Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson–Crick‐like T–HgII–T Base Pairs

The metallo DNA duplex containing mercury‐mediated T–T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B‐form DNA duplex containing two consecutive T–Hg^II–T base pairs. The Hg^II ion occupies the center between two T residues. The N3‐Hg^II bond distance is 2.0 Å. The relatively short Hg^II‐Hg^II distance (3.3 Å) observed in consecutive T–Hg^II–T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B‐form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg^II. The structure of the metallo DNA duplex itself and the Hg^II‐induced structural switching from the nonhelical form to the B‐form provide the basis for structure‐based design of metal‐conjugated nucleic acid nanomaterials.     

Development of a Metal‐Ion‐Mediated Base Pair for Electron Transfer in DNA

A new C‐nucleoside structurally based on the hydroxyquinoline ligand was synthesized that is able to form stable pairs in DNA in both the absence and the presence of metal ions. The interactions between the metal centers in adjacent Cu^II‐mediated base pairs in DNA were probed by electron paramagnetic resonance (EPR) spectroscopy. The metal–metal distance falls into the range of previously reported values. Fluorescence studies with a donor–DNA–acceptor system indicate that photoinduced charge‐transfer processes across these metal‐ion‐mediated base pairs in DNA occur more efficiently than over natural base pairs.     

Sequence‐Dependent Duplex Stabilization upon Formation of a Metal‐Mediated Base Pair

An artificial nucleoside surrogate with 1H‐imidazo[4,5‐f][1,10]phenanthroline ( P ) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal‐mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective Ag^I‐mediated base pairs strongly depends on the sequence context. Quantum mechanical/molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B‐DNA duplex.     

Metal‐Ion Selectivity of Chemically Modified Uracil Pairs in DNA Duplexes

DNA duplexes containing 5‐modified uracil pairs (5‐bromo, 5‐fluoro, and 5‐cyanouracil) bind selectivity to metal ions. Their selectivity is sensitive to the pH value of the solution (see picture), as the acidities of the modified uracil bases vary according to the electron‐withdrawing properties of the substituents.

     

Conformational Tuning of Magnetic Interactions in Metal–DNA Complexes

The alignment of Cu ²⁺ ions along a modified DNA helix is studied with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S‐en) metalated base pairs (MBPs). The conformational motion of H‐MBP leads to the interlinking of the H‐MBPs by an extended Cu‐O network that is ferromagnetic, whereas the conformational freezing of the S‐en‐MBP leads to an ordered pairwise‐stacked arrangement that is weakly antoferrimagnetic.

     

Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers

The double crossover junction (DX) is a fundamental building block for generating complex and varied structures from DNA. However, its implementation in functional devices is limited to the inherent properties of DNA itself. Here, we developed design strategies to generate the first metal–DX DNA tiles (DX_M) by site‐specifically functionalizing the tile crossovers with tetrahedral binding pockets that coordinate Cu^I. These DX junctions bind two Cu^I ions independently at distinct sites, display greater thermal stability than native DX tiles upon metalation, and melt in a cooperative fashion. In addition, the right‐handed helical chirality of DNA is transferred to the metal centers. Our tiles display high metal ion selectivity, such that Cu^II is spontaneously reduced to Cu^I in situ. By modifying our design over three generations of tiles, we elucidated the thermodynamic and geometric requirements for the successful assembly of DX_M tiles, which have direct applicability in developing robust, stable DNA‐based materials with electroactive, photoactive, and catalytic properties.     

Versatile Tailoring of Paddle‐Wheel ZnII Metal–Organic Frameworks through Single‐Crystal‐to‐Single‐Crystal Transformations

A new tetracarboxylate ligand having short and long arms formed 2D layer Zn^II coordination polymer 1 with paddle‐wheel secondary building units under solvothermal conditions. The framework undergoes solvent‐specific single crystal‐to‐single crystal (SC‐SC) transmetalation to produce 1_Cu . With a sterically encumbered dipyridyl linker, the same ligand forms non‐interpenetrated, 3D, pillared‐layer Zn^II metal–organic framework (MOF) 2 , which takes part in SC‐SC linker‐exchange reactions to produce three daughter frameworks. The parent MOF 2 shows preferential incorporation of the longest linker in competitive linker‐exchange experiments. All the 3D MOFs undergo complete SC‐SC transmetalation with Cu^II, whereby metal exchange in different solvents and monitoring of X‐ray structures revealed that bulky solvated metal ions lead to ordering of the shortest linker in the framework, which confirms that the solvated metal ions enter through the pores along the linker axis.     

