1
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Núñez-Villanueva D, Hunter CA. Replication of synthetic recognition-encoded oligomers by ligation of trimer building blocks. Org Chem Front 2023; 10:5950-5957. [PMID: 38022796 PMCID: PMC10661083 DOI: 10.1039/d3qo01717f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
The development of methods for replication of synthetic information oligomers will underpin the use of directed evolution to search new chemical space. Template-directed replication of triazole oligomers has been achieved using a covalent primer in conjunction with non-covalent binding of complementary building blocks. A phenol primer equipped with an alkyne was first attached to a benzoic recognition unit on a mixed sequence template via selective covalent ester base-pair formation. The remaining phenol recognition units on the template were then used for non-covalent binding of phosphine oxide oligomers equipped with an azide. The efficiency of the templated CuAAC reaction between the primer and phosphine oxide building blocks was investigated as a function of the number of H-bonds formed with the template. Increasing the strength of the non-covalent interaction between the template and the azide lead to a significant acceleration of the templated reaction. For shorter phosphine oxide oligomers intermolecular reactions compete with the templated process, but quantitative templated primer elongation was achieved with a phosphine oxide 3-mer building block that was able to form three H-bonds with the template. NMR spectroscopy and molecular models suggest that the template can fold, but addition of the phosphine oxide 3-mer leads to a complex with three H-bonds between phosphine oxide and phenol groups, aligning the azide and alkyne groups in a favourable geometry for the CuAAC reaction. In the product duplex, 1H and 31P NMR data confirm the presence of the three H-bonded base-pairs, demonstrating that the covalent and non-covalent base-pairs are geometrically compatible. A complete replication cycle was carried out starting from the oligotriazole template by covalent attachment of the primer, followed by template-directed elongation, and hydrolysis of the the ester base-pair in the resulting duplex to regenerate the template and liberate the copy strand. We have previously demonstrated sequence-selective oligomer replication using covalent base-pairing, but the trimer building block approach described here is suitable for replication of sequence information using non-covalent binding of the monomer building blocks to a template.
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Affiliation(s)
- Diego Núñez-Villanueva
- 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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2
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Rosa-Gastaldo D, Dalla Valle A, Marchetti T, Gabrielli L. Sequence-selective duplex formation and template effect in recognition-encoded oligoanilines. Chem Sci 2023; 14:8878-8888. [PMID: 37621420 PMCID: PMC10445429 DOI: 10.1039/d3sc00880k] [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: 02/16/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
A new family of duplex-forming recognition encoded oligomers, capable of sequence selective duplex formation and template directed synthesis, was developed. Monomers equipped with both amine and aldehyde groups were functionalized with 2-trifluoromethylphenol or phosphine oxide as H-bond recognition units. Duplex formation and assembly properties of homo- and hetero-oligomers were studied by 19F and 1H NMR experiments in chloroform. The designed backbone prevents the undesired 1,2-folding allowing sequence-selective duplex formation, and the stability of the antiparallel duplex is 3-fold higher than the parallel arrangement. Dynamic combinatorial chemistry was exploited for the templated synthesis of complementary oligomers, showing that an aniline dimer can template the formation of the complementary imine. The key role of the H-bond recognition confers to the system the ability to discriminate a mutated donor monomer incapable of H-bonding. Sequence selective duplex formation combined with the template effect makes this system an attractive target for further studies.
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Affiliation(s)
- Daniele Rosa-Gastaldo
- Dipartimento di Scienze Chimiche, Università degli studi di Padova via Marzolo 1 35131 Padova Italy
| | - Andrea Dalla Valle
- Dipartimento di Scienze Chimiche, Università degli studi di Padova via Marzolo 1 35131 Padova Italy
| | - Tommaso Marchetti
- Dipartimento di Scienze Chimiche, Università degli studi di Padova via Marzolo 1 35131 Padova Italy
| | - Luca Gabrielli
- Dipartimento di Scienze Chimiche, Università degli studi di Padova via Marzolo 1 35131 Padova Italy
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3
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Lewandowski B, Schäfer RJB, Cotter E, Harangozo D, Wennemers H. Catalytic templated length-controlled oligomerization. Faraday Discuss 2023; 244:119-133. [PMID: 37185626 DOI: 10.1039/d3fd00002h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Templated synthesis is an intriguing strategy for the length-controlled synthesis of oligomers. Traditionally, such reactions require stoichiometric amounts of the template with respect to the product. Recently we reported catalytic macrocyclic templates that promote oligomerization of a small molecule substrate with a remarkable degree of length control. Herein we present our efforts toward creating linear templates for catalytic length-controlled oligomer synthesis.
