA duplex containing one dcaU-dcaU mismatch (ΔT m = +16.1 °C). In contrast, a duplex containing a hydrogen-bonded dcaU-A pair was destabilized in the presence of GdIII (ΔT m = -3.5 °C). The GdIII-dependent base pairing of dcaU bases was applied to control the hybridization preference of DNA in response to metal ions. The hybridization partner of a dcaU-containing strand was reversibly exchanged by the addition and removal of GdIII ions. Since the incorporation of a single dcaU base can switch the hybridization behavior of DNA, the bifacial dcaU base would be a versatile building block for imparting metal responsiveness to DNA assemblies, allowing the rational design of dynamic DNA systems.

CuII-mediated DNA base pairing of a triazole-4-carboxylate nucleoside prepared by click chemistry.

Artificial metal-mediated DNA base pairing is a promising strategy for creating highly functionalized DNA supramolecules. Here we report a novel ligand-type triazole-4-carboxylate (TazC) nucleoside that is readily prepared by the click reaction. TazC nucleosides were found to form a stable TazC-CuII-TazC base pair inside DNA duplexes, resulting in CuII-specific duplex stabilization (ΔTm = +7.7 °C). This study demonstrates that the triazole derivatives are useful in the development of metal-mediated base pairing.

Synthesis and molecular structural studies of racemic chiral-at-vanadium(V) complexes using an unsymmetric achiral phenolic bidentate ligand.

Mononuclear oxovanadium(V) complexes [V(O)XL (1: X = Ot-Bu, 2: X = Cl)] [H2L: 2,2'-methylene bis(4,6-di-tert-butylphenol)(4'-tert-butyl-6'-(1-adamantyl)phenol)] directed towards asymmetric catalysis have been synthesised as racemic compounds using an unsymmetric and achiral phenolic bidentate ligand (H2L), and NMR and UV-vis absorption spectroscopies, single-crystal X-ray diffraction, and IR spectroscopy revealed their racemic chiral-at-vanadium structures in solution and in the crystal. In addition, theoretical calculations revealed that the HOMO-LUMO energy gap is smaller for unsymmetric ligands, which promotes d-orbital splitting of the metal centre.

CuII-mediated stabilisation of DNA duplexes bearing consecutive ethenoadenine lesions and its application to a metal-responsive DNAzyme.

Metal-mediated nucleobase pairing can play a central role in the expression of metal-responsive DNA functions. We report the CuII-mediated stabilisation of DNA duplexes bearing damaged nucleobases, 1,N6-ethenoadenine (εA), as metal-binding sites, which was utilised to construct a metal-responsive DNAzyme. Consecutive incorporation of three or more εA-εA mismatch pairs allowed for CuII-dependent significant duplex stabilisation through metal-mediated εA-CuII-εA base pairing. Subsequently, a split DNAzyme with three εA-CuII-εA base pairs was strategically designed. The activity of the εA-modified DNAzyme was enhanced by 5.3-fold upon addition of CuII ions. This study demonstrates the utility of εA lesions for building metal-responsive DNA architectures.

Correction: Highly selective acid-catalyzed olefin isomerization of limonene to terpinolene by kinetic suppression of overreactions in a confined space of porous metal-macrocycle frameworks.

[This corrects the article DOI: 10.1039/D2SC01561G.].

Highly selective acid-catalyzed olefin isomerization of limonene to terpinolene by kinetic suppression of overreactions in a confined space of porous metal-macrocycle frameworks.

Natural enzymes control the intrinsic reactivity of chemical reactions in the natural environment, giving only the necessary products. In recent years, challenging research on the reactivity control of terpenes with structural diversity using artificial host compounds that mimic such enzymatic reactions has been actively pursued. A typical example is the acid-catalyzed olefin isomerization of (+)-limonene, which generally gives a complex mixture due to over-isomerization to thermodynamically favored isomers. Herein we report a highly controlled conversion of (+)-limonene by kinetic suppression of over-isomerization in a confined space of a porous metal-macrocycle framework (MMF) equipped with a Brønsted acid catalyst. The terminal double bond of (+)-limonene migrated to one neighbor, preferentially producing terpinolene. This reaction selectivity was in stark contrast to the homogeneous acid-catalyzed reaction in bulk solution and to previously reported catalytic reactions. X-ray structural analysis and examination of the reaction with adsorption inhibitors suggest that the reactive substrates may bind non-covalently to specific positions in the confined space of the MMF, thereby inhibiting the over-isomerization reaction. The nanospaces of the MMF with substrate binding ability are expected to enable highly selective synthesis of a variety of terpene compounds.

N-Heterocyclic carbene-based C-centered Au(I)-Ag(I) clusters with intense phosphorescence and organelle-selective translocation in cells.

Photoluminescent gold clusters are functionally variable chemical modules by ligand design. Chemical modification of protective ligands and introduction of different metals into the gold clusters lead to discover unique chemical and physical properties based on their significantly perturbed electronic structures. Here we report the synthesis of carbon-centered Au(I)-Ag(I) clusters with high phosphorescence quantum yields using N-heterocyclic carbene ligands. Specifically, a heterometallic cluster [(C)(AuI-L)6AgI2]4+, where L denotes benzimidazolylidene-based carbene ligands featuring N-pyridyl substituents, shows a significantly high phosphorescence quantum yield (Φ = 0.88). Theoretical calculations suggest that the carbene ligands accelerate the radiative decay by affecting the spin-orbit coupling, and the benzimidazolylidene ligands further suppress the non-radiative pathway. Furthermore, these clusters with carbene ligands are taken up into cells, emit phosphorescence and translocate to a particular organelle. Such well-defined, highly phosphorescent C-centered Au(I)-Ag(I) clusters will enable ligand-specific, organelle-selective phosphorescence imaging and dynamic analysis of molecular distribution and translocation pathways in cells.

Metal-mediated DNA base pairing of easily prepared 2-oxo-imidazole-4-carboxylate nucleotides.

Metal-mediated DNA base pairs, which consist of two ligand-type artificial nucleobases and a bridging metal ion, have attracted increasing attention in recent years as a different base pairing mode from natural base pairing. Metal-mediated base pairing has been extensively studied, not only for metal-dependent thermal stabilisation of duplexes, but also for metal assembly by DNA templates and construction of functional DNAs that can be controlled by metals. Here, we report the metal-mediated base paring properties of a novel 2-oxo-imidazole-4-carboxylate (ImOC) nucleobase and a previously reported 2-oxo-imidazole-4-carboxamide (ImOA) nucleobase, both of which can be easily derived from a commercially available uridine analogue. The ImOC nucleobases were found to form stable ImOC-CuII-ImOC and ImOC-HgII-ImOC base pairs in the presence of the corresponding metal ions, leading to an increase in the duplex melting temperature by +20 °C and +11 °C, respectively. The ImOC bases did not react with other divalent metal ions and showed superior metal selectivity compared to similar nucleobase design reported so far. The ImOC-CuII-ImOC base pair was much more stable than mismatch pairs with other natural nucleobases, confirming the base pair specificity in the presence of CuII. Furthermore, we demonstrated the quantitative assembly of three CuII ions inside a DNA duplex with three consecutive ImOC-ImOC pairs, showing great potential of DNA-template based CuII nanoarray construction. The study of easily-prepared ImOC base pairs will provide a new design strategy for metal-responsive DNA materials.