Metal-Mediated Assembly of 1,N6-Ethenoadenine: From Surfaces to DNA Duplexes

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 Cu^II-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 Cu^II-dependent significant duplex stabilisation through metal-mediated εA-Cu^II-εA base pairing. Subsequently, a split DNAzyme with three εA-Cu^II-εA base pairs was strategically designed. The activity of the εA-modified DNAzyme was enhanced by 5.3-fold upon addition of Cu^II ions. This study demonstrates the utility of εA lesions for building metal-responsive DNA architectures.

Benzothiazole-substituted 1,3-diaza-2-oxophenoxazine as a luminescent nucleobase surrogate for silver(I)-mediated base pairing

A benzothiazole-substituted derivative (X) of 1,3-diaza-2-oxophenoxazine was evaluated with respect to its ability to engage in Ag(I)-mediated homo base pair formation in two different DNA duplexes. The metal binding was determined by a combination of temperature-dependent UV spectroscopy, CD spectroscopy, and fluorescence spectroscopy, indicating the incorporation of two Ag(I) ions to generate a dinuclear X-Ag(I)₂-X base pair. Interestingly, a luminescence increase was observed upon metal binding. Theoretical luminescence spectra were calculated using time-dependent density functional theory (TDDFT) for all possible Ag(I)-mediated X : X base pair geometries to identify the species responsible for the increase in luminescence. The study shows that even bulky non-planar artificial nucleobases can be applied to form stabilizing metal-mediated base pairs.

Triggering Copper(II)-Mediated Base Pair Formation by Light

Metal-mediated base pairs enable a site-specific incorporation of transition metal ions into nucleic acid structures. The resulting nucleic acid-metal complex conjugates are of interest in the context of functionalized nucleic acids, as they bear metal-based functionality. It is desirable to devise nucleic acids with an externally triggered metal-binding affinity, as this may allow regulating this functionality. Toward this end, a caged deoxyribonucleoside analog H^NPP was devised for the site-specific binding of copper(II) ions upon irradiation by light, based on the ligand 3-hydroxy-2-methylpyridin-4(1H)-one (H) and the photocleavable 2-(2-nitrophenyl)propoxy protecting group (NPP). The formation of both H-Cu(II)-H homo base pairs and H-Cu(II)-X hetero base pairs (involving a second artificial deoxyribonucleoside X, based on imidazole-4-carboxylate) was achieved upon irradiation of DNA duplexes bearing the respective H^NPP:H^NPP or H^NPP:X mispairs in the presence of copper(II) ions. The H-Cu(II)-X pair shows an exceptional DNA duplex stabilization of up to 43 °C upon its formation, exceeding that of the H-Cu(II)-H pair. It therefore represents one of the most stabilizing Cu(II)-mediated base pairs reported so far. Our findings expand the scope of light-triggered metal-mediated base pair formation by introducing a copper(II)-binding ligand.

Crystallographic Structure of Novel Types of AgI -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids

Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of Ag^I ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of Ag^I -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing Ag^I -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of Ag^I -mediated base pairs in the central region. The bent duplex structure induced by the addition of Ag^I ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.

Silver(I)-mediated base pairing in DNA involving the artificial nucleobase 7,8-dihydro-8-oxo-1,N6-ethenoadenine

The artificial nucleobase 7,8-dihydro-8-oxo-1,N⁶-ethenoadenine (X) was investigated with respect to its ability to engage in Ag(I)-mediated base pairing in DNA. Spectroscopic data indicate the formation of dinuclear X-Ag(I)₂-X homo base pairs and mononuclear X-Ag(I)-C base pairs (C, cytosine). Density functional theory calculations and molecular dynamics simulations indicate that the nucleobase changes from its lactam tautomeric form prior to the formation of the Ag(I)-mediated base pair to the lactim form after the incorporation of the Ag(I) ions. Fluorescence spectroscopy indicates that the two Ag(I) ions of the homo base pair are incorporated sequentially. Isothermal titration calorimetry confirms that the affinity of one of the Ag(I) ions is about tenfold higher than that of the other Ag(I) ion. The computational analysis by means of density functional theory confirms a much larger reaction energy for the incorporation of the first Ag(I) ion. The thermal stabilization upon the formation of the dinuclear Ag(I)-mediated homo base pair exceeds the one previously observed for the closely related nucleobase 1,N⁶-ethenoadenine by far, despite very similar structures. This additional stabilization may stem from the presence of water molecules engaged in hydrogen bonding with the additional oxygen atom of the artificial nucleobase X. The highly stabilizing Ag(I)-mediated base pair is a valuable addition to established dinuclear metal-mediated base pairs.

