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.     

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove

In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.     

Modular Synthesis and Dynamics of a Variety of Donor–Acceptor Interlocked Compounds Prepared by Click Chemistry

A series of donor–acceptor [2]‐, [3]‐, and [4]rotaxanes and self‐complexes ([1]rotaxanes) have been synthesized by a threading‐followed‐by‐stoppering approach, in which the precursor pseudorotaxanes are fixed by using Cu^I‐catalyzed Huisgen 1,3‐dipolar cycloaddition to attach the required stoppers. This alternative approach to forming rotaxanes of the donor–acceptor type, in which the donor is a 1,5‐dioxynaphthalene unit and the acceptor is the tetracationic cyclophane cyclobis(paraquat‐p‐phenylene), proceeds with enhanced yields relative to the tried and tested synthetic strategies, which involve the clipping of the cyclophane around a preformed dumbbell containing π‐electron‐donating recognition sites. The new synthetic approach is amenable to application to highly convergent sequences. To extend the scope of this reaction, we constructed [2]rotaxanes in which one of the phenylene rings of the tetracationic cyclophane is perfluorinated, a feature which significantly weakens its association with π‐electron‐rich guests. The activation barrier for the shuttling of the cyclophane over a spacer containing two triazole rings was determined to be (15.5±0.1) kcal mol^?1 for a degenerate two‐station [2]rotaxane, a value similar to that previously measured for analogous degenerate compounds containing aromatic or ethylene glycol spacers. The triazole rings do not seem to perturb the shuttling process significantly; this property bodes well for their future incorporation into bistable molecular switches.     

Interaction of dinuclear ruthenium(II) supramolecular cylinders with DNA: sequence-specific binding, unwinding, and photocleavage

Metallosupramolecular chemistry was used to design a new class of synthetic agents, namely, tetracationic supramolecular cylinders, that bind strongly and noncovalently in the major groove of DNA. To gain additional information on interactions of the cylinders with DNA we explored DNA unwinding and sequence-specific binding properties, as well as DNA photonuclease activity of ruthenium(II) metallosupramolecular cylinder [Ru(2)L(3)](4+), where L is a bis-pyridylimine ligand. We found that [Ru(2)L(3)](4+) unwinds negatively supercoiled plasmid DNA and exhibits binding preference to regular alternating purine-pyrimidine sequences in a similar way to the [Fe(2)L(3)](4+) analogue. Photocleavage studies showed that, unlike [Fe(2)L(3)](4+), [Ru(2)L(3)](4+) induces single-strand breaks on irradiation by visible and UVA light and cleaves DNA mainly at guanine residues contained preferentially in regularly alternating purine-pyrimidine nucleotides. As [Ru(2)L(3)](4+) binds and cleaves DNA in a sequence-dependent manner, it may provide a useful tool for basic and applied biology, such as for controlled manipulation of the genome.     

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.     

Interactions of cationic porphyrins with double-stranded oligodeoxynucleotides: a study by electrospray ionisation mass spectrometry

Electrospray ionisation mass spectrometry (ESI-MS), electrospray ionisation tandem mass spectrometry (ESI-MS/MS) and Ultraviolet-visible (UV-vis) spectroscopy were used to investigate the non-covalent interactions between small oligonucleotide duplexes with the GC motif and a group of cationic meso(N-methylpyridynium-4-yl)porphyrins (four free bases with one to four positive charges, and the zinc complex of the tetracationic free base).The results obtained point to outside binding of the porphyrins, with the binding strength increasing with the number of positive charges. Fragmentations involving losses from both chains were observed for the porphyrins with N-methylpyridinium-4-yl groups in opposite meso positions.     

From Packed “Sandwich” to “Russian Doll”: Assembly by Charge‐Transfer Interactions in Cucurbit[10]uril

As the host possessing the largest cavity in the cucurbit[n]uril (CB[n]) family, CB[10] has previously displayed unusual recognition and assembly properties with guests but much remains to be explored. Herein, we present the recognition properties of CB[10] toward a series of bipyridinium guests including the tetracationic cyclophane known as blue box along with electron‐rich guests and detail the influence of encapsulation on the charge‐transfer interactions between guests. For the mono‐bipyridinium guest (methylviologen, MV ²⁺), CB[10] not only forms 1:1 and 1:2 inclusion complexes, but also enhances the charge‐transfer interactions between methylviologen and dihydroxynaphthalene ( HN ) by mainly forming the 1:2:1 packed “sandwich” complex (CB[10] ? 2 MV ²⁺ ?HN ). For guest 1 with two bipyridinium units, an interesting conformational switching from linear to “U” shape is observed by adding catechol to the solution of CB[10] and the guest. For the tetracationic cyclophane‐blue box, CB[10] forms a stable 1:1 inclusion complex; the two bipyridinium units tilt inside the cavity of CB[10] according to the X‐ray crystal structure. Finally, a supramolecular “Russian doll” was built up by threading a guest through the cavities of both blue box and CB[10].     

