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At least 19 recordsLinked to original sources

PubMed2001

Self-assembly of rings, catenanes, and a doubly braided catenane containing gold(I): the hinge-group effect in diacetylide ligands.

Reaction of the flexible dialkynyldigold(I) precursors X(4-C6H4OCH2C-CAu)2 with 1,4-bis(diphenylphosphino)butane gave complexes of formula [[[mu-X(4-C6H4OCH2CCAu)2[mu-(Ph2PCH2CH2CH2CH2PPh2)]]n]. The complexes exist as 25-membered ring compounds with n = 1 when X = O or S, as [2]catenanes with n = 2 when X = CH2 or CMe2, and as a unique doubly braided [2]catenane, containing interlocked 50-membered rings with n = 4 when X = cyclohexylidene. These compounds form easily and selectively by self-assembly; reasons for the selectivity are also discussed.

Journal Article↗

PubMedDate not supplied

Model carbyne vs ideal and DNA catenanes.

The structure and stability of two-component carbyne catenanes, viewed as model compounds for DNA catenanes, have been estimated by molecular mechanics (MM) calculations. The carbyne catenane molecules studied were composed from interwined cyclic molecules constituted solely from carbon atoms bonded by alternating single and triple bonds. The total number of carbon atoms in molecules studied was set to 60, and the complementary sizes of the catenane components varied. The component cycles were entangled by 2, 4, ..., 11 crossings. For the catenanes with the number of crossings equal to six and seven more than one catenane topological type was considered. The calculated MM strain energy of carbyne catenanes was correlated with the averaged crossing number and length-to-diameter ratio of ideal catenanes as well as the electrophoretic mobility and sedimentation coefficient of DNA catenanes. To observe these correlations, for each topological type of carbyne catenane, it was necessary to find the proportion of the sizes of the two catenane components at which the MM strain energy is the lowest. Then, the values of these energies were correlated with characteristics of ideal and real DNA catenanes. The fits are significant and nonlinear.

Algorithms↗

PubMed1999

Self-Assembling Calix[4]arene [2]Catenanes. Preorganization, Conformation, Selectivity, and Efficiency.

A novel class of preorganized U-shape calix[4]arene clefts, dicationic salts 3a,c,e.2Cl, 3b.2PF(6)(), and 3f.2Br, consisting of one cone calix[4]arene and two bipyridine residues being linked by an aliphatic chain, have been designed and synthesized as precursors for self-assembly of calix[4]arene [2]catenanes by utilizing pi-stacking interactions between the hydroquinone and bipyridinium units. Conformationally flexible 6.2PF(6)() and cone 10.2Cl, whose conformation is fixed by two propyloxy groups on the lower rim, were also prepared in order to explore the effects of conformation and hydrogen bonding of the calix[4]arene moiety on self-assembly. For all reactions, bis-p-phenylene-34-crown ether-10 (11) was employed as the donor component. Alternate cone [2]catenane 13.4Cl is obtained in 8% yield from reaction of ethylene-incorporating 3a.2Cl and 1,4-bis(bromomethyl)benzene (12a). Three cone and one conformationally flexible [2]catenanes were obtained in moderate to good yields from reactions of propylene-incorporating 3b.PF(6)() and 3c.2Cl with 12a, 1,3-bis(bromomethyl)benzene (12b) or 4,4'-(bromomethyl)biphenyl (12c). Both cone and partial cone [2]catenanes were generated in moderate yields from butylene-incorporating 3c.2Cl with four tert-butyl groups on the calix[4]arene moiety and with 12a. In contrast, only cone [2]catenane was obtained from similar tert-butyl-free cleft 3d.2Cl. Cone and conformationally flexible [2]catenanes were obtained in moderate yields, respectively, from the reactions of 3d.2Cl and 3e.2Cl with 12c. No catenanes were isolated from reaction of phenylene-incorporating 3f.2Br or 6.2Cl, whereas reaction of 10.2Cl afforded cone [2]catenane in low yield. It was demonstrated that hydrogen bonding, which may be destroyed after catenation, within the calix[4]arene moiety is crucial for efficient self-assembly of the [2]catenanes. The dynamic (1)H NMR and absorption spectra and luminescent properties of the [2]catenanes were investigated, which reveal that incorporation of calix[4]arene into the tetracationic cyclophane reduces pi-stacking interactions between the donor and acceptor units and catenation has substantial influence on conformational distributions of the calix[4]arene moiety. The results demonstrate the versatility of calix[4]arene derivatives as building blocks in the construction of supramolecular structures.

