The Renaissance of Metal-Pyrimidine Nucleobase Coordination Chemistry

Chemical structures, biological activities, and medicinal potentials of amine compounds detected from Aloe species

Unrestricted interest in Aloe species has grown rapidly, and a lot of research is currently being done to learn more about the properties of the various Aloe constituents. Organic compounds containing amine as functional group are present in a vivid variety of compounds, namely, amino acids, hormones, neurotransmitters, DNA, alkaloids, dyes, etc. These compounds have amine functional groups that have various biological activities, which make them responsible for medicinal potential in the form of pharmaceutical, nutraceutical, and cosmeceutical applications. Consequently, the present review work provides an indication of the amines investigated in Aloe species and their therapeutic uses. Various amine compounds of the Aloe species have effective biological properties to treat diseases. Generally, the genus Aloe has various active amine-containing compounds to combat diseases when humans use them in various forms.

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.

Ru-Controlled Thymine Tautomerization Frozen by a k1(O)-, k2(N,O)-Metallacycle: An Experimental and Theoretical Approach

The reaction of mer-(Ru(H)₂(CO)(PPh₃)₃) (1) with one equivalent of thymine acetic acid (THAcH) unexpectedly produces the macrocyclic dimer k¹(O), k²(N,O)-(Ru(CO)(PPh₃)₂THAc)₂ (4) and, concomitantly, the doubly coordinated species k¹(O), k²(O,O)-(Ru(CO)(PPh₃)₂THAc) (5). The reaction promptly forms a complicated mixture of Ru-coordinated mononuclear species. With the aim of shedding some light in this context, two plausible reaction paths were proposed by attributing the isolated or spectroscopically intercepted intermediates on the basis of DFT-calculated energetic considerations. The cleavage of the sterically demanding equatorial phosphine in the mer-species releases enough energy to enable self-aggregation, producing the stable, symmetric 14-membered binuclear macrocycle of 4. The k¹-acetate iminol (C=N-OH) unit of the mer-tautomer k¹(O)-(Ru(CO)(PPh₃)₂(THAc)) (2) likely exhibits a stronger nucleophilic aptitude than the prevalent N(H)-C(O) amido species, thus accomplishing extra stabilization through concomitant k²(N,O)-thymine heteroleptic side-chelation. Furthermore, both the ESI-Ms and IR simulation spectra validated the related dimeric arrangement in solution, in agreement with the X-ray determination of the structure. The latter showed tautomerization to the iminol form. The ¹H NMR spectra in chlorinated solvents of the kinetic mixture showed the simultaneous presence of 4 and the doubly coordinated 5, in rather similar amounts. THAcH added in excess preferentially reacts with 2 or trans-k²(O,O)-(RuH(CO)(PPh₃)₂THAc) (3) rather than attacking the starting Complex 1, promptly forming the species of 5. The proposed reaction paths were inferred by spectroscopically monitoring the intermediate species, for which the results were strongly dependent on the of conditions the reaction (stoichiometry, solvent polarity, time, and the concentration of the mixture). The selected mechanism proved to be more reliable, due to the final dimeric product stereochemistry.

The Full Cytosine-Cytosine Base Paring: Self-Assembly and Crystal Structure

The synthesis of self-assembly systems that can mimic partial biological behaviours require ingenious and delicate design. For decades, scientists are committed to exploring new base pairing patterns using hydrogen bonds directed self-assembly of nucleotides. A fundamental question is the adaptive circumstance of the recognition between base pairs, namely, how solvent conditions affect the domain of base pairs. Towards this question, three nucleotide complexes based on 2'-deoxycytidine-5'-monophosphate (dCMP) and cytidine-5'-monophosphate (CMP) were synthesized in different solvents and pH values, and an unusual cytosine-cytosine base paring pattern (named full C : C base pairing) has been successfully obtained. Systematic single crystal analysis and ¹ H NMR titration spectra have been performed to explore factors influencing the formation of base paring patterns. Moreover, supramolecular chirality of three complexes were studied using circular dichroism (CD) spectroscopy in solution and solid-state combined with crystal structure analysis.