Silver(I) Coordination in Silver(I)-Mediated Homo Base Pairs of 6-Pyrazolylpurine in DNA Duplexes Involves the Watson-Crick Edge

DNA duplexes comprising 6‐(1H‐pyrazol‐1‐yl)‐9H‐purine (6PP), 1‐deaza‐6PP (^1D6PP), 7‐deaza‐6PP (^7D6PP) and 1,7‐dideaza‐6PP (^1,7D6PP) 2′‐deoxyribonucleosides, respectively, were investigated towards their ability to form metal‐mediated base pairs in the presence of Ag^I. In 6PP and ^7D6PP, the Ag^I ion can coordinate to the nucleobase via the endocyclic N1 nitrogen atom, that is, via the Watson–Crick edge. In contrast, this nitrogen atom is not available in ^1D6PP and ^1,7D6PP, so that in ^1D6PP an Ag^I coordination is only possible via the Hoogsteen edge (N7). Reference duplexes with either adenine:adenine mispairs or canonical adenine:thymine base pairs were used to investigate the impact of the pyrazolyl moiety on the Ag^I‐binding properties. To determine the thermal and structural duplex stabilities in the absence or presence of Ag^I, all duplexes were examined by UV and circular dichroism spectroscopic studies. These investigations shed light on the question of whether N1‐ or N7‐coordination is preferred in purine‐based metal‐mediated base pairs.

Nucleobase Pair-Metal Dimer/Dinuclear Metal Cation Interaction: A Theoretical Study

Nucleobase pair-metal dimer/dinuclear metal cation interactions play an important role in biological applications because of their highly symmetrical structures and high stabilities. In this work, we have selected five adenine-adenine hydrogen bonding, adenine-thymine (AT), adenine-uracil, adenine-adenine stacking pairs, and Watson-Crick AT stacking pairs and studied their interaction with the coinage metal dimer M2 and M2 2+ metal cations, where M = Ag, Au, and Cu. Quantum chemical calculations have been carried out with density functional theory (DFT) and time-dependent DFT (TDDFT) methods. Electronic structures were analyzed by the partial density of states method. During interactions, we find that M-M distances are shorter than the sum of van der Waals radii of the corresponding two homocoinage metal atoms, which show the existence of significant metallophilic interactions. Results indicated that nucleobase-M2 2+ complexes are stronger as compared to nucleobase-M2 complexes. Also, the replacement of the hydrogen bond by the dinuclear metal cation-coordinated bond forms more stable alternative metallo-DNA sequences in AAST base pairs. TDDFT calculations reveal that nucleobase-Cu2 complexes and nucleobase-Ag2 2+/Au2 2+ complexes can be used for fluorescent markers and logic gate applications. Atom-in-molecules analysis predicted the noncovalent interaction in these complexes.