Journal Article↗

PubMed2001

DOSY study on dynamic catenation: self-assembly of a [3]catenane as a meta-stable compound from twelve simple components.

Synthesis of [2]catenane 6 has been successfully achieved by the combination of Pd complex 1 and pyridines 2 and 3 at a molar ratio of 2:1:1 in D20. A mixture of square molecule 4 (prepared from 1 and 2) and macrocycle 5 (obtained from 1 and 3), in which the final ratio of 1, 2, and 3 was kept 2:1:1 reorganizes in D2O/CD3OD (1:1) to form 6 within one day. However, the same mixture in D2O shows the formation of novel [3]catenane 7 along with the [2]catenane. In order to make 7, the theoretical ratio of components 1, 2, and 3 should be 3:1:2. Thus, deliberately maintaining such ratio of the above-mentioned molecules, a higher proportion of the [3]catenane is observed in D2O as found from 1H NMR spectra of the system. Reorganization of the twelve components to form [3]catenane is supported by studies with the DOSY method. This method is a first attempt to separate, from a mixture, either catenanes or any other supramolecular self-assembly structures. CSI-MS studies further support the assigned catenane super structures 6 and 7. All the results indicate that the [2]catenane is thermodynamically the most stable structure, while the [3]catenane is a meta-stable self-assembly.

DNA↗

PubMed1994

Stereoselectivity of DNA catenane fusion by resolvase.

Communications between distant sites on DNA often depend on the way in which the sites are connected. For example, site-specific recombination catalysed by Tn3 resolvase is most efficient when the 114-base-pair res recombination sites are directly repeated in the same DNA molecule. In vitro a supercoiled plasmid substrate containing two directly repeated res sites gives a resolution product in which the two recombinant circles are topologically linked as a simple (two-noded) catenane (Fig. 1a). Resolvase is highly selective in forming this product rather than unlinked circles or more complex catenanes. It does not catalyse recombination between sites on separate supercoiled molecules, or between inverted sites in the same supercoiled molecule. Tn3 resolution removes four negative supercoils from the substrate, an energetically favourable change which may drive the reaction: in relaxed or nicked circular substrates, resolution is incomplete and slower. Resolvase can catalyse fusion of the circles of a nicked or relaxed catenane, giving a single unknotted circular product. The fusion is the precise topological reversal of resolution, introducing four negative supercoils into a relaxed catenane substrate, and should therefore not proceed if the catenane is already negatively supercoiled. Here we study recombination between res sites in non-supercoiled DNA circles linked into simple catenanes. We used (+2) and (-2) catenanes, which differ only in the direction in which one circle is threaded through the other (Fig. 2a). Although stereoselectivity is a feature of enzyme catalysis, it is not obvious how resolvase can distinguish between these subtly different catenane diastereomers. A model for the intertwining of the res site DNA in the catalytically active complex predicts that only the (-2) catenane will recombine, giving unknotted and 4-noded knot circular products. We have confirmed this prediction for the Tn3 and Tn21 resolvases.

DNA, Circular↗

PubMed1993

Monte Carlo analysis of the conformation of DNA catenanes.

We used a Monte Carlo method to study the conformational properties of catenanes between two nicked DNA rings. We calculated the writhe induced by catenation as a function of the linking number between the two rings. The simulations modeled catenated rings of equal size as well as rings differing in length by a factor of 3. For both classes of catenanes, the calculated values of writhe agreed very well with the experimental measurements of catenation-induced supercoiling made by Wasserman et al. Therefore, the equilibrium value of DNA twist is not changed significantly by catenation. We found that the induced writhe increased linearly with catenane linking number, but was independent of DNA length and of effective helical diameter. We conclude that induced writhe is a general feature of catenation, and that it depends primarily on the ratio of lengths of the linked rings and the number of catenane interlocks. In contrast, catenane conformation varied qualitatively with catenation linking number, DNA length, and double helix diameter. At the values of these parameters for catenanes isolated from cells, catenane conformations were strikingly irregular. Nonetheless, the local concentration of two sites on separate but linked rings increased greatly with catenane linking number. This increase is similar to that brought about by (-) supercoiling to DNA sites in cis.

