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Núñez-Villanueva D, Hunter CA. Replication of synthetic recognition-encoded oligomers by ligation of trimer building blocks. Org Chem Front 2023; 10:5950-5957. [PMID: 38022796 PMCID: PMC10661083 DOI: 10.1039/d3qo01717f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
The development of methods for replication of synthetic information oligomers will underpin the use of directed evolution to search new chemical space. Template-directed replication of triazole oligomers has been achieved using a covalent primer in conjunction with non-covalent binding of complementary building blocks. A phenol primer equipped with an alkyne was first attached to a benzoic recognition unit on a mixed sequence template via selective covalent ester base-pair formation. The remaining phenol recognition units on the template were then used for non-covalent binding of phosphine oxide oligomers equipped with an azide. The efficiency of the templated CuAAC reaction between the primer and phosphine oxide building blocks was investigated as a function of the number of H-bonds formed with the template. Increasing the strength of the non-covalent interaction between the template and the azide lead to a significant acceleration of the templated reaction. For shorter phosphine oxide oligomers intermolecular reactions compete with the templated process, but quantitative templated primer elongation was achieved with a phosphine oxide 3-mer building block that was able to form three H-bonds with the template. NMR spectroscopy and molecular models suggest that the template can fold, but addition of the phosphine oxide 3-mer leads to a complex with three H-bonds between phosphine oxide and phenol groups, aligning the azide and alkyne groups in a favourable geometry for the CuAAC reaction. In the product duplex, 1H and 31P NMR data confirm the presence of the three H-bonded base-pairs, demonstrating that the covalent and non-covalent base-pairs are geometrically compatible. A complete replication cycle was carried out starting from the oligotriazole template by covalent attachment of the primer, followed by template-directed elongation, and hydrolysis of the the ester base-pair in the resulting duplex to regenerate the template and liberate the copy strand. We have previously demonstrated sequence-selective oligomer replication using covalent base-pairing, but the trimer building block approach described here is suitable for replication of sequence information using non-covalent binding of the monomer building blocks to a template.
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Affiliation(s)
- Diego Núñez-Villanueva
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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2
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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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3
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Rajmane A, Jadhav S, Kumbhar A. N, O-polydentate ligands for palladium-catalyzed cross-coupling reactions (Part III). J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2021.122147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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4
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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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5
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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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6
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Horváth AK. Correct classification and identification of autocatalysis. Phys Chem Chem Phys 2021; 23:7178-7189. [PMID: 33734272 DOI: 10.1039/d1cp00224d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is generally accepted that autocatalysis is a kinetic phenomenon, where a product of a reacting system functions as a catalyst. Consequently, the reaction proceeds faster upon adding the corresponding product to the unreacted mixture of reactants providing an unequivocal possibility of how a system may be identified either experimentally or theoretically as an autocatalysis. Once this is approved, it often results in sigmoidal concentration-time profiles, though it is neither a necessary nor sufficient prerequisite because appropriate mechanistic and parametric conditions must be met to give rise to the appearance of this kinetic feature. Several mass action type kinetic models producing sigmoidal concentration-time profiles are systematically analyzed to clarify their correct characterization and classification. This procedure has led us to refine the definitions of autocatalysis and autocatalyst. A kinetic phenomenon where a product of the overall chemical event serves as a catalyst for at least one of its subsystems or for the whole system itself is called autocatalysis. This definition makes it clear that in the case of autocatalysis, the concentration of autocatalyst necessarily increases during the course of any real overall chemical or biochemical reaction. The way it is achieved thereby provides a suitable tool to classify autocatalytic processes by their elucidated and fine mechanistic details.
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Affiliation(s)
- Attila K Horváth
- Department of Inorganic Chemistry, Faculty of Sciences, University of Pécs, Pécs, Hungary.
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Núñez-Villanueva D, Hunter CA. Replication of Sequence Information in Synthetic Oligomers. Acc Chem Res 2021; 54:1298-1306. [PMID: 33554599 PMCID: PMC7931443 DOI: 10.1021/acs.accounts.0c00852] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 12/12/2022]
Abstract
The holy grail identified by Orgel in his 1995 Account was the development of novel chemical systems that evolve using reactions in which replication and information transfer occur together. There has been some success in the adaption of nucleic acids to make artificial analogues and in templating oligomerization reactions to form synthetic homopolymers, but replication of sequence information in synthetic polymers remains a major unsolved problem. In this Account, we describe our efforts in this direction based on a covalent base-pairing strategy to transfer sequence information between a parent template and a daughter copy. Oligotriazoles, which carry information as a sequence of phenol and benzoic acid side chains, have been prepared from bifunctional monomers equipped with an azide and an alkyne. Formation of esters between phenols and benzoic acids is used as the equivalent of nucleic base pairing to covalently attach monomer building blocks to a template oligomer. Sequential protection of the phenol side chains on the template, ester coupling of the benzoic acid side chains, and deprotection and ester coupling of the phenol side chains allow quantitative selective base-pair formation on a mixed sequence template. Copper catalyzed azide alkyne cycloaddition (CuAAC) is then used to oligomerize the monomers on the template. Finally, cleavage of the ester base pairs in the product duplex by hydrolysis releases the copy strand. This covalent template-directed synthesis strategy has been successfully used to copy the information encoded in a trimer template into a sequence-complementary oligomer in high yield.The use of covalent base pairing provides opportunities to manipulate the nature of the information transferred in the replication process. By using traceless linkers to connect the phenol and benzoic acid units, it is possible to carry out direct replication, reciprocal replication, and mutation. These preliminary results are promising, and methods have been developed to eliminate some of the side reactions that compete with the CuAAC process that zips up the duplex. In situ end-capping of the copy strand was found to be an effective general method for blocking intermolecular reactions between product duplexes. By selecting an appropriate concentration of an external capping agent, it is also possible to intercept macrocyclization of the reactive chain ends in the product duplex. The other side reaction observed is miscoupling of monomer units that are not attached to adjacent sites on the template, and optimization is required to eliminate these reactions. We are still some way from an evolvable synthetic polymer, but the chemical approach to molecular replication outlined here has some promise.
