Molecular Recognition of a Three-Way DNA Junction by a Metallosupramolecular Helicate

Y-DNA melting: a short tale of three scales

We address some aspects of the thermal denaturation of Y-DNA-the three-way junction-on three different length scales: the effect of chain concentration on the extrinsic melting behaviour within a simple kinetic approach, the exponent of the loop entropy in intrinsic melting as it appears in statistical mechanics models, and the microscopics of stacking within the junction from molecular dynamics simulations. Our results suggest that a multiscale approach is needed to properly describe the denaturation properties of these systems. We propose experiments which can also shed light on the melting of short and long duplex DNA sequences.

Ruthenium polypyridyl complexes and their modes of interaction with DNA: is there a correlation between these interactions and the antitumor activity of the compounds?

Various interaction modes between a group of six ruthenium polypyridyl complexes and DNA have been studied using a number of spectroscopic techniques. Five mononuclear species were selected with formula [Ru(tpy)L₁L₂]⁽²⁻ⁿ⁾⁺, and one closely related dinuclear cation of formula [{Ru(apy)(tpy)}₂{μ-H₂N(CH₂)₆NH₂}]⁴⁺. The ligand tpy is 2,2′:6′,2″-terpyridine and the ligand L₁ is a bidentate ligand, namely, apy (2,2′-azobispyridine), 2-phenylazopyridine, or 2-phenylpyridinylmethylene amine. The ligand L₂ is a labile monodentate ligand, being Cl⁻, H₂O, or CH₃CN. All six species containing a labile L₂ were found to be able to coordinate to the DNA model base 9-ethylguanine by ¹H NMR and mass spectrometry. The dinuclear cationic species, which has no positions available for coordination to a DNA base, was studied for comparison purposes. The interactions between a selection of four representative complexes and calf-thymus DNA were studied by circular and linear dichroism. To explore a possible relation between DNA-binding ability and toxicity, all compounds were screened for anticancer activity in a variety of cancer cell lines, showing in some cases an activity which is comparable to that of cisplatin. Comparison of the details of the compound structures, their DNA binding, and their toxicity allows the exploration of structure–activity relationships that might be used to guide optimization of the activity of agents of this class of compounds.

DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes

In this paper, we review recent DNA-binding agents that are expected to influence the field of DNA-targeting. We restrict ourselves to binders for which the three-dimensional structure in complex with DNA or RNA has been determined by X-ray crystallography or NMR. Furthermore, we primarily focus on unprecedented ways of targeting peculiar DNA structures, such as junctions, quadruplexes, and duplex DNAs different from the B-form. Classical binding modes of small molecular weight compounds to DNA, i.e. groove binding, intercalation and covalent addition are discussed in those cases where the structures represent a novelty. In addition, we review 3D structures of triple-stranded DNA, of the so-called Peptide Nucleic Acids (PNAs), which are oligonucleotide bases linked by a polypeptide backbone, and of aptamers, which are DNA or RNA receptors that are designed combinatorially. A discussion on perspectives in the field of DNA-targeting and on sequence recognition is also provided.

Chiral metallo-supramolecular complexes selectively recognize human telomeric G-quadruplex DNA

Here, we report the first example that one enantiomer of a supramolecular cylinder can selectively stabilize human telomeric G-quadruplex DNA. The P-enantiomer of this cylinder has a strong preference for G-quadruplex over duplex DNA and, in the presence of sodium, can convert G-quadruplexes from an antiparallel to a hybrid structure. The compound's chiral selectivity and its ability to discriminate quadruplex DNA have been studied by DNA melting, circular dichroism, gel electrophoresis, fluorescence spectroscopy and S1 nuclease cleavage. The chiral supramolecular complex has both small molecular chemical features and the large size of a zinc-finger-like DNA-binding motif. The complex is also convenient to synthesize and separate enantiomers. These results provide new insights into the development of chiral anticancer agents for targeting G-quadruplex DNA.

Tris[μ-2,2'-(azinodimethylidyne)diphenolato-κO,N:N',O']diiron(III) tetra-hydro-furan tetra-solvate

In the title binuclear iron(III) complex, [Fe(2)(C(14)H(10)N(2)O(2))(3)]·4C(4)H(8)O or [Fe(2)(salda)(3)]·4THF [H(2)salda = 2,2'-(azinidimethyl-ene)diphenolate and THF is tetra-hydro-furan], the ligand possesses a rotationally flexible single N-N bond. Three dinucleating O,N:N',O'-donor ligands provide three diazine (=N-N=) bridges between the metal ions, yielding a binuclear triple helicate structure with crystallographic C(2) symmetry, the rotation axis bis-ecting one N-N bond.

