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1.
J Org Chem ; 86(19): 13491-13502, 2021 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-34514788

RESUMO

In this study we found that 2,6-dimethanolpyridine displays good complementarity toward di(ethylene glycol) for the complexation of Na+ ions, allowing us to use this recognition system for the efficient synthesis of hetero[2]catenanes; indeed, it allowed us to attach multiple copies of [2]catenanes to branched systems presenting multiple isophthalaldehyde units. When we attempted to form a catenane from a preformed macrocycle featuring only a single di(ethylene glycol) unit, reacting it with a di(ethylene glycol) derivative presenting two amino termini, isophthalaldehyde, and templating Na+ ions [i.e., with the aim of using di(ethylene glycol)·Na+·di(ethylene glycol) recognition to template the formation of the interlocked imino macrocycle], the yields of the hetero[2]catenane and homo[2]catenane, comprising two imino macrocyclic units, were both poor (14% and 7%, respectively). In contrast, when one or two 2,6-dimethanolpyridine units were present in the preformed macrocycles, their reactions with the same diamine, dialdehyde, and Na+ ions provided the hetero[2]catenanes with high selectivity and efficiency (44% and 64% yields, respectively), with minimal formation of the competing homo[2]catenane. The high complementary of the 2,6-dimethanolpyridine·Na+·di(ethylene glycol) ligand pair allowed us to synthesize [2]catenane dimers and trimers directly from corresponding isophthalaldehyde-presenting cores, with yields, after subsequent reduction and methylation, of 42% and 31%, respectively.


Assuntos
Catenanos , Etilenoglicol , Antracenos , Íons , Espectroscopia de Ressonância Magnética
2.
J Biotechnol ; 325: 271-279, 2021 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-33065139

RESUMO

Protein topology engineering has emerged as a new dimension to alter protein stability and function. Inspired by the art of nature, where backbone cyclization is frequently adopted to enhance the stability of natural peptide products and thermostable enzymes; herein, we report protein topology engineering of an industrial thermolabile gamma lactamase via catenation. Two different protein catenanes were successfully constructed via SpyTag/SpyCatcher modules and two different peptide dimer domains. The designed protein catenanes were functionally synthesized in Escherichia coli. A comparison of their biochemical properties revealed that protein topology played a key role in the stability of gamma lactamase. Protein catenation enhanced both the thermo- and proteolytic stabilities of gamma lactamase. Gamma lactamase was stabilized by ∼8 °C in one of the catenated forms. Moreover, Cat1-MhIHL-V54L and Cat2-MhIHL-V54L displayed 1.8- and 2.4-fold higher enzyme efficiencies (Kcat/Km), respectively, than the unattenuated enzyme. Therefore, our results proved that protein catenane construction could be a general strategy to strengthen industrial biocatalysts by mechanisms distinct from those of the conventional direct evolution schemes, whereby our results offer wide applications in the fine chemical industry.


Assuntos
Catenanos , Proteínas , Antracenos , Engenharia de Proteínas , Estabilidade Proteica
3.
Small ; 16(6): e1905987, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31917513

RESUMO

Mechanically interlocked molecules have marked a breakthrough in the field of topological chemistry and boosted the vigorous development of molecular machinery. As an archetypal example of the interlocked molecules, catenanes comprise macrocycles that are threaded through one another like links in a chain. Inspired by the transition metal-templated approach of catenanes synthesis, the hierarchical assembly of DNA origami catenanes templated by gold nanoparticles is demonstrated in this work. DNA origami catenanes, which contain two, three or four interlocked rings are successfully created. In particular, the origami rings within the individual catenanes can be set free with respect to one another by releasing the interconnecting gold nanoparticles. This work will set the basis for rich progress toward DNA-based molecular architectures with unique structural programmability and well-defined topology.