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Affiliation(s)
- Diego Núñez-Villanueva
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher A. Hunter
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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9
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Abstract
![]()
Genetic biopolymers utilize defined
sequences and monomer-specific
molecular recognition to store and transfer information. Synthetic
polymers that mimic these attributes using reversible covalent chemistry
for base-pairing pose unique synthetic challenges. Here, we describe
a solid-phase synthesis methodology for the efficient construction
of ethynyl benzene oligomers with specific sequences of aniline and
benzaldehyde subunits. Handling these oligomers is complicated by
the fact that they often exhibit multiple conformations because of
intra- or intermolecular pairing. We describe conditions that allow
the dynamic behavior of these oligomers to be controlled so that they
may be manipulated and characterized without needing to mask the recognition
units with protecting groups.
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Affiliation(s)
- Kyle R. Strom
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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10
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Sawato T, Yamaguchi M. Synthetic Chemical Systems Involving Self‐Catalytic Reactions of Helicene Oligomer Foldamers. Chempluschem 2020; 85:2017-2038. [DOI: 10.1002/cplu.202000489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/18/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Tsukasa Sawato
- Department of Organic Chemistry Graduate School of Pharmaceutical Sciences Tohoku University Aoba Sendai 980-8578 Japan
| | - Masahiko Yamaguchi
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
- Department of Organic Chemistry Graduate School of Pharmaceutical Sciences Tohoku University Aoba Sendai 980-8578 Japan
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11
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Hanopolskyi AI, Smaliak VA, Novichkov AI, Semenov SN. Autocatalysis: Kinetics, Mechanisms and Design. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Anton I. Hanopolskyi
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Viktoryia A. Smaliak
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Alexander I. Novichkov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Sergey N. Semenov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
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12
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Paraja M, Hao X, Matile S. Polyether Natural Product Inspired Cascade Cyclizations: Autocatalysis on π-Acidic Aromatic Surfaces. Angew Chem Int Ed Engl 2020; 59:15093-15097. [PMID: 32181559 DOI: 10.1002/anie.202000681] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Indexed: 01/03/2023]
Abstract
Anion-π catalysis functions by stabilizing anionic transition states on aromatic π surfaces, thus providing a new approach to molecular transformation. The delocalized nature of anion-π interactions suggests that they serve best in stabilizing long-distance charge displacements. Aiming therefore for an anionic cascade reaction that is as charismatic as the steroid cyclization is for conventional cation-π biocatalysis, reported here is the anion-π-catalyzed epoxide-opening ether cyclizations of oligomers. Only on π-acidic aromatic surfaces having a positive quadrupole moment, such as hexafluorobenzene to naphthalenediimides, do these polyether cascade cyclizations proceed with exceptionally high autocatalysis (rate enhancements kauto /kcat >104 m-1 ). This distinctive characteristic adds complexity to reaction mechanisms (Goldilocks-type substrate concentration dependence, entropy-centered substrate destabilization) and opens intriguing perspectives for future developments.
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Affiliation(s)
- Miguel Paraja
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Xiaoyu Hao
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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Paraja M, Hao X, Matile S. Polyether Natural Product Inspired Cascade Cyclizations: Autocatalysis on π‐Acidic Aromatic Surfaces. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Miguel Paraja
- Department of Organic Chemistry University of Geneva Geneva Switzerland
| | - Xiaoyu Hao
- Department of Organic Chemistry University of Geneva Geneva Switzerland
| | - Stefan Matile
- Department of Organic Chemistry University of Geneva Geneva Switzerland
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Horváth AK. Law of Mass Action Type Chemical Mechanisms for Modeling Autocatalysis and Hypercycles: Their Role in the Evolutionary Race. Chemphyschem 2020; 21:1703-1710. [PMID: 32367607 PMCID: PMC7496691 DOI: 10.1002/cphc.202000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 01/21/2023]
Abstract
One of our most appealing challenge is to unravel the role of a presumably autocatalytic system in controlling the origin and spreading of Life on our entire planet. Here we show that in the simplest autocatalytic loop involving reactions capable of self-replication and obeying law of mass action kinetics, concentration growth of the autocatalyst may be characterized by parametrization of direct and autocatalytic pathways rather than by kinetic orders of the autocatalyst. Extending this model by feasible elementary steps allows us to outline super-exponential growth where kinetic order of the autocatalyst is higher than unity. Furthermore, it is shown in case of the simplest hypercycle that such a situation might appear where the otherwise more sluggish autocatalytic route receives a decisive support from the crosscatalytic pathway to become an apparently stronger autocatalytic loop even if the other route contains a more efficient autocatalysis. If the hypercycle is performed under flow conditions selection of autocatalyst depends on kinetic and flow parameters influenced by external factors mimicking that the most adaptive loop of hypercycle eventually finds its wining way in the evolutionary race.
