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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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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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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
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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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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
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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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Debnath S, Ghosh S, Kumar D, Vasudev PG, Satpati P, Chatterjee S. Effect of differential backbone di-substitution of gamma amino acid residues on the conformation and assembly of their Fmoc derivatives in solid and solution states. Chem Asian J 2022; 17:e202200356. [PMID: 35603989 DOI: 10.1002/asia.202200356] [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: 04/06/2022] [Revised: 05/23/2022] [Indexed: 11/11/2022]
Abstract
We studied the effect of variable backbone dimethyl-substitution of γ amino acid residues (γ 2,2 , γ 3,3 and γ 4,4 ) on the conformation and assembly, in crystals and solution of their Fmoc derivatives. Crystal structure of γ 2,2 and γ 4,4 derivatives showed distinct conformations (open/close for γ 2,2 /γ 4,4 ) that differed in torsion angles, hydrogen-bonding and most importantly the π-π Fmoc-stacking interactions (relatively favorable for γ 4,4 -close). Fmoc derivatives existed in an equilibrium between major-monomeric (low energy, non-hydrogen bonded) and minor-dimeric (high energy, hydrogen bonded) populations in solution. Rate of major/minor population exchange was dependent on the position of substitution, highest being for γ 4,4 derivative. In solution, assembly of Fmoc derivatives was solvent dependent, but it was independent of the position of geminal substitution. Crystallization was primarily governed by the stabilization of high-energy dimer by favorable π-π stacking involving Fmoc moieties. High free-energy of the dimers (γ 2,2 -close, γ 3,3 -open/close) offset favorable stacking interactions and hindered crystallization.
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Affiliation(s)
- Swapna Debnath
- Indian Institute of Technology Guwahati, Department of chemistry, INDIA
| | - Suvankar Ghosh
- Indian Institute of Technology Guwahati, Bioscience and Bioengineering, INDIA
| | - Dinesh Kumar
- CSIR-CIMAP: Central Institute of Medicinal and Aromatic Plants CSIR, Plant Biotechnology Division, INDIA
| | - Prema G Vasudev
- CSIR-CIMAP: Central Institute of Medicinal and Aromatic Plants CSIR, Plant Biotechnology Division, INDIA
| | - Priyadarshi Satpati
- Indian Institute of Technology Guwahati, Bioscience and BIoengineering, INDIA
| | - Sunanda Chatterjee
- Indian Institute of Technology Guwahati, CHEMISTRY, IIT GUWAHATI, 781039, GUWAHATI, INDIA
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Li H, Kou L, Liang L, Li B, Zhao W, Yang XJ, Wu B. Anion-coordination-driven single-double helix switching and chiroptical molecular switching based on oligoureas. Chem Sci 2022; 13:4915-4921. [PMID: 35655878 PMCID: PMC9067589 DOI: 10.1039/d2sc00876a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/02/2022] [Indexed: 11/21/2022] Open
Abstract
Synthetic foldamers with helical conformation are widely seen, but controllable interconversion amongst different geometries (helical structure and sense) is challenging. Here, a family of oligourea (tetra-, penta-, and hexa-) ligands bearing stereocenters at both ends are designed and shown to switch between single and double helices with concomitant inversion of helical senses upon anion coordination. The tetraurea ligand forms a right-handed single helix upon chloride anion (Cl-) binding and is converted into a left-handed double helix when phosphate anion (PO4 3-) is coordinated. The helical senses of the single and double helices are opposite, and the conversion is further found to be dependent on the stoichiometry of the ligand and phosphate anion. In contrast, only a single helix is formed for the hexaurea ligand with the phosphate anion. This distinction is attributed to the fact that the characteristic phosphate anion coordination geometry is satisfied by six urea moieties with twelve H-bonds. Our study revealed unusual single-double helix interconversion accompanied by unexpected chiroptical switching of helical senses.
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Affiliation(s)
- Hongfei Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
| | - Lei Kou
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
| | - Lin Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Boyang Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
| | - Wei Zhao
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Xiao-Juan Yang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Biao Wu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
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A complementary pairing. Nat Rev Chem 2021; 5:599. [PMID: 37118419 DOI: 10.1038/s41570-021-00322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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