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Weigel RK, Alabi CA. Duplex-forming oligocarbamates with tunable nonbonding sites. Chem Sci 2024; 15:9138-9146. [PMID: 38903212 PMCID: PMC11186313 DOI: 10.1039/d4sc00242c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/11/2024] [Indexed: 06/22/2024] Open
Abstract
In biopolymers such as proteins and nucleic acids, monomer sequence encodes for highly specific intra- and intermolecular interactions that direct self-assembly into complex architectures with high fidelity. This remarkable structural control translates into precise control over the properties of the biopolymer. Polymer scientists have sought to achieve similarly precise control over the structure and function of synthetic assemblies. A common strategy for achieving this goal has been to exploit existing biopolymers, known to associate with specific geometries and stoichiometries, for the assembly of synthetic building blocks. However, such systems are neither scalable nor amenable to the relatively harsh conditions required by various materials science applications, particularly those involving non-aqueous environments. To overcome these limitations, we have synthesized sequence-defined oligocarbamates (SeDOCs) that assemble into duplexes through complementary hydrogen bonds between thymine (T) and diaminotriazine (D) pendant groups. The SeDOC platform makes it simple to incorporate non-hydrogen-bonding sites into an oligomer's array of recognition motifs, thereby enabling an investigation into this unexplored handle for controlling the hybridization of complementary ligands. We successfully synthesized monovalent, divalent, and trivalent SeDOCs and characterized their self-assembly via diffusion ordered spectroscopy, 1H-NMR titration, and isothermal titration calorimetry. Our findings reveal that the binding strength of monovalent oligomers with complementary pendant groups is entropically driven and independent of monomer sequence. The results further show that the hybridization of multivalent oligomers is cooperative, that their binding enthalpy (ΔH) and entropy (TΔS) depend on monomer sequence, and that sequence-dependent changes in ΔH and TΔS occur in tandem to minimize the overall change in binding free energy.
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Affiliation(s)
- R Kenton Weigel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University Ithaca New York USA
| | - Christopher A Alabi
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University Ithaca New York USA
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2
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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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3
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Maier JM, Valenzuela SA, van der Stok A, Menta AK, Shimizu Y, Ngo PH, Ellington AD, Anslyn EV. Peptide Macrocyclization Guided by Reversible Covalent Templating. Chemistry 2023; 29:e202301949. [PMID: 37475574 PMCID: PMC10592230 DOI: 10.1002/chem.202301949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
The creation of complementary products via templating is a hallmark feature of nucleic acid replication. Outside of nucleic acid-like molecules, the templated synthesis of a hetero-complementary copy is still rare. Herein we describe one cycle of templated synthesis that creates homomeric macrocyclic peptides guided by linear instructing strands. This strategy utilizes hydrazone formation to pre-organize peptide oligomeric monomers along the template on a solid support resin, and microwave-assisted peptide synthesis to couple monomers and cyclize the strands. With a flexible templating strand, we can alter the size of the complementary macrocycle products by increasing the length and number of the binding peptide oligomers, showing the potential to precisely tune the size of macrocyclic products. For the smaller macrocyclic peptides, the products can be released via hydrolysis and characterized by ESI-MS.
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Affiliation(s)
- Josef M Maier
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Aevi van der Stok
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Arjun K Menta
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yuka Shimizu
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Phuoc H Ngo
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew D Ellington
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
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4
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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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5
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Greenlee AJ, Chen H, Wendell CI, Moore JS. Tandem Imine Formation and Alkyne Metathesis Enabled by Catalyst Choice. J Org Chem 2022; 87:8429-8436. [PMID: 35678630 DOI: 10.1021/acs.joc.2c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three-rung molecular ladder 8 was prepared in one pot via tandem imine condensation and alkyne metathesis. Catalyst VI is demonstrated to successfully engender the metathesis of imine-bearing substrate 7, while catalyst III does not. The susceptibility of catalyst VI to deactivation by hydrolysis and ligand exchange is demonstrated. Assembly and disassembly of ladder 8 in one pot were demonstrated in the presence and absence of a Lewis acid catalyst.
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Affiliation(s)
- Andrew J Greenlee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Heyu Chen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chloe I Wendell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jeffrey S Moore
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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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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7
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Zou YQ, Hu B, Chen L, Ji T, Yang M, Yang CA. Novel pH- and thermoresponsive supramolecular dendronized copolymer. IRANIAN POLYMER JOURNAL 2021. [DOI: 10.1007/s13726-020-00873-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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9
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Abstract
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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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10
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Leguizamon SC, Dunn MF, Scott TF. Sequence-directed dynamic covalent assembly of base-4-encoded oligomers. Chem Commun (Camb) 2020; 56:7817-7820. [PMID: 32618971 DOI: 10.1039/d0cc01083a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
As an information-bearing biomacromolecule, DNA is encoded in base-4, where each residue site can be occupied by any one of four nucleobases. Mimicking the information dense, sequence-selective hybridization of DNA, we demonstrate two orthogonal dynamic covalent interactions to effect the selective assembly of molecular ladders and grids from base-4-encoded oligo(peptoid)s.
