1
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Weigel RK, Alabi CA. Duplex-forming oligocarbamates with tunable nonbonding sites. Chem Sci 2024; 15:9138-9146. [PMID: 38903212 PMCID: PMC11186313 DOI: 10.1039/d4sc00242c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/11/2024] [Indexed: 06/22/2024] Open
Abstract
In biopolymers such as proteins and nucleic acids, monomer sequence encodes for highly specific intra- and intermolecular interactions that direct self-assembly into complex architectures with high fidelity. This remarkable structural control translates into precise control over the properties of the biopolymer. Polymer scientists have sought to achieve similarly precise control over the structure and function of synthetic assemblies. A common strategy for achieving this goal has been to exploit existing biopolymers, known to associate with specific geometries and stoichiometries, for the assembly of synthetic building blocks. However, such systems are neither scalable nor amenable to the relatively harsh conditions required by various materials science applications, particularly those involving non-aqueous environments. To overcome these limitations, we have synthesized sequence-defined oligocarbamates (SeDOCs) that assemble into duplexes through complementary hydrogen bonds between thymine (T) and diaminotriazine (D) pendant groups. The SeDOC platform makes it simple to incorporate non-hydrogen-bonding sites into an oligomer's array of recognition motifs, thereby enabling an investigation into this unexplored handle for controlling the hybridization of complementary ligands. We successfully synthesized monovalent, divalent, and trivalent SeDOCs and characterized their self-assembly via diffusion ordered spectroscopy, 1H-NMR titration, and isothermal titration calorimetry. Our findings reveal that the binding strength of monovalent oligomers with complementary pendant groups is entropically driven and independent of monomer sequence. The results further show that the hybridization of multivalent oligomers is cooperative, that their binding enthalpy (ΔH) and entropy (TΔS) depend on monomer sequence, and that sequence-dependent changes in ΔH and TΔS occur in tandem to minimize the overall change in binding free energy.
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Affiliation(s)
- R Kenton Weigel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University Ithaca New York USA
| | - Christopher A Alabi
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University Ithaca New York USA
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2
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Dhiman M, Cons R, Evans ON, Smith JT, Anderson CJ, Cabot R, Soloviev DO, Hunter CA. Selective Duplex Formation in Mixed Sequence Libraries of Synthetic Polymers. J Am Chem Soc 2024; 146:9326-9334. [PMID: 38529806 PMCID: PMC10995991 DOI: 10.1021/jacs.4c01381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/06/2024] [Accepted: 03/14/2024] [Indexed: 03/27/2024]
Abstract
Recognition-encoded melamine oligomers (REMO) are synthetic polymers that feature an alternating 1,3,5-triazine-piperazine backbone and side-chains equipped with either a phenol or phosphine oxide recognition unit. An automated method for the solid-phase synthesis (SPS) of REMO of any specified sequence has been developed starting from dichlorotriazine monomer building blocks. Complementary homo-oligomers with either six phenols or six phosphine oxides were synthesized and shown to form a stable duplex in nonpolar solvents by NMR denaturation experiments. The duplex was covalently trapped by equipping the ends of the oligomers with an azide and an alkyne group and using a copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. The SPS methodology was adapted to synthesize mixed sequence libraries by using a mixture of two different dichlorotriazine building blocks in each coupling cycle of an oligomer synthesis. The resulting libraries contain statistical mixtures of all possible sequences. The self-assembly properties of these libraries were screened by using the CuAAC reaction to trap any duplexes present. In mixed sequence libraries of 6-mers, the trapping experiments showed that only sequence-complementary oligomers formed duplexes at micromolar concentrations in dichloromethane. The automated synthesis approach developed here provides access to large libraries of mixed sequence synthetic polymers, and the covalent trapping experiment provides a convenient tool for screening functional properties of mixtures. The results suggest high-fidelity sequence-selective duplex formation in mixtures of 6-mer sequences of the REMO architecture.
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Affiliation(s)
- Mohit Dhiman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Ronan Cons
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Oliver N. Evans
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Joseph T. Smith
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Cecilia J. Anderson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Rafel Cabot
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Daniil O. Soloviev
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher A. Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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3
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Weigel RK, Rangamani A, Alabi CA. Synthetically encoded complementary oligomers. Nat Rev Chem 2023; 7:875-888. [PMID: 37973830 DOI: 10.1038/s41570-023-00556-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
Creating the next generation of advanced materials will require controlling molecular architecture to a degree typically achieved only in biopolymers. Sequence-defined polymers take inspiration from biology by using chain length and monomer sequence as handles for tuning structure and function. These sequence-defined polymers can assemble into discrete structures, such as molecular duplexes, via reversible interactions between functional groups. Selectivity can be attained by tuning the monomer sequence, thereby creating the need for chemical platforms that can produce sequence-defined polymers at scale. Developing sequence-defined polymers that are specific for their complementary sequence and achieve their desired binding strengths is critical for producing increasingly complex structures for new functional materials. In this Review Article, we discuss synthetic platforms that produce sequence-defined, duplex-forming oligomers of varying length, strength and association mode, and highlight several analytical techniques used to characterize their hybridization.