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Affiliation(s)
- Bartosz Lewandowski
- Laboratory of Organic Chemistry, D-CHAB, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.
| | - Rebecca J B Schäfer
- Laboratory of Organic Chemistry, D-CHAB, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.
| | - Etienne Cotter
- Laboratory of Organic Chemistry, D-CHAB, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.
| | - Dora Harangozo
- Laboratory of Organic Chemistry, D-CHAB, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.
| | - Helma Wennemers
- Laboratory of Organic Chemistry, D-CHAB, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.
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4
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Qureshi B, Juritz J, Poulton JM, Beersing-Vasquez A, Ouldridge TE. A universal method for analyzing copolymer growth. J Chem Phys 2023; 158:104906. [PMID: 36922142 DOI: 10.1063/5.0133489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerization has been studied theoretically in a number of contexts, often by considering a Markov process in which monomers are added or removed from the growing tip of a long copolymer. To date, the analysis of the most general models of this class has necessitated simulation. We present a general method for analyzing such processes without resorting to simulation. Our method can be applied to models with an arbitrary network of sub-steps prior to addition or removal of a monomer, including non-equilibrium kinetic proofreading cycles. Moreover, the approach allows for a dependency of addition and removal reactions on the neighboring site in the copolymer and thermodynamically self-consistent models in which all steps are assumed to be microscopically reversible. Using our approach, thermodynamic quantities such as chemical work; kinetic quantities such as time taken to grow; and statistical quantities such as the distribution of monomer types in the growing copolymer can be directly derived either analytically or numerically from the model definition.
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Affiliation(s)
- Benjamin Qureshi
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jordan Juritz
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jenny M Poulton
- Foundation for Fundamental Research on Matter (FOM), Institute for Atomic and Molecular Physics (AMOLF), 1098 XE Amsterdam, The Netherlands
| | | | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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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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Jia C, Zhang Y, Wang Y, Gao J, Raza A, Ogawa T, Wada S, Xie D, Wang JY. Positively charged and neutral drug-loaded liposomes as the aerosolized formulations for the efficacy assessment of tumor metastases to lungs. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.104081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Núñez-Villanueva D, Hunter CA. Effect of backbone flexibility on covalent template-directed synthesis of linear oligomers. Org Biomol Chem 2022; 20:8285-8292. [PMID: 36226964 PMCID: PMC9629452 DOI: 10.1039/d2ob01627c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Covalent template-directed synthesis can be used to replicate synthetic oligomers, but success depends critically on the conformational properties of the backbone. Here we investigate how the choice of monomer building block affects the flexibility of the backbone and in turn the efficiency of the replication process for a series of different triazole oligomers. Two competing reaction pathways were identified for monomers attached to a template, resulting in the formation of either macrocyclic or linear products. For flexible backbones, macrocycles and linear oligomers are formed at similar rates, but a more rigid backbone gave exclusively the linear product. The experimental results are consistent with ring strain calculations using molecular mechanics: products with low ring strain (20-30 kJ mol-1) formed rapidly, and products with high ring strain (>100 kJ mol-1) were not observed. Template-directed replication of linear oligomers requires monomers that rigid enough to prevent the formation of undesired macrocycles, but not so rigid that the linear templating pathway leading to the duplex is inhibited. Molecular mechanics calculations of ring strain provide a straightforward tool for assessing the flexibility of potential backbones and the viability different monomer designs before embarking on synthesis.
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Affiliation(s)
- Diego Núñez-Villanueva
- 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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8
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Núñez-Villanueva D, Hunter CA. Replication of a synthetic oligomer using chameleon base-pairs. Chem Commun (Camb) 2022; 58:11005-11008. [PMID: 36094173 DOI: 10.1039/d2cc04580j] [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
Salt bridges were used to attach polymerisable amidine monomers to an oligomeric benzoic acid template. CuAAC oligomerisation reactions in the presence of a benzoic acid 3-mer template gave the amidine 3-mer copy as the major product. Cleavage of ester linkers was used to hydrolyse off the amidine recognition units and convert the product into a benzoic acid 3-mer copy of the original template.