Assuntos
Catenanos , DNA Catenado , Ouro , Nanopartículas Metálicas , Catenanos/química , DNA/química , DNA Catenado/química , Ouro/química , Nanopartículas Metálicas/química
4.
Biochem J ; 477(2): 509-524, 2020 01 31.
Artigo em Inglês | MEDLINE | ID: mdl-31930351

RESUMO

DNA hemicatenanes (HCs) are four-way junctions in which one strand of a double-stranded helix is catenated with one strand of another double-stranded DNA. Frequently mentioned as DNA replication, recombination and repair intermediates, they have been proposed to participate in the spatial organization of chromosomes and in the regulation of gene expression. To explore potential roles of HCs in genome metabolism, we sought to purify proteins capable of binding specifically HCs by fractionating nuclear extracts from HeLa cells. This approach identified three RNA-binding proteins: the Tudor-staphylococcal nuclease domain 1 (SND1) protein and two proteins from the Drosophila behavior human splicing family, the paraspeckle protein component 1 and the splicing factor proline- and glutamine-rich protein. Since these proteins were partially pure after fractionation, truncated forms of these proteins were expressed in Escherichia coli and purified to near homogeneity. The specificity of their interaction with HCs was re-examined in vitro. The two truncated purified SND1 proteins exhibited specificity for HCs, opening the interesting possibility of a link between the basic transcription machinery and HC structures via SND1.


Assuntos
Catenanos/metabolismo , DNA/genética , Endonucleases/genética , Transcrição Genética , Animais , Catenanos/química , Cromossomos/genética , Replicação do DNA/genética , Proteínas de Ligação a DNA/genética , Endonucleases/metabolismo , Células HeLa , Humanos , Fator de Processamento Associado a PTB/genética , Ligação Proteica/genética , Proteínas de Ligação a RNA/genética , Recombinação Genética/genética
6.
Nat Protoc ; 14(10): 2818-2855, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31511665

RESUMO

Mechanically interlocked DNA nanostructures are useful as flexible entities for operating DNA-based nanomachines. Interlocked structures made of double-stranded (ds) DNA components can be constructed by irreversibly threading them through one another to mechanically link them. The interlocked components thus remain bound to one another while still permitting large-amplitude motion about the mechanical bond. The construction of interlocked dsDNA architectures is challenging because it usually involves the synthesis and modification of small dsDNA nanocircles of various sizes, dependent on intrinsically curved DNA. Here we describe the design, generation, purification, and characterization of interlocked dsDNA structures such as catenanes, rotaxanes, and daisy-chain rotaxanes (DCRs). Their construction requires precise control of threading and hybridization of the interlocking components at each step during the assembly process. The protocol details the characterization of these nanostructures with gel electrophoresis and atomic force microscopy (AFM), including acquisition of high-resolution AFM images obtained in intermittent contact mode in liquid. Additional functionality can be conferred on the DNA architectures by incorporating proteins, molecular switches such as photo-switchable azobenzene derivatives, or fluorophores for studying their mechanical behavior by fluorescence quenching or fluorescent resonance energy transfer experiments. These modified interlocked DNA architectures provide access to more complex mechanical devices and nanomachines that can perform a variety of desired functions and operations. The assembly of catenanes can be completed in 2 d, and that of rotaxanes in 3 d. Addition of azobenzene functionality, fluorophores, anchor groups, or the site-specific linkage of proteins to the nanostructure can extend the time line.


Assuntos
Catenanos/química , DNA/química , Nanoestruturas/química , Nanotecnologia/métodos , Hibridização de Ácido Nucleico/métodos , Rotaxanos/química , DNA/síntese química , Luz , Microscopia de Força Atômica
7.
Molecules ; 23(9)2018 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-30189687