Computer Simulation↗

PubMed2000

Regioselective template synthesis, X-ray structure, and chiroptical properties of a topologically chiral sulfonamide catenane.

The synthesis of a topologically chiral in,out-bis-sulfonamide catenane and its "dimer" are reported. The structures of the amide wheel and of the catenane were resolved by X-ray analysis. NMR-titration of the monosulfonamide-wheel yielded conclusive association constants supporting the proposed regioselective mechanism of the catenane formation. The enantioseparation of the catenane via chiral HPLC was successful. The enantiomers show pronounced Cotton effects in the aromatic region of the CD-spectrum. Since the template synthesis was carried out leading to the in-oriented sulfonamide-wheel blocked with an N-methyl group at its reactive sulfonamide functionality, the catenane represents the first monofunctional topologically chiral amide-based catenane. Reaction with 1,2-bis(2-iodoethoxy)ethane led to a bis-catenane containing two topological units. The meso- and the RR/SS-isomers represent a new type of topological diastereomers.

Chromatography, High Pressure Liquid↗

PubMed2001

Dual-mode "co-conformational" switching in catenanes incorporating bipyridinium and dialkylammonium recognition sites.

Three [2]catenanes and three [3]catenanes incorporating one or two pi-electron-rich macrocyclic polyethers and one pi-electron-deficient polycationic cyclophane have been synthesized in yields ranging from 4 to 38%. The pi-electron-rich macrocyclic components possess either two 1,4-dioxybenzene or two 1.5-dioxynaphthalene recognition sites. The pi-electron-deficient cyclophane components incorporate two bipyridinium and either one or two dialkylammonium recognition sites. The template-directed syntheses of these catenanes rely on i) pi...pi stacking interactions between the dioxyarene and bipyridinium recognition sites, ii) C-H...O hydrogen bonds between some of the bipyridinium hydrogen atoms and some of the polyether oxygen atoms, and iii) C-H...pi interactions between some of the dioxyarene hydrogen atoms and the aromatic spacers separating the bipyridinium units. The six catenanes were characterized by mass spectrometry and by both 1H and 13C NMR spectroscopy. The absorption spectra and the electrochemical properties of the catenanes have been investigated and compared with those exhibited by the component macrocycles and by related known catenanes. Broad and weak absorption bands in the visible region, originating from charge-transfer (CT) interactions between electron-donor and electron-acceptor units, have been observed. Such charge-transfer interactions are responsible for the quenching of the potentially fluorescent excited states of the aromatic units of the macrocyclic polyether components. The redox behavior of these novel compounds has been investigated and correlations among the observed redox potentials are illustrated and discussed. The catenanes undergo co-conformational switching upon one-electron reduction of the two bipyridinium units. One of them--in its reduced form--can be also switched by acid/base inputs and exhibits AND logic behavior. The co-conformational rearrangements induced by the redox and acid/base stimulations lend themselves to exploitation in the development of molecular-level machines and logic gates.

Journal Article↗

PubMed2002

Self-assembly of gold(I) rings and reversible formation of organometallic [2]catenanes.