Mapping H+ in the Nanoscale (A2C4)2-Ag8 Fluorophore

When strands of DNA encapsulate silver clusters, supramolecular optical chromophores develop. However, how a particular structure endows a specific spectrum remains poorly understood. Here, we used neutron diffraction to map protonation in (A₂C₄)₂-Ag₈, a green-emitting fluorophore with a "Big Dipper" arrangement of silvers. The DNA host has two substructures with distinct protonation patterns. Three cytosines from each strand collectively chelate handle-like array of three silvers, and calorimetry studies suggest Ag⁺ cross-links. The twisted cytosines are further joined by hydrogen bonds from fully protonated amines. The adenines and their neighboring cytosine from each strand anchor a dipper-like group of five silvers via their deprotonated endo- and exocyclic nitrogens. Typically, exocyclic amines are strongly basic, so their acidification and deprotonation in (A₂C₄)₂-Ag₈ suggest that silvers perturb the electron distribution in the aromatic nucleobases. The different protonation states in (A₂C₄)₂-Ag₈ suggest that atomic level structures can pinpoint how to control and tune the electronic spectra of these nanoscale chromophores.

Intramolecular Folding of PolyT Oligonucleotides Induced by Cooperative Binding of Silver(I) Ions

Ag⁺-bridged T-Ag⁺-T was recently discovered in a Ag⁺-DNA nanowire crystal, but it was reported that Ag⁺ had little to no affinity to T nucleobases and T-rich oligonucleotides in solution. Therefore, the binding mode for the formation of this type of novel metallo base pair in solution is elusive. Herein, we demonstrate that Ag⁺ can interact with polyT oligonucleotides once the concentration of Ag⁺ in solution exceeds a threshold value. The threshold value is independent of the concentration of the polyT oligonucleotide but is inversely proportional to the length of the polyT oligonucleotide. The polyT oligonucleotides are intramolecularly folded due to their positively cooperative formation and the stack of T-Ag⁺-T base pairs, resulting in the 5'- and 3'-ends being in close proximity to each other. The intramolecular Ag⁺-folded polyT oligonucleotide has a higher thermal stability than the duplex and can be reversibly modulated by cysteine.

Tug-of-War between DNA Chelation and Silver Agglomeration in DNA-Silver Cluster Chromophores

Supramolecular chromophores form when a DNA traps silvers that then coalesce into clusters with discrete, molecular electronic states. However, DNA strands are polymeric ligands that disperse silvers and thus curb agglomeration. We study this competition using two chromophores that share three common components: a dimeric DNA scaffold, Ag⁺-nucleobase base pairs, and Ag⁰ chromophores. The DNA host C₄-A₂-iC₄T mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "i") directions. The backbone directions must alternate to form the two silver clusters, and this interdependence supports a silver-linked structure. This template creates two chromophores with distinct sizes, charges, and hence spectra: (C₄-A₂-iC₄T)₂/Ag₁₁⁷⁺ with λ_abs/λ_em = 430/520 nm and (C₄-A₂-iC₄T)₂/Ag₁₄⁸⁺ with λ_abs/λ_em = 510/630 nm. The Ag⁺ and Ag⁰ constituents in these partially oxidized clusters are linked with structural elements in C₄-A₂-iC₄T. Ag⁺ alone binds sparsely but strongly to form C₄-A₂-iC₄T/3-4 Ag⁺ and (C₄-A₂-iC₄T)₂/7-8 Ag⁺ complexes, and these stoichiometries suggest that Ag⁺ cross-links pairs of cytosines to form a hairpin with a metallo-C₄/iC₄ duplex and an adenine loop. The Ag⁰ are chemically orthogonal because they can be oxidatively etched without disrupting the underlying Ag⁺-DNA matrix, and their reactivity is attributed to their valence electrons and weaker chelation by the adenines. These studies suggest that Ag⁺ disperses with the cytosines to create an adenine binding pocket for the Ag⁰ cluster chromophores.

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).

2-Trifluoromethyl-6-mercurianiline Nucleotide, a Sensitive 19F NMR Probe for Hg(II)-mediated Base Pairing

A 2-trifluoromethylaniline C-nucleoside was synthesized, incorporated in the middle of an oligonucleotide, and mercurated. The affinity of the mercurated oligonucleotide toward complementary strands placing each of the canonical nucleobases opposite to the organomercury nucleobase analogue was examined by ultraviolet (UV), circular dichroism (CD), and 19F NMR spectroscopy analyses. According to the UV melting profile analysis, the organomercury nucleobase analogue showed increased affinities in the order T > G > C > A. The CD profiles indicated the typical B-type helix in each case. The 19F resonance signal proved sensitive for the local environmental changes, showing clearly distinct signals for the duplexes with different opposing nucleobases. Furthermore, valuable information on the mercurated oligonucleotide and its binding to complementary strands at varying temperature could be obtained by 19F NMR spectroscopy.