Ruthenium(II) arene complexes with oligocationic triarylphosphine ligands: Synthesis, DNA interactions and in vitro properties

The synthesis, DNA binding properties and cytotoxicity of a series of Ru(II)-arene complexes containing oligocationic ammonium-functionalized triarylphosphines, of the type Ru(p-cymene)Cl₂(L) (L = oligocationic phosphine), are reported. The complexes are highly charged (the overall charge states being +3 and +6) and circular dichroism spectroscopy and gel electrophoresis studies indicate that the compounds interact strongly with DNA via electrostatic interactions. Despite forming strong interactions with DNA, the complexes exhibit only modest cytotoxicities on the human ovarian cancer cell lines A2780 and A2780cisR.     

Minor groove binding of a novel tetracationic diviologen

Novel tetracationic diviologen compounds of the general formula CH3(CH2)nV2+(CH2)6V2+(CH2)nCH3 (where V2+ = 4,4'-bipyridinium and n = 5 or 11) were investigated as electrochemical reporters of DNA duplex formation. These compounds bind to both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) when the DNA is either present in solution or immobilized at electrode surfaces. Binding to thiolated ssDNA and dsDNA immobilized at Au electrodes was characterized using the electrochemical response for the reduction of the V2+ state to the V+ (viologen radical cation) state. An analysis of the charge for this reduction provided isotherms and binding constants for binding of these diviologens to both forms of immobilized DNA. Saturation of the binding is achieved at solution concentrations near 20 microM. For both the n = 5 and 11 diviologens, binding to ssDNA is driven by electrostatic charge neutralization. For the n = 11 case, the binding is cooperative. In the presence of dsDNA, the n = 11 diviologen exhibits a unique reduction potential for the V2+/+ redox couple that is shifted approximately 100 mV negative of that in the presence of ssDNA. This new electrochemical signature is attributed to the reduction of viologen groups bound in the minor groove of the DNA duplex. For dsDNA in solution, an increase in the thermal denaturation temperature (Tm) from 60 to 66 degrees C as a function of the n = 11 diviologen concentration confirmed its interaction with the duplex. Circular dichroism (CD) spectroscopy also was used to investigate the binding of both the V2+ and V+ redox states of the n = 11 diviologen to dsDNA in solution. For the V+ state, a CD signal was observed that is consistent with the presence of face-to-face pi dimers of the viologen groups. This unambiguously demonstrates the binding of this redox state of the diviologen in the dsDNA minor groove and the formation of such dimers in the minor groove.     

Incorporation of a Non‐Natural Arginine Analogue into a Cyclic Peptide Leads to Formation of Positively Charged Nanofibers Capable of Gene Transfection

Functionalization of the tetracationic cyclic peptide (Ka)₄ with a single guanidiniocarbonyl pyrrole (GCP) moiety, a weakly basic but highly efficient arginine analogue, completely alters the self‐assembly properties of the peptide. In contrast to the nonfunctionalized peptide 2 , which does not self‐assemble, GCP‐containing peptide 1 forms cationic nanofibers of micrometer length. These aggregates are efficient gene transfection vectors. DNA binds to their cationic surface and is efficiently delivered into cells.     

Dimeric and trimeric tetrathiafulvalenes with strong intramolecular interactions in the oxidized states

New dimeric and trimeric TTF derivatives with methylenedithio spacers (1a,b, 2a, and 2b) have been synthesized. X-ray structure analysis revealed that TTF units of the dimer 1b adopted distorted face-to-face overlapping arrangement both in intra- and intermolecular stacking. Cyclic voltammetric study indicated that trimeric 2a was in favor of taking di- and tetracationic states, while the dimeric 1a was in favor of taking a monocation. The absorption spectroscopic study suggested an existence of the strong face-to-face interaction particularly in di-, tri-, and tetracationic state of the trimeric TTF derivatives.     