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Affiliation(s)
- R Kenton Weigel
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Adithya Rangamani
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher A Alabi
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
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4
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Iadevaia G, Hunter CA. Recognition-Encoded Synthetic Information Molecules. Acc Chem Res 2023; 56:712-727. [PMID: 36894535 PMCID: PMC10035037 DOI: 10.1021/acs.accounts.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
ConspectusNucleic acids represent a unique class of highly programmable molecules, where the sequence of monomer units incorporated into the polymer chain can be read through duplex formation with a complementary oligomer. It should be possible to encode information in synthetic oligomers as a sequence of different monomer units in the same way that the four different bases program information into DNA and RNA. In this Account, we describe our efforts to develop synthetic duplex-forming oligomers composed of sequences of two complementary recognition units that can base-pair in organic solvents through formation of a single H-bond, and we outline some general guidelines for the design of new sequence-selective recognition systems.The design strategy has focused on three interchangeable modules that control recognition, synthesis, and backbone geometry. For a single H-bond to be effective as a base-pairing interaction, very polar recognition units, such as phosphine oxide and phenol, are required. Reliable base-pairing in organic solvents requires a nonpolar backbone, so that the only polar functional groups present are the donor and acceptor sites on the two recognition units. This criterion limits the range of functional groups that can be produced in the synthesis of oligomers. In addition, the chemistry used for polymerization should be orthogonal to the recognition units. Several compatible high yielding coupling chemistries that are suitable for the synthesis of recognition-encoded polymers are explored. Finally, the conformational properties of the backbone module play an important role in determining the supramolecular assembly pathways that are accessible to mixed sequence oligomers.Almost all complementary homo-oligomers will form duplexes provided the product of the association constant for formation of a base-pair and the effective molarity for the intramolecular base-pairing interactions that zip up the duplex is significantly greater than one. For these systems, the structure of the backbone does not play a major role, and the effective molarities for duplex formation tend to fall in the range 10-100 mM for both rigid and flexible backbones. For mixed sequences, intramolecular H-bonding interactions lead to folding. The competition between folding and duplex formation depends critically on the conformational properties of the backbone, and high-fidelity sequence-selective duplex formation is only observed for backbones that are sufficiently rigid to prevent short-range folding between bases that are close in sequence. The final section of the Account highlights the prospects for functional properties, other than duplex formation, that might be encoded with sequence.
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Affiliation(s)
- Giulia Iadevaia
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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5
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Samokhvalova S, Lutz JF. Macromolecular Information Transfer. Angew Chem Int Ed Engl 2023; 62:e202300014. [PMID: 36696359 DOI: 10.1002/anie.202300014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/26/2023]
Abstract
Macromolecular information transfer can be defined as the process by which a coded monomer sequence is communicated from one macromolecule to another. In such a transfer process, the information sequence can be kept identical, transformed into a complementary sequence or even translated into a different molecular language. Such mechanisms are crucial in biology and take place in DNA→DNA replication, DNA→RNA transcription and RNA→protein translation. In fact, there would be no life on Earth without macromolecular information transfer. Mimicking such processes with synthetic macromolecules would also be of major scientific relevance because it would open up new avenues for technological applications (e.g. data storage and processing) but also for the creation of artificial life. In this important context, this minireview summarizes recent research about information transfer in synthetic oligomers and polymers. Medium- and long-term perspectives are also discussed.
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Affiliation(s)
- Svetlana Samokhvalova
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
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6
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Strom KR, Szostak JW. Folding and Duplex Formation in Sequence-Defined Aniline Benzaldehyde Oligoarylacetylenes. J Am Chem Soc 2022; 144:18350-18358. [PMID: 36174969 PMCID: PMC9562438 DOI: 10.1021/jacs.2c06268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In all known genetic
polymers, molecular recognition
via hydrogen
bonding between complementary subunits underpins their ability to
encode and transmit information, to form sequence-defined duplexes,
and to fold into catalytically active forms. Reversible covalent interactions
between complementary subunits provide a different way to encode information,
and potentially function, in sequence-defined oligomers. Here, we
examine six oligoarylacetylene trimers composed of aniline and benzaldehyde
subunits. Four of these trimers self-pair to form two-rung duplex
structures, and two form macrocyclic 1,3-folded structures. The equilibrium
proportions of these structures can be driven to favor each of the
observed structures almost entirely depending upon the concentration
of trimers and an acid catalyst. Quenching the acidic trimer solutions
with an organic base kinetically traps all species such that they
can be isolated and characterized. Mixtures of complementary trimers
form exclusively sequence-specific 3-rung duplexes. Our results suggest
that reversible covalent bonds could in principle guide the formation
of more complex folded conformations of longer oligomers.
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Affiliation(s)
- Kyle R Strom
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
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7
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Leguizamon SC, Scott TF. Mimicking DNA Functions with Abiotic, Sequence-Defined Polymers. POLYM REV 2021. [DOI: 10.1080/15583724.2021.2014519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Samuel C. Leguizamon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Timothy F. Scott
- Department of Chemical Engineering, Monash University, Clayton, VIC, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, VIC, Australia
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8
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Rosa-Gastaldo D, Pečiukėnas V, Hunter CA, Gabrielli L. Duplex vs. folding: tuning the self-assembly of synthetic recognition-encoded aniline oligomers. Org Biomol Chem 2021; 19:8947-8954. [PMID: 34622914 DOI: 10.1039/d1ob01882e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the challenges in the realization of synthetic oligomers capable of sequence-selective duplex formation is intramolecular folding interaction between complementary recognition units. To assess whether complementary hetero-oligomers can assemble into high fidelity duplex structures, the competing folding equilibria must be carefully considered. A family of recognition-encoded aniline oligomers were assembled via reductive amination of dianiline linkers and dialdehyde monomers, which were equipped with either a 2-trifluoromethylphenol or a phosphine oxide H-bond recognition unit. To test the possibility of 1,2-folding in mixed sequence oligomers, the self-assembly properties of the homo- and hetero-dimers were characterised by 19F and 1H NMR titration and dilution experiments in toluene and in chloroform. Three different systems were investigated with variations in the steric bulk around the H-bond acceptor unit and the length of the dianiline linker. For two systems, the hetero-dimers folded with intramolecular H-bonding in the monomeric state, reducing stability of the intermolecular duplex by two to three orders of magnitude compared with the corresponding homo-oligomers. However, the use of a long rigid linker as the backbone connecting two monomer units successfully prevents 1,2-folding and leads to the formation of a stable mixed sequence duplex in toluene.