Chemical reduction of Ag+ to Ag employing organic electron donors: evaluation of the effect of Ag+-mediated cytosine-cytosine base pairing on the aggregation of Ag nanoparticles

Ag⁺-mediated base pairing is valuable for synthesising DNA-based silver nanoparticles (AgNPs) and nanoclusters (AgNCs). Recently, we reported the formation of a [Ag(cytidine)₂]⁺ complex in dimethyl sulfoxide (DMSO), which facilitated the evaluation of the effect of cytosine-Ag⁺-cytosine (C-Ag⁺-C) base pairing on the degree of AgNP aggregation in solution. As an aprotic solvent, DMSO was expected to dissolve the [Ag(cytidine)₂]⁺ complex, and powerful reducing agents, such as organic electron donors. In this study, the chemical reduction of a cytidine/Ag⁺ system using a powerful reducing agent tetrakis(dimethylamino)ethylene (TDAE) was investigated. ¹H/¹³C/¹⁵N NMR spectroscopic evidence was obtained to identify the iminium dication (TDAE²⁺), which is an oxidised form of TDAE. The results were compared with those obtained using another organic electron donor, tetrathiafulvalene (TTF), which exhibits a relatively lower reduction activity than TDAE. AgNPs prepared via redox reaction between [Ag(cytidine)₂]⁺ and organic electron donors (TDAE and TTF) were characterised using UV-Vis spectroscopy and nanoparticle tracking analysis. It was found that the formation of C-Ag⁺-C base pairing inhibited the aggregation of AgNPs in solution. In addition, in the presence of cytidine, the total concentration of the AgNP solution was affected by the reduction activity of the reducing agent.

Two Co(II) coordination polymers: magnetic properties and application values against chronic subdural hematoma

In this current experiment, by applying the mixed-ligand synthesis method, two coordination polymers (CPs) containing Co(II) were created triumphantly with reaction between 1,3-bis(1-imidazoly)benzene (mbib) and Co(II) salts with the aid of diverse carboxylic ligands, and their chemical formulae are [Co₃(opda)₃(mbib)₄(H₂O)₄]·2H₂O (1, H₂opda is 1,2-phenylenediacetic acid) and [Co(mpda)(mbib)]·H₂O (2, H₂mpda is 1,3-phenylenediacetic acid). The two compounds' magnetic performances suggest that between the adjacent metal ions, there present the antiferromagnetic coupling. The evaluation of their treatment activity against chronic subdural hematoma was carried out and the relevant mechanism was studied simultaneously. Firstly, before the treatment of compound, the chronic subdural hematoma was generated. Furthermore, the enzyme-linked immunosorbent assay detection kit was implemented and in hematoma capsule, the anti-inflammatory cytokines level and pro-inflammatory cytokines level was detected. Additionally, the cytotoxicity of compounds 1 and 2 on the normal human cells was determined with Cell Counting Kit-8 assay. Above all, we proved compound 1 decreased the pro-inflammatory cytokines content and increased the anti-inflammatory cytokines content in the hematoma capsule, which is much stronger than that of compound 2. Both compounds 1 and 2 showed no cytotoxicity on the normal human cells.

Effect of cytosine-Ag+-cytosine base pairing on the redox potential of the Ag+/Ag couple and the chemical reduction of Ag+ to Ag by tetrathiafulvalene

The redox properties of metallo-base pairs remain to be elucidated. Herein, we report the detailed 1H/13C/109Ag NMR spectroscopic and cyclic voltammetric characterisation of the [Ag(cytidine)2]+ complex as isolated cytosine-Ag+-cytosine (C-Ag+-C) base pairs. We also performed comparative studies between cytidine/Ag+ and other nucleoside/Ag+ systems by using cyclic voltammetry measurements. In addition, to evaluate the effect of [Ag(cytidine)2]+ formation on the chemical reduction of Ag+ to Ag, we utilised the redox reaction between Ag+ and tetrathiafulvalene (TTF). We found that Ag+-mediated base pairing lowers the redox potential of the Ag+/Ag couple. In addition, C-Ag+-C base pairing makes it more difficult to reduce captured Ag+ ions than in other nucleoside/Ag+ systems. Remarkably, the cytidine/Ag+ system can be utilised to control the redox potential of the Ag+/Ag couple in DMSO. This feature of the cytidine/Ag+ system may be exploited for Ag nanoparticle synthesis by using the redox reaction between Ag+ and TTF.