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Affiliation(s)
- Attila K. Horváth
- Department of Inorganic ChemistryFaculty of SciencesUniversity of PécsIfjúság u. 6.H-7624PécsHungary
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Núñez-Villanueva D, Hunter CA. Molecular replication using covalent base-pairs with traceless linkers. Org Biomol Chem 2019; 17:9660-9665. [PMID: 31691702 DOI: 10.1039/c9ob02336d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A unique feature of kinetically inert covalent base-pairing is that the nature of the chemical information that is transferred can be modulated by changing the chemical connectivity between the two bases. Formation of esters between phenols and benzoic acids has been used as a base-pairing strategy for sequence information transfer in template-directed synthesis of linear oligomers, but the copy strand produced by this process has the complementary sequence to the template strand. It is possible to form a base-pair between two benzoic acids by using a hydroquinone linker, which is eliminated when the product duplex is hydrolysed. Using this approach, covalent template-directed synthesis was carried out using a benzoic acid 3-mer template to produce an identical copy. This direct replication process was used in iterative rounds of replication leading to an increase of the population of the copied oligomer.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Christopher A Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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Wet-Dry Cycling Delays the Gelation of Hyperbranched Polyesters: Implications to the Origin of Life. Life (Basel) 2019; 9:life9030056. [PMID: 31266241 PMCID: PMC6789768 DOI: 10.3390/life9030056] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/11/2019] [Accepted: 06/28/2019] [Indexed: 11/17/2022] Open
Abstract
In extant biology, biopolymers perform multiple crucial functions. The biopolymers are synthesized by enzyme-controlled biosystems that would not have been available at the earliest stages of chemical evolution and consist of correctly sequenced and/or linked monomers. Some of the abiotic "messy" polymers approximate some functions of biopolymers. Condensation polymers are an attractive search target for abiotic functional polymers since principal polymers of life are produced by condensation and since condensation allows for the accurate construction of high polymers. Herein the formation of hyperbranched polyesters that have been previously used in the construction of enzyme-like catalytic complexes is explored. The experimental setup compares between the branched polyesters prepared under mild continuous heating and the wet-dry cycling associated with environmental conditions, such as dew formation or tidal activities. The results reveal that periodic wetting during which partial hydrolysis of the polyester occurs, helps to control the chain growth and delays the gel transition, a mechanism contributing to the tar formation. Moreover, the NMR and mass spec analyses indicate that continuously dried samples contain higher quantities of crosslinked and macrocyclic products, whereas cycled systems are enriched in branched structures. Ostensibly, environmental conditions have the ability to exert a rudimentary pressure to selectively enrich the polyesterification products in polymers of different structures and properties. At the early stages of chemical evolution, in the absence of biological machinery, this example of environmental control could have been for selectivity in chemical systems. As expected in marginally controlled systems, the identification of each component of the heterogeneous system has proved challenging, but it is not crucial for drawing the conclusions.
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Núñez-Villanueva D, Ciaccia M, Iadevaia G, Sanna E, Hunter CA. Sequence information transfer using covalent template-directed synthesis. Chem Sci 2019; 10:5258-5266. [PMID: 31191881 PMCID: PMC6540929 DOI: 10.1039/c9sc01460h] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/22/2019] [Indexed: 12/14/2022] Open
Abstract
Kinetically inert ester bonds were used to attach monomers to a template, dictating the sequence of the polymer product.
Template-directed synthesis is the biological method for the assembly of oligomers of defined sequence, providing the molecular basis for replication and the process of evolution. To apply analogous processes to synthetic oligomeric molecules, methods are required for the transfer of sequence information from a template to a daughter strand. We show that covalent template-directed synthesis is a promising approach for the molecular replication of sequence information in synthetic oligomers. Two monomer building blocks were synthesized: a phenol monomer and a benzoic acid monomer, each bearing an alkyne and an azide for oligomerization via copper catalyzed azide alkyne cycloaddition (CuAAC) reactions. Stepwise synthesis was used to prepare oligomers, where information was encoded as the sequence of phenol (P) and benzoic acid (A) units. Ester base-pairing was used to attach monomers to a mixed sequence template, and CuAAC was used to zip up the backbone. Hydrolysis of the ester base-pairs gave back the starting template and the sequence complementary copy. When the AAP trimer was used as the template, the complementary sequence PPA was obtained as the major product, with a small amount of scrambling resulting in PAP as a side-product. This covalent base-pairing strategy represents a general approach that can be implemented in different formats for the replication of sequence information in synthetic oligomers.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Maria Ciaccia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Elena Sanna
- 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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18
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Abstract
Template assistance allows organic reactions to occur under highly dilute conditions-where intermolecular reactions often fail to proceed-by bringing reactants into close spatial proximity. This strategy has been elegantly applied to numerous systems, but always with the retention of at least one of the templating groups in the product. In this report, we describe a traceless, templated amide-forming ligation that proceeds at low micromolar concentration under aqueous conditions in the presence of biomolecules. We utilized the unique features of an acylboronate-hydroxylamine ligation, in which covalent bonds are broken in each of the reactants as the new amide bond is formed. By using streptavidin as a template and acylboronates and O-acylhydroxylamines bearing desthiobiotins that are cleaved upon amide formation, we demonstrate that traceless, templated ligation occurs rapidly even at submicromolar concentrations. The requirement for a close spatial orientation of the functional groups-achieved upon binding to streptavidin-is critical for the observed enhancement in the rate and quantity of product formed.