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Affiliation(s)
| | - Vytautas Pečiukėnas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Luca Gabrielli
- Department of Chemistry, University of Padova, via Marzolo 1, Padova, 35131, Italy.
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9
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Iadevaia G, Swain JA, Núñez-Villanueva D, Bond AD, Hunter CA. Folding and duplex formation in mixed sequence recognition-encoded m-phenylene ethynylene polymers. Chem Sci 2021; 12:10218-10226. [PMID: 34377409 PMCID: PMC8336474 DOI: 10.1039/d1sc02288a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/30/2021] [Indexed: 11/21/2022] Open
Abstract
Oligomers equipped with complementary recognition units have the potential to encode and express chemical information in the same way as nucleic acids. The supramolecular assembly properties of m-phenylene ethynylene polymers equipped with H-bond donor (D = phenol) and H-bond acceptor (A = phosphine oxide) side chains have been investigated in chloroform solution. Polymerisation of a bifunctional monomer in the presence of a monofunctional chain stopper was used for the one pot synthesis of families of m-phenylene ethynylene polymers with sequences ADnA or DAnD (n = 1-5), which were separated by chromatography. All of the oligomers self-associate due to intermolecular H-bonding interactions, but intramolecular folding of the monomeric single strands can be studied in dilute solution. NMR and fluorescence spectroscopy show that the 3-mers ADA and DAD do not fold, but there are intramolecular H-bonding interactions for all of the longer sequences. Nevertheless, 1 : 1 mixtures of sequence complementary oligomers all form stable duplexes. Duplex stability was quantified using DMSO denaturation experiments, which show that the association constant for duplex formation increases by an order of magnitude for every base-pairing interaction added to the chain, from 103 M-1 for ADA·DAD to 105 M-1 for ADDDA·DAAAD. Intramolecular folding is the major pathway that competes with duplex formation between recognition-encoded oligomers and limits the fidelity of sequence-selective assembly. The experimental approach described here provides a practical strategy for rapid evaluation of suitability for the development of programmable synthetic polymers.
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Affiliation(s)
- Giulia Iadevaia
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jonathan A Swain
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Diego Núñez-Villanueva
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Andrew D Bond
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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10
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Troselj P, Bolgar P, Ballester P, Hunter CA. High-Fidelity Sequence-Selective Duplex Formation by Recognition-Encoded Melamine Oligomers. J Am Chem Soc 2021; 143:8669-8678. [PMID: 34081864 PMCID: PMC8213060 DOI: 10.1021/jacs.1c02275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Melamine oligomers composed of repeating triazine-piperidine units and equipped with phenol and phosphine oxide side-chains form H-bonded duplexes. The melamine backbone provides sufficient rigidity to prevent intramolecular folding of oligomers up to three recognition units in length, leading to reliable duplex formation between sequence complementary oligomers. NMR spectroscopy and isothermal titration calorimetry (ITC) were used to characterize the self-assembly properties of the oligomers. For length-complementary homo-oligomers, duplex formation in toluene is characterized by an increase in stability of an order of magnitude for every base-pair added to the chain. NMR spectra of dilute solutions of the AD 2-mer show that intramolecular H-bonding between neighboring recognition units on the chain (1,2-folding) does not occur. NMR spectra of dilute solutions of both the AAD and the ADD 3-mer show that 1,3-folding does not take place either. ITC was used to characterize interactions between all pairwise combinations of the six different 3-mer sequences, and the sequence complementary duplexes are approximately an order of magnitude more stable than duplexes with a single base mismatch. High-fidelity duplex formation combined with the synthetic accessibility of the monomer building blocks makes these systems attractive targets for further investigation.
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Affiliation(s)
- Pavle Troselj
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Peter Bolgar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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11
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Aksakal R, Mertens C, Soete M, Badi N, Du Prez F. Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004038. [PMID: 33747749 PMCID: PMC7967060 DOI: 10.1002/advs.202004038] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/22/2020] [Indexed: 05/19/2023]
Abstract
In the last decade, the field of sequence-defined polymers and related ultraprecise, monodisperse synthetic macromolecules has grown exponentially. In the early stage, mainly articles or reviews dedicated to the development of synthetic routes toward their preparation have been published. Nowadays, those synthetic methodologies, combined with the elucidation of the structure-property relationships, allow envisioning many promising applications. Consequently, in the past 3 years, application-oriented papers based on discrete synthetic macromolecules emerged. Hence, material science applications such as macromolecular data storage and encryption, self-assembly of discrete structures and foldamers have been the object of many fascinating studies. Moreover, in the area of life sciences, such structures have also been the focus of numerous research studies. Here, it is aimed to highlight these recent applications and to give the reader a critical overview of the future trends in this area of research.
