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Lee S, Song G, Jeong KS. Stimuli-Responsive Molecular Duplexes Displaying Duplex-to-Duplex Switching. Angew Chem Int Ed Engl 2024:e202410884. [PMID: 38937392 DOI: 10.1002/anie.202410884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 06/29/2024]
Abstract
Synthetic duplexes with high stabilities have promising potential for mimicking biomolecular functions and developing supramolecular smart materials. Herein, we describe the synthesis and stimuli-responsive properties of molecular duplexes derived from indolocarbazole-pyridine (I-P) oligomers. These duplexes adopt nonclassical helical structures, stabilized by I-P hydrogen-bonding pairs in anhydrous chlorinated solvents. Notably, the longest duplex 62 (11-mer)2 displays remarkable stability, forming twenty hydrogen bonds; its exchange energy barrier was determined to be ΔG≠=22.0 kcal ⋅ mol-1 at 75 °C in anhydrous (CDCl2)2. Upon the addition of water, a hydrated duplex 62 (11-mer)2⊃10H2O was formed, with one water molecule inserted between each I-P hydrogen-bonding pair. The Hill coefficient (n) for this process is 6.1, demonstrating extremely positive cooperativity. Conversely, the hydrated duplex 62 (11-mer)2⊃10H2O was completely converted into the original anhydrous duplex 62 (11-mer)2 when the temperature was increased. Interconversion between these two distinct duplexes can be repeatedly carried out by varying the temperature. Furthermore, reversible switching between hetero-duplexes and homo-duplexes was also demonstrated by controlling the temperature, with concomitant changes in the characteristic emission signals.
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Affiliation(s)
- Seungwon Lee
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Geunmoo Song
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Kyu-Sung Jeong
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
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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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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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5
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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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6
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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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7
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Duan HZ, Hu C, Li YL, Wang SH, Xia Y, Liu X, Wang J, Chen YX. Genetically Encoded Phosphine Ligand for Metalloprotein Design. J Am Chem Soc 2022; 144:22831-22837. [DOI: 10.1021/jacs.2c09683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Hua-Zhen Duan
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Cheng Hu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, P.R. China
| | - Yue-Lin Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Shi-Hao Wang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Yan Xia
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, P.R. China
| | - Xiaohong Liu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, P.R. China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, P.R. China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
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8
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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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9
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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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10
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Abstract
It is challenging to increase the rigidity of a macromolecule while maintaining solubility. Established strategies rely on templating by dendrons, or by encapsulation in macrocycles, and exploit supramolecular arrangements with limited robustness. Covalently bonded structures have entailed intramolecular coupling of units to resemble the structure of an alternating tread ladder with rungs composed of a covalent bond. We introduce a versatile concept of rigidification in which two rigid-rod polymer chains are repeatedly covalently associated along their contour by stiff molecular connectors. This approach yields almost perfect ladder structures with two well-defined π-conjugated rails and discretely spaced nanoscale rungs, easily visualized by scanning tunnelling microscopy. The enhancement of molecular rigidity is confirmed by the fluorescence depolarization dynamics and complemented by molecular-dynamics simulations. The covalent templating of the rods leads to self-rigidification that gives rise to intramolecular electronic coupling, enhancing excitonic coherence. The molecules are characterized by unprecedented excitonic mobility, giving rise to excitonic interactions on length scales exceeding 100 nm. Such interactions lead to deterministic single-photon emission from these giant rigid macromolecules, with potential implications for energy conversion in optoelectronic devices.
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11
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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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12
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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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13
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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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14
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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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16
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Gabrielli L, Hunter CA. Supramolecular catalysis by recognition-encoded oligomers: discovery of a synthetic imine polymerase. Chem Sci 2020; 11:7408-7414. [PMID: 34123021 PMCID: PMC8159439 DOI: 10.1039/d0sc02234a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
All key chemical transformations in biology are catalysed by linear oligomers. Catalytic properties could be programmed into synthetic oligomers in the same way as they are programmed into proteins, and an example of the discovery of emergent catalytic properties in a synthetic oligomer is reported. Dynamic combinatorial chemistry experiments designed to study the templating of a recognition-encoded oligomer by the complementary sequence have uncovered an unexpected imine polymerase activity. Libraries of equilibrating imines were formed by coupling diamine linkers with monomer building blocks composed of dialdehydes functionalised with either a trifluoromethyl phenol (D) or phosphine oxide (A) H-bond recognition unit. However, addition of the AAA trimer to a mixture of the phenol dialdehyde and the diamine linker did not template the formation of the DDD oligo-imine. Instead, AAA was found to be a catalyst, leading to rapid formation of long oligomers of D. AAA catalysed a number of different imine formation reactions, but a complementary phenol recognition group on the aldehyde reaction partner is an essential requirement. Competitive inhibition by an unreactive phenol confirmed the role of H-bonding in substrate recognition. AAA accelerates the rate of imine formation in toluene by a factor of 20. The kinetic parameters for this enzyme-like catalysis are estimated as 1 × 10-3 s-1 for k cat and the dissociation constant for substrate binding is 300 μM. The corresponding DDD trimer was found to catalyse oligomerisation the phosphine oxide dialdehyde with the diamine linker, suggesting an important role for the backbone in catalysis. This unexpected imine polymerase activity in a duplex-forming synthetic oligomer suggests that there are many interesting processes to be discovered in the chemistry of synthetic recognition-encoded oligomers that will parallel those found in natural biopolymers.