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Affiliation(s)
- Alberto Osuna Gálvez
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
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Sawato T, Saito N, Yamaguchi M. Chemical Systems Involving Two Competitive Self-Catalytic Reactions. ACS OMEGA 2019; 4:5879-5899. [PMID: 31459737 PMCID: PMC6648109 DOI: 10.1021/acsomega.9b00133] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/13/2019] [Indexed: 06/10/2023]
Abstract
Self-catalytic reactions are chemical phenomena, in which a product catalyzes the reactions of substrates further to yield products. A significant amplification of product concentration occurs during the reactions in a dilute solution, which exhibit notable properties such as sigmoidal kinetics, seeding effects, and thermal hysteresis. Chemical systems involving two competitive self-catalytic reactions can be considered, in which the competitive formation of two products occurs, which is affected by environmental changes, subtle perturbations, and fluctuations, and notable chemical phenomena appear such as formation of different structures in response to slow/fast temperature changes, chiral symmetry breaking, shortcut in reaction time, homogeneous-heterogeneous transitions, and mechanical responses. Studies on such chemical systems provide understanding on biological systems and can also be extended to the development of novel functional materials.
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20
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MacCulloch T, Buchberger A, Stephanopoulos N. Emerging applications of peptide-oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterials. Org Biomol Chem 2019; 17:1668-1682. [PMID: 30483688 DOI: 10.1039/c8ob02436g] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Peptide-oligonucleotide conjugates (POCs) are covalent constructs that link a molecule like DNA to a synthetic peptide sequences. These materials merge the programmable self-assembly of oligonucleotides with the bioactivity and chemical diversity of polypeptides. Recent years have seen the widespread use of POCs in a range of fields, driven the by relative advantages of each molecular type. In this review, we will present an overview of the synthesis and application of POCs, with an emphasis on emerging areas where these molecules will have a unique impact. We first discuss two main strategies for synthesizing POCs from synthetic monomers such as phosphoramidites and functionalized amino acids. We then describe four key fields of research in POCs: (1) biomaterials for interfacing with, and controlling the behavior of cells; (2) hybrid self-assembling systems that balance peptide and oligonucleotide intermolecular forces; (3) template-enhanced coupling of POCs into larger molecules; and (4) display of peptides on self-assembled oligonucleotide scaffolds. We also highlight several promising areas for future applications in each of these four directions, and anticipate ever increasing uses of POCs in interdisciplinary research.
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Affiliation(s)
- Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe AZ, USA.
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21
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Núñez-Villanueva D, Ciaccia M, Hunter CA. Cap control: cyclic versus linear oligomerisation in covalent template-directed synthesis. RSC Adv 2019; 9:29566-29569. [PMID: 35531529 PMCID: PMC9071899 DOI: 10.1039/c9ra07233k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
Covalent template-directed synthesis was used to oligomerise monomer building blocks in a controlled manner to give exclusively the linear trimer. Competing reaction pathways were blocked by addition of a large excess of a monomeric capping agent. At a concentration of 1 mM, the cap selectively prevented further reaction of the product chain ends to give polymeric and macrocyclic products, but did not interfere with the templating process. The right concentration of capping agent is required to control the product distribution in covalent template-directed synthesis of linear oligomers using CuAAC.![]()
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Affiliation(s)
| | - Maria Ciaccia
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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22
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Lai G, Luh TY. Polynorbornene-based Template for Polymer Synthesis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20170354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Guoqiao Lai
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Tien-Yau Luh
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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23
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Bag BG, Ghorai S, Panja SK, Dinda SK, Paul K. First in situ vesicular self-assembly of ‘binols’ generated by a two-component aerobic oxidation reaction. RSC Adv 2018; 8:29155-29163. [PMID: 35547996 PMCID: PMC9084448 DOI: 10.1039/c8ra06488a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/07/2018] [Indexed: 11/25/2022] Open
Abstract
Generation of vesicular self-assemblies from natural and synthetic components has been in the frontiers of research in recent years for an improved understanding of the self-assembly process and also because of its prospective and realized applications in the areas of advanced materials, biotechnology and medicine. In the present work, we report the first example of the in situ generation of vesicular self-assemblies during an aerobic coupling reaction. The two precursor 2-naphthol units, having hydrogen bond donor–acceptor groups with appended alkyl chains, yielded binol (2,2′-dihydroxy-1,1′-binaphthyl) derivatives by aerobic coupling that spontaneously self-assembled in situ, yielding vesicular self-assemblies and gels. The morphology of the self-assemblies has been characterized by various optical, electron and atomic force microscopic techniques. The vesicular self-assemblies obtained in the liquids were capable of entrapping fluorophores such as rhodamine-B and carboxy fluorescein including the anticancer drug doxorubicin. The entrapped fluorophores could also be released by sonication or by rupture of vesicles. The supramolecular gels obtained in binary solvent mixtures showed improved gelation abilities with increase in the alkyl chain lengths as reflected by their minimum gelator concentration (mgcs) values, gel to sol transition temperatures (Tgel) and rheology properties. The results described here are also the first demonstration of gelation during an aerobic coupling reaction. Binol derivatives, obtained by aerobic coupling of two 2-naphthol derivatives having H-bond donor–acceptor groups and appended alkyl chains, spontaneously self-assembled in situ yielding vesicular self-assemblies and gels.![]()
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Affiliation(s)