DNA binding of dinuclear iron(II) metallosupramolecular cylinders. DNA unwinding and sequence preference

[Fe₂L₃]⁴⁺ (L = C₂₅H₂₀N₄) is a synthetic tetracationic supramolecular cylinder (with a triple helical architecture) that targets the major groove of DNA and can bind to DNA Y-shaped junctions. To explore the DNA-binding mode of [Fe₂L₃]⁴⁺, we examine herein the interactions of pure enantiomers of this cylinder with DNA by biochemical and molecular biology methods. The results have revealed that, in addition to the previously reported bending of DNA, the enantiomers extensively unwind DNA, with the M enantiomer being the more efficient at unwinding, and exhibit preferential binding to regular alternating purine–pyrimidine sequences, with the M enantiomer showing a greater preference. Also, interestingly, the DNA binding of bulky cylinders [Fe₂(L-CF₃)₃]⁴⁺ and [Fe₂(L-Ph)₃]⁴⁺ results in no DNA unwinding and also no sequence preference of their DNA binding was observed. The observation of sequence-preference in the binding of these supramolecular cylinders suggests that a concept based on the use of metallosupramolecular cylinders might result in molecular designs that recognize the genetic code in a sequence-dependent manner with a potential ability to affect the processing of the genetic code.

Towards a molecular dynamics consensus view of B-DNA flexibility

We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility.

New trends for metal complexes with anticancer activity

Medicinal inorganic chemistry can exploit the unique properties of metal ions for the design of new drugs. This has, for instance, led to the clinical application of chemotherapeutic agents for cancer treatment, such as cisplatin. The use of cisplatin is, however, severely limited by its toxic side-effects. This has spurred chemists to employ different strategies in the development of new metal-based anticancer agents with different mechanisms of action. Recent trends in the field are discussed in this review. These include the more selective delivery and/or activation of cisplatin-related prodrugs and the discovery of new non-covalent interactions with the classical target, DNA. The use of the metal as scaffold rather than reactive centre and the departure from the cisplatin paradigm of activity towards a more targeted, cancer cell-specific approach, a major trend, are discussed as well. All this, together with the observation that some of the new drugs are organometallic complexes, illustrates that exciting times lie ahead for those interested in 'metals in medicine'.

Click-connected ligand scaffolds: macrocyclic chelates for asymmetric hydrogenation

Click chemistry is used to construct ligand scaffolds for a series of chiral diphosphites. Enantioselectivity as high as 97% ee is obtained using these click ligands in rhodium-catalyzed asymmetric hydrogenation. Control experiments and spectroscopic data suggest that a 16-membered P,P-macrocyclic Rh(I) chelate is formed.

Metallo-intercalators and metallo-insertors

Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In particular, the study of transition metal complexes that bind DNA with specificity has been a burgeoning field. This growth has been due in large part to the useful properties of metal complexes, which possess a wide array of photophysical attributes and allow for the modular assembly of an ensemble of recognition elements. Here we review recent experiments in our laboratory aimed at the design and study of octahedral metal complexes that bind DNA non-covalently and target reactions to specific sites. Emphasis is placed both on the variety of methods employed to confer site-specificity and upon the many applications for these complexes. Particular attention is given to the family of complexes recently designed that target single base mismatches in duplex DNA through metallo-insertion.

Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics

Guanine-rich DNA sequences can form G-quadruplexes stabilized by stacked G–G–G–G tetrads in monovalent cation-containing solution. The length and number of individual G-tracts and the length and sequence context of linker residues define the diverse topologies adopted by G-quadruplexes. The review highlights recent solution NMR-based G-quadruplex structures formed by the four-repeat human telomere in K⁺ solution and the guanine-rich strands of c-myc, c-kit and variant bcl-2 oncogenic promoters, as well as a bimolecular G-quadruplex that targets HIV-1 integrase. Such structure determinations have helped to identify unanticipated scaffolds such as interlocked G-quadruplexes, as well as novel topologies represented by double-chain-reversal and V-shaped loops, triads, mixed tetrads, adenine-mediated pentads and hexads and snap-back G-tetrad alignments. The review also highlights the recent identification of guanine-rich sequences positioned adjacent to translation start sites in 5′-untranslated regions (5′-UTRs) of RNA oncogenic sequences. The activity of the enzyme telomerase, which maintains telomere length, can be negatively regulated through G-quadruplex formation at telomeric ends. The review evaluates progress related to ongoing efforts to identify small molecule drugs that bind and stabilize distinct G-quadruplex scaffolds associated with telomeric and oncogenic sequences, and outlines progress towards identifying recognition principles based on several X-ray-based structures of ligand–G-quadruplex complexes.

