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Afari MNK, Lönnberg T. Base-Filling in Double-Helical Nucleic Acids. ChemistryOpen 2024:e202400088. [PMID: 38709096 DOI: 10.1002/open.202400088] [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: 03/18/2024] [Revised: 04/10/2024] [Indexed: 05/07/2024] Open
Abstract
Base-filling, i. e., post-synthetic furnishing of an oligonucleotide scaffold with base moieties or their analogues, is an interesting alternative to the conventional approach of sequential coupling of building blocks (modified or otherwise). Reversible attachment of the base moieties is particularly attractive as it allows the use of dynamic combinatorial chemistry and usually leads to higher fidelity. This concept article summarizes the various backbones and coupling reactions used for base-filling over the past fifteen years, discusses the impact of base stacking and pairing on efficiency and fidelity and highlights potential and realized applications.
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Affiliation(s)
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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2
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Shirvani P, Fayyazi N, Van Belle S, Debyser Z, Christ F, Saghaie L, Fassihi A. Design, synthesis, in silico studies, and antiproliferative evaluations of novel indolin-2-one derivatives containing 3-hydroxy-4-pyridinone fragment. Bioorg Med Chem Lett 2022; 70:128784. [PMID: 35569690 DOI: 10.1016/j.bmcl.2022.128784] [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: 02/06/2022] [Revised: 04/30/2022] [Accepted: 05/09/2022] [Indexed: 11/25/2022]
Abstract
Keeping in view the pharmacological properties of indolinones as promising scaffold as kinase inhibitors, herein, a novel series of 3-hydrazonoindolin-2-one derivatives bearing 3-hydroxy-4-pyridinone moiety were synthesized, studied by molecular docking, and fully characterized by spectroscopic techniques. All the prepared compounds were evaluated for their cytotoxicity attributes against a panel of tumor cell lines, including non-small cell lung cancer (A549), breast carcinoma (MCF-7), acute myeloid leukemia (AML), and chronic myeloid leukemia (CML). They displayed moderate to promising antiproliferative effects toward A549 and MCF-7 cells but remarkable results against AML and CML. Especially, compound 10k was found to be more potent against AML (EC50 = 0.69 μM) compare to the other halogen-substituted derivatives. FMS-like tyrosine kinase 3 (FLT3) is known to be expressed in AML cancer cells. The molecular docking studies demonstrated that our prepared compounds were potentially bound to AML active site through essential H-bond and other vital interactions with critical binding residues.
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Affiliation(s)
- Pouria Shirvani
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib, 817416-73461, Isfahan, Iran
| | - Neda Fayyazi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib, 817416-73461, Isfahan, Iran; Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Siska Van Belle
- Department of Pharmacological and Pharmaceutical Sciences, Laboratory of Molecular Virology and Gene Therapy, KU Leuven, Belgium
| | - Zeger Debyser
- Department of Pharmacological and Pharmaceutical Sciences, Laboratory of Molecular Virology and Gene Therapy, KU Leuven, Belgium
| | - Frauke Christ
- Department of Pharmacological and Pharmaceutical Sciences, Laboratory of Molecular Virology and Gene Therapy, KU Leuven, Belgium
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib, 817416-73461, Isfahan, Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib, 817416-73461, Isfahan, Iran.
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3
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Caillaud K, Ladavière C. Water‐soluble (poly)acylhydrazones: Syntheses and Applications. MACROMOL CHEM PHYS 2022. [DOI: 10.1002/macp.202200064] [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]
Affiliation(s)
- Kilian Caillaud
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères Université Claude Bernard Lyon1, INSA Lyon, Université Jean Monnet Villeurbanne Cédex F‐69622 France
| | - Catherine Ladavière
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères Université Claude Bernard Lyon1, INSA Lyon, Université Jean Monnet Villeurbanne Cédex F‐69622 France
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4
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Synthesis and DNA binding of new adenine derivatives incorporating 5-((Alkylthio)-1,3,4-oxadiazol-2-yl)methyl moiety. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2211-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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5
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Beierle JM, Ura Y, Ghadiri MR, Leman LJ. Templated Self-Assembly of Dynamic Peptide Nucleic Acids. Biochemistry 2017; 57:160-172. [PMID: 28832127 DOI: 10.1021/acs.biochem.7b00656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Template-directed macromolecule synthesis is a hallmark of living systems. Inspired by this natural process, several fundamentally novel mechanisms for template-directed assembly of nucleic acid analogues have been developed. Although these approaches have broad significance, including potential applications in biotechnology and implications for the origins of life, there are unresolved challenges in how to characterize in detail the complex assembly equilibria associated with dynamic templated reactions. Here we describe mechanistic studies of template-directed dynamic assembly for thioester peptide nucleic acid (tPNA), an informational polymer that responds to selection pressures under enzyme-free conditions. To overcome some of the inherent challenges of mechanistic studies of dynamic oligomers, we designed, synthesized, and implemented tPNA-DNA conjugates. The DNA primer region affords a high level of control over the location and register of the tPNA backbone in relation to the template strand. We characterized the degree and kinetics of dynamic nucleobase mismatch correction at defined backbone positions. Furthermore, we report the fidelity of dynamic assembly in tPNA as a function of position along the peptide backbone. Finally, we present theoretical studies that explore the level of fidelity that can be expected for an oligomer having a given hybridization affinity in dynamic templated reactions and provide guidance for the future development of sequence self-editing polymers and materials. As our results demonstrate, the use of molecular conjugates of constitutionally static and dynamic polymers establishes a new methodology for expediting the characterization of the complex chemical equilibria that underlie the assembly of dynamic informational polymers.