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Affiliation(s)
- Luca Gabrielli
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK .,Department of Chemistry, University of Padova via F. Marzolo 1 Padova 35131 Italy
| | - Christopher A Hunter
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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17
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Gao SC, Wan K, Fang X, Li YX, Xue M, Yang Y. Determination of association constants and FRET in hydrazide-based molecular duplex strands. Org Chem Front 2020. [DOI: 10.1039/d0qo00746c] [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
The association constants for the hydrazide-based molecular duplex strands can be determined via monitoring the pyrene excimer emission. By mixing pyrene and perylene labelled oligomers, supramolecular substitution reactions induced efficient FRET.
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Affiliation(s)
- Shi-Chang Gao
- School of Science
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Kang Wan
- School of Science
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Xu Fang
- School of Science
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Yong-Xue Li
- School of Science
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Min Xue
- School of Science
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Yong Yang
- School of Science
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
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18
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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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19
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Ng AWH, Yee C, Au‐Yeung HY. Radial Hetero[5]catenanes: Peripheral Isomer Sequences of the Interlocked Macrocycles. Angew Chem Int Ed Engl 2019; 58:17375-17382. [DOI: 10.1002/anie.201908576] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/05/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Antony Wing Hung Ng
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Chi‐Chung Yee
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Ho Yu Au‐Yeung
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
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20
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Ng AWH, Yee C, Au‐Yeung HY. Radial Hetero[5]catenanes: Peripheral Isomer Sequences of the Interlocked Macrocycles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Antony Wing Hung Ng
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Chi‐Chung Yee
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Ho Yu Au‐Yeung
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
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21
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Hebel M, Riegger A, Zegota MM, Kizilsavas G, Gačanin J, Pieszka M, Lückerath T, Coelho JAS, Wagner M, Gois PMP, Ng DYW, Weil T. Sequence Programming with Dynamic Boronic Acid/Catechol Binary Codes. J Am Chem Soc 2019; 141:14026-14031. [PMID: 31436970 PMCID: PMC6743217 DOI: 10.1021/jacs.9b03107] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Indexed: 12/25/2022]
Abstract
The development of a synthetic code that enables a sequence programmable feature like DNA represents a key aspect toward intelligent molecular systems. We developed herein the well-known dynamic covalent interaction between boronic acids (BAs) and catechols (CAs) into synthetic nucleobase analogs. Along a defined peptide backbone, BA or CA residues are arranged to enable sequence recognition to their complementary strand. Dynamic strand displacement and errors were elucidated thermodynamically to show that sequences are able to specifically select their partners. Unlike DNA, the pH dependency of BA/CA binding enables the dehybridization of complementary strands at pH 5.0. In addition, we demonstrate the sequence recognition at the macromolecular level by conjugating the cytochrome c protein to a complementary polyethylene glycol chain in a site-directed fashion.
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Affiliation(s)
- Marco Hebel
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Andreas Riegger
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Maksymilian M. Zegota
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Gönül Kizilsavas
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jasmina Gačanin
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Michaela Pieszka
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Thorsten Lückerath
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jaime A. S. Coelho
- Research Institute
for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Manfred Wagner
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Pedro M. P. Gois
- Research Institute
for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - David Y. W. Ng
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic
Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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22
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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
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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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23
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Szczypiński FT, Hunter CA. Building blocks for recognition-encoded oligoesters that form H-bonded duplexes. Chem Sci 2019; 10:2444-2451. [PMID: 30881672 PMCID: PMC6385898 DOI: 10.1039/c8sc04896g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/03/2019] [Indexed: 12/20/2022] Open
Abstract
A long-short base-pairing scheme hinders intramolecular folding and allows the use of flexible backbones in duplex-forming oligomers.
Competition from intramolecular folding is a major challenge in the design of synthetic oligomers that form intermolecular duplexes in a sequence-selective manner. One strategy is to use very rigid backbones that prevent folding, but this design can prejudice duplex formation if the geometry is not exactly right. The alternative approach found in nucleic acids is to use bases (or recognition units) that have different dimensions. A long-short base-pairing scheme makes folding geometrically difficult and is compatible with the flexible backbones that are required to guarantee duplex formation. A monomer building block equipped with a long hydrogen bond donor (phenol, D) recognition unit and a monomer building block equipped with a short hydrogen bond acceptor (phosphine oxide, A) recognition unit were prepared with differentially protected alcohol and carboxylic acid groups. These compounds were used to synthesise the homo and hetero-sequence 2-mers AA, DD and AD. 19F and 31P NMR experiments were used to characterize the assembly properties of these compounds in toluene solution. AA and DD form a stable doubly-hydrogen-bonded duplex with an effective molarity of 20 mM for formation of the second intramolecular hydrogen bond. AD forms a duplex of similar stability. There is no evidence of intramolecular folding in the monomeric state of this compound, which shows that the long-short base-pairing scheme is effective. The ester coupling chemistry used here is an attractive method for the synthesis of long oligomers, and the properties of the 2-mers indicate that this molecular architecture should give longer mixed sequence oligomers that show high fidelity sequence-selective duplex formation.
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Affiliation(s)
- Filip T Szczypiński
- 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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24
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Szczypiński FT, Gabrielli L, Hunter CA. Emergent supramolecular assembly properties of a recognition-encoded oligoester. Chem Sci 2019. [DOI: 10.1039/c9sc01669d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An oligoester containing an alternating sequence of hydrogen bonding donor and acceptor side-chains forms a supramolecular architecture that resembles the kissing stem-loops motif found in folded RNA.
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Affiliation(s)
| | - Luca Gabrielli
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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