- Braja G. Bag
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore 721102
- India
| | - Subrata Ghorai
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore 721102
- India
| | - Saikat K. Panja
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore 721102
- India
| | - Shaishab K. Dinda
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore 721102
- India
| | - Koushik Paul
- Department of Chemistry and Chemical Technology
- Vidyasagar University
- Midnapore 721102
- India
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24
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O’Reilly RK, Turberfield AJ, Wilks TR. The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery. Acc Chem Res 2017; 50:2496-2509. [PMID: 28915003 PMCID: PMC5746846 DOI: 10.1021/acs.accounts.7b00280] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Precise control over reactivity and molecular
structure is a fundamental
goal of the chemical sciences. Billions of years of evolution by natural
selection have resulted in chemical systems capable of information
storage, self-replication, catalysis, capture and production of light,
and even cognition. In all these cases, control over molecular structure
is required to achieve a particular function: without structural control,
function may be impaired, unpredictable, or impossible. The
search for molecules with a desired function is often achieved
by synthesizing a combinatorial library, which contains many or all
possible combinations of a set of chemical building blocks (BBs),
and then screening this library to identify “successful”
structures. The largest libraries made by conventional synthesis are
currently of the order of 108 distinct molecules. To put
this in context, there are 1013 ways of arranging the 21
proteinogenic amino acids in chains up to 10 units long. Given that
we know that a number of these compounds have potent biological activity,
it would be highly desirable to be able to search them all to identify
leads for new drug molecules. Large libraries of oligonucleotides
can be synthesized combinatorially and translated into peptides using
systems based on biological replication such as mRNA display, with
selected molecules identified by DNA sequencing; but these methods
are limited to BBs that are compatible with cellular machinery. In
order to search the vast tracts of chemical space beyond nucleic acids
and natural peptides, an alternative approach is required. DNA-templated
synthesis (DTS) could enable us to meet this challenge.
DTS controls chemical product formation by using the specificity of
DNA hybridization to bring selected reactants into close proximity,
and is capable of the programmed synthesis of many distinct products
in the same reaction vessel. By making use of dynamic, programmable
DNA processes, it is possible to engineer a system that can translate
instructions coded as a sequence of DNA bases into a chemical structure—a
process analogous to the action of the ribosome in living organisms
but with the potential to create a much more chemically diverse set
of products. It is also possible to ensure that each product molecule
is tagged with its identifying DNA sequence. Compound libraries synthesized
in this way can be exposed to selection against suitable targets,
enriching successful molecules. The encoding DNA can then be amplified
using the polymerase chain reaction and decoded by DNA sequencing.
More importantly, the DNA instruction sequences can be mutated and
reused during multiple rounds of amplification, translation, and selection.
In other words, DTS could be used as the foundation for a system of
synthetic molecular evolution, which could allow us to efficiently
search a vast chemical space. This has huge potential to revolutionize
materials discovery—imagine being able to evolve molecules
for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety
of reactions can be performed on a DNA template. Complex architectures
and autonomous “DNA robots” have been implemented for
the controlled assembly of BBs, and these mechanisms have in turn
enabled the one-pot synthesis of large combinatorial libraries. Indeed,
DTS libraries are being exploited by pharmaceutical companies and
have already found their way into drug lead discovery programs. This
Account explores the processes involved in DTS and highlights the
challenges that remain in creating a general system for molecular
discovery by evolution.
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Affiliation(s)
- Rachel K. O’Reilly
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew J. Turberfield
- Clarendon
Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Thomas R. Wilks
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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25
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Lanier KA, Williams LD. The Origin of Life: Models and Data. J Mol Evol 2017; 84:85-92. [PMID: 28243688 PMCID: PMC5371624 DOI: 10.1007/s00239-017-9783-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/14/2017] [Indexed: 11/03/2022]
Abstract
A general framework for conventional models of the origin of life (OOL) is the specification of a ‘privileged function.’ A privileged function is an extant biological function that is excised from its biological context, elevated in importance over other functions, and transported back in time to a primitive chemical or geological environment. In RNA or Clay Worlds, the privileged function is replication. In Metabolism-First Worlds, the privileged function is metabolism. In Thermal Vent Worlds, the privileged function is energy harvesting from chemical gradients. In Membrane Worlds, the privileged function is compartmentalization. In evaluating these models, we consider the contents and properties of the Universal Gene Set of life, which is the set of orthologous genes conserved throughout the tree of life and found in every living system. We also consider the components and properties of the Molecular Toolbox of Life, which contains twenty amino acids, eight nucleotides, glucose, polypeptide, polynucleotide, and several other components. OOL models based on privileged functions necessarily depend on “takeovers” to transition from previous genetic and catalytic systems to the extant DNA/RNA/protein system, requiring replacement of one Molecular Toolbox with another and of one Universal Gene Set with another. The observed robustness and contents of the Toolbox of Life and the Universal Gene Set over the last 3.7 billion years are thought to be post hoc phenomena. Once the takeover processes are acknowledged and are reasonably considered, the privileged function models are seen to be extremely complex with low predictive power. These models require indeterminacy and plasticity of biological and chemical processes.
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Affiliation(s)
- Kathryn A Lanier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA.