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Affiliation(s)
- Resat Aksakal
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Chiel Mertens
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Matthieu Soete
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Nezha Badi
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Filip Du Prez
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
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12
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Taura D, Wang X, Ito M, Yashima E. Selective formation of spiroborate-based double-stranded hetero-helicates assisted by donor–acceptor interactions. Org Chem Front 2021. [DOI: 10.1039/d1qo00286d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel spiroborate-based double-stranded hetero-helicate is selectively formed through donor–acceptor interactions between the central electron-rich porphyrin and electron-deficient naphthalene diimide units.
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Affiliation(s)
- Daisuke Taura
- Department of Molecular and Macromolecular Chemistry
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Xiang Wang
- Department of Molecular and Macromolecular Chemistry
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Masaki Ito
- Department of Molecular and Macromolecular Chemistry
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Eiji Yashima
- Department of Molecular and Macromolecular Chemistry
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
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13
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Santoro A, Holub J, Fik‐Jaskółka MA, Vantomme G, Lehn J. Dynamic Helicates Self‐Assembly from Homo‐ and Heterotopic Dynamic Covalent Ligand Strands. Chemistry 2020; 26:15664-15671. [DOI: 10.1002/chem.202003496] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/17/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Antonio Santoro
- Laboratoire de Chimie Supramoléculaire, ISIS Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
- Present address: Department of Chemical, Biological, Pharmaceutical and Environmental Sciences University of Messina Viale F. Stagno d'Alcontres 31 98166 Messina Italy
| | - Jan Holub
- Laboratoire de Chimie Supramoléculaire, ISIS Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
- Present address: Institute of Chemical Research of Catalonia (ICIQ) Avinguda Països Catalans 16 43007 Tarragona Spain
| | - Marta A. Fik‐Jaskółka
- Laboratoire de Chimie Supramoléculaire, ISIS Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
- Present address: Faculty of Chemistry Adam Mickiewicz University Uniwersytetu Poznańskiego 8 61-614 Poznań Poland
- Present address: Centre for Advanced Technology Adam Mickiewicz University Uniwersytetu Poznańskiego 10 61-614 Poznań Poland
| | - Ghislaine Vantomme
- Laboratoire de Chimie Supramoléculaire, ISIS Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
- Present address: Institute for Complex Molecular Systems Laboratory of Macromolecular and Organic Chemistry Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Jean‐Marie Lehn
- Laboratoire de Chimie Supramoléculaire, ISIS Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
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14
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Affiliation(s)
- Jean‐François Lutz
- Université de Strasbourg, CNRSInstitut Charles Sadron, UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
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15
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Strom KR, Szostak JW, Prywes N. Transfer of Sequence Information and Replication of Diimine Duplexes. J Org Chem 2019; 84:3754-3761. [PMID: 30855962 PMCID: PMC7547894 DOI: 10.1021/acs.joc.9b00095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The
ability of the biopolymers RNA and DNA to store and transfer
information is essential to life. Herein, we demonstrate template-directed
replication in a set of dimer duplexes that use reversible covalent
bonds to form base-pairing interactions. Binary sequence information
was encoded as a sequence of aniline and benzaldehyde subunits linked
together by a diethynyl benzene backbone. These dimers formed sequence-specific,
imine-linked duplexes, which could be separated and used as templates
for the synthesis of daughter duplexes with identical sequences.
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Affiliation(s)
- Kyle R Strom
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States
| | - Noam Prywes
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States
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16
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Schneider HJ. Strain effects determine the performance of artificial allosteric systems: calixarenes as models. Chem Commun (Camb) 2019; 55:3433-3444. [PMID: 30843901 DOI: 10.1039/c9cc00573k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
It is shown that the performance of allosteric systems regarding the efficiency and the speed of response depends critically on the strain energy of the equilibrating conformers and of the corresponding interconversion transition state. The affinity of a substrate A can be large enough to overcome in the absence of an effector E by induced fit the strain involved in the formation of an optimal conformation for binding A. The efficiency as given by the ratio KAE/KA of binding constants in the presence or absence of an effector is, for many published synthetic allosteric systems, relatively low; in practice this means that these only function within rather limited concentration ranges. A small KAE/KA ratio means that the binding strength of A or the corresponding signal will increase only little by adding an effector, and may need higher concentration of E. Implementation of steric distortion in the minor conformer can lead to reduced binding of A in the absence of the effector E. Destabilization of conformers can also result from the inclusion of high energy water molecules within a cavity. Furthermore, until now it has been overlooked that strain in the transition state can lead to reaction times of up to days, and thus to the neglect of experimental observation. The role of conformational changes within an allosteric molecule is characterized with a variety of calixarenes and other compound classes, offering a clue for the design of more efficient synthetic systems with high cooperativity.
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Affiliation(s)
- Hans-Jörg Schneider
- FR Organische Chemie, Universität des Saarlandes, D 66041 Saarbrücken, Germany.
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17
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Tai CY, Fu JH, Lee YH, He YJ, Wang SC, Chan YT. Facile synthesis of multicomponent heterobimetallic metallomacrocycles through selective metal–ligand coordination. Chem Commun (Camb) 2019; 55:6289-6292. [DOI: 10.1039/c9cc02430a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Through selective coordination, three heterobimetallic ZnII–PdII/PtII metallomacrocycles have been constructed by either a stepwise or a one-pot self-assembly protocol.
