DNA modified with metal complexes: Applications in the construction of higher order metal–DNA nanostructures

Chemistry of organometallic nucleic acid components: personal perspectives and prospects for the future

Organometallic modifications of biologically important compounds such as drugs, secondary natural products, peptides, and nucleic acids, to name just a few, represent a well-established strategy for the development of new anticancer and antimicrobial agents. Supported by these reasons, over 12 years ago, we initiated a research program into organometallic modifications of nucleic acid components. This account summarizes key results regarding the synthetic chemistry and biological activities of the obtained compounds. As synthetic chemists, our main goal over the last 12 years has been to develop new strategies that allow for the exploration of the chemical space of organometallic nucleic acid components. Accordingly, we have developed a Michael addition reaction-based methodology that enabled the synthesis of an entirely new class of glycol nucleic acid (GNA) constituents. Concerning GNA chemistry, we also reported the synthesis of the first-ever ferrocenyl GNA-RNA "mixed" dinucleoside phosphate analog. Recently, we developed a Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition reaction-based approach for the synthesis of novel 1,2,3-triazole-linked ("click") nucleosides. The high value of this approach is because it allows for the introduction of functional (e.g., luminescent and redox-active) groups that protrude from the main oligomer sequence. With respect to biological activity studies, we identified several promising anticancer and antimicrobial compounds. Furthermore, we found that simple ferrocenyl-nucleobase conjugates have potential as modulators of Aβ21-40 amyloid aggregation. The final section of this article serves as a guide for future studies, as it presents some challenging goals yet to be achieved within the rapidly growing field of nucleic acid chemistry.

Monomeric copper(II) complexes with unsymmetrical salen environment: Synthesis, characterization and study of biological activities

Three new ONNO-donor tetradentate unsymmetrical salen ligands were synthesized by using o-phenyl diamine with substituted salicylaldehydes followed by a two-step reaction methodology. These three ligands by reaction with Cu(OAc)2.4H2O produced three new monomeric Cu(II) complexes, [CuII(L1-3)] (1-3). Elemental analysis, IR, UV-vis, NMR, and HR-ESI-MS techniques were used to analyze and characterize all the synthesized ligands and their corresponding metal complexes. Molecular structures of 1-3 were confirmed by the single-crystal-XRD analysis. Furthermore, the DNA binding ability of these complexes was checked through UV-vis, fluorescence spectroscopy, and also by circular dichroism studies. All the complexes were found to show an intercalation mode of binding with the Kb value in the range of 104-105 M-1. Finally, 1-3 was tested against two malignant (HeLa and A549) and non-cancerous (NIH-3T3) cell lines to check their in vitro antiproliferative activities. Among all, 1 is the most cytotoxic of the series having IC50 values of 5.7 ± 0.9 and 6.0 ± 0.3 μM against HeLa and A549 cell lines, respectively. This result is also consistent with the DNA binding order. Furthermore, the apoptotic mode of cell death of all the complexes was also evaluated by DAPI, AO/EB, and Annexin V-FITC/PI double staining assays.

Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly Polarized Light

Control over the stereochemistry of metal-organic cages can give rise to useful functions that are entwined with chirality, such as stereoselective guest binding and chiroptical applications. Here, we report a chiral CuI12L4 pseudo-octahedral cage that self-assembled from condensation of triaminotriptycene, aminoquinaldine, and diformylpyridine subcomponents around CuI templates. The corners of this cage consist of six head-to-tail dicopper(I) helicates whose helical chirality can be controlled by the addition of enantiopure 1,1'-bi-2-naphthol (BINOL) during the assembly process. Chiroptical and nuclear magnetic resonance (NMR) studies elucidated the process and mechanism of stereochemical information transfer from BINOL to the cage during the assembly process. Initially formed CuI(BINOL)2 thus underwent stereoselective ligand exchange during the formation of the chiral helicate corners of the cage, which determined the overall cage stereochemistry. The resulting dicopper(I) helicate corners of the cage were also shown to generate circularly polarized luminescence.