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26
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He C, Gállego I, Laughlin B, Grover MA, Hud NV. A viscous solvent enables information transfer from gene-length nucleic acids in a model prebiotic replication cycle. Nat Chem 2016; 9:318-324. [PMID: 28338690 DOI: 10.1038/nchem.2628] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/23/2016] [Indexed: 11/09/2022]
Abstract
Many hypotheses concerning the nature of early life assume that genetic information was once transferred through the template-directed synthesis of RNA, before the emergence of coded enzymes. However, attempts to demonstrate enzyme-free, template-directed synthesis of nucleic acids have been limited by 'strand inhibition', whereby transferring information from a template strand in the presence of its complementary strand is inhibited by the stability of the template duplex. Here, we use solvent viscosity to circumvent strand inhibition, demonstrating information transfer from a gene-length template (>300 nt) within a longer (545 bp or 3 kb) duplex. These results suggest that viscous environments on the prebiotic Earth, generated periodically by water evaporation, could have facilitated nucleic acid replication-particularly of long, structured sequences such as ribozymes. Our approach works with DNA and RNA, suggesting that viscosity-mediated replication is possible for a range of genetic polymers, perhaps even for informational polymers that may have preceded RNA.
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Affiliation(s)
- Christine He
- School of Chemical &Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Isaac Gállego
- School of Chemistry &Biochemistry, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Brandon Laughlin
- School of Chemistry &Biochemistry, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Martha A Grover
- School of Chemical &Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Nicholas V Hud
- School of Chemistry &Biochemistry, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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27
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Aleman Garcia MA, Hu Y, Willner I. Switchable supramolecular catalysis using DNA-templated scaffolds. Chem Commun (Camb) 2016; 52:2153-6. [PMID: 26701068 DOI: 10.1039/c5cc08873a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Switchable β-cyclodextrin (β-CD)-induced hydrolysis of m-tert-butylphenyl acetate is demonstrated in the presence of supramolecular β-CD/adamantane oligonucleotide scaffolds. In one system, a duplex between a β-CD-functionalized nucleic acid and an adamantane-nucleic acid leads to a switchable catalytic system. In a second system, a β-CD/adamantane duplex is cooperatively generated by K(+)-stabilized G-quadruplex units. The binding of hemin to the second system yields a bifunctional DNA scaffold with alternate catalytic functions.
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Affiliation(s)
- Miguel Angel Aleman Garcia
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Yuwei Hu
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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28
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Catalano MJ, Price NE, Gates KS. Effective molarity in a nucleic acid-controlled reaction. Bioorg Med Chem Lett 2016; 26:2627-30. [PMID: 27117430 DOI: 10.1016/j.bmcl.2016.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 12/30/2022]
Abstract
Positioning of reactive functional groups within a DNA duplex can enable chemical reactions that otherwise would not occur to an appreciable extent. However, few studies have quantitatively defined the extent to which the enforced proximity of reaction partners in duplex DNA can favor chemical processes. Here, we measured substantial effective molarities (as high as 25M) afforded by duplex DNA to a reaction involving interstrand cross-link formation between 2'-deoxyadenosine and a 2-deoxyribose abasic (Ap) site.
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Affiliation(s)
- Michael J Catalano
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Nathan E Price
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States; University of Missouri, Department of Biochemistry, 125 Chemistry Building, Columbia, MO 65211, United States.
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29
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Frisch H, Nie Y, Raunser S, Besenius P. pH‐Regulated Selectivity in Supramolecular Polymerizations: Switching between Co‐ and Homopolymers. Chemistry 2015; 21:3304-9. [DOI: 10.1002/chem.201406281] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Hendrik Frisch
- Organic Chemistry Institute and CeNTech, Westfälische Wilhelms‐Universität Münster, Corrensstrasse 40, 48149 Münster (Germany)
| | - Yan Nie
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto‐Hahn‐Strasse 11, 44227 Dortmund (Germany)
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto‐Hahn‐Strasse 11, 44227 Dortmund (Germany)
| | - Pol Besenius
- Organic Chemistry Institute and CeNTech, Westfälische Wilhelms‐Universität Münster, Corrensstrasse 40, 48149 Münster (Germany)
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30
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Barbeyron R, Martin AR, Jean-Jacques Vasseur JJV, Michael Smietana MS. DNA-templated borononucleic acid self assembly: a study of minimal complexity. RSC Adv 2015. [DOI: 10.1039/c5ra20767c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The minimal degree of sequence complexity needed for DNA-templated self-assembly of bifunctional oligonucleotides able to form internucleosidic boronate linkages has been studied.
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Affiliation(s)
- Renaud Barbeyron
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
| | - Anthony R. Martin
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
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31
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Abstract
This review discusses the template-directed preparation of sequence-defined polymers.
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32
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Zhang Y, Li Y, Zhang X, Jiang X. Sulfide synthesis through copper-catalyzed C–S bond formation under biomolecule-compatible conditions. Chem Commun (Camb) 2015; 51:941-4. [DOI: 10.1039/c4cc08367a] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here an efficient, mild and biomolecule-compatible method for constructing C–S bonds.