The reaction of the digold(I) diacetylide [(AuCCCH2OC6H4)2CMe2] with diphosphane ligands can lead to formation of either macrocyclic ring complexes or [2]catenanes by self-assembly. This gives an easy route to rare organometallic [2]catenanes, and the effect of the diphosphane ligand on the selectivity of self-assembly is studied. With diphosphane ligands Ph2P(CH2)xPPh2, the simple ring complex [Au2[(CCCH2OC6H4)2CMe2](Ph2P(CH2)xPPh2)] is formed selectively when x = 2, but the [2]catenanes [Au2[(CCCH2OC6H4)2CMe2](Ph2P(CH2)xPPh2)]2 are formed when x = 4 or 5. When x = 3, a mixture of the simple ring and [2]catenane is formed, along with the "double-ring" complex, [Au4[(CCCH2OC6H4)2CMe2]2(Ph2P(CH2)3PPh2)2] and a "hexamer" Au2[(CCCH2OC6H4)2CMe2](Ph2P(CH2)3PPh2)]6] whose structure is not determined. A study of the equilibria between these complexes by solution NMR techniques gives insight into the energetics and mechanism of [2]catenane formation. When the oligomer [(AuCCCH2OC6H4)2CMe2] was treated with a mixture of two diphosphane ligands, or when two [2]catenane complexes [[Au2[(CCCH2OC6H4)2CMe2](diphosphane)]2] were allowed to equilibrate, only the symmetrical [2]catenanes were formed. The diphosphanes Ph2PCCPPh2, trans-[Ph2PCH=CHPPh2] and (Ph2PC5H4)2Fe give the corresponding ring complexes [Au2[(CCCH2OC6H4)2CMe2](diphosphane)], and the chiral, unsymmetrical diacetylide [Au2[(CCCH2OC6H4C(Me)(CH2CMe2)C6H3OCH2CC)] gives macrocyclic ring complexes with all diphosphane ligands Ph2P(CH2)xPPh2 (x = 2-5).

Journal Article↗

PubMed1995

Analysis of the structure of dimeric DNA catenanes by electron microscopy.

We analyzed the structure of open-circular and supercoiled dimeric DNA catenanes generated by site-specific recombination in vitro. Electron microscopy of open-circular catenanes shows that the number of duplex crossings in a plane is a linear function of the number of catenane interlinks (Ca/2), and that the length of the catenane axis is constant, independent of Ca. These relationships are similar to those observed with supercoiled DNA. Statistical analyses reveal, however, that the conformations of the individual rings of the catenanes are similar to those of unlinked circles. The distribution of distances between randomly chosen points on separate rings depends strongly on Ca and is consistent with a sharp decrease in the center-of-mass separation between rings with increasing Ca. Singly linked supercoiled catenanes are seen by microscopy to be linked predominantly through terminal loops in the respective superhelices. The observations suggest that chain entropy is a major factor determining the conformation of DNA catenanes.

DNA↗

PubMed2002

Gold(I) macrocycles and topologically chiral [2]catenanes.

The design and synthesis of a new type of topologically chiral [2]catenane is reported. The compounds are formed easily by self-assembly on reaction of the oligomeric digold(I) diacetylide precursor complex [[4-BrC(6)H(4)CH(4-C(6)H(4)OCH(2)CCAu)(2)](n)] with diphosphine ligands. Reactions with the diphosphines PP = bis(diphenylphosphinophoshino)acetylene, trans-1,2-bis(diphenylphosphino)ethylene, bis(diphenylphosphino)ethane, and 1,1'-bis(diphenylphosphino)ferrocene yield simple ring complexes [4-BrC(6)H(4)CH(4-C(6)H(4)OCH(2)CCAu)(2)(mu-PP)] as the only products, since the spacer groups in the diphosphines are not long enough or are too bulky to allow catenane formation. Reaction with PP = bis(diphenylphosphino)propane or bis(diphenylphosphino)butane gave [2]catenane complexes [[4-BrC(6)H(4)CH(4-C(6)H(4)OCH(2)CCAu)(2)(mu-PP)](2)], whose structures are confirmed crystallographically. The macrocyclic ring compounds have C(s) symmetry but, as a result of the presence of the unsymmetrical "hinge group" 4-BrC(6)H(4)CH, the [2]catenanes have C(2) symmetry and so are topologically chiral. In favorable cases, the formation of the [2]catenane can be proved by NMR spectroscopy since catenane formation leads to nonequivalence of most ring atoms. The formation of the [2]catenanes was successfully predicted based on the conformation of the precursor bis(phenol), and it is argued that the methods used should be more generally applicable to the synthesis of functionally substituted supermolecules of interest for application in molecular devices.