Synthesis and chemical transformations of glycol nucleic acid (GNA) nucleosides

Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol nucleic acid (GNA) is constructed from a three-carbon 1,2-propanediol (propylene glycol) backbone attached to a nucleobase entity, representing the simplest known XNA. This review is intended to present GNA nucleosides from a synthetic chemistry perspective-a perspective that serves as a starting point for biological studies. Therefore this account focuses on synthetic methods for GNA nucleoside synthesis, as well as their postsynthetic chemical transformations. The properties and biological activity of GNA constituents are also highlighted. A literature survey shows four major approaches toward GNA nucleoside scaffold synthesis. These approaches pertain to glycidol ring-opening, Mitsunobu, SN2, and dihydroxylation reactions. The general arsenal of reactions used in GNA chemistry is versatile and encompasses the Sonogashira reaction, Michael addition, silyl-Hilbert-Johnson reaction, halogenation, alkylation, cyclization, Rh-catalyzed N-allylation, Sharpless catalytic dihydroxylation, and Yb(OTf)3-catalyzed etherification. Additionally, various phosphorylation reactions have enabled the synthesis of diverse types of GNA nucleotides, dinucleoside phosphates, phosphordiamidites, and oligos. Furthermore, recent advances in GNA chemistry have resulted in the synthesis of previously unknown redox-active (ferrocenyl) and luminescent (pyrenyl and phenanthrenyl) GNA nucleosides, which are also covered in this review.

Replacement of the phosphodiester backbone between canonical nucleosides with a dirhenium carbonyl "click" linker-a new class of luminescent organometallic dinucleoside phosphate mimics

The first-in-class luminescent dinucleoside phosphate analogs with a [Re₂(μ-Cl)₂(CO)₆(μ-pyridazine)] "click" linker as a replacement for the natural phosphate group are reported together with the synthesis of luminescent adenosine and thymidine derivatives having the [Re₂(μ-Cl)₂(CO)₆(μ-pyridazine)] entity attached to positions 5' and 3', respectively. These compounds were synthesized by applying inverse-electron-demand Diels-Alder and copper(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition reactions in three or four steps. The obtained compounds exhibited orange emission (λ_PL ≈ 600 nm, Φ_PL ≈ 0.10, and τ = 0.33-0.61 μs) and no toxicity (except for one nucleoside) to human HeLa cervical epithelioid and Ishikawa endometrial adenocarcinoma cancer cells in vitro. Furthermore, the compounds' ability to inhibit the growth of Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli bacterial strains was moderate and only observed at a high concentration of 100 μM. Confocal microscopy imaging revealed that the "dirhenium carbonyl" dinucleosides and nucleosides localized mainly in the membranous structures of HeLa cells and uniformly inside S. aureus and E. coli bacterial cells. An interesting finding was that some of the tested compounds were also found in the nuclei of HeLa cells.

Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions

Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.

N-Methoxy-1,3-oxazinane nucleic acids (MOANAs) - a configurationally flexible backbone modification allows post-synthetic incorporation of base moieties

(2R,3S)-4-(Methoxyamino)butane-1,2,3-triol was converted into a protected phosphoramidite building block and incorporated into the middle of a short DNA oligonucleotide. O1 and O3 of the (2R,3S)-4-(methoxyamino)butane-1,2,3-triol were engaged in phosphodiester linkages, leaving O2 and the methoxyamino function available to form an N-methoxy-1,3-oxazinane ring through reaction with an aldehyde. In modified oligonucleotides thus obtained, the oxazinane ring formally replaces the furanose ring and the aldehyde, the base moiety of natural nucleosides. The feasibility of synthesizing base-modified oligonucleotides by this approach was demonstrated with several aromatic and aliphatic aldehydes featuring various functional groups.

Recent advances in constructing high-order DNA structures

Molecular self-assembly is widely used in the fields of biosensors, molecular devices, efficient catalytic materials, and medical biomaterials. As the carrier of genetic information, DNA is a kind of biomacromolecule composed of deoxyribonucleotide units. DNA nanotechnology extends DNA of its original properties as a molecule that stores and transmits genetic information from its biological environment. By taking advantage of its unique base pairing and inherent biocompatibility to produce structurally-defined supramolecular structures. With the continuously development of DNA technology, the assembly method of DNA nanostructures is not only limited on the basis of DNA hybridization but also other biochemical interactions. In this review, we summarize the latest methods used to construct high-order DNA nanostructures. The problems of DNA nanostructures are discussed and the future directions in this field are provided.