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Affiliation(s)
- Diego Núñez-Villanueva
- 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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9
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Battaglia AM, Pahlavanlu P, Grignon E, An SY, Seferos DS. High Active Material Loading in Organic Electrodes Enabled by a Multifunctional Binder. ACS APPLIED MATERIALS & INTERFACES 2022; 14:42298-42307. [PMID: 36083595 DOI: 10.1021/acsami.2c10070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Organic electrodes are promising candidates for next-generation lithium-ion batteries due to their low cost and sustainable nature; however, they often suffer from very low conductivity and active material loadings. The conventional binder used in organic-based Li-ion batteries is poly(vinylidene fluoride) (PVDF), yet it is electrochemically inactive and thus occupies volume and mass without storing energy. Here, we report an organic mixed ionic-electronic conducting polymer, poly[norbornene-1,2-bis(C(O)OPEDOT)]25-b-[norbornene-1,2-bis-(C(O)PEG12)]25 denoted PEDOT-b-PEG for simplicity, as a cathode binder to address the aforementioned issues. The polymer contains a poly(3,4-ethylenedioxythiophene) (PEDOT) functionality to provide electronic conductivity, as well as poly(ethylene glycol) (PEG) chains to impart ionic conductivity to the cathode composite. We compare electrodes containing a perylene diimide (PDI) active material, conductive carbon, and a polymeric binder (either PVDF or PEDOT-b-PEG) with different weight ratios to study the impact of active material loading and type of binder on the performance of the cell. The lithium-ion cells prepared with the PEDOT-b-PEG polymer binder result in higher capacities and decreased impedance at all active material loadings compared to cathodes prepared with the PVDF-containing electrodes, demonstrating potential as a new binder to achieve higher active material loadings in organic electrodes. The strategy of preparing these polymers should be broadly applicable to other classes of mixed polymer conductors.
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Affiliation(s)
- Alicia M Battaglia
- Department of Chemistry, University of Toronto, 80 Street George Street, Toronto, Ontario M5S 3H6, Canada
| | - Paniz Pahlavanlu
- Department of Chemistry, University of Toronto, 80 Street George Street, Toronto, Ontario M5S 3H6, Canada
| | - Eloi Grignon
- Department of Chemistry, University of Toronto, 80 Street George Street, Toronto, Ontario M5S 3H6, Canada
| | - So Young An
- Department of Chemistry, University of Toronto, 80 Street George Street, Toronto, Ontario M5S 3H6, Canada
| | - Dwight S Seferos
- Department of Chemistry, University of Toronto, 80 Street George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
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10
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Núñez-Villanueva D, Hunter CA. H-Bond Templated Oligomer Synthesis Using a Covalent Primer. J Am Chem Soc 2022; 144:17307-17316. [PMID: 36082527 PMCID: PMC9501907 DOI: 10.1021/jacs.2c08119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Template-directed synthesis of nucleic acids in the polymerase
chain reaction is based on the use of a primer, which is elongated
in the replication process. The attachment of a high affinity primer
to the end of a template chain has been implemented for templating
the synthesis of triazole oligomers. A covalent ester base-pair was
used to attach a primer to a mixed sequence template. The resulting
primed template has phenol recognition units on the template, which
can form noncovalent base-pairs with phosphine oxide monomers via
H-bonding, and an alkyne group on the primer, which can react with
the azide group on a phosphine oxide monomer. Competition reactions
between azides bearing phosphine oxide and phenol recognition groups
were used to demonstrate a substantial template effect, due to H-bonding
interactions between the phenols on the template and phosphine oxides
on the azide. The largest rate acceleration was observed when a phosphine
oxide 2-mer was used, because this compound binds to the template
with a higher affinity than compounds that can only make one H-bond.
The 31P NMR spectrum of the product duplex shows that the
H-bonds responsible for the template effect are present in the product,
and this result indicates that the covalent ester base-pairs and noncovalent
H-bonded base-pairs developed here are geometrically compatible. Following
the templated reaction, it is possible to regenerate the template
and liberate the copy strand by hydrolysis of the ester base-pair
used to attach the primer, thus completing a formal replication cycle.