Controlling electron transfer in donor-bridge-acceptor molecules using cross-conjugated bridges

Photoinitiated charge separation (CS) and recombination (CR) in a series of donor-bridge-acceptor (D-B-A) molecules with cross-conjugated, linearly conjugated, and saturated bridges have been compared and contrasted using time-resolved spectroscopy. The photoexcited charge transfer state of 3,5-dimethyl-4-(9-anthracenyl)julolidine (DMJ-An) is the donor, and naphthalene-1,8:4,5-bis(dicarboximide) (NI) is the acceptor in all cases, along with 1,1-diphenylethene, trans-stilbene, diphenylmethane, and xanthone bridges. Photoinitiated CS through the cross-conjugated 1,1-diphenylethene bridge is about 30 times slower than through its linearly conjugated trans-stilbene counterpart and is comparable to that observed through the diphenylmethane bridge. This result implies that cross-conjugation strongly decreases the π orbital contribution to the donor-acceptor electronic coupling so that electron transfer most likely uses the bridge σ system as its primary CS pathway. In contrast, the CS rate through the cross-conjugated xanthone bridge is comparable to that observed through the linearly conjugated trans-stilbene bridge. Molecular conductance calculations on these bridges show that cross-conjugation results in quantum interference effects that greatly alter the through-bridge donor-acceptor electronic coupling as a function of charge injection energy. These calculations display trends that agree well with the observed trends in the electron transfer rates.     

Anomalous NMR behavior of meso compounds with remote stereogenic centers on addition of chiral shift reagent or chiral solvating agent

A problem has arisen in using chiral shift reagents (CSR) and chiral solvating agents (CSA) to determine meso and racemic forms of diastereoisomers in which the stereogenic centers of the molecules are separated by achiral spacers. It is found that NMR signals of both meso and racemic forms of diastereoisomers may exhibit doubling on addition of CSR/CSA, which means that unequivocal assignments cannot be made without characterizing the effects for separate meso and racemic forms; this is particularly important for additions of CSR/CSA at relatively low concentrations, which always result in the splitting of some NMR signals of diastereoisomers. The phenomenon is demonstrated in the (31)P NMR spectra of meso and racemic forms of three spermine-bridged gem-disubstituted cyclotriphosphazatrienes, 1a-c, and compared with analogous achiral molecules, the per-substituted spermine-bridged cyclotriphosphazatrienes 2a-d. As expected, only one set of (31)P NMR signals was observed for the achiral compounds 2a-d, even on addition of CSA. Two sets of (31)P NMR ABX multiplets corresponding to meso and racemic diastereoisomers were observed for compounds 1a-c; on addition of CSA, the signals of at least one of the multiplets for each compound separated into more than the expected groups of three lines with an intensity distribution of 2:1:1. To understand this phenomenon, the meso and racemic forms of 1a and 1b and the meso form of 1c have been separated and characterized by X-ray crystallography. On addition of CSA to the racemic forms of 1a and 1b, the (31)P NMR spectrum shows the expected doubling of signals, but, unexpectedly, the same is observed for each of the meso forms of 1a-c. Analogous results using both CSA and CSR have been obtained for the meso and racemic forms of the diastereoisomeric piperazine-bridged macrocyclic-phosphazene compound, 3, whereas no effect was observed for the two meso forms of the doubly bridged macrocyclic-phosphazene compound 4. The phenomenon of doubling of the (31)P NMR signals of the meso form of singly bridged cyclotriphosphazatrienes, 1a-c and 3, is explained by consideration of the equilibrium in solution of independent complexation of a chiral ligand with molecules that have two chiral cyclophosphazene moieties separated by an achiral spacer group. The results show that the stereogenicity of such diastereoisomeric molecules in solution cannot be characterized unequivocally by NMR measurements on addition of either CSR or CSA.     

Single-step electron transfer on the nanometer scale: ultra-fast charge shift in strongly coupled zinc porphyrin-gold porphyrin dyads