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Affiliation(s)
- John M Beierle
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yasuyuki Ura
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - M Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke J Leman
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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6
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Isenegger PG, Pfaltz A. Mass Spectrometric Back Reaction Screening of Quasi-Enantiomeric Products as a Mechanistic Tool. CHEM REC 2016; 16:2534-2543. [PMID: 27417883 DOI: 10.1002/tcr.201600072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 11/12/2022]
Abstract
In this account, we discuss a mass spectrometric method that enables unambiguous identification of intermediates involved in the enantioselective step of a catalytic cycle. This method, which we originally developed for rapid evaluation of chiral catalysts, is based on monitoring the back reaction of mass-labeled quasi-enantiomeric products by ESI-MS. In this way, the intrinsic enantioselectivity of a chiral catalyst can be determined directly by quantification of catalytically relevant intermediates. By comparing the results from the forward and back reaction, direct evidence for the involvement of a catalytic intermediate in the enantioselective step can be obtained. In addition, insights about the energy profile of the catalytic cycle may be gained. The potential of back reaction screening as a mechanistic tool is demonstrated for organocatalytic aldol reactions, 1,4-additions of aldehydes to nitroolefins, Diels-Alder reactions, Michael additions, and Morita-Baylis-Hillman reactions.
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Affiliation(s)
- Patrick G Isenegger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Andreas Pfaltz
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
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7
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Herrmann A. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures. Chem Soc Rev 2014; 43:1899-933. [PMID: 24296754 DOI: 10.1039/c3cs60336a] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.
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Affiliation(s)
- Andreas Herrmann
- Firmenich SA, Division Recherche et Développement, Route des Jeunes 1, B. P. 239, CH-1211 Genève 8, Switzerland.
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8
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Li Z, Liu W, Hao A. Gel–sol–gel′ evolution triggered by formic acid. Colloids Surf A Physicochem Eng Asp 2014. [DOI: 10.1016/j.colsurfa.2014.03.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Vaidya N, Walker SI, Lehman N. Recycling of informational units leads to selection of replicators in a prebiotic soup. ACTA ACUST UNITED AC 2013; 20:241-52. [PMID: 23438753 DOI: 10.1016/j.chembiol.2013.01.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/30/2012] [Accepted: 01/03/2013] [Indexed: 11/15/2022]
Abstract
Prebiotic chemical reactions would have been greatly aided by a process whereby living materials could have been recycled under conditions of limiting resources. Recombination of RNA fragments is a viable means of recycling but has not been demonstrated. Using systems based on the Azoarcus group I intron ribozyme, computational Monte Carlo studies indicate that a moderate level of recycling activity, spontaneous or catalyzed, leads to the most robust selection scenarios. It is interesting that recycling leads to a threshold effect where a dominant species suddenly jumps to fixation. In conjunction, laboratory studies with the Azoarcus ribozyme corroborate these results, showing that mixtures of scrambled and/or deleteriously mutated molecules can recycle their component fragments to generate fully functional recombinase ribozymes. These studies highlight the importance of recombination and recycling jointly in the advent of living systems.