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Affiliation(s)
- Diego Núñez-Villanueva
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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11
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Laurent Q, Sakai N, Matile S. An Orthogonal Dynamic Covalent Chemistry Tool for Ring-Opening Polymerization of Cyclic Oligochalcogenides on Detachable Helical Peptide Templates. Chemistry 2022; 28:e202200785. [PMID: 35416345 PMCID: PMC9324982 DOI: 10.1002/chem.202200785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Indexed: 12/13/2022]
Abstract
A model system is introduced as a general tool to elaborate on orthogonal templation of dynamic covalent ring‐opening polymerization (ODC‐TROP). The tool consists of 310 helical peptides as unprecedented templates and semicarbazones as orthogonal dynamic covalent linkers. With difficult‐to‐control 1,2‐dithiolanes, ODC‐TROP on the level of short model oligomers occurs with high templation efficiency, increasing and diminishing upon helix stabilization and denaturation, respectively. Further, an anti‐templated conjugate with mispositioned monomers gave reduced templation upon helix twisting. Even with the “unpolymerizable” 1,2‐diselenolanes, initial studies already afford mild templation efficiency. These proof‐of‐principle results promise that the here introduced tool, recyclable and enabling late‐stage side chain modification, will be useful to realize ODC‐TROP of intractable or unknown cyclic dynamic covalent monomers for dynamer materials as well as cellular uptake and signaling applications.
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Affiliation(s)
- Quentin Laurent
- Department of Organic Chemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, 1211, Geneva, Switzerland
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12
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Juritz J, Poulton JM, Ouldridge TE. Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions. J Chem Phys 2022; 156:074103. [DOI: 10.1063/5.0077865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jordan Juritz
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jenny M. Poulton
- Foundation for Fundamental Research on Matter (FOM), Institute for Atomic and Molecular Physics (AMOLF), 1098 XE Amsterdam, The Netherlands
| | - Thomas E. Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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13
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Fasano F, Bolgar P, Iadevaia G, Hunter CA. Supramolecular template-directed synthesis of triazole oligomers. Chem Sci 2022; 13:13085-13093. [PMID: 36425510 PMCID: PMC9667925 DOI: 10.1039/d2sc04155c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
Sandwich complexes formed by two zinc porphyrins and a diamine ligand (DABCO) have been used as a supramolecular template to direct the synthesis of triazole oligomers. Monomer units equipped with two polymerizable functional groups, an alkyne and an azide, were attached to the template via ester bonds between a phenol unit on the monomer and benzoic acid units on the porphyrin. Self-assembly of the zinc porphyrins by addition of DABCO led to a supramolecular complex containing four of the monomer units, two on each porphyrin. CuAAC oligomerisation was carried out in the presence of a chain capping agent to prevent intermolecular reactions between the templated products, which carry reactive chain ends. The templated-directed oligomerisation resulted in selective formation of a duplex, which contains two identical chains of triazole oligomers connecting the porphyrin linkers. The effective molarity for the intramolecular CuAAC reactions on the template is 3–9 mM, and because the triazole backbone has a direction, the product duplex was obtained as a 4 : 1 mixture of the parallel and antiparallel isomers. Hydrolysis of the ester bonds connecting the oligomers to the template gave a single product, the phenol 2-mer, in excellent yield. The introduction of a supramolecular element into the template considerably broadens the scope of the covalent template-directed oligomerisation methodology that we previously developed for the replication of sequence information in synthetic oligomers. A supramolecular metalloporphyrin assembly was used as a disposable template for controlling the oligomerisation of covalently attached monomer building blocks to give a linear oligomeric product that is not accessible via untemplated reactions.![]()
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Affiliation(s)
- Francesco Fasano
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Peter Bolgar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Giulia Iadevaia
- 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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14
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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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15
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Zhang X, Gou F, Wang X, Wang Y, Ding S. Easily Functionalized and Readable Sequence-Defined Polytriazoles. ACS Macro Lett 2021; 10:551-557. [PMID: 35570766 DOI: 10.1021/acsmacrolett.1c00145] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Developing sequence-defined skeletons that could be conveniently characterized and functionalized with diverse side groups is attractive but challenging. Here we report one novel sequence-defined polytriazole structure bearing side groups at its triazole rings. Its construction was facilely accessed by the iterative employments of azidation and iridium-catalyzed cycloaddition of azide with internal 1-thioalkyne (IrAAC) in solution phase. The easy preparation of 1-thioalkyne monomers and the excellent tolerance of IrAAC enable the introduction of diverse functional side chains to this architecture. The obtained sequence was effectively characterized by tandem mass spectrometry owing to the efficient fractures of both of the Csp3-S and Csp3-N bonds in its backbone, indicating its potential utilization in high-capacity digital polymer developments. Further successful application of this structure in building monodisperse macromolecules exhibiting aggregation-induced emission (AIE) characteristics demonstrates its expected application in functional material fabrications.