Sequence dependence of Pd(II)-mediated base pairing by palladacyclic nucleobase surrogates

A C-nucleoside derivative of phenylpyridine or the respective palladacycle was incorporated at either 3'- or 5'-terminus of a short oligodeoxynucleotide. Hybridization properties of these modified oligonucleotides were studied in a fluorescence-based competition assay in addition to conventional UV melting temperature analysis and compared with those of a previously prepared analogue featuring the modified nucleoside in the middle of the sequence. With the unpalladated phenylpyridine oligonucleotides, UV melting temperature qualitatively correlated with the ability to displace a strand from a double helix in the competition assay, decreasing in the order 5' > 3' > middle. Corresponding results on the palladacyclic oligonucleotides were more difficult to interpret but both UV melting and competition experiments revealed a decrease in the duplex stability upon palladation in most cases. On the other hand, dependence of the UV melting temperature on the identity of the canonical nucleobase opposite to the modified nucleobase analogue was much more pronounced with the palladacyclic duplexes than with their unpalladated counterparts. Furthermore, UV melting profiles of the palladacyclic duplexes featured an additional transition at a temperature exceeding the melting temperature of the unmodified part of the duplex. Taken together, these results lend support to the idea of Pd(II)-mediated base pairs that are highly stable but incompatible with the geometry of a double helix.

Organomercury Nucleic Acids: Past, Present and Future

Synthetic efforts towards nucleosides, nucleotides, oligonucleotides and nucleic acids covalently mercurated at one or more of their base moieties are summarized, followed by a discussion of the proposed, realized and abandoned applications of this unique class of compounds. Special emphasis is given to fields in which active research is ongoing, notably the use of HgII -mediated base pairing to improve the hybridization properties of oligonucleotide probes. Finally, this minireview attempts to anticipate potential future applications of organomercury nucleic acids.

A Gadolinium(III) Complex Based on the Thymine Nucleobase with Properties Suitable for Magnetic Resonance Imaging

The paramagnetic gadolinium(III) ion is used as contrast agent in magnetic resonance (MR) imaging to improve the lesion detection and characterization. It generates a signal by changing the relaxivity of protons from associated water molecules and creates a clearer physical distinction between the molecule and the surrounding tissues. New gadolinium-based contrast agents displaying larger relaxivity values and specifically targeted might provide higher resolution and better functional images. We have synthesized the gadolinium(III) complex of formula [Gd(thy)₂(H₂O)₆](ClO₄)₃·2H₂O (1) [thy = 5-methyl-1H-pyrimidine-2,4-dione or thymine], which is the first reported compound based on gadolinium and thymine nucleobase. 1 has been characterized through UV-vis, IR, SEM-EDAX, and single-crystal X-ray diffraction techniques, and its magnetic and relaxometric properties have been investigated by means of SQUID magnetometer and MR imaging phantom studies, respectively. On the basis of its high relaxivity values, this gadolinium(III) complex can be considered a suitable candidate for contrast-enhanced magnetic resonance imaging.

On the Heterogeneous Nature of Cisplatin-1-Methyluracil Complexes: Coexistence of Different Aggregation Modes and Partial Loss of NH3 Ligands as Likely Explanation

The conversion of the 1 : 1-complex of Cisplatin with 1-methyluracil (1MeUH), cis-[Pt(NH3 )2 (1MeU-N3)Cl] (1 a) to the aqua species cis-[Pt(NH3 )2 (1MeU-N3)(OH2 )]+ (1 b), achieved by reaction of 1 a with AgNO3 in water, affords a mixture of compounds, the composition of which strongly depends on sample history. The complexity stems from variations in condensation patterns and partial loss of NH3 ligands. In dilute aqueous solution, 1 a, and dinuclear compounds cis-[(NH3 )2 (1MeU-N3)Pt(μ-OH)Pt(1MeU-N3)(NH3 )2 ]+ (3) as well as head-tail cis-[Pt2 (NH3 )4 (μ-1MeU-N3,O4)2 ]2+ (4) represent the major components. In addition, there are numerous other species present in minor quantities, which differ in metal nuclearity, stoichiometry, stereoisomerism, and Pt oxidation state, as revealed by a combination of 1 H NMR and ESI-MS spectroscopy. Their composition appears not to be the consequence of a unique and repeating coordination pattern of the 1MeU ligand in oligomers but rather the coexistence of distinctly different condensation patterns, which include μ-OH, μ-1MeU, and μ-NH2 bridging and combinations thereof. Consequently, the products obtained should, in total, be defined as a heterogeneous mixture rather than a mixture of oligomers of different sizes. In addition, a N2 complex, [Pt(NH3 )(1MeU)(N2 )]+ appears to be formed in gas phase during the ESI-MS experiment. In the presence of Na+ ions, multimers n of 1 a with n=2, 3, 4 are formed that represent analogues of non-metalated uracil quartets found in tetrastranded RNA.