Journal Article↗

PubMed2000

[2]Catenane assembly from calix[4]arene crown ethers [In Process Citation]

A variety of novel calix[4]arene-incorporating crown ethers with or without intramolecular hydrogen bonding have been prepared by two efficient methods and utilized as donor rings to assemble calix[4]arene [2]catenanes based on pi-stacking interaction between hydroquinone and bipyridinium units. Treatment of calix[4]arene crown ethers 4, 10a, or 10b, whose cone conformation was fixed by intramolecular hydrogen bonding within the calix[4]arene moiety, with dicationic salt 15 x 2PF6 and dibromide 16 afforded the corresponding [2]catenanes 17a x 4PF6, 17b x 4PF6, and 17c x 4PF6 in 20%, 53%, and 55% yields, respectively, whereas from the reactions of 15 x 2PF6 and dibromide 16 in the presence of conformationally flexible 11 or 12 with a cone conformation kept by two propyl groups, [2]catenanes 18 x 4PF6 and 19 x 4PF6 were obtained in 12% and 6% yields. [2]Catenanes 21a x 4Cl, 21b x 4Cl, and 21c x 4Cl, incorporating calix[4]arene in both the donor and acceptor rings, were also successfully assembled from 10a or 10b, 16, and dicationic salts 20a x 2PF6 or 20b x 2PF6. The dynamic 1H NMR and absorption spectra of the [2]catenanes have been investigated, which revealed a strongest donor-acceptor interaction in 17a x 4PF6 and that the cone [2]catenanes 17a-c x 4PF6 can isomerize to the partial cone isomer at high temperature. The difference of the dynamic properties of these catenanes was discussed. The results demonstrate that catenation is one new general method to change the conformational distributions of calix[4]arenes.

Journal Article↗

PubMed2006

Oligothiophene catenanes and knots: a theoretical study.

Oligothiophene [2]catenanes and knots containing up to 28 thiophene units have been studied at the BHandHLYP/3-21G level of theory. Small knots (less than 22 thiophene units) and [2]catenanes (less than 18 thiophene units) are strained molecules. Larger knots and [2]catenanes are almost strain-free. [2]Catenanes and knots having less than 18 and 24 units, respectively, show transversal electronic coupling destroying one-dimensionality of molecules reflecting in smaller band gaps compared to larger knots and catenanes. Ionization potentials of knots and catenanes are always higher compared to that of lineal oligomers due to less effective conjugation. Polaron formation in catenanes is delocalized only over one ring, leaving another intact. In the case of a knot containing 22 thiophene units, estimated polaron delocalization is 8 to 9 repeating units.

Journal Article↗

PubMed2003

Photoinduced electron transfer between the interlocked components of porphyrin catenanes: effect of the presence of nonequivalent reduction sites on the charge recombination rate.

[2]Catenanes made up of several polyether-strapped porphyrin macrocycles interlinked with the cyclic electron acceptor cyclobis(paraquat-p-phenylene) were spectroscopically, photophysically, and electrochemically characterized. The catenanes exhibit very rich redox behavior due to the presence of several different and interacting electro-active subunits. The redox patterns represent useful "fingerprints" that provide detailed information on the electronic interactions and the chemical environments that the electroactive subunits experience in the supramolecular arrays. A photoinduced electron transfer from the porphyrin excited state (charge separation CS) occurs with tau=20 ps in the catenanes with a larger strap and faster than 20 ps (instrumental resolution) in the catenanes with a shorter strap. The resulting charge-separated state recombines to the ground state (charge recombination CR) with lifetimes similar in all cases, 41+/-4 ps. Comparison of the electron transfer rates CS and CR in the host-guest complexes of the same porphyrins with the noncyclic electron acceptor paraquat, indicate slower reactions in the [2]catenanes. This behavior is assigned to the different separation between reacting partners determined by the type of bond (weak interaction or mechanical) and to a two-step consecutive electron transfer to different sites of the macrocyclic electron acceptor in the catenanes which retards charge recombination.

Journal Article↗

PubMed1980

Formation and resolution of DNA catenanes by DNA gyrase.