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Affiliation(s)
- Xueyan Zhang
- State Key Laboratory of Organic−Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Fuqi Gou
- State Key Laboratory of Organic−Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaojun Wang
- State Key Laboratory of Organic−Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yong Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Shengtao Ding
- State Key Laboratory of Organic−Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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16
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Núñez-Villanueva D, Hunter CA. Replication of Sequence Information in Synthetic Oligomers. Acc Chem Res 2021; 54:1298-1306. [PMID: 33554599 PMCID: PMC7931443 DOI: 10.1021/acs.accounts.0c00852] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 12/12/2022]
Abstract
The holy grail identified by Orgel in his 1995 Account was the development of novel chemical systems that evolve using reactions in which replication and information transfer occur together. There has been some success in the adaption of nucleic acids to make artificial analogues and in templating oligomerization reactions to form synthetic homopolymers, but replication of sequence information in synthetic polymers remains a major unsolved problem. In this Account, we describe our efforts in this direction based on a covalent base-pairing strategy to transfer sequence information between a parent template and a daughter copy. Oligotriazoles, which carry information as a sequence of phenol and benzoic acid side chains, have been prepared from bifunctional monomers equipped with an azide and an alkyne. Formation of esters between phenols and benzoic acids is used as the equivalent of nucleic base pairing to covalently attach monomer building blocks to a template oligomer. Sequential protection of the phenol side chains on the template, ester coupling of the benzoic acid side chains, and deprotection and ester coupling of the phenol side chains allow quantitative selective base-pair formation on a mixed sequence template. Copper catalyzed azide alkyne cycloaddition (CuAAC) is then used to oligomerize the monomers on the template. Finally, cleavage of the ester base pairs in the product duplex by hydrolysis releases the copy strand. This covalent template-directed synthesis strategy has been successfully used to copy the information encoded in a trimer template into a sequence-complementary oligomer in high yield.The use of covalent base pairing provides opportunities to manipulate the nature of the information transferred in the replication process. By using traceless linkers to connect the phenol and benzoic acid units, it is possible to carry out direct replication, reciprocal replication, and mutation. These preliminary results are promising, and methods have been developed to eliminate some of the side reactions that compete with the CuAAC process that zips up the duplex. In situ end-capping of the copy strand was found to be an effective general method for blocking intermolecular reactions between product duplexes. By selecting an appropriate concentration of an external capping agent, it is also possible to intercept macrocyclization of the reactive chain ends in the product duplex. The other side reaction observed is miscoupling of monomer units that are not attached to adjacent sites on the template, and optimization is required to eliminate these reactions. We are still some way from an evolvable synthetic polymer, but the chemical approach to molecular replication outlined here has some promise.
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Affiliation(s)
- Diego Núñez-Villanueva
- 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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17
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Núñez-Villanueva D, Hunter CA. Controlled mutation in the replication of synthetic oligomers. Chem Sci 2021; 12:4063-4068. [PMID: 34163677 PMCID: PMC8179503 DOI: 10.1039/d0sc06770a] [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: 12/10/2020] [Accepted: 01/29/2021] [Indexed: 12/24/2022] Open
Abstract
Replication of sequence information with mutation is the molecular basis for the evolution of functional biopolymers. Covalent template-directed synthesis has been used to replicate sequence information in synthetic oligomers, and the covalent base-pairs used in these systems provide an opportunity to manipulate the outcome of the information transfer process through the use of traceless linkers. Two new types of covalent base-pair have been used to introduce mutation in the replication of an oligotriazole, where information is encoded as the sequence of benzoic acid and phenol monomer units. When a benzoic acid-benzoic acid base-pairing system was used, a direct copy of a benzoic acid homo-oligomer template was obtained. When a phenol-benzoic acid base-pairing system was used, a reciprocal copy, the phenol homo-oligomer, was obtained. The two base-pairing systems are isosteric, so they can be used interchangeably, allowing direct and reciprocal copying to take place simultaneously on the same template strand. As a result, it was possible to introduce mutations in the replication process by spiking the monomer used for direct copying with the monomer used for reciprocal copying. The mutation rate is determined precisely by the relative proportions of the two monomers. The ability to introduce mutation at a controlled rate is a key step in the development of synthetic systems capable of evolution, which requires replication with variation.