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Affiliation(s)
- S C Leguizamon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - M F Dunn
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - T F Scott
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA and Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia. and Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
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11
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Leguizamon SC, Scott TF. Sequence-selective dynamic covalent assembly of information-bearing oligomers. Nat Commun 2020; 11:784. [PMID: 32034159 PMCID: PMC7005811 DOI: 10.1038/s41467-020-14607-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/21/2020] [Indexed: 01/03/2023] Open
Abstract
Relatively robust dynamic covalent interactions have been employed extensively to mediate molecular self-assembly reactions; however, these assembly processes often do not converge to a thermodynamic equilibrium, instead yielding mixtures of kinetically-trapped species. Here, we report a dynamic covalent self-assembly process that mitigates kinetic trapping such that multiple unique oligomers bearing covalently coreactive pendant groups are able to undergo simultaneous, sequence-selective hybridization with their complementary strands to afford biomimetic, in-registry molecular ladders with covalent rungs. Analogous to the thermal cycling commonly employed for nucleic acid melting and annealing, this is achieved by raising and lowering the concentration of a multi-role reagent to effect quantitative dissociation and subsequently catalyze covalent bond rearrangement, affording selective assembly of the oligomeric sequences. The hybridization specificity afforded by this process further enabled information encoded in oligomers to be retrieved through selective hybridization with complementary, mass-labeled sequences. Dynamic covalent interactions have been employed to mediate molecular self-assembly reactions but often do not converge to a thermodynamic equilibrium and yield a mixture of kinetically trapped species. Here, the authors show a sequence-selective, dynamic covalent self-assembly process that mitigates kinetic trapping to afford biomimetic molecular ladders with covalent rungs.
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Affiliation(s)
- Samuel C Leguizamon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Timothy F Scott
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA. .,Macromolecular Science and Engineering Program, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Chemical Engineering, Monash University, Clayton, VIC, 3800, Australia. .,Department of Materials Science and Engineering, Monash University, Clayton, VIC, 3800, Australia.
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12
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Leguizamon SC, Alqubati AF, Scott TF. Temperature-mediated molecular ladder self-assembly employing Diels–Alder cycloaddition. Polym Chem 2020. [DOI: 10.1039/d0py01296c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Thermal annealing of sequence-defined, maleimide- and furan-bearing oligomers enables sequence-selective hybridization to afford molecular ladders incorporating Diels–Alder adduct-based rungs.
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Affiliation(s)
| | | | - Timothy F. Scott
- Department of Chemical Engineering
- Monash University
- Clayton
- Australia
- Department of Materials Science and Engineering
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13
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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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14
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Cencer MM, Greenlee AJ, Moore JS. Quantifying Error Correction through a Rule-Based Model of Strand Escape from an [n]-Rung Ladder. J Am Chem Soc 2019; 142:162-168. [DOI: 10.1021/jacs.9b08958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Morgan M. Cencer
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrew J. Greenlee
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jeffrey S. Moore
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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15
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Pattillo CC, Moore JS. A tetrahedral molecular cage with a responsive vertex. Chem Sci 2019; 10:7043-7048. [PMID: 31588271 PMCID: PMC6676470 DOI: 10.1039/c9sc02047k] [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: 04/25/2019] [Accepted: 06/09/2019] [Indexed: 12/27/2022] Open
Abstract
Dynamic covalent chemistry (DCC) is a widely used method for the self-assembly of three-dimensional molecular architectures. The orthogonality of dynamic reactions is emerging as a versatile strategy for controlling product distributions in DCC, yet the application of this approach to the synthesis of 3D organic molecular cages is limited. We report the first system which employs the orthogonality of alkyne metathesis and dynamic imine exchange to prepare a molecular cage with a reversibly removable vertex. This study demonstrates the rational and controlled application of chemical orthogonality in DCC to prepare organic cages of expanded functionality which respond to chemical stimuli.
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Affiliation(s)
- Christopher C Pattillo
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , USA .
| | - Jeffrey S Moore
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , USA .
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16
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Dunn MF, Wei T, Zuckermann RN, Scott TF. Aqueous dynamic covalent assembly of molecular ladders and grids bearing boronate ester rungs. Polym Chem 2019. [DOI: 10.1039/c8py01705k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mimicking the self-assembly of nucleic acid sequences into double-stranded molecular ladders that incorporate hydrogen bond-based rungs, dynamic covalent interactions enable the fabrication of molecular ladder and grid structures with covalent bond-based rungs.
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Affiliation(s)
- Megan F. Dunn
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor
- USA
| | - Tao Wei
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor
- USA
| | | | - Timothy F. Scott
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor
- USA
- Macromolecular Science and Engineering
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17
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Zhou Z, Palermo EF. Templated Ring-Opening Metathesis (TROM) of Cyclic Olefins Tethered to Unimolecular Oligo(thiophene)s. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00998] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhe Zhou
- Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Edmund F. Palermo
- Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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18
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Fu X, Li Z, Wei J, Sun J, Li Z. Schiff base and reductive amination reactions of α-amino acids: a facile route toward N-alkylated amino acids and peptoid synthesis. Polym Chem 2018. [DOI: 10.1039/c8py00924d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Polypeptoids are a promising class of peptidomimetic polymers for applications in biotechnology, but the polymers prepared by solution polymerization have limited side-chain functionalities due to synthetic difficulty.
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Affiliation(s)
- Xiaohui Fu
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department; School of Polymer Science and Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- China
| | - Zheng Li
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department; School of Polymer Science and Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- China
| | - Jirui Wei
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department; School of Polymer Science and Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- China
| | - Jing Sun
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department; School of Polymer Science and Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- China
| | - Zhibo Li
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department; School of Polymer Science and Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- China
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19
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Wei T, Furgal JC, Scott TF. In situ deprotection and dynamic covalent assembly using a dual role catalyst. Chem Commun (Camb) 2017; 53:3874-3877. [DOI: 10.1039/c7cc01028a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Sc(OTf)3 is employed as a dual role catalyst to effect the in situ deprotection and dynamic covalent assembly of oligo(peptoid)s.
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Affiliation(s)
- T. Wei
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor
- USA
| | - J. C. Furgal
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor
- USA
| | - T. F. Scott
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor
- USA
- Macromolecular Science and Engineering
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