The selective synthesis of metallanucleosides and metallanucleotides: a new tool for the functionalization of nucleic acids

Purinyl N-directed aroylation of 6-arylpurine ribo- and 2'-deoxyribonucleosides, and mechanistic insights

The purinyl ring contains four embedded nitrogen atoms of varying basicities. Selective utilization of these ring nitrogen atoms can lead to relatively facile remote functionalization, yielding modified purinyl motifs that are otherwise not easily obtained. Herein, we report previously undescribed N-directed aroylation of 6-arylpurine ribo and the more labile 2'-deoxyribonucleosides. Kinetic isotope analysis as well as reaction with a well-defined dimeric, palladated 9-benzyl 6-arylpurine provided evidence for N-directed cyclometallation as a key step, with a plausible rate-limiting C-H bond cleavage. Radical inhibition experiments indicate the likely intermediacy of aroyl radicals. The chemistry surmounts difficulties often posed in the functionalization of polynitrogenated and polyoxygenated nucleosidic structures that possess complex reactivities and a labile glycosidic bond that is more sensitive in the 2'-deoxy substrates.

Organometallic modification confers oligonucleotides new functionalities

To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.

Phosphorescent Ir(III) complexes derived from purine nucleobases

We report the preparation and the study of new types of neutral and cationic phosphorescent heteroleptic Ir(III) complexes derived from 6-phenylpurine nucleosides and nucleotides. Neutral complexes of general formula Ir(C^N)₂(acac) 7, and 8a-c (HC^N = 9-substituted-6-phenyl purine) are orange-red emissive upon photoexcitation, with short lifetimes and good quantum yields (0.42-0.65) in both PMMA films and 2-MeTHF at room temperature. In turn, cationic complexes [Ir(C^N)₂(dtb-bpy)][PF₆] 9, 12a and 12c (dtb-bpy = 4,4'-di-tert-butyl-2,2'-dipyridine) are yellow-green emitters with moderate quantum yields (0.24-0.32).

Controllable synthesis of two adenosine 5'-monophosphate nucleotide coordination polymers via pH regulation: crystal structure and chirality

Two types of Cu(ii)-AMP-4,4'-bipy coordination polymers, {[Cu(AMP)(4,4'-bipy)(H₂O)₃]·5H₂O}n (1) and {[Cu₂(HAMP)₂(4,4'-bipy)₂(H₂O)₄]·2NO₃·11H₂O}n (2) (Na₂AMP = adenosine 5'-monophosphate disodium salt), were synthesised through pH control. X-ray single-crystal diffraction analysis revealed that 1 and 2 are one-dimensional (1D) coordinating coordination polymers. The nucleotide in 1 was not protonated whereas that in 2 was protonated. With the protonated NO₃^- in 2 entering the crystal lattice, it plays a role in balancing the charge. The chirality was studied using solid-state circular dichroism (CD) spectroscopy based on the analysis of crystal structures.

Self-assembled nanostructures of phosphomolybdate, nucleobase and metal ions synthesis and their in vitro cytotoxicity studies on cancer cell lines

The ability of the multidentate nucleobases, adenine and thymine, to coordinate polyoxometalate and metal ions leading to the formation of self-assembled nanostructures and their strong cytotoxicity toward cancer cell lines have been demonstrated. A unique synthetic approach is developed to make a series of functional nanoscale hybrid materials consisting of nucleobases (adenine and thymine) and phosphomolybdic acid (PMA) through solid state chemical reaction and self-assembly process. Adenine was protonated through its ring nitrogen, while the ketone group in thymine was protonated during the addition of PMA to these nucleobases. The self-assembled nanostructures formed as a result of the electrostatic interaction between the protonated nucleobases and polyanionic PMA. To promote the base pairing between the nucleobases, chloroaurate ions and silver ions were added to each PMA/adenine and PMA/thymine nanostructures. The complexation between the nucleobases and the added metal ions was found to drive the formation of subsequent self-assembled nanostructures. All the materials were screened for their anticancer activity against breast (MDAMB-231) and prostate (PC-3) cancer cells, and non-cancerous keratinocyte cells HaCaT. PMA/adenine/[AuCl4]- and PMA/thymine/Ag+ nanostructures were found to have strong anti-cancer activity, while PMA/adenine/Ag+, PMA/thymine/[AuCl4]-, and PMA/pdenine, PMA/thymine nanostructures did not exhibit such activity. The unique redox properties of these materials and the self-assembly of the PMA and metal ions were the major factors responsible for the cytotoxicity. This unique approach of making functional nanomaterials incorporate the nucleobase, PMA and metal ions using solid state self-assembly and their anti-cancer applications are considered to be an effective approach for the development of inorganic nucleoside analogue bio-pharmaceutical agents.

Sequential Reactions of Alkynes on an Iridium(III) Single Site

Sequential insertion of terminal alkynes on Ir^III cyclometalated complexes allow the formation of novel metallapolycycles in a controlled and efficient manner. ortho-Methylarylethynyl derivatives led to an unprecedented cascade combination of three fundamental processes (C-C bond formation, C(sp³ )-H activation, and reductive coupling) on a single Ir^III center, in a process compatible with functionalized biomolecules and photoactive substrates. The reaction with tert-butylacetylene led to a [6,5,4]-polycycle that incorporates an iridacyclobutenylidene in its structure. The sequence is a multicomponent reaction in which the metal not only promotes the different steps but also determines their stereoselectivity. This is an elegant example of the synergy between a metal-promoting reaction and a symmetry-defined stereochemistry.