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Affiliation(s)
- Chang-You Tai
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
| | - Jun-Hao Fu
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
| | - Yin-Hsuan Lee
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
| | - Yun-Jui He
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
| | - Shi-Cheng Wang
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
| | - Yi-Tsu Chan
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
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18
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Swain J, Iadevaia G, Hunter CA. H-Bonded Duplexes based on a Phenylacetylene Backbone. J Am Chem Soc 2018; 140:11526-11536. [PMID: 30179469 PMCID: PMC6148443 DOI: 10.1021/jacs.8b08087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Indexed: 11/30/2022]
Abstract
Complementary phenylacetylene oligomers equipped with phenol and phosphine oxide recognition sites form stable multiply H-bonded duplexes in toluene solution. Oligomers were prepared by Sonogashira coupling of diiodobenzene and bis-acetylene building blocks in the presence of monoacetylene chain terminators. The product mixtures were separated by reverse phase preparative high-pressure liquid chromatography to give a series of pure oligomers up to seven recognition units in length. Duplex formation between length complementary homo-oligomers was demonstrated by 31P NMR denaturation experiments using dimethyl sulfoxide as a competing H-bond acceptor. The denaturation experiments were used to determine the association constants for duplex formation, which increase by nearly 2 orders of magnitude for every phenol-phosphine oxide base-pair added. These experiments show that the phenylacetylene backbone supports formation of extended duplexes with multiple cooperative intermolecular H-bonding interactions, and together with previous studies on the mixed sequence phenylacetylene 2-mer, suggest that this supramolecular architecture is a promising candidate for the development of synthetic information molecules that parallel the properties of nucleic acids.
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Affiliation(s)
- Jonathan
A. Swain
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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19
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Iadevaia G, Núñez-Villanueva D, Stross AE, Hunter CA. Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers. Org Biomol Chem 2018; 16:4183-4190. [PMID: 29790563 PMCID: PMC5989393 DOI: 10.1039/c8ob00819a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 04/30/2018] [Indexed: 01/06/2023]
Abstract
Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.
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Affiliation(s)
- Giulia Iadevaia
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
| | - Diego Núñez-Villanueva
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
| | - Alexander E. Stross
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
| | - Christopher A. Hunter
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
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20
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Yamasaki Y, Shio H, Amimoto T, Sekiya R, Haino T. Majority-Rules Effect and Allostery in Molecular Recognition of Calix[4]arene-Based Triple-Stranded Metallohelicates. Chemistry 2018; 24:8558-8568. [DOI: 10.1002/chem.201800997] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/09/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Yutaro Yamasaki
- Department of Chemistry, Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi- Hiroshima 739-8526 Japan
| | - Hidemi Shio
- Department of Chemistry, Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi- Hiroshima 739-8526 Japan
| | - Tomoko Amimoto
- Natural Science Center for Basic Research and Development; Hiroshima University; 1-3-1 Kagamiyama Higashi- Hiroshima 739-8526 Japan
| | - Ryo Sekiya
- Department of Chemistry, Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi- Hiroshima 739-8526 Japan
| | - Takeharu Haino
- Department of Chemistry, Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi- Hiroshima 739-8526 Japan
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21
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22
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Stross A, Iadevaia G, Núñez-Villanueva D, Hunter CA. Sequence-Selective Formation of Synthetic H-Bonded Duplexes. J Am Chem Soc 2017; 139:12655-12663. [PMID: 28857551 PMCID: PMC5627343 DOI: 10.1021/jacs.7b06619] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 11/30/2022]
Abstract
Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M-1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor-acceptor sequences are avoided.
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Affiliation(s)
- Alexander
E. Stross
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Diego Núñez-Villanueva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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23
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Núñez-Villanueva D, Iadevaia G, Stross AE, Jinks MA, Swain JA, Hunter CA. H-Bond Self-Assembly: Folding versus Duplex Formation. J Am Chem Soc 2017; 139:6654-6662. [PMID: 28470070 PMCID: PMC5469522 DOI: 10.1021/jacs.7b01357] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 01/05/2023]
Abstract
Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Alexander E. Stross
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Michael A. Jinks
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Jonathan A. Swain
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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24
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Núñez-Villanueva D, Hunter CA. Homochiral oligomers with highly flexible backbones form stable H-bonded duplexes. Chem Sci 2017; 8:206-213. [PMID: 28451167 PMCID: PMC5308278 DOI: 10.1039/c6sc02995g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/02/2016] [Indexed: 12/24/2022] Open
Abstract
Two homochiral building blocks featuring a protected thiol, an alkene and a H-bond recognition unit (phenol or phosphine oxide) have been prepared. Iterative photochemical thiol-ene coupling reactions were used to synthesize oligomers containing 1-4 phosphine oxide and 1-4 phenol recognition sites. Length-complementary H-bond donor and H-bond acceptor oligomers were found to form stable duplexes in toluene. NMR titrations and thermal denaturation experiments show that the association constant and the enthalpy of duplex formation increase significantly for every additional H-bonding unit added to the chain. There is an order of magnitude increase in stability for each additional H-bonding interaction at room temperature indicating that all of the H-bonding sites are fully bound to their complements in the duplexes. The backbone of the thiol-ene duplexes is a highly flexible alkane chain, but this conformational flexibility does not have a negative impact on binding affinity. The average effective molarity for the intramolecular H-bonding interactions that zip up the duplexes is 18 mM. This value is somewhat higher than the EM of 14 mM found for a related family of duplexes, which have the same recognition units but a more rigid backbone prepared using reductive amination chemistry. The flexible thiol-ene AAAA·DDDD duplex is an order of magnitude more stable than the rigid reductive amination AAAA·DDDD duplex. The backbone of the thiol-ene system retains much of its conformational flexibility in the duplex, and these results show that highly flexible molecules can make very stable complexes, provided there is no significant restriction of degrees of freedom on complexation.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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25
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Yashima E, Ousaka N, Taura D, Shimomura K, Ikai T, Maeda K. Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions. Chem Rev 2016; 116:13752-13990. [PMID: 27754649 DOI: 10.1021/acs.chemrev.6b00354] [Citation(s) in RCA: 1198] [Impact Index Per Article: 149.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In this review, we describe the recent advances in supramolecular helical assemblies formed from chiral and achiral small molecules, oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been observed in or achieved by biological systems. In addition, a brief historical overview of the helical assemblies of small molecules and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described.