RESUMO

DNA catenanes are characterized by their flexible and dynamic motions and have been regarded as one of the key players in sophisticated DNA-based molecular machines. There, the linking number (Lk) between adjacent interlocked rings is one of the most critical factors, since it governs the feasibility of dynamic motions. However, there has been no established way to synthesize catenanes in which Lk is controlled to a predetermined value. This paper reports a new methodology to selectively synthesize Lk 1 catenanes composed of single-stranded DNA rings, in which these rings can most freely rotate each other due to minimal inter-ring interactions. To the mixture for the synthesis, two holder strands (oligonucleotides of 18⁻46 nt) were added, and the structure of the quasi-catenane intermediate was interlocked through Watson⁻Crick base pairings into a favorable conformation for Lk 1 catenation. The length of the complementary part between the two quasi-rings was kept at 10 bp or shorter. Under these steric constraints, two quasi-rings were cyclized with the use of T4 DNA ligase. By this simple procedure, the formation of undesired topoisomers (Lk ≥ 2) was almost completely inhibited, and Lk 1 catenane was selectively prepared in high yield up to 70 mole%. These Lk 1 catenanes have high potentials as dynamic parts for versatile DNA architectures.


Assuntos
Catenanos/química , DNA de Cadeia Simples/química , Nanoestruturas/química , Conformação de Ácido Nucleico , Oligonucleotídeos/química
8.
Molecules ; 23(5)2018 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-29751658

RESUMO

Catenanes with desymmetrized ring components can undergo co-conformational rearrangements upon external stimulation and can form the basis for the development of molecular rotary motors. We describe the design, synthesis and properties of a [2]catenane consisting of a macrocycle-the 'track' ring-endowed with two distinct recognition sites (a bipyridinium and an ammonium) for a calix[6]arene-the 'shuttle' ring. By exploiting the ability of the calixarene to thread appropriate non-symmetric axles with directional selectivity, we assembled an oriented pseudorotaxane and converted it into the corresponding oriented catenane by intramolecular ring closing metathesis. Cyclic voltammetric experiments indicate that the calixarene wheel initially surrounds the bipyridinium site, moves away from it when it is reduced, and returns in the original position upon reoxidation. A comparison with appropriate model compounds shows that the presence of the ammonium station is necessary for the calixarene to leave the reduced bipyridinium site.


Assuntos
Calixarenos/química , Catenanos/química , Modelos Moleculares , Conformação Molecular , Catenanos/síntese química , Técnicas de Química Sintética , Espectroscopia de Ressonância Magnética , Estrutura Molecular
9.
Proc Natl Acad Sci U S A ; 115(38): 9391-9396, 2018 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-29735677

RESUMO

The coordinated motion of many individual components underpins the operation of all machines. However, despite generations of experience in engineering, understanding the motion of three or more coupled components remains a challenge, known since the time of Newton as the "three-body problem." Here, we describe, quantify, and simulate a molecular three-body problem of threading two molecular rings onto a linear molecular thread. Specifically, we use voltage-triggered reduction of a tetrazine-based thread to capture two cyanostar macrocycles and form a [3]pseudorotaxane product. As a consequence of the noncovalent coupling between the cyanostar rings, we find the threading occurs by an unexpected and rare inchworm-like motion where one ring follows the other. The mechanism was derived from controls, analysis of cyclic voltammetry (CV) traces, and Brownian dynamics simulations. CVs from two noncovalently interacting rings match that of two covalently linked rings designed to thread via the inchworm pathway, and they deviate considerably from the CV of a macrocycle designed to thread via a stepwise pathway. Time-dependent electrochemistry provides estimates of rate constants for threading. Experimentally derived parameters (energy wells, barriers, diffusion coefficients) helped determine likely pathways of motion with rate-kinetics and Brownian dynamics simulations. Simulations verified intercomponent coupling could be separated into ring-thread interactions for kinetics, and ring-ring interactions for thermodynamics to reduce the three-body problem to a two-body one. Our findings provide a basis for high-throughput design of molecular machinery with multiple components undergoing coupled motion.