Construction of hydrogen bonding and coordination networks based on ethynylpyridine-appended nucleobases

A series of ethynylpyridine-appended nucleobases have been designed, synthesized, characterized and employed for the formation of crystalline molecular networks by hydrogen/coordination bonding.

Covalently Mercurated Molecular Beacon for Discriminating the Canonical Nucleobases

A highly nucleobase-discriminating metalated nucleoside analogue, 3-fluoro-2-mercuri-6-methylaniline, was incorporated into an oligonucleotide molecular beacon. Fluorescence emission spectra were measured after the addition of four different complementary strands, in which the nucleobase opposite the metalated analogue varies. The fluorescence results showed a clear binding selectivity at room temperature, in the order G>T>C>A. The selectivity is based on the different affinities between the metalated nucleoside analogue and the canonical nucleobases. The synthesized probe is capable of robust discrimination between the two purine as well as the two pyrimidine bases by fluorescence at room temperature, and more sophisticated temperature analysis allows clear separation of every canonical nucleobase. The probe would, hence, be a suitable method for the detection of single nucleotide polymorphisms.

Metal-Mediated Base Pairing of Rigid and Flexible Benzaldoxime Metallacycles

Oligonucleotides incorporating a central C-nucleoside with either a rigid or flexible benzaldoxime base moiety have been synthesized, and the hybridization properties of their metallacyclic derivatives have been studied by UV melting experiments. In all cases, the metallated duplexes were less stable than their unmetallated counterparts, and the metallacyclic nucleobases did not show a clear preference for any of the canonical nucleobases as a base-pairing partner. With palladated oligonucleotides, increased flexibility translated to less severe destabilization, whereas the opposite was true for the mercurated oligonucleotides; this reflects the greater difficulties in accommodating a rigid PdII -mediated base pair than a rigid HgII -mediated base pair within the base stack of a double helix.

Functional Systems Derived from Nucleobase Self-assembly

Dynamic and reversible non-covalent interactions endow synthetic systems and materials with smart adaptive functions that allow them to response to diverse stimuli, interact with external agents, or repair structural defects. Inspired by the outstanding performance and selectivity of DNA in living systems, scientists are increasingly employing Watson-Crick nucleobase pairing to control the structure and properties of self-assembled materials. Two sets of complementary purine-pyrimidine pairs (guanine:cytosine and adenine:thymine(uracil)) are available that provide selective and directional H-bonding interactions, present multiple metal-coordination sites, and exhibit rich redox chemistry. In this review, we highlight several recent examples that profit from these features and employ nucleobase interactions in functional systems and materials, covering the fields of energy/electron transfer, charge transport, adaptive nanoparticles, porous materials, macromolecule self-assembly, or polymeric materials with adhesive or self-healing ability.

Synthesis, X-ray characterization and regium bonding interactions of a trichlorido(1-hexylcytosine)gold(iii) complex

Herein we report the synthesis and X-ray characterization of a gold(iii) complex of 1-hexylcytosine via N(3). The AuCl₃N complexes stack on top of each other by reciprocal [AuCl] regium bonding interactions. After the first example 35 years ago, this is the second available structure of a cytosine nucleobase model complexed to gold(iii).

1,8-Dimercuri-6-Phenyl-1H-Carbazole as a Monofacial Dinuclear Organometallic Nucleobase

A C-nucleoside with 6-phenyl-1H-carbazole as the base moiety has been synthesized and incorporated in the middle of an oligonucleotide. Mercuration of this modified residue at positions 1 and 8 gave the first example of an oligonucleotide featuring a monofacial dinuclear organometallic nucleobase. The dimercurated oligonucleotide formed stable duplexes with unmodified oligonucleotides placing either cytosine, guanine, or thymine opposite to the organometallic nucleobase. A highly stabilizing (ΔT_m =7.3 °C) Hg^II -mediated base pair was formed with thymine. According to DFT calculations performed at the PBE0DH level of theory, this base pair is most likely dinuclear, with the two Hg^II ions coordinated to O2 and O4 of the thymine base.