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Affiliation(s)
- Eiji Yashima
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University , Chikusa-ku, Nagoya 464-8603, Japan
| | - Naoki Ousaka
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University , Chikusa-ku, Nagoya 464-8603, Japan
| | - Daisuke Taura
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University , Chikusa-ku, Nagoya 464-8603, Japan
| | - Kouhei Shimomura
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University , Chikusa-ku, Nagoya 464-8603, Japan
| | - Tomoyuki Ikai
- Graduate School of Natural Science and Technology, Kanazawa University , Kakuma-machi, Kanazawa 920-1192, Japan
| | - Katsuhiro Maeda
- Graduate School of Natural Science and Technology, Kanazawa University , Kakuma-machi, Kanazawa 920-1192, Japan
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26
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Stross AE, Iadevaia G, Hunter CA. Mix and match recognition modules for the formation of H-bonded duplexes. Chem Sci 2016; 7:5686-5691. [PMID: 30034707 PMCID: PMC6022071 DOI: 10.1039/c6sc01884j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/24/2016] [Indexed: 11/21/2022] Open
Abstract
Oligomeric molecules equipped with complementary H-bond recognition sites form stable duplexes in non-polar solvents. The use of a single H-bond between a good H-bond donor and a good H-bond acceptor as the recognition motif appended to a non-polar backbone leads to an architecture with interchangeable recognition alphabets. The interactions of three different families of H-bond acceptor oligomers (pyridine, pyridine N-oxide or phosphine oxide recognition module) with a family of H-bond donor oligomers (phenol recognition module) are compared. All three donor-acceptor combinations form stable duplexes, where the stability of the 1 : 1 complex increases with increasing numbers of recognition modules. The effective molarity for formation of intramolecular H-bonds that lead to zipping up of the duplex (EM) increases with decreasing flexibility of the recognition modules: 14 mM for the phosphine oxides which are connected to the backbone via a flexible linker; 40 mM for the pyridine N-oxides which have three fewer degrees of torsional freedom, and 80 mM for the pyridines where the geometry of the H-bond is more directional. However, the pyridine-phenol H-bond is an order of magnitude weaker than the other two types of H-bond, so overall the pyridine N-oxides form the most stable duplexes with the highest degree of cooperativity. The results show that it is possible to use different recognition motifs with the same duplex architecture, and this makes it possible to tune overall stabilities of the complexes by varying the components.
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Affiliation(s)
- Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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27
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Iadevaia G, Stross AE, Neumann A, Hunter CA. Mix and match backbones for the formation of H-bonded duplexes. Chem Sci 2016; 7:1760-1767. [PMID: 28936325 PMCID: PMC5592378 DOI: 10.1039/c5sc04467g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/18/2015] [Indexed: 11/21/2022] Open
Abstract
The formation of well-defined supramolecular assemblies involves competition between intermolecular and intramolecular interactions, which is quantified by effective molarity. Formation of a duplex between two oligomers equipped with recognition sites displayed along a non-interacting backbone requires that once one intermolecular interaction has been formed, all subsequent interactions take place in an intramolecular sense. The efficiency of this process is governed by the geometric complementarity and conformational flexibility of the backbone linking the recognition sites. Here we report a series of phosphine oxide H-bond acceptor AA 2-mers and phenol H-bond donor DD 2-mers, where the two recognition sites are connected by isomeric backbone modules that vary in geometry and flexibility. All AA and DD combinations form stable AA·DD duplexes, where two cooperative H-bonds lead to an increase in stability of an order of magnitude compared with the corresponding A·D complexes that can only form one H-bond. For all six possible backbone combinations, the effective molarity for duplex formation is approximately constant (7-20 mM). Thus strict complementarity and high degrees of preorganisation are not required for efficient supramolecular assembly. Provided there is some flexibility, quite different backbone modules can be used interchangeably to construct stable H-bonded duplexes.
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Affiliation(s)
- Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Anja Neumann
- Department of Chemistry , University of Sheffield , Sheffield S3 7HF , UK
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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28
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Progress in Heterocyclic Metallosupramolecular Construction. ADVANCES IN HETEROCYCLIC CHEMISTRY 2016. [DOI: 10.1016/bs.aihch.2016.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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29
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Stross AE, Iadevaia G, Hunter CA. Cooperative duplex formation by synthetic H-bonding oligomers. Chem Sci 2015; 7:94-101. [PMID: 29861969 PMCID: PMC5950798 DOI: 10.1039/c5sc03414k] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/15/2015] [Indexed: 01/12/2023] Open
Abstract
Flexible phenol-phosphine oxide oligomers show promise as a new class of synthetic information molecule.