Controllable DNA strand displacement by independent metal-ligand complexation

Introduction of artificial metal-ligand base pairs can enrich the structural diversity and functional controllability of nucleic acids. In this work, we revealed a novel approach by placing a ligand-type nucleoside as an independent toehold to control DNA strand-displacement reactions based on metal-ligand complexation. This metal-mediated artificial base pair could initiate strand invasion similar to the natural toehold DNA, but exhibited flexible controllability to manipulate the dynamics of strand displacement that was only governed by its intrinsic coordination properties. External factors that influence the intrinsic properties of metal-ligand complexation, including metal species, metal concentrations and pH conditions, could be utilized to regulate the strand dynamics. Reversible control of DNA strand-displacement reactions was also achieved through combination of the metal-mediated artificial base pair with the conventional toehold-mediated strand exchange by cyclical treatments of the metal ion and the chelating reagent. Unlike previous studies of embedded metal-mediated base pairs within natural base pairs, this metal-ligand complexation is not integrated into the nucleic acid structure, but functions as an independent toehold to regulate strand displacement, which would open a new door for the development of versatile dynamic DNA nanotechnologies.

Cisplatin adducts of DNA as precursors for nanostructured catalyst materials

The synthesis and characterisation of novel metal-modified DNA precursors for fuel cell catalyst development are described. Material precursors in the form of metal-DNA complexes were prepared through the reaction of DNA with cisplatin at various loadings and spectroscopically tested to confirm the platinum binding mode and the degree of complexation. The surface morphology of the DNA-metal material was analysed by Scanning Transmission Electron Microscopy (STEM), which revealed the extent of platinum nanocluster formation, with low metal loadings leading to observation of individual platinum atoms. Electrochemical measurements showed a greater electrocatalytic activity for the hydrogen evolution reaction (HER) with increased platinum loadings, shifting the half wave potential, E _1/2, away from the glassy carbon limit towards that of a bulk Pt electrode. This is explained further by Tafel plots, from which a change in the mechanism of the apparent rate limiting step for proton reduction from a Volmer to a Heyrovsky mechanism is postulated as the platinum loading increases.

Boron clusters as a platform for new materials: composites of nucleic acids and oligofunctionalized carboranes (C2B10H12) and their assembly into functional nanoparticles

Nucleic acids are key biomolecules in all life forms. These biomolecules can encode and transfer information via Watson-Crick base-pairing interactions and can form double-stranded structures between complementary sequences with high precision. These properties make nucleic acids extremely successful in applications in materials science as nanoconstruction materials. Herein, we describe a method for the automated synthesis of "oligopeds", which are building blocks based on the boron cluster structure equipped with short DNA adapters; these building blocks assemble into functional nanoparticles. The obtained, well defined, torus-like structures are the first DNA nanoconstructs based on a boron cluster scaffold. The results indicate the potential of boron clusters in DNA nanoconstruction and open the way for the design of entirely new types of buildings blocks based on polyhedral heteroborane geometry and its unique properties. The use of antisense oligonucleotides as DNA adapters illustrates one of the possible applications of the obtained nanoconstructs as vectors for therapeutic nucleic acids.

On the Enzymatic Formation of Metal Base Pairs with Thiolated and pKa -Perturbed Nucleotides

The formation of artificial metal base pairs is an alluring and versatile method for the functionalization of nucleic acids. Access to DNA functionalized with metal base pairs is granted mainly by solid-phase synthesis. An alternative, yet underexplored method, envisions the installation of metal base pairs through the polymerization of modified nucleoside triphosphates. Herein, we have explored the possibility of using thiolated and pK_a -perturbed nucleotides for the enzymatic construction of artificial metal base pairs. The thiolated nucleotides S2C, S6G, and S4T as well as the fluorinated analogue 5FU are readily incorporated opposite a templating S4T nucleotide through the guidance of metal cations. Multiple incorporation of the modified nucleotides along with polymerase bypass of the unnatural base pairs are also possible under certain conditions. The thiolated nucleotides S4T, S4T, S2C, and S6G were also shown to be compatible with the synthesis of modified, high molecular weight single-stranded (ss)DNA products through TdT-mediated tailing reactions. Thus, sulfur-substitution and pK_a perturbation represent alternative strategies for the design of modified nucleotides compatible with the enzymatic construction of metal base pairs.

