Models of Putative (AH)G(AH)G Nucleobase Quartets

Mixed guanine, adenine base quartets: possible roles of protons and metal ions in their stabilization

Structural variations of the well-known guanine quartet (G₄) motif in nucleic acid structures, namely substitution of two guanine bases (G) by two adenine (A) nucleobases in mutual trans positions, are discussed and studied by density functional theory (DFT) methods. This work was initiated by three findings, namely (1) that GA mismatches are compatible with complementary pairing patterns in duplex-DNA structures and can, in principle, be extended to quartet structures, (2) that GA pairs can come in several variations, including with a N1 protonated adeninium moiety (AH), and (3) that cross-linking of the major donor sites of purine nucleobases (N1 and N7) by transition metal ions of linear coordination geometries produces planar purine quartets, as demonstrated by some of us in the past. Here, possible structures of mixed AGAG quartets both in the presence of protons and alkali metal ions are discussed, and in particular, the existence of a putative four-purine, two-metal motif.

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.

The exocyclic amino group of adenine in PtII and PdII complexes: a critical comparison of the X-ray crystallographic structural data and gas phase calculations

A detailed computational (DFT level of theory) study regarding the nature of the exocyclic amino group, N6H₂, of the model nucleobase 9-methyladenine (9MeA) and its protonated (9MeAH⁺) and deprotonated forms (9MeA_-H), free and metal-complexed, has been conducted. The metals are Pt^II and Pd^II, bonded to nitrogen-containing co-ligands (NH₃, dien, bpy), with N1, N6, and N7 being the metal-binding sites, individually or in different combinations. The results obtained from gas phase calculations are critically compared with X-ray crystallography data, whenever possible. In the majority of cases, there is good qualitative agreement between calculated and experimentally determined C6-N6 bond lengths, but calculated values always show a trend to larger values, by 0.02-0.08 Å. Both methods indicate, with few exceptions, a high degree of double-bond character of C6-N6, consistent with an essentially sp²-hybridized N6 atom. The shortest values for C6-N6 distances in X-ray crystal structures are around 1.30 Å. Exceptions refer to cases in which DFT calculations suggest the existence of a hydrogen bond with N6H₂ acting as a H bond acceptor, hence a situation with N6 having undergone a substantial hybridization shift toward sp³. Nevertheless, even in these cases the C6-N6 bond (1.392 Å) is still halfway between a typical C-N single bond (1.48 Å) and a typical C=N double bond (1.28 Å). This scenario is, however, not borne out by X-ray crystallographic results, and is attributed to the absence of counter anions and solvent molecules in the calculated structures.

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.

Mixed adenine/guanine quartets with three trans-a2 Pt(II) (a=NH(3) or MeNH(2)) cross-links: linkage and rotational isomerism, base pairing, and loss of NH(3)

Of the numerous ways in which two adenine and two guanines (N9 positions blocked in each) can be cross-linked by three linear metal moieties such as trans-a2 Pt(II) (with a=NH3 or MeNH2 ) to produce open metalated purine quartets with exclusive metal coordination through N1 and N7 sites, one linkage isomer was studied in detail. The isomer trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)}2 ][(ClO4 )6 ]⋅3H2 O (1) (with 9-EtA=9-ethyladenine and 9-MeGH=9-methylguanine) was crystallized from water and found to adopt a flat Z-shape in the solid state as far as the trinuclear cation is concerned. In the presence of excess 9-MeGH, a meander-like construct, trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)2 }][(ClO4 )6 ]⋅[(9-MeGH)2 ]⋅7 H2 O (2) is formed, in which the two extra 9-MeGH nucleobases are hydrogen bonded to the two terminal platinated guanine ligands of 1. Compound 1, and likewise the analogous complex 1 a (with NH3 ligands only), undergo loss of an ammonia ligand and formation of NH4 (+) when dissolved in [D6 ]DMSO. From the analogy between the behavior of 1 and 1 a it is concluded that a NH3 ligand from the central Pt atom is lost. Addition of 1-methylcytosine (1-MeC) to such a DMSO solution reveals coordination of 1-MeC to the central Pt. In an analogous manner, 9-MeGH can coordinate to the central Pt in [D6 ]DMSO. It is proposed that the proton responsible for formation of NH4 (+) is from one of the exocyclic amino groups of the two adenine bases, and furthermore, that this process is accompanied by a conformational change of the cation from Z-form to U-form. DFT calculations confirm the proposed mechanism and shed light on possible pathways of this process. Calculations show that rotational isomerism is not kinetically hindered and that it would preferably occur previous to the displacement of NH3 by DMSO. This displacement is the most energetically costly step, but it is compensated by the proton transfer to NH3 and formation of U(-H(+) ) species, which exhibits an intramolecular hydrogen bond between the deprotonated N6H(-) of one adenine and the N6H2 group of the other adenine. Finally the question is examined, how metal cross-linking patterns in closed metallacyclic quartets containing two adenine and two guanine nucleobases influence the overall shape (square, rectangle, trapezoid) and the planarity of a metalated purine quartet.