Footprints of Nanoscale DNA-Silver Cluster Chromophores via Activated-Electron Photodetachment Mass Spectrometry

DNA-templated silver clusters (AgC) are fluorescent probes and biosensors whose electronic spectra can be tuned by their DNA hosts. However, the underlying rules that relate DNA sequence and structure to DNA-AgC fluorescence and photophysics are largely empirical. Here, we employ 193 nm activated electron photodetachment (a-EPD) mass spectrometry as a hybrid MS³ approach to gain structural insight into these nanoscale chromophores. Two DNA-AgC systems are investigated with a 20 nt single-stranded DNA (ssDNA) and a 28 nt hybrid hairpin/single-stranded DNA (hpDNA). Both oligonucleotides template Ag₁₀ clusters, but the two complexes are distinct chromophores: the former has a violet absorption at 400 nm with no observable emission, while the latter has a blue-green absorption at 490 nm with strong green emission at 550 nm. Via identification of both apo and holo (AgC-containing) sequence ions generated upon a-EPD and mapping areas of sequence dropout, specific DNA regions that encapsulate the AgC are assigned and attributed to the coordination with the DNA nucleobases. These a-EPD footprints are distinct for the two complexes. The ssDNA contacts the cluster via four nucleobases (CCTT) in the central region of the strand, whereas the hpDNA coordinates the cluster via 13 nucleobases (TTCCCGCCTTTTG) in the double-stranded region of the hairpin. This difference is consistent with prior X-ray scattering spectra and suggests that the clusters can adapt to different DNA hosts. More importantly, the a-EPD footprints directly identify the nucleobases that are in direct contact with the AgC. As these contacting nucleobases can tune the electronic structures of the Ag core and protect the AgC from collisional quenching in solution, understanding the DNA-silver contacts within these complexes will facilitate future biosensor designs.

Silver-Mediated Homochiral and Heterochiral α-dC/β-dC Base Pairs: Synthesis of α-dC through Glycosylation and Impact of Consecutive, Isolated, and Multiple Metal Ion Pairs on DNA Stability

Isolated and consecutive heterochiral α-dC- base pairs have been incorporated into 12-mer oligonucleotide duplexes at various positions, thereby replacing Watson-Crick pairs. To this end, a new synthesis of the α-d anomer of dC has been developed, and oligonucleotides containing α-dC residues have been synthesized. Silver-mediated base pairs were formed upon the addition of silver ions. Furthermore, we have established that heterochiral α-dC-dC base pairs can approach the stability of a Watson-Crick pair, whereas homochiral dC-dC pairs are significantly less stable. A positional change of the silver-mediated base pairs affects the duplex stability and reveals the nearest-neighbor influence. When the number of silver ions was equivalent to the number of duplex base pairs (12), non-melting silver-rich complexes were formed. Structural changes have been supported by circular dichroism (CD) spectra, which showed that the B-DNA structure was maintained whilst the silver ion concentration was low. At high silver ion concentration, silver-rich complexes displaying different CD spectra were formed.

Concerted dynamics of metallo-base pairs in an A/B-form helical transition

Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-HgII-T metallo base pairs separated by six canonical base pairs. NMR experiments reveal a 3:1 ratio of well-resolved structures in dynamic equilibrium. The major species contains two (N3)T-HgII-(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-HgII-(N4)C base pairs and greater A-form characteristics. Ten-fold different 1J coupling constants (15N,199Hg) are observed for (N3)C-HgII (114 Hz) versus (N4)C-HgII (1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-HgII-T base pairs are coupled to a global conformational exchange between the helices. These observations inspired the design of a repetitive DNA sequence capable of undergoing a global B-to-A-form helical transition upon adding HgII, demonstrating that C-HgII-T has unique switching potential in DNA-based materials and devices.

3-Fluoro-2-mercuri-6-methylaniline Nucleotide as a High-Affinity Nucleobase-Specific Hybridization Probe

A 3-fluoro-6-methylaniline nucleoside was synthesized and incorporated into an oligonucleotide, and its ability to form mercury-mediated base pairs was studied. UV melting experiments revealed increased duplex stability with thymine, guanine, and cytosine opposite to the probe and a clear nucleobase-specific binding preference (T > G > C > A). Moreover, the 3-fluoro group was utilized as a spin label that showed distinct ¹⁹F NMR resonance shifts depending on the complementary nucleobase, providing more detailed information on Hg(II)-mediated base pairing.