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Affiliation(s)
- Nilesh Vaidya
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA
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10
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Design and synthesis of N-alkyl-N′-substituted 2,4-dioxo-3,4-dihydropyrimidin-1-diacylhydrazine derivatives as ecdysone receptor agonist. Bioorg Med Chem 2013; 21:4687-97. [DOI: 10.1016/j.bmc.2013.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/07/2013] [Accepted: 05/08/2013] [Indexed: 01/22/2023]
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11
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Mac DH, Sattar A, Chandrasekhar S, Yadav JS, Grée R. Synthesis of new 4-methyl-3-piperidones via an iron-catalyzed intramolecular tandem isomerization–aldolisation process. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.08.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Hocková D, Keough DT, Janeba Z, Wang TH, de Jersey J, Guddat LW. Synthesis of Novel N-Branched Acyclic Nucleoside Phosphonates As Potent and Selective Inhibitors of Human, Plasmodium falciparum and Plasmodium vivax 6-Oxopurine Phosphoribosyltransferases. J Med Chem 2012; 55:6209-23. [DOI: 10.1021/jm300662d] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dana Hocková
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences of the Czech Republic, vvi Flemingovo
nam. 2, CZ-166 10 Prague 6, Czech Republic
| | - Dianne T. Keough
- The School of Chemistry and Molecular Biosciences,
The University of Queensland, Brisbane, 4072 QLD, Australia
| | - Zlatko Janeba
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences of the Czech Republic, vvi Flemingovo
nam. 2, CZ-166 10 Prague 6, Czech Republic
| | - Tzu-Hsuan Wang
- The School of Chemistry and Molecular Biosciences,
The University of Queensland, Brisbane, 4072 QLD, Australia
| | - John de Jersey
- The School of Chemistry and Molecular Biosciences,
The University of Queensland, Brisbane, 4072 QLD, Australia
| | - Luke W. Guddat
- The School of Chemistry and Molecular Biosciences,
The University of Queensland, Brisbane, 4072 QLD, Australia
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13
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Khomyakova EA, Zubin EM, Smirnov IP, Pozmogova GE, Stetsenko DA, Oretskaya TS. DNA or RNA oligonucleotide 2'-hydrazides for chemoselective click-type ligation with carbonyl compounds. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:577-84. [PMID: 21888548 DOI: 10.1080/15257770.2011.586010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
An efficient method for the synthesis of DNA or RNA oligonucleotide 2'-hydrazides is described. Fully deprotected oligonucleotides containing a hydrazide group at the 2'-position of a uridine residue were obtained by a novel two-step procedure: periodate cleavage of an oligonucleotide with 1,2-diol group followed by conversion of the aldehyde to hydrazide with an extended linker arm using a homobifunctional reagent succinic dihydrazide and NaBH(3)CN. The resulting oligonucleotide 2'-hydrazides were efficiently conjugated by a click-type reaction at acidic pH to aliphatic or aromatic aldehydes with or without NaBH(3)CN reduction to afford novel 2'-conjugates.
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Affiliation(s)
- Elena A Khomyakova
- Department of Chemistry, A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonossov Moscow State University, Leninskie Gory, Moscow, Russia
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14
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15
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Lin Z, Emge TJ, Warmuth R. Multicomponent assembly of cavitand-based polyacylhydrazone nanocapsules. Chemistry 2011; 17:9395-405. [PMID: 21735498 DOI: 10.1002/chem.201100527] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Indexed: 01/09/2023]
Abstract
The thermodynamically controlled syntheses of different di-, tetra-, and hexacavitand polyacylhydrazone nanocapsules are reported. [2+4]-, [4+8]-, and [6+12]-nanocapsules assemble upon reacting a tetraformyl cavitand with two equivalents of isophthalic dihydrazide, or terephthalic dihydrazide in the presence of trifluoroacetic acid, whereby the building blocks are linked together through 8, 16, or 24 newly formed acylhydrazone bonds. Futhermore, the reaction of the tetraformylcavitands with different trigonal planar trihydrazides, simultaneously leads to the formation of [2+4]- and [6+8]-nanocapsules in varying ratios that depend on the cavitand to trihydrazide ratio and the nature of the cavitand and trihydrazide building blocks. The product ratios are rationalized with the different conformational strain of the acylhydrazone linkages in these nanocapsules. Diffusion NMR experiments with the hexacavitand polyacylhydrazone nanocapsules yield solvodynamic radii that range from 1.6 to 2.5 nm, consistent with estimates from force field calculations, and support, that these capsules have solvent filled, spherical interiors, the sizes of which approaches those of smaller proteins.