Assuntos
Fenômenos Biofísicos , Modelos Teóricos , Movimento (Física) , Termodinâmica , Algoritmos , Catenanos/química , Difusão , Eletroquímica , Cinética , Simulação de Dinâmica Molecular , Rotaxanos/química
10.
Methods Mol Biol ; 1703: 153-159, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29177740

RESUMO

Hemicatenane is a structure that forms when two DNA duplexes are physically linked through a single-stranded crossover. It is proposed to be an intermediate resulting from double Holliday junction (dHJ) dissolution, repair of replication stalled forks and late stage replication. Our previous study has shown that hemicatenane can be synthesized and dissolved in vitro by hyperthermophilic type IA topoisomerases. Here we present the protocol of hemicatenane synthesis and its structure detection by 2D agarose gel electrophoresis. The generated product can be used as a substrate to study the biochemical mechanism of hemicatenane processing reactions.


Assuntos
Catenanos/síntese química , DNA Topoisomerases Tipo I/metabolismo , Nanoarchaeota/enzimologia , Proteínas Arqueais/metabolismo , Catenanos/metabolismo , Replicação do DNA , Eletroforese em Gel Bidimensional , Conformação de Ácido Nucleico
11.
Curr Opin Biotechnol ; 48: 159-167, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-28505598

RESUMO

Interlocked molecular architectures are well known in supramolecular chemistry and are widely used for various applications like sensors, molecular machines and logic gates. The use of DNA for constructing these interlocked structures has increased significantly within the current decade. Because of Watson-Crick base pairing rules, DNA is an excellent material for the self-assembly of well-defined interlocked nanoarchitectures. These DNA nanostructures exhibit sufficient stability, good solubility in aqueous media, biocompatibility, and can be easily combined with other biomolecules in bio-hybrid nano-assemblies. Therefore, the study of novel DNA-based interlocked systems is of interest for nanotechnology, synthetic biology, supramolecular chemistry, biotechnology, and for sensing purposes. Here we summarize recent developments and applications of interlocked supramolecular architectures made of DNA. Examples illustrating that these systems can be precisely controlled by switching on and off the molecular motion of its mechanically trapped components are discussed. Introducing different triggers into such systems creates molecular assemblies capable of performing logic gate operations and/or catalytic activity control. Interlocked DNA-based nanostructures thus represent promising frameworks for building increasingly complex and dynamic nanomachines with highly controllable functionality.


Assuntos
DNA/química , Nanotecnologia/métodos , Catenanos/química , Nanoestruturas/química , Conformação de Ácido Nucleico , Rotaxanos/química
12.
J Am Chem Soc ; 138(43): 14214-14217, 2016 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-27768305

RESUMO

Lasso peptides exist naturally in a threaded state as [1]rotaxanes, and we reasoned that lasso peptides cleaved in their loop region could serve as building blocks for catenanes. Mutagenesis of the lasso peptide microcin J25 (MccJ25) with two cysteine residues followed by cleavage of the peptide with trypsin led to a [2]rotaxane structure that self-assembled into a [3]catenane and [4]catenanes at room temperature in aqueous solution. The [3]catenane represents the smallest ring size of a catenane composed solely of polypeptide segments. The NMR structure of the [3]catenane was determined, suggesting that burial of hydrophobic residues may be a driving force for assembly of the catenane structure.


Assuntos
Catenanos/química , Peptídeos/química , Animais , Modelos Moleculares , Conformação Proteica , Temperatura
13.
Genes Dev ; 30(19): 2158-2172, 2016 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-27737959

RESUMO

Compaction of chromosomes is essential for accurate segregation of the genome during mitosis. In vertebrates, two condensin complexes ensure timely chromosome condensation, sister chromatid disentanglement, and maintenance of mitotic chromosome structure. Here, we report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of these complexes, cause microcephaly. In addition, hypomorphic Ncaph2 mice have significantly reduced brain size, with frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis. Such DNA bridges also arise in condensin-deficient patient cells, where they are the consequence of failed sister chromatid disentanglement during chromosome compaction. This results in chromosome segregation errors, leading to micronucleus formation and increased aneuploidy in daughter cells. These findings establish "condensinopathies" as microcephalic disorders, with decatenation failure as an additional disease mechanism for microcephaly, implicating mitotic chromosome condensation as a key process ensuring mammalian cerebral cortex size.