The synthesis, electrochemical properties, and photoinduced electron transfer processes of a series of three novel zinc(II)-gold(III) bisporphyrin dyads (ZnP--S--AuP(+)) are described. The systems studied consist of two trisaryl porphyrins connected directly in the meso position via an alkyne unit to tert-(phenylenethynylene) or penta(phenylenethynylene) spacers. In these dyads, the estimated center to center interporphyrin separation distance varies from 32 to 45 A. The absorption, emission, and electrochemical data indicate that there are strong electronic interactions between the linked elements, thanks to the direct attachment of the spacer on the porphyrin ring through the alkyne unit. At room temperature in toluene, light excitation of the zinc porphyrin results in almost quantitative formation of the charge shifted state (.+)ZnP--S--AuP(.), whose lifetime is in the order of hundreds of picoseconds. In this solvent, the charge-separated state decays to the ground state through the intermediate population of the zinc porphyrin triplet excited state. Excitation of the gold porphyrin leads instead to rapid energy transfer to the triplet ZnP. In dichloromethane the charge shift reactions are even faster, with time constants down to 2 ps, and may be induced also by excitation of the gold porphyrin. In this latter solvent, the longest charge-shifted lifetime (tau=2.3 ns) was obtained with the penta-(phenylenethynylene) spacer. The charge shift reactions are discussed in terms of bridge-mediated super-exchange mechanisms as electron or hole transfer. These new bis-porphyrin arrays, with strong electronic coupling, represent interesting molecular systems in which extremely fast and efficient long-range photoinduced charge shift occurs over a long distance. The rate constants are two to three orders of magnitude larger than for corresponding ZnP--AuP(+) dyads linked via meso-phenyl groups to oligo-phenyleneethynylene spacers. This study demonstrates the critical impact of the attachment position of the spacer on the porphyrin on the electron transfer rate, and this strategy can represent a useful approach to develop molecular photonic devices for long-range charge separations.     

Modified expanded corrole-ferrocene conjugates: syntheses, structure and properties

Syntheses, characterization and properties of expanded corrole-ferrocene conjugates are reported. Ferrocenyl group are covalently linked to the corrole macrocycle through three different spacers groups. The synthetic strategy involved prior insertion of ferrocene with spacers to the dipyrromethane unit followed by a "3+2" acid-catalyzed oxidative coupling methodology. The optical and emission data of the expanded corrole-ferrocene conjugates depend on the nature and length of the spacer groups and the maximum effects are seen where ferrocene is directly linked to the meso carbon of macrocycle. The single crystal X-ray structure of two expanded corrole-ferrocene conjugates; [22]pentaphyrin (1.1.0.1.0) with different meso substituents, clearly reveal shortening of the C-C bond length linking the meso carbon and the aryl substituent containing the ferrocene moiety relative to meso aryl substituents without ferrocene. The results suggest that an electronic interaction between the two pi systems. Electrochemical data reveal harder oxidation for the ferrocene unit in the conjugates relative to free ferrocene; this suggests the electron donating nature of the ferrocene. The first corrole ring oxidation shows easier oxidation relative to 1 and the magnitude of shifts in potential is inversely proportional to the length of spacer. The molecular first hyperpolarizabilities (beta) measured at 1064 nm by HRS method vary in the range 20-32x10(-30) esu and imply that the beta values can be increased by enhancing the number of mobile electrons in the conjugation. The conjugates form 1:1 metal complex with the Rh(I) where rhodium is coordinated to one amino and one imino nitrogen of the dipyrromethane unit.     

Effects of the nature of counterions in solution on interactions of phenoxazones, xanthones, and carbazoles containing benzo-crown groups with DNA

The interactions of DNA with phenoxazones, xanthones, and carbazoles containing the (benzo-18-crown-6)-4′-yl and (benzo-15-crown-5)-4′-yl radicals bonded to the chromophore via spacers of different lengths in the presence of Na⁺ and K⁺ ions were studied by spectrophotometry, circular dichroism, and dynamic birefringence. The thermodynamic parameters of the binding of the compounds with DNA and changes in the macromolecular parameters of the DNA molecule during complexation were determined. Based on the results of these studies, we suggested the models of bonding of these compounds to the double helix of DNA. It is shown that the mode of DNA binding with a phenoxazone derivative containing two (benzo-15-crown-5)-4′-yl radicals bonded via a fragment of glycine to chromophore depends on the type of the counterion in solution. In the presence of Na⁺, the chromophore is intercalated into the double helix of DNA; in the presence of K⁺, it is bound to DNA in the form of a dimer outside the double helix. The type of the counterion does not affect the mode of binding of other crown-containing compounds of actinocin with DNA. For compounds containing the (benzo-18-crown-6)-4′-yl radical, the mode of binding to DNA adepends only on the spacer length.     