DNA Modified with Boron⁻Metal Cluster Complexes [M(C₂B₉H11)₂]-Synthesis, Properties, and Applications

Together with tremendous progress in biotechnology, nucleic acids, while retaining their status as "molecules of life", are becoming "molecular wires", materials for the construction of molecular structures at the junction between the biological and abiotic worlds. Herein, we present an overview of the approaches for incorporating metal centers into nucleic acids based on metal⁻boron cluster complexes (metallacarboranes) as the metal carriers. The methods are modular and versatile, allowing practical access to innovative metal-containing DNA for various applications, such as nucleic acid therapeutics, electrochemical biosensors, infrared-sensitive probes, and building blocks for nanoconstruction.

High definition polyphosphoesters: between nucleic acids and plastics

Nucleic acids and synthetic polyphosphoester materials have been distinct fields – this review shows how these areas now comprise a continuum.

Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block

The DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag⁺-base bonding rather than by Watson-Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies.

Cu(I) complexes of bis(methyl)(thia/selena) salen ligands: Synthesis, characterization, redox behavior and DNA binding studies

Mononuclear cuprous complexes 1 and 2, [{CH₃E(o-C₆H₄)CH=NCH₂}₂Cu]ClO₄; E=S/Se, have been synthesized by the reaction of bis(methyl)(thia/selena) salen ligands and [Cu(CH₃CN)₄]ClO₄. Both the products were characterized by elemental analysis, ESI-MS, FT-IR, ¹H/¹³C/⁷⁷Se NMR, and cyclic voltammetry. The complexes possess tetrahedral geometry around metal center with the N₂S₂/N₂Se₂ coordination core. Cyclic voltammograms of complexes 1 and 2 displayed reversible anodic waves at E_1/2=+0.08V and +0.10V, respectively, corresponding to the Cu(I)/Cu(II) redox couple. DNA binding studies of both the complexes were performed applying absorbance, fluorescence and molecular docking techniques. Competitive binding experiment of complexes with ct-DNA against ethidium bromide is performed to predict the mode of binding. The results indicate the groove binding mode of complexes 1 and 2 to DNA. The binding constants revealed the strong binding affinity of complexes towards ct-DNA.

The first X-ray structure of a silver–nucleotide complex: interaction of ion Ag(i) with cytidine-5′-monophosphate

The synthesis and X-ray characterization of an unprecedented complex of Ag(i) with cytidine-5′-monophosphate (HCMP) is reported. The coordination of Ag(i) to HCMP is via both the N3 and O2 atoms of two cytosine moieties and the phosphate group, generating a MOF.

Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA

An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between "choose-maximum" (choose a base pair giving the maximum β for each step) and "choose-minimum" (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

Metal-responsive structural transformation between artificial DNA duplexes and three-way junctions

Metal-responsive structural transformation between DNA duplexes and three-way junction structures was demonstrated utilizing artificial oligonucleotides modified with a 2,2’-bipyridine ligand.

DNA three-way junctions (3WJs) are essential structural motifs for DNA nanoarchitectures and DNA-based materials. We report herein a metal-responsive structural transformation between DNA duplexes and 3WJs using artificial oligonucleotides modified with a 2,2′-bipyridine (bpy) ligand. A mixture of bpy-modified DNA strands and natural complementary strands were self-assembled exclusively into duplexes without any transition metal ions, while they formed 3WJs in the presence of Ni^II ions. This transformation was induced by the formation of an interstrand Ni^II(bpy)₃ complex, which served as a template for the 3WJ assembly. Altering the amount and identity of the metal ion regulated the 3WJ induction efficiency. Removal of the metal using EDTA quantitatively regenerated the duplexes. The metal-dependent structural conversion shown here has many potential applications in the development of stimuli-responsive DNA materials.

Macrocyclic Metal Complex-DNA Conjugates for Electrochemical Sensing of Single Nucleobase Changes in DNA

The direct incorporation of macrocyclic cyclidene complexes into DNA via automated synthesis results in a new family of metal-functionalized DNA derivatives that readily demonstrate their utility through the ability of one redox-active copper(II)-containing strand to distinguish electrochemically between all four canonical DNA nucleobases at a single site within a target sequence of DNA.