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Affiliation(s)
- Yonghong Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- Department of Chemistry
- East China Normal University
- Shanghai 200062
- P. R. China
| | - Yiming Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- Department of Chemistry
- East China Normal University
- Shanghai 200062
- P. R. China
| | - Xiaomei Zhang
- Chengdu Institute of Organic Chemistry
- Chinese Academy of Sciences
- Chengdu 610041
- P. R. China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- Department of Chemistry
- East China Normal University
- Shanghai 200062
- P. R. China
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33
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Brewer A, Davis AP. Chiral encoding may provide a simple solution to the origin of life. Nat Chem 2014; 6:569-74. [PMID: 24950314 DOI: 10.1038/nchem.1981] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 05/14/2014] [Indexed: 11/09/2022]
Abstract
The route by which the complex and specific molecules of life arose from the 'prebiotic soup' remains an unsolved problem. Evolution provides a large part of the answer, but this requires molecules that can carry information (that is, exist in many variants) and can replicate themselves. The process is commonplace in living organisms, but not so easy to achieve with simple chemical systems. It is especially difficult to contemplate in the chemical chaos of the prebiotic world. Although popular in many quarters, the notion that RNA was the first self-replicator carries many difficulties. Here, we present an alternative view, suggesting that there may be undiscovered self-replication mechanisms possible in much simpler systems. In particular, we highlight the possibility of information coding through stereochemical configurations of substituents in organic polymers. We also show that this coding system leads naturally to enantiopurity, solving the apparent problem of biological homochirality.
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Affiliation(s)
- Ashley Brewer
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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34
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Vázquez O, Seitz O. Templated native chemical ligation: peptide chemistry beyond protein synthesis. J Pept Sci 2014; 20:78-86. [PMID: 24395765 DOI: 10.1002/psc.2602] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 11/22/2013] [Accepted: 11/22/2013] [Indexed: 12/11/2022]
Abstract
Native chemical ligation (NCL) is a powerful method for the convergent synthesis of proteins and peptides. In its original format, NCL between a peptide containing a C-terminal thioester and another peptide offering an N-terminal cysteine has been used to enable protein synthesis of unprotected peptide fragments. However, the applications of NCL extend beyond the scope of protein synthesis. For instance, NCL can be put under the control of template molecules. In such a scenario, NCL enables the design of conditional reaction systems in which, peptide bond formation occurs only when a specific third party molecule is present. In this review, we will show how templates can be used to control the reactivity and chemoselectivity of NCL reactions. We highlight peptide and nucleic-acid-templated NCL reactions and discuss potential applications in nucleic acid diagnosis, origin-of-life studies and gene-expression-specific therapies.
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Affiliation(s)
- Olalla Vázquez
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
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35
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36
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Bissette AJ, Fletcher SP. Mechanisms of Autocatalysis. Angew Chem Int Ed Engl 2013; 52:12800-26. [DOI: 10.1002/anie.201303822] [Citation(s) in RCA: 273] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Indexed: 12/17/2022]
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37
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Dutta S, Fülöp A, Mokhir A. Fluorogenic, Catalytic, Photochemical Reaction for Amplified Detection of Nucleic Acids. Bioconjug Chem 2013; 24:1533-42. [DOI: 10.1021/bc400152n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Subrata Dutta
- Institute of Organic Chemistry
II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 42, 91054 Erlangen, Germany
| | - Annabelle Fülöp
- Institute of Organic Chemistry
II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 42, 91054 Erlangen, Germany
| | - Andriy Mokhir
- Institute of Organic Chemistry
II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 42, 91054 Erlangen, Germany
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38
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Jiménez-Balsa A, Dodero VI, Mascareñas JL. Toward encoding reactivity using double-stranded DNA. Sequence-dependent native chemical ligation of DNA binding polyamides. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.05.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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39
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Ke YZ, Ji RJ, Wei TC, Lee SL, Huang SL, Huang MJ, Chen CH, Luh TY. Well-Defined Condensation Polymers with Narrow Polydispersity via Unsymmetrical Ladderphanes by Sequential Polymerization. Macromolecules 2013. [DOI: 10.1021/ma4012363] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yuan-Zhen Ke
- Department
of Chemistry, National Taiwan University, Taipei, Taiwan 106
- Shanghai
Institute of Organic
Chemistry, Chinese Academy of Sciences,
345 Lingling Lu, Shanghai, China 200032
| | - Ren-Jie Ji
- Department
of Chemistry, National Taiwan University, Taipei, Taiwan 106
- Shanghai
Institute of Organic
Chemistry, Chinese Academy of Sciences,
345 Lingling Lu, Shanghai, China 200032
| | - Te-Chung Wei
- Department
of Chemistry, National Taiwan University, Taipei, Taiwan 106
| | - Shern-Long Lee
- Department
of Chemistry, National Taiwan University, Taipei, Taiwan 106
| | - Shou-Ling Huang
- Department
of Chemistry, National Taiwan University, Taipei, Taiwan 106
| | - Min-Jie Huang
- Department
of Chemistry, National Taiwan University, Taipei, Taiwan 106
| | - Chun-hsien Chen
- Department
of Chemistry, National Taiwan University, Taipei, Taiwan 106
| | - Tien-Yau Luh
- Department
of Chemistry, National Taiwan University, Taipei, Taiwan 106
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40
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Gorska K, Winssinger N. Reactions templated by nucleic acids: more ways to translate oligonucleotide-based instructions into emerging function. Angew Chem Int Ed Engl 2013; 52:6820-43. [PMID: 23794204 DOI: 10.1002/anie.201208460] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Indexed: 12/30/2022]
Abstract
The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.