A Metal–Organic Framework/DNA Hybrid System as a Novel Fluorescent Biosensor for Mercury(II) Ion Detection

Mercury(II) ions have emerged as a widespread environmental hazard in recent decades. Despite different kinds of detection methods reported to sense Hg²⁺, it still remains a challenging task to develop new sensing molecules to replenish the fluorescence‐based apparatus for Hg²⁺ detection. This communication demonstrates a novel fluorescent sensor using UiO‐66‐NH₂ and a T‐rich FAM‐labeled ssDNA as a hybrid system to detect Hg²⁺ sensitively and selectively. To the best of our knowledge, it has rarely been reported that a MOF is utilized as the biosensing platform for Hg²⁺ assay.     

Highly Stable Double‐Stranded DNA Containing Sequential Silver(I)‐Mediated 7‐Deazaadenine/Thymine Watson–Crick Base Pairs

The oligonucleotide d(TX)₉, which consists of an octadecamer sequence with alternating non‐canonical 7‐deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double‐stranded DNA through the formation of hydrogen‐bonded Watson–Crick base pairs. dsDNA with metal‐mediated base pairs was then obtained by selectively replacing W‐C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag⁺ ions, and its stability is significantly enhanced in the presence of Ag⁺ ions while its double‐helix structure is retained. Temperature‐dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)‐mediated base pairs. This strategy could become useful for preparing stable metallo‐DNA‐based nanostructures.     

Expanding the Toolbox of Metal–Phenolic Networks via Enzyme‐Mediated Assembly

Functional coatings are of considerable interest because of their fundamental implications for interfacial assembly and promise for numerous applications. Universally adherent materials have recently emerged as versatile functional coatings; however, such coatings are generally limited to catechol, (ortho‐diphenol)‐containing molecules, as building blocks. Here, we report a facile, biofriendly enzyme‐mediated strategy for assembling a wide range of molecules (e.g., 14 representative molecules in this study) that do not natively have catechol moieties, including small molecules, peptides, and proteins, on various surfaces, while preserving the molecule's inherent function, such as catalysis (≈80 % retention of enzymatic activity for trypsin). Assembly is achieved by in situ conversion of monophenols into catechols via tyrosinase, where films form on surfaces via covalent and coordination cross‐linking. The resulting coatings are robust, functional (e.g., in protective coatings, biological imaging, and enzymatic catalysis), and versatile for diverse secondary surface‐confined reactions (e.g., biomineralization, metal ion chelation, and N‐hydroxysuccinimide conjugation).     

Single‐Walled Metal–Organic Nanotube Built from a Simple Synthon

A conformationally flexible triazole‐carboxylic acid ligand derived from an L ‐amino acid, namely, 4 H‐1,2,4‐triazol‐4‐yl‐acetic acid (αHGlytrz), has been exploited to synthesize a structurally diverse and functionally intriguing metal–organic framework with CuSiF₆. The crystal structure reveals a novel single‐walled metal–organic nanotube (SWMONT), namely, {[Cu₃(μ₃‐OH)(H₂O)₃(Glytrz)₃] ? SiF₆ ? 8 H₂O ? X}_∞ ( 1 ), (where X=disordered lattice water molecules) having a pore size as large as zeolites. Compound 1 was synthesized as crystals, as powder, or as layers by precipitation/electrodeposition. Mercury intrusion porosimetry demonstrates the ability of this material to store metallic mercury, after a pressure treatment, contrary to previous literature examples.     