Reprogramming the assembly of unmodified DNA with a small molecule

The ability of DNA to store and encode information arises from base pairing of the four-letter nucleobase code to form a double helix. Expanding this DNA 'alphabet' by synthetic incorporation of new bases can introduce new functionalities and enable the formation of novel nucleic acid structures. However, reprogramming the self-assembly of existing nucleobases presents an alternative route to expand the structural space and functionality of nucleic acids. Here we report the discovery that a small molecule, cyanuric acid, with three thymine-like faces, reprogrammes the assembly of unmodified poly(adenine) (poly(A)) into stable, long and abundant fibres with a unique internal structure. Poly(A) DNA, RNA and peptide nucleic acid (PNA) all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, which brings together poly(A) triplexes with a subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen-bonding molecules can be used to induce the assembly of nucleic acids in water, which leads to new structures from inexpensive and readily available materials.

Base-modified NAD and AMP derivatives and their activity against bacterial DNA ligases

We report the chemical synthesis and conformational analysis of a collection of 2-, 6- and 8-substituted derivatives of β-NAD(+) and AMP, and their biochemical evaluation against NAD(+)-dependent DNA ligases from Escherichia coli and Mycobacterium tuberculosis. Bacterial DNA ligases are validated anti-microbial targets, and new strategies for their inhibition are therefore of considerable scientific and practical interest. Our study includes several pairs of β-NAD(+) and AMP derivatives with the same substitution pattern at the adenine base. This has enabled the first direct comparison of co-substrate and inhibitor behaviour against bacterial DNA ligases. Our results suggest that an additional substituent in position 6 or 8 of the adenine base in β-NAD(+) is detrimental for activity as either co-substrate or inhibitor. In contrast, substituents in position 2 are not only tolerated, but appear to give rise to a new mode of inhibition, which targets the conformational changes these DNA ligases undergo during catalysis. Using a molecular modelling approach, we highlight that these findings have important implications for our understanding of ligase mechanism and inhibition, and may provide a promising starting point for the rational design of a new class of inhibitors against NAD(+)-dependent DNA ligases.

Regioselectivity of the C-metalation of 6-furylpurine: importance of directing effects

We report the C-metalation of 6-furylpurine with Pt(2+), Pd(2+), and Hg(2+). The ligand binds the metal ions in a bidentate fashion, involving the N7 purine atom and one of the furyl carbon atoms. The regioselectivity is determined by the metal ion. Pt(2+) and Pd(2+) coordinate the furyl moiety in its β position and Hg(2+) in its electronically preferred α position.

On the use of metal purine derivatives (M=Ir, Rh) for the selective labeling of nucleosides and nucleotides

The reactions of neutral or cationic IrIII and RhIII derivatives of phenyl purine nucleobases with unsymmetrical alkynes produce new metallacycles in a predictable manner, which allows for the incorporation of either photoactive (anthracene or pyrene) or electroactive (ferrocene) labels in the nucleotide or nucleoside moiety. The reported methodology (metalation of the purine derivative and subsequent marker insertion) could be used for the postfunctionalization and unambiguous labeling of oligonucleotides.

A versatile methodology for the regioselective C⁸-metalation of purine bases

Purine nucleobases are excellent ligands for metal ions, forming normally coordinative Werner-type bonds by utilizing the N donor atoms of the nucleobase skeleton. Here we show that purines such as 8-chlorocaffeine and 8-bromo-9-methyladenine react with [Pt(PPh3)4] under oxidative addition of the C(8)-halogen bond to the metal center. The resulting Pt(II) complexes feature a C(8)-bound ylidene ligand. Protonation of the ylidene at the N(7/9)-atom yields complexes bearing a protic N-heterocyclic carbene ligand derived from the purine base with an NMe,NH-substitution pattern.

Cyclometalated [Cp*M(C^X)] (M = Ir, Rh; X = N, C, O, P) complexes

Isolated and well-defined cyclometalated iridium/rhodium complexes that contain a Cp*M–C (M = Ir, Rh) bond stabilised by the intramolecular coordination of neutral donor atoms (N, C, O or P), together with their applications, were summarized.

Purinyl N1-directed aromatic C-H oxidation in 6-arylpurines and 6-arylpurine nucleosides

Palladium-catalyzed C-H bond activation and oxidation of C6 arylpurines as well as C6 arylpurine nucleosides can be accomplished using Pd(OAc)2/PhI(OAc)2 in CH3CN. Despite the presence of four nitrogen atoms in the purine moiety as well as the polyoxygenated saccharide and a labile glycosidic bond in the nucleosides, these reactions can be effectively conducted. Notably, the generally more labile 2'-deoxyribonucleosides also undergo reaction. The reaction conditions can be tuned to yield either monoacetoxylated or diacetoxylated products predominantly. In the course of these investigations, a dimeric Pd(II)-containing cyclopalladated C6 naphthylpurine derivative has been obtained and crystallographically characterized. This compound is competent in catalyzing the oxidization with PhI(OAc)2, indicating its plausible intermediacy in the chemistry. The X-ray structure of a monoacetoxylated product from this reaction has also been obtained.