Differential stabilization of adenine quartets by anions and cations

We have investigated the structures and stabilities of four different adenine quartets with alkali and halide ions in the gas phase and in water, using dispersion-corrected density functional theory at the BLYP-D/TZ2P level. First, we examine the empty quartets and how they interact with alkali cations and halide anions with formation of adenine quartet–ion complexes. Second, we examine the interaction in a stack, in which a planar adenine quartet interacts with a cation or anion in the periphery as well as in the center of the quartet. Interestingly, for the latter situation, we find that both cations and anions can stabilize a planar adenine quartet in a stack.

A ditopic ion-pair receptor based on stacked nucleobase quartets

Pass the salt, please! State-of-the-art computations indicate that the stacking complex of a guanine quartet and an adenine quartet (G(4)A(4)) can function as a potent ditopic receptor for NaCl in aqueous solution (see picture; Na(+), Cl(-) yellow, O red, N blue, C black, H white).

Unusual Dimeric Zn(II)-cytosine complexes: New models of the interaction of Zn(II) with DNA and RNA

Synthesis and crystal structure of two Zn(II) dimer complexes with 1-methylcytosine (1-MeC) are reported. In complex [Zn(2)Cl(4)(mu-1-MeC-O2,N3)(2)] (1), two 1-MeC ligands are bridging two ZnCl(2) moieties. In [Zn(2)(1-MeC-N3)(4)(mu-SO(4))(2)].2H(2)O (2), the sulfates act as bridging ligands and 1-MeC are linked via N3 to Zn(II) as terminal ligands. Both complexes represent the first examples of Zn(II)-pyrimidine dimers. The potential biological significance of 1 and 2 is discussed.

Four-Stranded Coordination Helices Containing Silver−Adenine (Purine) Metallaquartets

This Communication describes structures of a family of silver-adenine (purine) metallaquartets that occur in a four-stranded coordination motif, bearing a close resemblance to nucleic acid quadruplexes. Using modified purine frameworks, it is further demonstrated that subtle variations in nucleobase heterocycle are tolerable and a metallaquartet is obtained irrespective of the substitution, thus suggesting a high-propensity silver-adenine interaction to achieve quartet structures. All of the solid-state structures studied were orthorhombic, belonging to the Fdd2 space group.

Molecular recognition of adeninium cations on anionic metal-oxalato frameworks: an experimental and theoretical analysis

Reactions of adenine with water-soluble oxalato complexes at acidic pH give the compounds (1H,9H-ade)2[Cu(ox)2(H2O)] (1) [H2ade=adeninium cation (1+), ox=oxalato ligand (2-)] and (3H,7H-ade)2[M(ox)2(H2O)2].2H2O [M(II)=Co (2), Zn (3)]. The X-ray single crystal analyses show that the supramolecular architecture of all compounds is built up of anionic sheets of metal-oxalato-water complexes and ribbons of cationic nucleobases among them to afford lamellar inorganic-organic hybrid materials. The molecular recognition process between the organic and the inorganic frameworks determines the isolated tautomeric form of the adeninium cation found in the crystal structures: the canonical 1H,9H for compound 1, and the first solid-state characterized 3H,7H-adeninium tautomer for compounds 2 and 3. Density functional theory calculations have been performed to study the stability of the protonated nucleobase forms and their hydrogen-bonded associations by comparing experimental and theoretical results.