Stable Hg(II)-mediated base pairs with a phenanthroline-derived nucleobase surrogate in antiparallel-stranded DNA

Metal-mediated base pairs involving artificial nucleobases have emerged as a promising means for the site-specific functionalization of nucleic acids with metal ions. In this context, a GNA-appended (GNA: glycol nucleic acid) nucleoside analogue containing the artificial nucleobase 1H-imidazo[4,5-f][1,10]phenanthroline (P) has already been applied successfully in a variety of homo- and heteroleptic metal-mediated base pairs, mainly involving Ag(I) ions. Herein, we report a thorough investigation of the Hg(II)-binding properties of P when incorporated into antiparallel-stranded DNA duplexes. The artificial nucleobase P is able to form Hg(II)-mediated homoleptic base pairs of the type P-Hg(II)-P with a [2 + 2] coordination environment. In addition, the heteroleptic P-Hg(II)-T pair was investigated. The addition of a stoichiometric amount of Hg(II) to a duplex comprising either a P:P pair or a P:T pair stabilizes the DNA duplex by 4.3 °C and 14.5 °C, respectively. The P-Hg(II)-T base pair, hence, represents the most stabilizing non-organometallic Hg(II)-mediated base pair reported to date. The formation of the Hg(II)-mediated base pairs was investigated by means of temperature-dependent UV spectroscopy and CD spectroscopy.

Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads

The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of Ag^I -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.

1,3,9-Triaza-2-oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self-Base Pairs with Three AgI Ions in a Duplex

Metal-mediated base pairs (MMBPs) formed by natural or artificial nucleobases have recently been developed. The metal ions can be aligned linearly in a duplex by MMBP formation. The development of a three- or more-metal-coordinated MMBPs has the potential to improve the conductivity and enable the design of metal ion architectures in a duplex. This study aimed to develop artificial self-bases coordinated by three linearly aligned Ag^I ions within an MMBP. Thus, artificial nucleic acids with a 1,3,9-triaza-2-oxophenoxazine (9-TAP) nucleobase were designed and synthesized. In a DNA/DNA duplex, self-base pairs of 9-TAP could form highly stable MMBPs with three Ag^I ions. Nine equivalents of Ag^I led to the formation of three consecutive 9-TAP self-base pairs with extremely high stability. The complex structures of 9-TAP MMBPs were determined by using electrospray ionization mass spectrometry and UV titration experiments. Highly stable self-9-TAP MMBPs with three Ag^I ions are expected to be applicable to new DNA nanotechnologies.

Copper(ii)-mediated base pairing involving the artificial nucleobase 3H-imidazo[4,5-f]quinolin-5-ol

A highly stabilizing Cu(ii)-mediated base pair is introduced into DNA using a large artificial nucleobase.

7-Methyl-6-furylpurine forms dinuclear metal complexes with N3,N9 coordination

Two dinuclear metal complexes bearing the purine derivative 7-methyl-6-furylpurine (1b) as a ligand are reported. In [Ag2(1b)2(DMSO)2](ClO4)2·DMSO and [Cu2(1b)2(NO3)2], two bridging purine derivatives coordinate the two metal ions via their N3 and N9 positions. In the silver(I) complex, the coordination environment of each metal ion is completed by a DMSO ligand, whereas an additional nitrato ligand coordinates to each copper(I) ion. The intramolecular Ag···Ag distance of 3.1069(5) Å is in agreement with the presence of a weak argentophilic interaction, whereas the Cu···Cu distance of 2.9382(4) Å is too long to be indicative of a cuprophilic interaction. The compounds represent the first examples of dinuclear complexes comprising two N3,N9-bridging purine derivatives without any additional bridging ligand.

A dinuclear Cu(i)-mediated complex: Theoretical studies of the G2Cu2 4+ cluster ion