Synthesis and cytotoxicity of dinuclear complexes containing ruthenium(II) bipyridyl units linked by a bis(pyridylimine) ligand

Enantiopure dinuclear ruthenium polypyridyl complexes of the form [Ru(2)(LL)(4)L(1)](PF(6))(4) (LL = 2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen); L(1)= C(25)H(20)N(4) a bis(pyridylimine) ligand containing a diphenylmethane spacer) have been synthesized using the chiral building blocks cis-[Ru(bpy)(2)(py)(2)](2+) and cis-[Ru(phen)(2)(py)(2)](2+). These dinuclear ruthenium complexes have been characterised using NMR, mass spectrometry, UV-visible absorbance, circular dichroism and linear dichroism. The compounds exhibit good photo and thermal stability. The extinction coefficient for the bpy complex at 478 nm is epsilon(478) = 15,700 mol(-1) cm(-1) dm(3) and for the phen complex is epsilon(478) = 24,900 mol(-1) cm(-1) dm(3). Both complexes have their longest wavelength (metal to ligand charge transfer) transition predominantly x/y (short axis)-polarised while the transitions at shorter wavelength are a mixture of x/y and z-polarisations, similar to both the copper helicate and iron triple helicate studied previously. Cytotoxicity studies reveal that the compounds are dramatically less active against cancer cell lines than the recently reported supramolecular cylinders prepared from the same bis(pyridylimine) ligand.     

A Double Plug–Socket System Capable of Molecular Keypad Locks through Controllable Photooxidation

Two robust divalent complexes have been successfully constructed by using complementary rigid spacers (anthracene vs. 1,4,5,8‐naphthalenediimide (NDI)) and two pairs of [24]crown‐8 ethers and secondary dialkylammonium functionalities as binding motifs. It was demonstrated that properly selected, rigid spacers are more efficient than flexible ones for achieving strong multivalent association. This is presumably due to the preorganization of the rigid spacers, the cooperation between charge‐transfer interactions of rigid spacers, and the complexation of the binding motifs. Furthermore, the intermolecular photoinduced electron transfer (PET) between rigid spacers in these robust complexes could be switched on and off by modulating their complexation through acid–base reactions, which is reminiscent of a plug–socket system capable of electron transfer. In addition, the self‐sensitized photooxidation of the divalent host with anthracene as a spacer can be completely inhibited after complexation with the divalent guests that contain NDI as spacers. This process could also be understood by invoking intermolecular PET and could be turned on and off through acid–base reactions. The photophysical and photochemical properties of these robust complexes have been interpreted as molecular keypad locks with alarm systems. Thus, a double plug–socket system and molecular keypad locks were successfully integrated inside robust multivalent systems and then the normal molecular devices were endowed with logic functions.     

Electrophoretic mobility of a cylindrical colloidal particle in a salt-free medium

Approximate expressions are derived for the electrophoretic mobility of dilute cylindrical colloidal particles in a salt-free medium containing only counterions. The cylinder is assumed to be infinitely long. It is shown that as in the case of a spherical particle, there is a certain critical value of the particle surface charge separating two cases. When the particle surface charge is lower than the critical value (case 1), the electrophoretic mobility increases with increasing particle surface charge per unit length. When the particle surface charge is higher than the critical value (case 2), the mobility becomes constant (for a cylinder in a transverse field) or the increase in the electrophoretic mobility with the particle surface charge becomes suppressed (for a cylinder in a tangential field). These phenomena are caused by the effect of counterion condensation in the vicinity of the particle surface. The critical value of the particle charge is essentially independent of the particle volume fraction phi for the dilute case, unlike the case of a sphere, in which case the critical charge value is proportional to ln(1/phi).     

New electronic and magnetic properties emerging from adsorption of organized organic layers

New electronic and magnetic properties are induced by the adsorption of closed packed monolayers on solid substrates. For many thiolated molecules self-assembled on gold, a surprisingly large paramagnetism is observed. In the case where the layers are made from chiral molecules, in addition an unexpectedly large electronic dichroism is observed, which manifests itself as spin specific electron transmission. This dichroism was observed for monolayers made from polyalanine and from DNA. Self-assembled monolayers of double-stranded DNA oligomers on gold interact with polarized electrons similarly to a strong and oriented magnetic field. The direction of the field for right-handed DNA is away from the substrate. Moreover, the layer shows very high paramagnetic susceptibility. Interestingly, thiolated single-stranded DNA oligomers on gold do not show this effect. All the observations can be rationalized by assuming organization induced charge transfer between the substrate and the organic layer. The charge transfer results in spin alignment of the transferred electrons/holes. While for achiral molecules the spin alignment varies among the domains, in the case of monolayer made from chiral molecules the alignment is the same across the entire sample. When magnetic field is applied, large magnetic moment is observed that results from orbital magnetism.