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Affiliation(s)
- Diego Núñez-Villanueva
- 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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18
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Pahlavanlu P, Cheng S, Battaglia AM, Hicks GEJ, Jarrett-Wilkins CN, Evariste S, Seferos DS. Templated approach to well-defined, oxidatively coupled conjugated polymers. Polym Chem 2021. [DOI: 10.1039/d0py01620a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Templated oxidative polymerization affords organic soluble, oxidatively doped PEDOT-based polymers with controlled molecular weights and low dispersities (Đ ∼ 1.2) for the first time.
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Affiliation(s)
| | - Susan Cheng
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
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19
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Abstract
This review offers a summary on the advances in the construction of 1,2,3-triazole-based sequence-defined oligomers and polymers through MAAC-based ISG or IEG strategies.
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Affiliation(s)
- Xiaojun Wang
- State Key Laboratory of Organic-Inorganic Composites
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Xueyan Zhang
- State Key Laboratory of Organic-Inorganic Composites
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Shengtao Ding
- State Key Laboratory of Organic-Inorganic Composites
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
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20
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Abstract
![]()
Genetic biopolymers utilize defined
sequences and monomer-specific
molecular recognition to store and transfer information. Synthetic
polymers that mimic these attributes using reversible covalent chemistry
for base-pairing pose unique synthetic challenges. Here, we describe
a solid-phase synthesis methodology for the efficient construction
of ethynyl benzene oligomers with specific sequences of aniline and
benzaldehyde subunits. Handling these oligomers is complicated by
the fact that they often exhibit multiple conformations because of
intra- or intermolecular pairing. We describe conditions that allow
the dynamic behavior of these oligomers to be controlled so that they
may be manipulated and characterized without needing to mask the recognition
units with protecting groups.
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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, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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21
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Knappert M, Jin T, Midgley SD, Wu G, Scherman OA, Grau-Crespo R, Colquhoun HM. Single-site binding of pyrene to poly(ester-imide)s incorporating long spacer-units: prediction of NMR resonance-patterns from a fractal model. Chem Sci 2020; 11:12165-12177. [PMID: 34123224 PMCID: PMC8162740 DOI: 10.1039/d0sc03730c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Co-polycondensation of the diimide-based diols N,N′-bis(2-hydroxyethyl)hexafluoroisopropylidene-diphthalimide, (HFDI), and N,N′-bis(2-hydroxy-ethyl)naphthalene-1,4,5,8-tetracarboxylic-diimide, (NDI), with aliphatic diacyl chlorides ClOC(CH2)xCOCl (x = 5 to 8) affords linear copoly(ester-imide)s. Such copolymers interact with pyrene via supramolecular binding of the polycyclic aromatic at NDI residues. This interaction results in upfield complexation shifts and sequence-related splittings of the NDI 1H NMR resonances, but gives a very different final resonance-pattern from the copolymer where x = 2. Computational modelling of the polymer with x = 5 suggests that each pyrene molecule binds to just a single NDI residue rather than by intercalation between a pair of NDI's at a tight chain-fold, as was found for x = 2. The new single-site binding model enables the pattern of 1H NMR resonances for copolymers with longer spacers (x = 5 to 8) to be reproduced and assigned by simulation from sequence-specific shielding factors based on a type of fractal known as the last-fraction Cantor set. As this type of fractal also enables an understanding of pairwise binding systems, it evidently provides a general numerical framework for supramolecular sequence-analysis in binary copolymers. Nine 1H NMR resonances assignable to specific copoly(ester-imide) sequences identified from a fractal model result from 1 : 1 supramolecular binding of pyrene to NDI residues.![]()
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Affiliation(s)
- Marcus Knappert
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6AD UK
| | - Tianqi Jin
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6AD UK
| | - Scott D Midgley
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6AD UK
| | - Guanglu Wu
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Ricardo Grau-Crespo