Recently, the T-Hg(ii)₂-A base pair containing two equivalents of Hg(ii) has been prepared and characterized experimentally, which implies that there might exist considerable stable metal-mediated base pairs holding two neighbouring metal centers. Here we report a quantum chemical study on geometries, electronic structures, and bonding of various G₂Cu₂ ⁴⁺ (G = guanine) isomers including one di-copper(i) unit. Different density functional methods [Becke 3-parameter-Lee-Yang-Parr, Perdew-Becke-Ernzerhof, Becke-Perdew, Density Functional Theory with Dispersion Corrections (DFT-D)] assign ambiguous relative energies to these isomers with the singlet and triplet states. High-level ab initio [domain-based local pair natural orbital (DLPNO) coupled-cluster with single and double excitations and DLPNO-coupled-cluster with single, double, and perturbative triple excitations] calculations confirm that the lowest-lying isomer of the G₂Cu₂ ⁴⁺ ion has C _2h symmetry with the singlet state and is comparable to the singly and doubly charged homologues (G₂Cu₂ ⁺ and G₂Cu₂ ²⁺). The extended transition state (ETS)-natural orbitals for the chemical valence (ETS-NOCV) calculations point out that it has larger instantaneous interaction energy and bond dissociation energy than the corresponding singly and doubly charged complexes due to its relatively stronger attractive energies and weaker Pauli repulsion. The orbital interactions in the quadruply charged cluster chiefly come from Cu₂ ⁴⁺ ← G⋯G π donations. The results may help the understanding of the bonding properties of other potential metal-base pair complexes with the electron transfer.

Surface modification and pattern formation by nucleobases and their coordination complexes

This review presents recent progress concerning the organization of nucleobases on highly ordered pyrolytic graphite (HOPG), mica, Cu(110) and Au(111) surfaces, followed by their studies using microscopy methods such as atomic force microscopy (AFM), scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). Interesting research prospects related to surface patterning by nucleobases, nucleobase-functionalized carbon nanotubes (CNTs) and metal–nucleobase coordination polymers are also discussed, which offer a wide array of functional molecules for advanced applications. Nucleobases and their analogs are able to invoke non-covalent interactions such as π–π stacking and hydrogen bonding, and possess the required framework to coordinate metal ions, giving rise to fascinating supramolecular architectures. The latter could be transferred to conductive substrates, such as HOPG and gold, for assessment by high-end tunneling microscopy under various conditions. Clear understanding of the principles governing nucleobase self-assembly and metal ion complexation, and precise control over generation of functional architectures, might lead to custom assemblies for targeted nanotechnological and nanomaterial applications.

This review highlights recent advancements in surface patterning of nucleobases, their analogs including nucleobase-CNT hybrids and metal complexes, using various microscopy techniques for nanotechnological applications.

Metal-mediated base pairs in parallel-stranded DNA

In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine-Ag(I)-cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.

Dinuclear Metal-Mediated Homo Base Pairs with Metallophilic Interactions: Theoretical Studies of G2M22+ (M = Cu, Ag, and Au) Ions

Dinuclear metal-mediated homo base pairs are interesting clusters with highly symmetric structures and significant stabilities. The geometric and electronic structures of G₂M₂²⁺ (G = Guanine, M = Cu, Ag or Au) cluster ions were studied with quantum chemical calculations. The lowest-energy isomers of G₂M₂²⁺ cluster ions have C_2h symmetries with an approximately antiparallel alignment of two sets of N-M∙∙∙O groups being formed in the planar structures. The M-M distances are shorter than the sum of van der Waals radii of corresponding two homo coinage metal atoms, showing that metallophilic interactions significantly exist in these complexes. They have the large HOMO−LUMO gaps of about 5.80 eV at the DFT level and the bond dissociation energies of more than 5.60 eV at the DFT/B3LYP level, indicating that these cluster dications are highly stable. The second lowest-energy isomers stabilized by an approximately parallel alignment of one set of O-M-O group and one set of N-M-N group are found to be close to the lowest-energy isomers in energy. The barrier between the two isomers of G₂M₂²⁺ cluster ions is significantly large, also showing that these lowest-energy isomers are very stable.

Metal-Mediated Base Pairs: From Characterization to Application

The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.

Directed adenine functionalization for creating complex architectures for material and biological applications

In this feature article, targeted design strategies are outlined for modified adenine nucleobase derivatives in order to construct metal-mediated discrete complexes, ring-expanded purine skeletons, linear and catenated coordination polymers, shape-selective MOFs, and purine-capped nanoparticles, with a wide range of applications from gas and solvent adsorption to bioimaging agents and anticancer metallodrugs. The success of such design strategies could be ascribed to the rich chemistry of purine and pyrimidine derivatives, versatile coordination behavior, ability to bind a host of metal ions, which could be further tuned by the introduction of additional functionalities, and their inherent propensity to hydrogen bond and exhibit π-π interactions. These noncovalent interactions produce stable frameworks and network solids that are useful as advanced materials, and the biocompatibility of these ligand complexes provides an impetus for assessing novel biological applications.