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Affiliation(s)
- Zhihua Lin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
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16
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Martin AR, Barvik I, Luvino D, Smietana M, Vasseur JJ. Dynamic and Programmable DNA-Templated Boronic Ester Formation. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007170] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Martin AR, Barvik I, Luvino D, Smietana M, Vasseur JJ. Dynamic and programmable DNA-templated boronic ester formation. Angew Chem Int Ed Engl 2011; 50:4193-6. [PMID: 21445950 DOI: 10.1002/anie.201007170] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 02/14/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Anthony R Martin
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, Place Bataillon, 34095 Montpellier, France
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18
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Capela MDF, Mosey NJ, Xing L, Wang R, Petitjean A. Amine Exchange in Formamidines: An Experimental and Theoretical Study. Chemistry 2011; 17:4598-612. [DOI: 10.1002/chem.201002389] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Indexed: 11/05/2022]
Affiliation(s)
- Marinha dF. Capela
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Nicholas J. Mosey
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Liyan Xing
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Ruiyao Wang
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
| | - Anne Petitjean
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7 L 3N6 (Canada), Fax: (+1) 613‐533‐6669
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19
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Dynamic Nanoplatforms in Biosensor and Membrane Constitutional Systems. CONSTITUTIONAL DYNAMIC CHEMISTRY 2011; 322:139-63. [DOI: 10.1007/128_2011_199] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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20
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Abstract
Dynamic combinatorial chemistry (DCC) is a powerful method for the identification of novel ligands for the molecular recognition of receptor molecules. The method relies on self-assembly processes to generate libraries of compounds under reversible conditions, allowing a receptor molecule to select the optimal binding ligand from the mixture. However, while DCC is now an established field of chemistry, there are limited examples of the application of DCC to nucleic acids. The requirement to conduct experiments under physiologically relevant conditions, and avoid reaction with, or denaturation of, the target nucleic acid secondary structure, limits the choice of the reversible chemistry, and presents restrictions on the building block design. This review will summarize recent examples of applications of DCC to the recognition of nucleic acids. Studies with duplex DNA, quadruplex DNA, and RNA have utilized mainly thiol disulfide libraries, although applications of imine libraries, in combination with metal coordination, have been reported. The use of thiol disulfide libraries produces lead compounds with limited biostability, and hence design of stable analogues or mimics is required for many applications.
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21
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Bowler FR, Diaz-Mochon JJ, Swift MD, Bradley M. DNA analysis by dynamic chemistry. Angew Chem Int Ed Engl 2010; 49:1809-12. [PMID: 20155766 DOI: 10.1002/anie.200905699] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Frank R Bowler
- School of Chemistry, University of Edinburgh, EH9 3JJ, Edinburgh, UK
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22
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Bowler F, Diaz-Mochon J, Swift M, Bradley M. DNA Analysis by Dynamic Chemistry. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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23
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Heemstra JM, Liu DR. Templated synthesis of peptide nucleic acids via sequence-selective base-filling reactions. J Am Chem Soc 2009; 131:11347-9. [PMID: 19722647 PMCID: PMC2726731 DOI: 10.1021/ja904712t] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The templated synthesis of nucleic acids has previously been achieved through the backbone ligation of preformed nucleotide monomers or oligomers. In contrast, here we demonstrate templated nucleic acid synthesis using a base-filling approach in which individual bases are added to abasic sites of a peptide nucleic acid (PNA). Because nucleobase substrates in this approach are not self-reactive, a base-filling approach may reduce the formation of nontemplated reaction products. Using either reductive amination or amine acylation chemistries, we observed efficient and selective addition of each of the four nucleobases to an abasic site in the middle of the PNA strand. We also describe the addition of single nucleobases to the end of a PNA strand through base filling, as well as the tandem addition of two bases to the middle of the PNA strand. These findings represent an experimental foundation for nonenzymatic information transfer through base filling.
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Affiliation(s)
- Jennifer M Heemstra
- Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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24
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Ura Y, Beierle JM, Leman LJ, Orgel LE, Ghadiri MR. Self-assembling sequence-adaptive peptide nucleic acids. Science 2009; 325:73-7. [PMID: 19520909 DOI: 10.1126/science.1174577] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Several classes of nucleic acid analogs have been reported, but no synthetic informational polymer has yet proven responsive to selection pressures under enzyme-free conditions. Here, we introduce an oligomer family that efficiently self-assembles by means of reversible covalent anchoring of nucleobase recognition units onto simple oligo-dipeptide backbones [thioester peptide nucleic acids (tPNAs)] and undergoes dynamic sequence modification in response to changing templates in solution. The oligomers specifically self-pair with complementary tPNA strands and cross-pair with RNA and DNA in Watson-Crick fashion. Thus, tPNA combines base-pairing interactions with the side-chain functionalities of typical peptides and proteins. These characteristics might prove advantageous for the design or selection of catalytic constructs or biomaterials that are capable of dynamic sequence repair and adaptation.
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Affiliation(s)
- Yasuyuki Ura
- Department of Chemistry and Skaggs Institute for Chemical Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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