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6AD UK
| | - Howard M Colquhoun
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6AD UK
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22
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Lutz JF. 100th Anniversary of Macromolecular Science Viewpoint: Toward Artificial Life-Supporting Macromolecules. ACS Macro Lett 2020; 9:185-189. [PMID: 35638671 DOI: 10.1021/acsmacrolett.9b00938] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Terrestrial Life is based on polymers. In all known living organisms, DNA stores genetic information, mutates, self-replicates, and guides the synthesis of messenger molecules. Although the function of nucleic acids is well-understood, the development of artificial macromolecular mimics remains very limited. Laboratory-synthesized nucleic acids still support Life, and some nucleic acids analogues exhibit biological functions. Yet, after hundred years of polymer science, no other type of Life-supporting macromolecule (i.e., non-nucleic acids) has ever been reported. In this context, the aim of the present viewpoint is to discuss important challenges that shall be addressed by polymer chemists to achieve artificial Life. Similarly to DNA, an artificial Life-supporting macromolecule shall store information, transfer information, and mutate. Many tools, such as sequence-defined polymer synthesis, polymer modification, supramolecular polymer chemistry, and dynamic chemistry, are already available to chemists to attain these properties. However, the design of artificial Life-supporting macromolecules is hindered by two main factors. First, the chemical search space is enormous, and it is difficult to predict promising structures, even with the help of combinatorial and chemoinformatic tools. Second, rational design is probably a limited approach to achieve macromolecules that shall be involved in nonequilibrium metabolic systems. Hence, a synergic combination of classical polymer chemistry with the more recent field of systems chemistry is probably the key toward the emergence of artificial Life-supporting macromolecules.
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Affiliation(s)
- Jean-François Lutz
- Université de Strasbourg, CNRS - UPR 22, Institut Charles Sadron, 23 rue du Loess, 67034 Strasbourg, France
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23
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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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24
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Li J, Leclercq M, Fossepré M, Surin M, Glinel K, Jonas AM, Fernandes AE. Discrete multifunctional sequence-defined oligomers with controlled chirality. Polym Chem 2020. [DOI: 10.1039/d0py00537a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New synthetic strategy leading to discrete poly(triazole-urethane) oligomers with a large range of functional side groups, programmable stereochemistry and sequentiality.
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Affiliation(s)
- Jie Li
- Institute of Condensed Matter and Nanosciences
- Bio- and Soft Matter
- Université catholique de Louvain
- 1348 Louvain-la-Neuve
- Belgium
| | - Maxime Leclercq
- Laboratory for Chemistry of Novel Materials
- Centre of Innovation and Research in Materials and Polymers (CIRMAP)
- University of Mons - UMONS
- 7000 Mons
- Belgium
| | - Mathieu Fossepré
- Laboratory for Chemistry of Novel Materials
- Centre of Innovation and Research in Materials and Polymers (CIRMAP)
- University of Mons - UMONS
- 7000 Mons
- Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials
- Centre of Innovation and Research in Materials and Polymers (CIRMAP)
- University of Mons - UMONS
- 7000 Mons
- Belgium
| | - Karine Glinel
- Institute of Condensed Matter and Nanosciences
- Bio- and Soft Matter
- Université catholique de Louvain
- 1348 Louvain-la-Neuve
- Belgium
| | - Alain M. Jonas
- Institute of Condensed Matter and Nanosciences
- Bio- and Soft Matter
- Université catholique de Louvain
- 1348 Louvain-la-Neuve
- Belgium
| | - Antony E. Fernandes
- Institute of Condensed Matter and Nanosciences
- Bio- and Soft Matter
- Université catholique de Louvain
- 1348 Louvain-la-Neuve
- Belgium
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25
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Gabrielli L, Núñez-Villanueva D, Hunter CA. Two-component assembly of recognition-encoded oligomers that form stable H-bonded duplexes. Chem Sci 2019; 11:561-566. [PMID: 32206273 PMCID: PMC7069511 DOI: 10.1039/c9sc04250d] [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] [Received: 08/23/2019] [Accepted: 11/19/2019] [Indexed: 12/17/2022] Open
Abstract
Imine chemistry was used to assemble oligomers displaying phenol and phosphine oxide side chains that selectively base-pair to give duplexes, which are stable in chloroform solution.