Mesityl phenanthroline-modified 2'-deoxyuridine for heteroleptic complexes in metal ion-mediated assembly of DNA

The synthesis of a new DNA building block that bears the metal ion ligand 2,9-bis-mesityl-3-ethynyl-phenanthroline attached to the 5-position of 2'-deoxyuridine is presented. In the presence of Zn(2+), Cu(2+), Fe(2+) and Ni(2+) the complex formation of an accordingly modified DNA double strand with a second DNA duplex bearing the 2,2':6',2''-terpyridine ligand was studied by optical spectroscopy. The selective formation of heteroleptic assemblies between the two different DNA pieces was evidenced by denaturing polyacrylamide gel electrophoresis.

Hierarchical coassembly of DNA-triptycene hybrid molecular building blocks and zinc protoporphyrin IX

Herein, we describe the successful construction of composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA)-DNA building blocks and zinc protoporphyrin IX (Zn PpIX). DNA-organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5'-C12-amine-terminated modified single strand DNA (ssDNA) and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE), reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA-TPA molecular building blocks as well as a model guest molecule within the DNA-TPA supramolecular self-assembly. The formation of fiber-like composite DNA nanostructures was observed. Native PAGE, circular dichroism (CD) and atomic force microscopy (AFM) have been utilized for analyzing the formation of DNA nanofibers after the coassembly. Computational methods were applied to discern the theoretical dimension of the DNA-TPA molecular building block of the nanofibers. A notable change in photocatalytic efficiency of Zn PpIX was observed when it was inside the TPA-DNA scaffold. The significant increase in ROS generation by Zn PpIX when trapped in this biocompatible DNA-TPA hybrid nanofiber may be an effective tool to explore photodynamic therapy (PDT) applications as well as photocatalytic reactions.

The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers

DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.

Homochiral self-assembly of biocoordination polymers: anion-triggered helicity and absolute configuration inversion

The different natures of the weakly coordinating anions - triflate or perchlorate - in the Cu2+-mediated self-assembly of cytidine monophosphate nucleotide play a fundamental role in the homochiral resolution process, yielding one-dimensional copper(ii) coordination polymers of opposite helicity that can be easily inverted, in a reversible way, by changing the nature of the anion as revealed by circular dichroism experiments both in solution and in the solid state.

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 (2py) PyrdC-(2py) PyrdC 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.

Silver mediated duplex-type complexes of pyrimidinophanes and their acyclic counterparts

Pyrimidinophanes revealed high extraction selectivity for Ag⁺ ions and afforded Ag⁺ mediated duplex-type complexes. Such coordination is realized due to the N1-atoms of the 2-thiocytosine fragments and the polymethylene spacer linking amine groups.

Synthesis of a multibranched porphyrin-oligonucleotide scaffold for the construction of DNA-based nano-architectures

The interest in the functionalization of oligonucleotides with organic molecules has grown considerably over the last decade. In this work, we report on the synthesis and characterization of porphyrin-oligonucleotide hybrids containing one to four DNA strands (P1-P4). The hybrid P4, which inserts one porphyrin and four DNA fragments, was combined with gold nanoparticles and imaged by transmission electron microscopy.

Ca2+ metal ion adducts with cytosine, cytidine and cytidine 5′-monophosphate: a comprehensive study of calcium reactivity towards building units of nucleic acids

Six new Ca(ii) adducts with cytosine (cyt), cytidine (H₂cyd) and cytidine 5′-monophosphate (CMP) are presented. H₂cyd and CMP show unprecedented binding sites for the calcium ion.

DNA modification under mild conditions by Suzuki-Miyaura cross-coupling for the generation of functional probes

Quick and clean: A method for Pd-catalyzed Suzuki-Miyaura cross-coupling to iododeoxyuridine (IdU) in DNA is described. Key to the reactivity is the choice of the ligand and the buffer. A covalent [Pd]-DNA intermediate was isolated and characterized. Photocrosslinking probes were generated to trap proteins that bind to epigenetic DNA modifications.