A DNA-binding copper(I) metallosupramolecular cylinder that acts as an artificial nuclease

The DNA binding of a dicationic pyridylimine-based dicopper(I) metallosupramolecular cylinder is reported together with its ability to act as an artificial nuclease. The cylinder binds strongly to DNA; more strongly than the spherical dication [Ru(phen)(3)](2+) (phen=1,10-phenanthroline), but more weakly than the corresponding tetracationic cylinders. DNA coiling effects are not observed with this dication, in contrast to the situation with the previously reported tetracationic cylinder involving a similar ligand. Linear dichroism (LD) data suggests that the dicopper cylinder binds in a different orientation from that of the tetracationic iron cylinder. Furthermore, the dicopper cylinder shows DNA-cleavage activity in the presence of peroxide. Of particular note is that the cylinder displays a marked and unusual ability to cleave both DNA strands at the same site, probably reflecting its dinuclear nature and possibly its mode of binding to the DNA.

Recognition of DNA three-way junctions by metallosupramolecular cylinders: gel electrophoresis studies

The interaction of metallosupramolecular cylinders with DNA three-way junctions has been studied by gel electrophoresis. A recent X-ray crystal structure of a palindromic oligonucleotide forming part of a complex with such a cylinder revealed binding at the heart of a three-way junction structure. The studies reported herein confirm that this is not solely an artefact of crystallisation and reveal that this is a potentially very powerful new mode of DNA recognition with wide scope. The cylinders are much more effective at stabilizing three-way junctions than simple magnesium di-cations or organic or metallo-organic tetra-cations, with the M cylinder enantiomer being more effective than P. The recognition is not restricted to three-way junctions formed from palindromic DNA with a central AT step at the junction; non-palindromic three-way junctions and those with GC steps are also stabilised. The cylinder is also revealed to stabilise other Y-shaped junctions, such as that formed at a fraying point in duplex DNA (for example, a replication fork), and other DNA three-way junction structures, such as those containing unpaired nucleotides, perhaps by opening up this structure to access the central cavity.

Design and Non-Covalent DNA Binding of Platinum(II) Metallacalix[4]arenes

A set of cyclic tetranuclear complexes of the metallacalix[4]arene type with formula [{Pt(en)(L)}(4)](4+) (en=ethylenediamine; 2: LH=5-chloro-2-hydroxypyrimidine (5-Cl-Hpymo); 3: LH=5-bromo-2-hydroxypyrimidine (5-Br-Hpymo); 4: LH=5-iodo-2-hydroxypyrimidine (5-I-Hpymo)) have been obtained from the reaction between cis-protected square-planar [Pt(en)(H(2)O)(2)](2+) metal entities and LH in aqueous media. Additionally, the binding properties of 2, 3, 4 and their congener [{Pt(en)(L)}(4)](4+) (1: LH=2-hydroxypyrimidine (Hpymo)) with calf thymus-DNA (ct-DNA) have been studied by using different techniques including circular and linear dichroism (CD and LD, respectively) and UV-visible absorbance spectroscopies, gel electrophoresis, fluorescence competitive-binding studies and atomic force microscopy (AFM). The results are consistent with significant non-covalent interactions taking place between the polynuclear cyclic species and ct-DNA. Moreover, gel electrophoresis, linear dichroism titrations and AFM images of ct-DNA with metallacalixarenes show ct-DNA coiling at low metallacalixarene concentrations and upon subsequent increments in metallacalixarene concentration ct-DNA can be seen to uncoil with concomitant formation of long and inflexible ct-DNA structures.

Supramolecular Chemistry in Water

Supramolecular chemistry in water is a constantly growing research area because noncovalent interactions in aqueous media are important for obtaining a better understanding and control of the major processes in nature. This Review offers an overview of recent advances in the area of water-soluble synthetic receptors as well as self-assembly and molecular recognition in water, through consideration of the functionalities that are used to increase the water solubility, as well as the supramolecular interactions and approaches used for effective recognition of a guest and self-assembly in water. The special features and applications of supramolecular entities in aqueous media are also described.

Diastereoselective Self-Assembly of Double-Stranded Helicates from Tröger's Base Derivatives

[structure: see text]. Several ligands based on the rigid, V-shaped structure of Tröger's base bearing 2,2'-bipyridine and 2-pyridylmethanimine moieties have been synthesized. These ligands undergo diastereoselective self-assembly to dinuclear double-stranded D2d-symmetric helicates upon coordination to copper(I) and silver(I) ions as elucidated by NMR techniques and ESI mass spectrometric methods.

Shape effects on the activity of synthetic major-groove binding ligands

In this work we present the results of a molecular simulation study of two different tetracationic bis iron(II) supramolecular cylinders interacting with DNA. One cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA; the second is a derivative of the first, with additional methyl groups attached so as to give a larger cylinder-radius. The simulations show that both cylinders bind strongly to the major groove of the DNA, and induce complex structural changes in A-T rich regions. Whereas the parent cylinder tends to bind along the major groove, the derivatised cylinder tends to twist so that only one end remains within the major groove. Both G-C rich and A-T rich binding sites for the derivatised cylinder are discussed.