A new family of recognition-encoded oligomers that form stable duplexes in chloroform have been prepared. Monomer building blocks composed of dialdehydes functionalised with either a trifluoromethylphenol or phosphine oxide H-bond recognition unit were prepared. The dialdehydes were coupled with diamines by imine formation and then reduction to give homo-oligomers between one and three recognition units in length. Duplex formation was characterised by 19F and 1H NMR titration experiments in toluene and in chloroform. For duplexes formed between length complementary H-bond donor and acceptor homo-oligomers, an order of magnitude increase in stability was observed for every base-pair added to the duplex in chloroform. The effective molarity for the intramolecular H-bonds responsible for zipping up the duplex is 30 mM, which results in the fully assembled duplex in all cases. The uniform increase in duplex stability with oligomer length suggests that the backbone structure and geometry is likely to be compatible with the formation of extended duplexes in longer oligomers.
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Affiliation(s)
- Luca Gabrielli
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - 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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26
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Núñez-Villanueva D, Hunter CA. Molecular replication using covalent base-pairs with traceless linkers. Org Biomol Chem 2019; 17:9660-9665. [PMID: 31691702 DOI: 10.1039/c9ob02336d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A unique feature of kinetically inert covalent base-pairing is that the nature of the chemical information that is transferred can be modulated by changing the chemical connectivity between the two bases. Formation of esters between phenols and benzoic acids has been used as a base-pairing strategy for sequence information transfer in template-directed synthesis of linear oligomers, but the copy strand produced by this process has the complementary sequence to the template strand. It is possible to form a base-pair between two benzoic acids by using a hydroquinone linker, which is eliminated when the product duplex is hydrolysed. Using this approach, covalent template-directed synthesis was carried out using a benzoic acid 3-mer template to produce an identical copy. This direct replication process was used in iterative rounds of replication leading to an increase of the population of the copied oligomer.
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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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27
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Ciaccia M, Núñez-Villanueva D, Hunter CA. Capping Strategies for Covalent Template-Directed Synthesis of Linear Oligomers Using CuAAC. J Am Chem Soc 2019; 141:10862-10875. [PMID: 31251047 DOI: 10.1021/jacs.9b04973] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Covalent templating provides an attractive solution to the controlled synthesis of linear oligomers because a template oligomer can be used to define the precise length and sequence of the product. If the monomer units are attached to the template using kinetically inert covalent bonds it should be possible to operate at high dilution to favor intramolecular over intermolecular reaction. However, for oligomerization reactions using copper-catalyzed azide alkyne cycloaddition (CuAAC) this is not the case. The rate-limiting step is formation of an activated copper complex, so any alkyne that is activated by copper reacts rapidly with the nearest available azide. As a result, every time a chain end alkyne is activated, rapid intermolecular reaction takes place with a different oligomer leading to the formation of higher order products. It proved possible to block these intermolecular reactions by adding an excess of an azide capping agent that intercepts the chain end of the growing oligomer on the template. By adjusting the concentration of the capping agent to compete effectively with the unwanted intermolecular reactions without interfering with the desired intramolecular reactions, it was possible to obtain quantitative yields of copy strands from covalent template-directed oligomerization reactions. Remarkably, the capping agent could also be used to control the stereochemistry of the duplex formed in the templated oligomerization reaction to give exclusively the antiparallel product.
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Affiliation(s)
- Maria Ciaccia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Diego Núñez-Villanueva
- 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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28
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Núñez-Villanueva D, Ciaccia M, Hunter CA. Cap control: cyclic versus linear oligomerisation in covalent template-directed synthesis. RSC Adv 2019; 9:29566-29569. [PMID: 35531529 PMCID: PMC9071899 DOI: 10.1039/c9ra07233k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
Covalent template-directed synthesis was used to oligomerise monomer building blocks in a controlled manner to give exclusively the linear trimer. Competing reaction pathways were blocked by addition of a large excess of a monomeric capping agent. At a concentration of 1 mM, the cap selectively prevented further reaction of the product chain ends to give polymeric and macrocyclic products, but did not interfere with the templating process. The right concentration of capping agent is required to control the product distribution in covalent template-directed synthesis of linear oligomers using CuAAC.![]()
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Affiliation(s)
| | - Maria Ciaccia
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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