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Affiliation(s)
- Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Universite de Strasbourg-CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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Gorska K, Winssinger N. Reaktionen an Nucleinsäuretemplaten: mehr Methoden zur Übersetzung Oligonucleotid-basierter Informationen in neue Funktionen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208460] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Percivalle C, Bartolo JF, Ladame S. Oligonucleotide-templated chemical reactions: pushing the boundaries of a nature-inspired process. Org Biomol Chem 2013; 11:16-26. [PMID: 23076879 DOI: 10.1039/c2ob26163d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Widespread in nature, oligonucleotide-templated reactions of phosphodiester bond formation have inspired chemists who are now applying this elegant strategy to the catalysis of a broad range of otherwise inefficient reactions. This review highlights the increasing diversity of chemical reactions that can be efficiently catalysed by an oligonucleotide template, using Watson-Crick base-pairing to bring both reagents in close enough proximity to react, thus increasing significantly their effective molarity. The applications of this elegant concept for nucleic acid sensing and controlled organic synthesis will also be discussed.
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Affiliation(s)
- Claudia Percivalle
- Department of Bioengineering, Imperial College London, South Kensington campus, London SW7 2AZ, UK
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Chen W, Schuster GB. Precise Sequence Control in Linear and Cyclic Copolymers of 2,5-Bis(2-thienyl)pyrrole and Aniline by DNA-Programmed Assembly. J Am Chem Soc 2013; 135:4438-49. [DOI: 10.1021/ja312507z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Wen Chen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Gary B. Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
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Barbeyron R, Wengel J, Vasseur JJ, Smietana M. Boronic acid-based autoligation of nucleic acids: influence of the nature of the 3′-end ribonucleotidic strand. MONATSHEFTE FUR CHEMIE 2012. [DOI: 10.1007/s00706-012-0881-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Spiropulos NG, Heemstra JM. Templating effect in DNA proximity ligation enables use of non-bioorthogonal chemistry in biological fluids. ARTIFICIAL DNA, PNA & XNA 2012; 3:123-8. [PMID: 23370267 DOI: 10.4161/adna.23842] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Here we describe the first example of selective reductive amination in biological fluids using split aptamer proximity ligation (StAPL). Utilizing the cocaine split aptamer, we demonstrate small-molecule-dependent ligation that is dose-dependent over a wide range of target concentrations in buffer, human blood serum and artificial urine medium. We explore the substrate binding preferences of the split aptamer and find that the cinchona alkaloids quinine and quinidine bind to the aptamer with higher affinity than cocaine. This increased affinity leads to improved detection limits for these small-molecule targets. We also demonstrate that linker length and hydrophobicity impact the efficiency of split aptamer ligation. The ability to carry out selective chemical transformations using non-bioorthogonal chemistry in media where competing reactive groups are present highlights the power of the increased effective molarity provided by DNA assembly. Obviating the need for bioorthogonal chemistry would dramatically expand the repertoire of chemical transformations available for use in templated reactions such as proximity ligation assays, in turn enabling the development of novel methods for biomolecule detection.
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Affiliation(s)
- Nicholas G Spiropulos
- Department of Chemistry, Center for Cell and Genome Science, University of Utah, Salt Lake City, UT USA
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Abstract
The single common feature of all biological systems is the dependence on self-assembly of molecular units to be morphed into well-defined functional architectures. Thanks to a dynamic equilibrium process, incorrect structural units are rejected with high levels of fidelity. The development of synthetic systems displaying similar attributes is an emerging field with wide applications from biotechnology to medicine. In this context, we developed a stimuli-responsive nucleic acid-based system relying on the reversible formation of cyclic boronate internucleosidic linkages. The dynamic assembly of this new borono-based helix has been accomplished through a DNA- and an RNA-templated autoligation process featuring a 5'-ended boronic acid oligonucleotide connecting to a 3'-ended ribonucleosidic oligonucleotide partner.
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Park S, Ikehata K, Watabe R, Hidaka Y, Rajendran A, Sugiyama H. Deciphering DNA-based asymmetric catalysis through intramolecular Friedel–Crafts alkylations. Chem Commun (Camb) 2012; 48:10398-400. [DOI: 10.1039/c2cc35625b] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Here we describe the first use of small-molecule binding to direct a chemical reaction between two nucleic acid strands. The reported reaction is a ligation between two fragments of a DNA split aptamer using strain-promoted azide-alkyne cycloaddition. Utilizing the split aptamer for cocaine, we demonstrate small-molecule-dependent ligation that is dose-dependent over a wide range of cocaine concentrations and is compatible with complex biological fluids such as human blood serum. Moreover, studies of split aptamer ligation at varying salt concentrations and using structurally similar analogues of cocaine have revealed new insight into the assembly and small-molecule binding properties of the cocaine split aptamer. The ability to translate the presence of a small-molecule target into the output of DNA ligation is anticipated to enable the development of new, broadly applicable small-molecule detection assays.
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Affiliation(s)
- Ashwani K Sharma
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
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Silverman SK. DNA as a versatile chemical component for catalysis, encoding, and stereocontrol. Angew Chem Int Ed Engl 2011; 49:7180-201. [PMID: 20669202 DOI: 10.1002/anie.200906345] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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Dutta S, Mokhir A. An autocatalytic chromogenic and fluorogenic photochemical reaction controlled by nucleic acids. Chem Commun (Camb) 2010; 47:1243-5. [PMID: 21103531 DOI: 10.1039/c0cc02508a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The autocatalytic photochemical reaction, which is potentially controlled by any selected nucleic acid, is highly sequence specific and not inhibited by its products, was developed. This reaction generates colored and fluorescent products, which can be monitored by the naked eye.
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Affiliation(s)
- Subrata Dutta
- Institute of Inorganic Chemistry, University of Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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