We have discovered that DNA gyrase interlocks duplex DNA circles to form catenanes and resolves catenanes into component monomers. The reactions were inhibited by novobiocin and oxolinic acid and required ATP, Mg++ and spermidine. DNA sequence homology is not involved in catenation, since hybrid catenanes were formed efficiently between supercoiled phi X174 and Col E1 DNA. Strikingly different results were obtained with native and relaxed Col E1 DNA substrates. Up to 50-60% of input native DNA was converted into oligomeric catenanes, predominantly dimers and trimers. Relaxed substrates were instead converted into vast interlocked networks and were occasionally knotted. Optimal catenation occurred only in the narrow range of 20-35 mM KCl; increased ionic strength blocked catenation completely but activated the back reaction of decatenation. Gyrase resolved both the oligomeric catenanes and interlocked networks it produced, as well as naturally occurring catenanes. These results imply that the mechanism of gyrase involves a transient double-strand break and passage of a DNA segment through the resulting gap. Gyrase is representative of a general class of enzymes, found in both procaryotic and eucaryotic cells, that facilitate diffusion of duplex DNA segments through each other and may thereby solve topological problems arising from the replication, recombination and condensation of DNA.

Bacteriocin Plasmids↗

PubMed1998

Geometry and physics of catenanes applied to the study of DNA replication.

The concept of ideal geometric configurations was recently applied to the classification and characterization of various knots. Different knots in their ideal form (i.e., the one requiring the shortest length of a constant-diameter tube to form a given knot) were shown to have an overall compactness proportional to the time-averaged compactness of thermally agitated knotted polymers forming corresponding knots. This was useful for predicting the relative speed of electrophoretic migration of different DNA knots. Here we characterize the ideal geometric configurations of catenanes (called links by mathematicians), i.e., closed curves in space that are topologically linked to each other. We demonstrate that the ideal configurations of different catenanes show interrelations very similar to those observed in the ideal configurations of knots. By analyzing literature data on electrophoretic separations of the torus-type of DNA catenanes with increasing complexity, we observed that their electrophoretic migration is roughly proportional to the overall compactness of ideal representations of the corresponding catenanes. This correlation does not apply, however, to electrophoretic migration of certain replication intermediates, believed up to now to represent the simplest torus-type catenanes. We propose, therefore, that freshly replicated circular DNA molecules, in addition to forming regular catenanes, may also form hemicatenanes.

Biophysical Phenomena↗

PubMed1998

Sedimentation and electrophoretic migration of DNA knots and catenanes.

Various site-specific recombination enzymes produce different types of knots or catenanes while acting on circular DNA in vitro and in vivo. By analysing the types of knots or links produced, it is possible to reconstruct the order of events during the reaction and to deduce the molecular "architecture" of the complexes that different enzymes form with DNA. Until recently it was necessary to use laborious electron microscopy methods to identify the types of knots or catenanes that migrate in different bands on the agarose gels used to analyse the products of the reaction. We reported recently that electrophoretic migration of different knots and catenanes formed on the same size DNA molecules is simply related to the average crossing number of the ideal representations of the corresponding knots and catenanes. Here we explain this relation by demonstrating that the expected sedimentation coefficient of randomly fluctuating knotted or catenated DNA molecules in solution shows approximately linear correlation with the average crossing number of ideal configurations of the corresponding knots or catenanes.

Centrifugation↗

PubMed1999

Topology of Xer recombination on catenanes produced by lambda integrase.

Xer site-specific recombination at the psi site from plasmid pSC101 displays topological selectivity, such that recombination normally occurs only between directly repeated sites on the same circular DNA molecule. This intramolecular selectivity is important for the biological role of psi, and is imposed by accessory proteins PepA and ArcA acting at accessory DNA sequences adjacent to the core recombination site. Here we show that the selectivity for intramolecular recombination at psi can be bypassed in multiply interlinked catenanes. Xer site-specific recombination occurred relatively efficiently between antiparallel psi sites located on separate rings of right-handed torus catenanes containing six or more nodes. This recombination introduced one additional node into the catenanes. Antiparallel sites on four-noded right-handed catenanes, the normal product of Xer recombination at psi, were not recombined efficiently. Furthermore, parallel psi sites on right-handed torus catenanes were not substrates for Xer recombination. These findings support a model in which psi sites are plectonemically interwrapped, trapping a precise number of supercoils that are converted to four catenation nodes by Xer strand exchange.

Bacteriophage lambda↗