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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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2
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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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3
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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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4
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Wang G, Yang Y, Liu H, Chen M, Jiang Z, Bai Q, Yuan J, Jiang Z, Li Y, Wang P. Modular Construction of a Tessellated Octahedron, its Hierarchical Spherical Aggregate Behavior, and Electrocatalytic CO
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Reduction Activity. Angew Chem Int Ed Engl 2022; 61:e202205851. [DOI: 10.1002/anie.202205851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Guotao Wang
- School of Metallurgy and Environment Central South University Changsha Hunan 410083 China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution Changsha Hunan 410083 China
| | - Yunna Yang
- School of Metallurgy and Environment Central South University Changsha Hunan 410083 China
| | - Hui Liu
- School of Metallurgy and Environment Central South University Changsha Hunan 410083 China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution Changsha Hunan 410083 China
| | - Mingzhao Chen
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou Key Laboratory for Clean Energy and Materials Guangzhou University Guangzhou 510006 China
| | - Zhiyuan Jiang
- Department of Organic and Polymer Chemistry Hunan Key Laboratory of Micro & Nano Materials Interface Science College of Chemistry and Chemical Engineering Central South University Changsha Hunan 410083 China
| | - Qixia Bai
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou Key Laboratory for Clean Energy and Materials Guangzhou University Guangzhou 510006 China
| | - Jie Yuan
- School of Chemistry and Chemical Engineering Henan Normal University Xinxiang Henan 453007 China
| | - Zhilong Jiang
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou Key Laboratory for Clean Energy and Materials Guangzhou University Guangzhou 510006 China
| | - Yiming Li
- Department of Organic and Polymer Chemistry Hunan Key Laboratory of Micro & Nano Materials Interface Science College of Chemistry and Chemical Engineering Central South University Changsha Hunan 410083 China
| | - Pingshan Wang
- Department of Organic and Polymer Chemistry Hunan Key Laboratory of Micro & Nano Materials Interface Science College of Chemistry and Chemical Engineering Central South University Changsha Hunan 410083 China
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou Key Laboratory for Clean Energy and Materials Guangzhou University Guangzhou 510006 China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution Changsha Hunan 410083 China
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5
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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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6
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Wang G, Yang Y, liu H, Chen M, Jiang Z, Bai Q, Yuan J, jiang Z, Li Y, Wang P. Modular Construction of a Tessellated Octahedron and its Hierarchical Spherical Aggregate Behavior. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Guotao Wang
- Central South University School of Metallurgy and Environment CHINA
| | - Yunna Yang
- Central South University School of Metallurgy and Environment CHINA
| | - Hui liu
- Central South University School of Metallurgy and Environment CHINA
| | - Mingzhao Chen
- Guangzhou University Institute of Environmental Research at Greater Bay Area CHINA
| | - Zhiyuan Jiang
- Central South University School of Chemistry and Chemical Engineering CHINA
| | - Qixia Bai
- Guangzhou University Institute of Environmental Research at Greater Bay Area CHINA
| | - Jie Yuan
- Henan Normal University School of Chemistry and Chemical Engineering CHINA
| | - Zhilong jiang
- Guangzhou University Institute of Environmental Research at Greater Bay Area CHINA
| | - Yiming Li
- Central South University College of Chemistry and Chemical Engineering CHINA
| | - Pingshan Wang
- Central South University College of Chemistry and Chemical Engineering 932 S. Lushan Rd. 410083 Changsha CHINA
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7
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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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8
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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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9
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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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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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