Assuntos
Adenosina Trifosfatases/genética , Proteínas de Ligação a DNA/genética , Microcefalia/genética , Mitose/genética , Complexos Multiproteicos/genética , Mutação/genética , Aneuploidia , Animais , Catenanos/metabolismo , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Células Cultivadas , Instabilidade Cromossômica/genética , Segregação de Cromossomos/genética , Feminino , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Micronúcleos com Defeito Cromossômico , Neurônios/patologia , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Células-Tronco
14.
J Am Chem Soc ; 138(16): 5172-85, 2016 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-27019201

RESUMO

Interlocked circular DNA nanostructures, e.g., catenanes or rotaxanes, provide functional materials within the area of DNA nanotechnology. Specifically, the triggered reversible reconfiguration of the catenane or rotaxane structures provides a means to yield new DNA switches and to use them as dynamic scaffolds for controlling chemical functions and positioning functional cargoes. The synthesis of two-ring catenanes and their switchable reconfiguration by pH, metal ions, or fuel/anti-fuel stimuli are presented, and the functions of these systems, as pendulum or rotor devices or as switchable catalysts, are described. Also, the synthesis of three-, five-, and seven-ring catenanes is presented, and their switchable reconfiguration using fuel/anti-fuel strands is addressed. Implementation of the dynamically reconfigured catenane structures for the programmed organization of Au nanoparticle (NP) assemblies, which allows the plasmonic control of the fluorescence properties of Au NP/fluorophore loads associated with the scaffold, and for the operation of logic gates is discussed. Interlocked DNA rotaxanes and their different synthetic approaches are presented, and their switchable reconfiguration by means of fuel/anti-fuel strands or photonic stimuli is described. Specifically, the use of the rotaxane as a scaffold to organize Au NP assemblies, and the control of the fluorescence properties with Au NP/fluorophore hybrids loaded on the rotaxane scaffold, are introduced. The future prospectives and challenges in the field of interlocked DNA nanostructures and the possible applications are discussed.


Assuntos
Catenanos/química , DNA/química , Nanoestruturas/química , Nanotecnologia/métodos , Técnicas de Química Sintética , DNA/síntese química , DNA Circular , Corantes Fluorescentes/química , Rotaxanos/química
15.
Chem Commun (Camb) ; 52(2): 319-22, 2016 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-26515104

RESUMO

[5]Catenanes were synthesized by olefin metathesis dimerization. The reaction of pseudorotaxanes, which were derived from a [2]catenane and one equivalent of an ammonium salt bearing two terminal olefins in dichloromethane, with a catalytic amount of Grubbs catalyst afforded linear [5]catenanes in 12% yield. Intermolecular and intramolecular olefin metathesis reactions were controlled by the length of the alkyl chain of the ammonium salts.


Assuntos
Alcenos/química , Compostos de Amônio/química , Catenanos/síntese química , Rotaxanos/química , Catálise , Dimerização , Estrutura Molecular , Espectroscopia de Prótons por Ressonância Magnética
16.
Cell Rep ; 13(11): 2587-2596, 2015 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-26686641

RESUMO

The type II topoisomerase TopoIV, which has an essential role in Escherichia coli chromosome decatenation, interacts with MukBEF, an SMC (structural maintenance of chromosomes) complex that acts in chromosome segregation. We have characterized the intracellular dynamics of individual TopoIV molecules and the consequences of their interaction with MukBEF clusters by using photoactivated-localization microscopy. We show that ~15 TopoIV molecules per cell are associated with MukBEF clusters that are preferentially localized to the replication origin region (ori), close to the long axis of the cell. A replication-dependent increase in the fraction of immobile molecules, together with a proposed catalytic cycle of ~1.8 s, is consistent with the majority of active TopoIV molecules catalyzing decatenation, with a minority maintaining steady-state DNA supercoiling. Finally, we show that the MukB-ParC interaction is crucial for timely decatenation and segregation of newly replicated ori DNA.