Enantiomeric resolution of supramolecular helicates with different surface topographies

The enantiomeric resolution of an extended range of di-metallo supramolecular triple-helical molecules are reported. The ligands for all complexes are symmetric with two units containing an aryl group linked via an imine bond to a pyridine. Alkyl substituents have been attached in different positions on the ligand backbone. Previous work on the parent compound, whose molecular formula is [Fe(2)(C(25)H(20)N(4))(3)]Cl4, showed that it could be resolved into enantiomerically pure solutions using cellulose and 20 mM aqueous sodium chloride. In this work a range of mobile phases have been investigated to see if the separation and speed of elution could be increased and the amount of NaCl co-eluted with the compounds decreased. Methanol, ethanol and acetonitrile were considered, together with aqueous NaCl : organic mixtures. Effective separation was most often achieved when using 90% acetonitrile : 10% 20 mM NaCl (aq) w/v, which gives scope for scaling up to incorporate the use of HPLC. The overall most efficient (i.e. fastest) separation was generally achieved where the cellulose column was packed with 20 mM NaCl (aq) and the column first eluted with 100% acetonitrile, then with 75% ethanol : 25% 20 mM NaCl (aq) until the M enantiomer had fully eluted and finally with 90% acetonitrile : 10% 20 mM NaCl (aq) until the P enantiomer had been collected. The sequence of eluents ensured minimum NaCl accompanying the enantiomers and minimum total solvent being required to elute the enantiomers, especially the second one, from the column. No helicate with a methyl group on the imine bond could be resolved and methyl groups on the pyridine rings also have an adverse effect on resolution.

Metal-based anticancer drugs: From a past anchored in platinum chemistry to a post-genomic future of diverse chemistry and biology

The field of metal-based anticancer drugs was initiated by cisplatin, one of the leading agents in clinical use. Cisplatin acts by binding to DNA and forming 1,2 intrastrand cross-links. Its importance is reflected by the fact that it is estimated that 50-70 % of cancer patients are treated with a platinum drug [7]. For some time, molecular designs in the metallo-drug field remained obdurately anchored in cis-diamine platinum(II) chemistry, but now the field is evolving rapidly with a variety of alternate and very diverse designs being explored. These designs give rise to new spectra of activity and potency and can circumvent cisplatin resistance. This critical review considers the existing clinical platinum drugs, and those currently in commercial development, alongside the new designs including ruthenium anticancer and antimetastatic drugs in clinical trials, polynuclear drugs, organometallic drugs, titanium and gallium drugs, and emerging supramolecular metallo-drugs that act on DNA by noncovalent interactions. The rapid evolution of the field is being informed by post-genomic knowledge and approaches, and further dramatic step-change breakthroughs can be expected as a result; harnessing this knowledge and responding to and taking advantage of this new environment requires integration of chemistry and biology research.

Synthetic metallomolecules as agents for the control of DNA structure

This tutorial review summarises B-DNA structure and metallomolecule binding modes and illustrates some DNA structures induced by molecules containing metallic cations. The effects of aquated metal ions, cobalt amines, ruthenium octahedral metal complexes, metallohelicates and platinum complexes such as cis-platin are discussed alongside the techniques of NMR, X-ray crystallography, gel electrophoresis, circular dichroism, linear dichroism and molecular dynamics. The review will be of interest to people interested in both DNA structure and roles of metallomolecules in biological systems.

Supramolecular DNA recognition

Non-covalent DNA-recognition by synthetic agents is surveyed in this tutorial review, and contrasted with biomolecular DNA-recognition. The principles and forces involved in DNA recognition are similar to those seen elsewhere in the wider field of supramolecular chemistry, although the size, surface dimensions and nature of DNA introduce new possibilities and challenges. Recent discoveries of new binding motifs, and new biological structural and genomic information from bioscience, are affording new opportunities for supramolecular chemistry, where shape, fit and orientation play such an important role.

Equilibrium shift by target DNA substrates for determination of DNA binding ligands

An equilibrium containing the thiol derivative of Hoechst33258 (Ht-SH), glutathione (G-SH), and the corresponding homo and hetero disulfides was shifted by the addition of the duplex DNA. It was shown from the analysis of the components that the hetero disulfide Ht-SS-G increased by binding with the DNA (CA14) with an A(3)T(3) binding motif for the structure of Hoechst33258, and that the different equilibrium shift was observed in the presence of CT14 with no A(3)T(3) binding motif.

DNA architecture: from G to Z

G-quadruplexes and Z-DNA are two important non-B forms of DNA architecture. Results on novel structural elements, folding and unfolding kinetics, and interactions with small molecules and proteins have been reported recently for these forms. These results will enhance our understanding of the biology of these structures and provide a platform for drug design.