A series of flexible oligomers equipped with phenol H-bond donors and phosphine oxide H-bond acceptors have been synthesised using reductive amination chemistry. H-bonding interactions between complementary oligomers leads to the formation of double-stranded complexes which were characterised using NMR titrations and thermal denaturation experiments. The stability of the duplex increases by one order of magnitude for every H-bonding group added to the chain. Similarly, the enthalpy change for duplex assembly and the melting temperature for duplex denaturation both increase with increasing chain length. These observations indicate that H-bond formation along the oligomers is cooperative despite the flexible backbone, and the effective molarity for intramolecular H-bond formation (14 mM) is sufficient to propagate the formation of longer duplexes using this approach. The product K EM, which is used to quantify chelate cooperativity is 5, which means that each H-bond is more than 80% populated in the assembled duplex. The modular design of these oligomers represents a general strategy for the design of synthetic information molecules that could potentially encode and replicate chemical information in the same way as nucleic acids.
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Affiliation(s)
- Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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30
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Kulkarni A, Dugasani SR. Photoelectric properties in metal ion modified DNA nanostructure. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2015:4359-4362. [PMID: 26737260 DOI: 10.1109/embc.2015.7319360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Due to specific or as designed self-assembly, DNA nanostructures gaining popularity in various nanoscale electronic applications. Herein, a novel divalent metal ion-DNA complex known as M-DNA have been investigated for its photoelectric characteristics. The increased conductivity of M-DNA thin films is attributed to the metal ion electrical and optical properties. The gate voltage effect along with illumination on the conductivity of M-DNA demonstrates that M-DNA can be used as an active element of a field-effect transistor. The Zn DNA shows maximum conductivity of 300μS/cm at 480 nm light illumination suggest that M-DNA can be utilized in nano-opto-electronics and bio-sensing applications.
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31
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Makiguchi W, Tanabe J, Yamada H, Iida H, Taura D, Ousaka N, Yashima E. Chirality- and sequence-selective successive self-sorting via specific homo- and complementary-duplex formations. Nat Commun 2015; 6:7236. [PMID: 26051291 PMCID: PMC4468858 DOI: 10.1038/ncomms8236] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 04/20/2015] [Indexed: 11/12/2022] Open
Abstract
Self-recognition and self-discrimination within complex mixtures are of fundamental importance in biological systems, which entirely rely on the preprogrammed monomer sequences and homochirality of biological macromolecules. Here we report artificial chirality- and sequence-selective successive self-sorting of chiral dimeric strands bearing carboxylic acid or amidine groups joined by chiral amide linkers with different sequences through homo- and complementary-duplex formations. A mixture of carboxylic acid dimers linked by racemic-1,2-cyclohexane bis-amides with different amide sequences (NHCO or CONH) self-associate to form homoduplexes in a completely sequence-selective way, the structures of which are different from each other depending on the linker amide sequences. The further addition of an enantiopure amide-linked amidine dimer to a mixture of the racemic carboxylic acid dimers resulted in the formation of a single optically pure complementary duplex with a 100% diastereoselectivity and complete sequence specificity stabilized by the amidinium–carboxylate salt bridges, leading to the perfect chirality- and sequence-selective duplex formation. The recognition and self-sorting of chiral molecules is a vital feature of many biomolecules. Here, the authors report chirality- and sequence-specific self-sorting of organic strands containing carboxylic acid or amidine groups, leading to selective duplex formation.
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Affiliation(s)
- Wataru Makiguchi
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Junki Tanabe
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hidekazu Yamada
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroki Iida
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Daisuke Taura
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Naoki Ousaka
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Eiji Yashima
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
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32
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Bazzicalupi C, Bianchi A, Biver T, Giorgi C, Santarelli S, Savastano M. Formation of Double-Strand Dimetallic Helicates with a Terpyridine-Based Macrocycle. Inorg Chem 2014; 53:12215-24. [DOI: 10.1021/ic502329s] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Carla Bazzicalupi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Antonio Bianchi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tarita Biver
- Department
of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi
3, 56124 Pisa, Italy
| | - Claudia Giorgi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Samuele Santarelli
- Eni S.p.A., Centro Ricerche per le Energie
non Convenzionali, Istituto Eni-Donegani, Via G. Fauser 4, 28100 Novara, Italy
| | - Matteo Savastano
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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Ayme JF, Beves JE, Campbell CJ, Leigh DA. The self-sorting behavior of circular helicates and molecular knots and links. Angew Chem Int Ed Engl 2014; 53:7823-7. [PMID: 24899408 PMCID: PMC4321334 DOI: 10.1002/anie.201404270] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Indexed: 11/10/2022]
Abstract
We report on multicomponent self-sorting to form open circular helicates of different sizes from a primary monoamine, Fe(II) ions, and dialdehyde ligand strands that differ in length and structure by only two oxygen atoms. The corresponding closed circular helicates that are formed from a diamine--a molecular Solomon link and a pentafoil knot--also self-sort, but up to two of the Solomon-link-forming ligand strands can be accommodated within the pentafoil knot structure and are either incorporated or omitted depending on the stage that the components are mixed.