Assuntos
Proteínas Cromossômicas não Histona/metabolismo , Segregação de Cromossomos , DNA Topoisomerase IV/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimologia , Proteínas Repressoras/metabolismo , Biocatálise , Catenanos/metabolismo , Proteínas Cromossômicas não Histona/genética , Cromossomos Bacterianos/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Microscopia de Fluorescência , Família Multigênica , Origem de Replicação , Proteínas Repressoras/genética , Imagem com Lapso de Tempo
17.
Chem Commun (Camb) ; 51(73): 13882-5, 2015 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-26225550

RESUMO

A topologically novel [2]rota[2]catenane containing both a pillar[5]arene-imidazolium based [2]rotaxane subunit and a crown ether-tetracationic cyclophane based [2]catenane one was designed and constructed. The structure of the [2]rota[2]catenane was thoroughly characterized by NMR spectra, MS spectrometry and single crystal X-ray diffraction analysis.


Assuntos
Catenanos/síntese química , Éteres de Coroa/química , Compostos de Amônio Quaternário/química , Rotaxanos/síntese química , Calixarenos , Catenanos/química , Estrutura Molecular , Rotaxanos/química
18.
Org Biomol Chem ; 13(26): 7313-22, 2015 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-26059864

RESUMO

Mechanically interlocked structures such as rotaxanes and catenanes provide a novel backbone for constructing functional materials with unique structural characteristics. In this study, we have designed and synthesized a series of photoswitchable rotaxanes and catenanes containing photochromic dithienylethene fragments using a template-directed clipping approach based on dynamic imine chemistry. Their structures have been confirmed using NMR, mass spectrometry and elemental analysis. Investigations into their photoisomerization properties indicated that these dithienylethene-based mechanically interlocked molecules have good reversibility and excellent fatigue resistance upon irradiation with UV or visible light. Interestingly, the mechanically interlocked molecules containing two dithienylethene backbones display around a 2-fold increase in the molar absorption coefficient compared with that of the mono dithienylethene derivative. Furthermore, the introduction of the fluorophore pyrene in the dithienylethene component facilitates these molecules to serve as fluorescent switches.


Assuntos
Alcenos/química , Catenanos/química , Processos Fotoquímicos , Rotaxanos/química , Iminas/química , Isomerismo , Fenômenos Mecânicos , Modelos Moleculares , Conformação Molecular
19.
Org Lett ; 17(11): 2804-7, 2015 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-25996900

RESUMO

Hierarchical self-assembly centered on metallacyclic scaffolds greatly facilitates the construction of mechanically interlocked structures. The formation of two [3]catenanes and one [4]molecular necklace is presented by utilizing the orthogonality of coordination-driven self-assembly and crown ether-based cryptand/paraquat derivative complexation. The threaded [3]catenanes and [4]molecular necklace were fabricated by using ten and nine total molecular components, respectively, from four and three unique species in solution, respectively. In all cases single supramolecular ensembles were obtained, attesting to the high degree of structural complexity made possible via self-assembly approaches.


Assuntos
Catenanos/química , Éteres de Coroa/química , Éteres Cíclicos/química , Paraquat/química , Rotaxanos/química , Bases de Schiff/química , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Estrutura Molecular
20.
Org Lett ; 17(9): 2158-61, 2015 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-25905465

RESUMO

Di-, tri-, and tetra(ethylene glycol) units in both dumbbell-shaped and macrocyclic molecules can be used as primary recognition units for the clipping of macrocycles in the presence of templating Na(+) ions to form corresponding [2]rotaxanes and [2]catenanes. One such tri(ethylene glycol)-containing [2]catenane behaves as a Na(+) ion-controllable molecular switch.


Assuntos
Catenanos/síntese química , Compostos Macrocíclicos/química , Sódio/química , Catenanos/química , Etilenoglicol/química , Íons , Espectroscopia de Ressonância Magnética , Estrutura Molecular , Rotaxanos/síntese química , Rotaxanos/química
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