Anomeric 5-Aza-7-deaza-2'-deoxyguanosines in Silver-Ion-Mediated Homo and Hybrid Base Pairs: Impact of Mismatch Structure, Helical Environment, and Nucleobase Substituents on DNA Stability

Nucleoside configuration (α-d vs. β-d), nucleobase substituents, and the helical DNA environment of silver-mediated 5-aza-7-deazaguanine-cytosine base pairs have a strong impact on DNA stability. This has been demonstrated by investigations on oligonucleotide duplexes with silver-mediated base pairs of α-d and β-d anomeric 5-aza-7-deaza-2'-deoxyguanosines and anomeric 2'-deoxycytidines incorporated in 12-mer duplexes. To this end, a new synthetic protocol has been developed to access the pure anomers of 5-aza-7-deaza-2'-deoxyguanosine by glycosylation of either the protected nucleobase or its salt followed by separation of the glycosylation products by crystallization and chromatography. Thermal stability measurements were performed on duplexes with α-d/α-d and β-d/β-d homo base pairs or α-d/β-d and β-d/α-d hybrid pairs within two sequence environments, positions 6 or 7, of oligonucleotide duplexes. The respective T_m stability increases observed after silver ion addition differ significantly. Homo base pairs with β-d/β-d or α-d/α-d nucleoside combinations are more stable than α-d/β-d hybrid base pairs. The positional switch of silver-ion-mediated base pairs has a significant impact on stability. Nucleobase substituents introduced at the 5-position of the dC site of silver-mediated base pairs affect base pair stability to a minor extent. Our investigation might lead to applications in the construction of bioinspired nanodevices, in DNA diagnostics, or metal-DNA hybrid materials.

Addressing the properties of "Metallo-DNA" with a Ag(i)-mediated supramolecular duplex

The silver-nucleoside complex [Ag(i)-(N3-cytidine)₂]⁺, 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA.

The silver-nucleoside complex [Ag(i)-(N3-cytidine)₂], 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA. A combination of complementary hydrogen-bonding, hydrophobic and argentophilic interactions drive the formation of a double-helix with a continuous silver core. Electrical measurements on 1 show that despite having Ag···Ag distances within <5% of the metallic radii, the material is electrically insulating. This is due to the electronic structure which features a filled valence band, an empty conduction band dominated by the ligand, and a band gap of 2.5 eV. Hence, as-prepared, such Ag(i)-DNA systems should not be considered molecular nanowires but, at best, proto-wires. The structural features seen in 1 are essentially retained in the corresponding organogel which exhibits thixotropic self-healing that can be attributed to the reversible nature of the intermolecular interactions. Photo-reduced samples of the gel exhibit luminescence confirming that these poly-cytidine sequences appropriately pre-configure silver ions for the formation of quantum-confined metal clusters in line with contemporary views on DNA-templated clusters. Microscopy data reveals the resulting metal cluster/particles are approximately spherical and crystalline with lattice spacing (111) similar to bulk Ag.

Atomic Structure of a Fluorescent Ag8 Cluster Templated by a Multistranded DNA Scaffold

Multinuclear silver clusters encapsulated by DNA exhibit size-tunable emission spectra and rich photophysics, but their atomic organization is poorly understood. Herein, we describe the structure of one such hybrid chromophore, a green-emitting Ag₈ cluster arranged in a Big Dipper-shape bound to the oligonucleotide A₂C₄. Three 3' cytosine metallo-base pairs stabilize a parallel A-form-like duplex with a 5' adenine-rich pocket, which binds a metallic, trapezoidal-shaped Ag₅ moiety via Ag-N bonds to endo- and exocyclic nitrogens of cytosine and adenine. The unique DNA configuration, constrained coordination environment, and templated Ag₈ cluster arrangement highlight the reciprocity between the silvers and DNA in adopting this structure. These first atomic details of a DNA-encapsulated Ag cluster fluorophore illuminate many aspects of biological assembly, nanoscience, and metal cluster photophysics.

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.

2,6-Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase

A C-nucleoside having 2,6-dimercuriphenol as the base moiety has been synthesized and incorporated into an oligonucleotide. NMR and UV melting experiments revealed the ability of this bifacial organometallic nucleobase surrogate to form stable dinuclear Hg^II -mediated base triples with adenine, cytosine, and thymine (or uracil) in solution as well as within a triple-helical oligonucleotide. A single Hg^II -mediated base triple between 2,6-dimercuriphenol and two thymines increased both Hoogsteen and Watson-Crick melting temperatures of a 15-mer pyrimidine⋅purine*pyrimidine triple helix by more than 10 °C relative to an unmodified triple helix of the same length. This novel binding mode could be exploited in targeting certain pathogenic nucleic acids as well as in DNA nanotechnology.