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Affiliation(s)
- Jean-François Ayme
- J.-F. Ayme, Prof. D. A. Leigh School of Chemistry, University of ManchesterOxford Road, Manchester M13 9PL (UK)
- Dr. J. E. Beves, Dr. C. J. Campbell, Prof. D. A. Leigh School of Chemistry, University of Edinburgh, The King's
BuildingsWest Mains Road, Edinburgh EH9 3JJ (UK)
| | - Jonathon E Beves
- J.-F. Ayme, Prof. D. A. Leigh School of Chemistry, University of ManchesterOxford Road, Manchester M13 9PL (UK)
- Dr. J. E. Beves, Dr. C. J. Campbell, Prof. D. A. Leigh School of Chemistry, University of Edinburgh, The King's
BuildingsWest Mains Road, Edinburgh EH9 3JJ (UK)
| | - Christopher J Campbell
- J.-F. Ayme, Prof. D. A. Leigh School of Chemistry, University of ManchesterOxford Road, Manchester M13 9PL (UK)
- Dr. J. E. Beves, Dr. C. J. Campbell, Prof. D. A. Leigh School of Chemistry, University of Edinburgh, The King's
BuildingsWest Mains Road, Edinburgh EH9 3JJ (UK)
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Ayme JF, Beves JE, Campbell CJ, Leigh DA. The Self-Sorting Behavior of Circular Helicates and Molecular Knots and Links. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404270] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Saito N, Shigeno M, Yamaguchi M. Two-Component Fibers/Gels and Vesicles Formed from Hetero-Double-Helices of Pseudoenantiomeric Ethynylhelicene Oligomers with Branched Side Chains. Chemistry 2012; 18:8994-9004. [DOI: 10.1002/chem.201200280] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/07/2012] [Indexed: 12/29/2022]
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Gan Q, Shang J, Kauffmann B, Wang Y, Bie F, Jiang H. A highly stable double helix of aromatic oligoamide comprised of fused ring aromatic units. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.081] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Aboshyan-Sorgho L, Cantuel M, Bernardinelli G, Piguet C. Looking for the origin of the switch between coordination-captured helicates and catenates. Dalton Trans 2012; 41:7218-26. [DOI: 10.1039/c2dt30414g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Borodkin GS, Borodkina IG, Garnovskii AD. Heteronuclear NMR spectroscopy in the coordination chemistry. RUSS J COORD CHEM+ 2011. [DOI: 10.1134/s1070328411070025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Mujahid A, Keppler M, Lieberzeit PA, Dickert FL. From mono- to polytopic interactions via hydrogen bonds — Capacitive sensor studies. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2011. [DOI: 10.1016/j.msec.2010.11.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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Li Y, Mullen KM, Sardinha J, Félix V, Beer PD. Clipping and stoppering anion templated synthesis of a [2]rotaxane host system. Dalton Trans 2011; 40:12180-90. [DOI: 10.1039/c1dt10887e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Jana P, Maity S, Maity SK, Haldar D. A new peptide motif in the formation of supramolecular double helices. Chem Commun (Camb) 2011; 47:2092-4. [DOI: 10.1039/c0cc04244g] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Stefankiewicz AR, Harrowfield J, Madalan A, Rissanen K, Sobolev AN, Lehn JM. Structural and metallo selectivity in the assembly of [2 × 2] grid-type metallosupramolecular species: Mechanisms and kinetic control. Dalton Trans 2011; 40:12320-32. [DOI: 10.1039/c1dt11226k] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Artur R Stefankiewicz
- Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg, 8, allée Gaspard Monge, 67083, Strasbourg, France
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Campbell VE, de Hatten X, Delsuc N, Kauffmann B, Huc I, Nitschke JR. Cascading transformations within a dynamic self-assembled system. Nat Chem 2010; 2:684-7. [DOI: 10.1038/nchem.693] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 04/30/2010] [Indexed: 11/09/2022]
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Belyakov PA, Kadentsev VI, Chizhov AO, Kolotyrkina NG, Shashkov AS, Ananikov VP. Mechanistic insight into organic and catalytic reactions by joint studies using mass spectrometry and NMR spectroscopy. MENDELEEV COMMUNICATIONS 2010. [DOI: 10.1016/j.mencom.2010.05.001] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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45
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Baptiste B, Zhu J, Haldar D, Kauffmann B, Léger JM, Huc I. Hybridization of Long Pyridine-Dicarboxamide Oligomers into Multi-Turn Double Helices: Slow Strand Association and Dissociation, Solvent Dependence, and Solid State Structures. Chem Asian J 2010; 5:1364-75. [DOI: 10.1002/asia.200900713] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Gan Q, Li F, Li G, Kauffmann B, Xiang J, Huc I, Jiang H. Heteromeric double helix formation by cross-hybridization of chloro-and fluoro-substituted quinoline oligoamides. Chem Commun (Camb) 2010; 46:297-9. [DOI: 10.1039/b910435f] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Yang H, Rys A, McLaughlin C, Sleiman H. Templated Ligand Environments for the Selective Incorporation of Different Metals into DNA. Angew Chem Int Ed Engl 2009; 48:9919-23. [DOI: 10.1002/anie.200904186] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Yang H, Rys A, McLaughlin C, Sleiman H. Templated Ligand Environments for the Selective Incorporation of Different Metals into DNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904186] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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49
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Yashima E, Maeda K, Iida H, Furusho Y, Nagai K. Helical Polymers: Synthesis, Structures, and Functions. Chem Rev 2009; 109:6102-211. [PMID: 19905011 DOI: 10.1021/cr900162q] [Citation(s) in RCA: 1261] [Impact Index Per Article: 84.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Eiji Yashima
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan, and Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Katsuhiro Maeda
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan, and Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Hiroki Iida
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan, and Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yoshio Furusho
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan, and Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kanji Nagai
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan, and Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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50
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Li Y, Mullen KM, Claridge TDW, Costa PJ, Felix V, Beer PD. Sulfate anion templated synthesis of a triply interlocked capsule. Chem Commun (Camb) 2009:7134-6. [PMID: 19921007 DOI: 10.1039/b915548a] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sulfate templation has been used in the synthesis of a novel tris-urea-based triply interlocked capsule, whose structure has been verified by DOSY NMR, mass spectrometry and molecular modelling investigations.
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Affiliation(s)
- Yitong Li
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, UK OX1 3TA
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