Metal-mediated DNA assembly with ligand-based nucleosides

Nucleic acids such as DNA are increasingly being applied in nanotechnology, as a result of their capability to self-assemble reversibly. The formal replacement of canonical base pairs by metal-mediated ones enables a site-specific introduction of metal-based functionality into these biomolecules, leading to the formation of predesigned metal arrays. This article offers an overview of structural aspects of metal-mediated base pairs, reviews recent advances in the field of metal-mediated base pairing and presents potential applications of the resulting metal-modified nucleic acids. It particularly focuses on recently developed metal-mediated base pairs with purine-derived nucleosides, gives an overview of metal-responsive systems relying on metal-mediated base pairs and summarizes various applications beyond metal-ion sensors.

Crystal structure of a DNA duplex containing four Ag(i) ions in consecutive dinuclear Ag(i)-mediated base pairs: 4-thiothymine–2Ag(i)–4-thiothymine

The crystal structures of 4-thiothymine–2Ag^I–4-thiothymine base pairs in B-form DNA duplexes have been solved.

Relative Strand Orientation in a DNA Duplex Controls the Nuclearity of a Metal-Mediated Base Pair

1,N⁶ -Ethenoadenine (ϵA) and cytosine (C) are able to form two different metal-mediated base pairs. When the glycosidic bonds are arranged in a cisoid manner (i.e., in antiparallel-stranded DNA), the ϵA:C mispair binds one Ag^I ion, leading to a mononuclear ϵA-Ag^I -C base pair that contains a synergistic hydrogen bond. In contrast, a transoid orientation of the glycosidic bonds (as found in parallel-stranded DNA) results in the formation of a dinuclear metal-mediated base pair ϵA-Ag^I₂ -C.

Luminescent Silver-Purine Double Helicate: Synthesis, Self-Assembly and Antibacterial Action

The synthesis, self-assembly and antibacterial activity of a luminescent silver-purine double helicate is reported. The structure of the newly synthesized silver-supported helicate [C₃₆ H₂₄ N₁₆ O₄ Cl₅ Ag₁ ] was unambiguously characterized by single-crystal X-ray crystallography. It exhibited a bright bluish-green emission (λ_max =460 nm), when excited with 380 nm light. Microscopic investigations showed that the complex has a propensity to self-assemble into nanospheres. The antibacterial activity of this silver-containing helicate was studied against both Gram-positive and Gram-negative bacteria. MIC (minimal inhibitory concentration) values showed that the complex is very active against Gram-negative bacteria. Further internalization of the silver complex into E. coli bacteria was mapped with the help of microscopic techniques. These results are significant as silver was recently found to enhance antibiotic action against Gram-negative bacteria, raising hope in countering severe bacterial infections.

A Dinuclear Mercury(II)-Mediated Base Pair in DNA

The first dinuclear metal-mediated base pair containing divalent metal ions has been prepared. A combination of the neutral bis(monodentate) purine derivative 1,N⁶ -ethenoadenine (ϵA), which preferentially binds two metal ions with a parallel alignment of the N-M bonds, and the canonical nucleobase thymine (T), which readily deprotonates in the presence of Hg^II and thereby partially compensates the charge accumulation due to the two closely spaced divalent metal ions, yields the dinuclear T-Hg^II₂ -ϵA base pair. This metal-mediated base pair stabilizes the DNA oligonucleotide duplex as shown by an increase of 8 °C in its melting temperature. Formation of the base pair was demonstrated by temperature-dependent UV spectroscopy as well as by titration experiments monitored by UV and CD spectroscopy.