Supramolecular architectures in metal(II) (Cd/Zn) halide/nitrate complexes of cytosine/5-fluorocytosine

Three new metal(II)-cytosine (Cy)/5-fluorocytosine (5FC) complexes, namely bis(4-amino-1,2-dihydropyrimidin-2-one-κN³)diiodidocadmium(II) or bis(cytosine)diiodidocadmium(II), [CdI₂(C₄H₅N₃O)₂], (I), bis(4-amino-1,2-dihydropyrimidin-2-one-κN³)bis(nitrato-κ²O,O')cadmium(II) or bis(cytosine)bis(nitrato)cadmium(II), [Cd(NO₃)₂(C₄H₅N₃O)₂], (II), and (6-amino-5-fluoro-1,2-dihydropyrimidin-2-one-κN³)aquadibromidozinc(II)-6-amino-5-fluoro-1,2-dihydropyrimidin-2-one (1/1) or (6-amino-5-fluorocytosine)aquadibromidozinc(II)-4-amino-5-fluorocytosine (1/1), [ZnBr₂(C₄H₅FN₃O)(H₂O)]·C₄H₅FN₃O, (III), have been synthesized and characterized by single-crystal X-ray diffraction. In complex (I), the Cd^II ion is coordinated to two iodide ions and the endocyclic N atoms of the two cytosine molecules, leading to a distorted tetrahedral geometry. The structure is isotypic with [CdBr₂(C₄H₅N₃O)₂] [Muthiah et al. (2001). Acta Cryst. E57, m558-m560]. In compound (II), each of the two cytosine molecules coordinates to the Cd^II ion in a bidentate chelating mode via the endocyclic N atom and the O atom. Each of the two nitrate ions also coordinates in a bidentate chelating mode, forming a bicapped distorted octahedral geometry around cadmium. The typical interligand N-H...O hydrogen bond involving two cytosine molecules is also present. In compound (III), one zinc-coordinated 5FC ligand is cocrystallized with another uncoordinated 5FC molecule. The Zn^II atom coordinates to the N(1) atom (systematic numbering) of 5FC, displacing the proton to the N(3) position. This N(3)-H tautomer of 5FC mimics N(3)-protonated cytosine in forming a base pair (via three hydrogen bonds) with 5FC in the lattice, generating two fused R₂²(8) motifs. The distorted tetrahedral geometry around zinc is completed by two bromide ions and a water molecule. The coordinated and nonccordinated 5FCs are stacked over one another along the a-axis direction, forming the rungs of a ladder motif, whereas Zn-Br bonds and N-H...Br hydrogen bonds form the rails of the ladder. The coordinated water molecules bridge the two types of 5FC molecules via O-H...O hydrogen bonds. The cytosine molecules are coordinated directly to the metal ion in each of the complexes and are hydrogen bonded to the bromide, iodide or nitrate ions. In compound (III), the uncoordinated 5FC molecule pairs with the coordinated 5FC ligand through three hydrogen bonds. The crystal structures are further stabilized by N-H...O, N-H...N, O-H...O, N-H...I and N-H...Br hydrogen bonds, and stacking interactions.

5-Aza-7-deaza-2'-deoxyguanosine and 2'-Deoxycytidine Form Programmable Silver-Mediated Base Pairs with Metal Ions in the Core of the DNA Double Helix

5-Aza-7-deaza-2'-deoxyguanosine (dZ) forms a silver-mediated base pair with dC. The metal ion pair represents a mimic of the H-bonded Watson-Crick dG-dC pair. The modified nucleoside displays a similar shape as the parent 2'-deoxyguanosine from which it can be constructed by transposition of nitrogen-7 to the bridgehead position-5. It lacks the major groove binding site as the positional change moves the dG- acceptor position from nitrogen-7 to nitrogen-1. As a shape mimic of dG, it fits nicely in the DNA double helix. The purine-pyrimidine dZ-dC hetero pair shows a relationship to the pyrimidine-pyrimidine dC-dC homo base pair. The dZ-dC pair forms a mismatch in the absence of silver ions and matches after addition of metal ions. Base-pair formation was verified on self-complementary 6-mer duplexes and 12-mer DNA with random composition by UV-dependent T_m measurements. Modified silver-mediated and hydrogen-bonded canonical base pairs can coexist. The dZ-Ag⁺ -dC base pair is slightly less stable than the dG-dC pair, shows sequence dependence, and consumes one or two silver ions. These properties make the dZ-Ag⁺ -dC pair suitable for programmable incorporation of silver ions in DNA which cannot be achieved by canonical base pairs. If the silver ion content is higher than the total number of base pairs the duplexes turn into very stable structures in which all base pairs are considered to be in the silver-mediated pairing mode.