Molecular Vise Approach to Create Metal‐Binding Sites in MOFs and Detection of Biomarkers

We report a new approach to create metal‐binding site in a series of metal–organic frameworks (MOFs), where tetratopic carboxylate linker, 4′,4′′,4′′′,4′′′′‐methanetetrayltetrabiphenyl‐4‐carboxylic acid, is partially replaced by a tritopic carboxylate linker, tris(4‐carboxybiphenyl)amine, in combination with monotopic linkers, formic acid, trifluoroacetic acid, benzoic acid, isonicotinic acid, 4‐chlorobenzoic acid, and 4‐nitrobenzoic acid, respectively. The distance between these paired‐up linkers can be precisely controlled, ranging from 5.4 to 10.8 Å, where a variety of metals, Mg²⁺, Al³⁺, Cr³⁺, Mn²⁺, Fe³⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Ag⁺, Cd²⁺ and Pb²⁺, can be placed in. The distribution of these metal‐binding sites across a single crystal is visualized by 3D tomography of laser scanning confocal microscopy with a resolution of 10 nm. The binding affinity between the metal and its binding‐site in MOF can be varied in a large range (observed binding constants, K_obs from 1.56×10² to 1.70×10⁴ L mol^?1), in aqueous solution. The fluorescence of these crystals can be used to detect biomarkers, such as cysteine, homocysteine and glutathione, with ultrahigh sensitivity and without the interference of urine, through the dissociation of metal ions from their binding sites.     

Additional Base‐Pair Formation in DNA Duplexes by a Double‐Headed Nucleotide

We have designed and synthesised a double‐headed nucleotide that presents two nucleobases in the interior of a dsDNA duplex. This nucleotide recognises and forms Watson–Crick base pairs with two complementary adenosines in a Watson–Crick framework. Furthermore, with judicious positioning in complementary strands, the nucleotide recognises itself through the formation of a T:T base pair. Thus, two novel nucleic acid motifs can be defined by using our double‐headed nucleotide. Both motifs were characterised by UV melting experiments, CD and NMR spectroscopy and molecular dynamics simulations. Both motifs leave the thermostability of the native dsDNA duplex largely unaltered. Molecular dynamics calculations showed that the double‐headed nucleotides are accommodated in the dsDNA by entirely local perturbations and that the modified duplexes retain an overall B‐type geometry with the dsDNA unwound by around 25 or 60°, respectively, in each of the modified motifs. Both motifs can be accommodated twice in a dsDNA duplex without incurring any loss of stability and extrapolating from this observation and the results of modelling, it is conceivable that both can be multiplied several times within a dsDNA duplex. These new motifs extend the DNA recognition repertoire and may form the basis for a complete series of double‐headed nucleotides based on all 16 base combinations of the four natural nucleobases. In addition, both motifs can be used in the design of nanoscale DNA structures in which a specific duplex twist is required.     

Pyrrolo‐dC Metal‐Mediated Base Pairs in the Reverse Watson–Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6‐Pyridinyl Residues on Fluorescence and Silver‐Ion Binding

Reverse Watson–Crick DNA with parallel‐strand orientation (ps DNA) has been constructed. Pyrrolo‐dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3‐d]pyrimidine base have been incorporated in 12‐ and 25‐mer oligonucleotide duplexes and utilized as silver‐ion binding sites. Thermal‐stability studies on the parallel DNA strands demonstrated extremely strong silver‐ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single ^2pyPyrdC–^2pyPyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver‐ion base pair that aligns 7‐deazapurine bases head‐to‐tail instead of head‐to‐head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson–Crick base pairs stabilized by a dinuclear silver‐mediated PyrdC pair.     

Theoretical Investigation of the Coupling between Hydrogen‐Atom Transfer and Stacking Interaction in Adenine–Thymine Dimers

Three different dimers of the adenine–thymine (A‐T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A‐T monomer system explains the role of the stacking interaction in the hydrogen‐atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N? N and N? O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N? N bridge than for the N? O one. Also, the two different mechanisms of two‐hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.