1
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Irving OJ, Matthews L, Coulthard S, Neely RK, Grant MM, Albrecht T. Sterically Enhanced Control of Enzyme-Assisted DNA Assembly. Chembiochem 2023; 24:e202300361. [PMID: 37681318 DOI: 10.1002/cbic.202300361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/15/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023]
Abstract
Traditional methods for the assembly of functionalised DNA structures, involving enzyme restriction and modification, present difficulties when working with small DNA fragments (<100 bp), in part due to a lack of control over enzymatic action during the DNA modification process. This limits the design flexibility and range of accessible DNA structures. Here, we show that these limitations can be overcome by introducing chemical modifications into the DNA that spatially restrict enzymatic activity. This approach, sterically controlled nuclease enhanced (SCoNE) DNA assembly, thereby circumvents the size limitations of conventional Gibson assembly (GA) and allows the preparation of well-defined, functionalised DNA structures with multiple probes for specific analytes, such as IL-6, procalcitonin (PCT), and a biotin reporter group. Notably, when using the same starting materials, conventional GA under typical conditions fails. We demonstrate successful analyte capture based on standard and modified sandwich ELISA and also show how the inclusion of biotin probes provides additional functionality for product isolation.
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Affiliation(s)
- Oliver J Irving
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Lauren Matthews
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Steven Coulthard
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Robert K Neely
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Melissa M Grant
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital, Birmingham Community Healthcare Trust), 5 Mill Pool Way, Edgbaston, Birmingham, B5 7EG, UK
| | - Tim Albrecht
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
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2
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Chandankar SS, Kondhare D, Leonard P, Seela F. Purine DNA Constructs Designed to Expand the Genetic Code: Functionalization, Impact of Ionic Forms, and Molecular Recognition of 7-Deazaxanthine-7-Deazapurine-2,6-diamine Base Pairs and Their Purine Counterparts. J Org Chem 2023; 88:13149-13168. [PMID: 37669119 DOI: 10.1021/acs.joc.3c01370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Purine DNA represents an alternative pairing system formed by two purines in the base pair with the recognition elements of Watson-Crick DNA. Base functionalization of 7-deaza-2'-deoxyxanthosine with ethynyl and octadiynyl residues led to clickable side chain derivatives with short and long linker arms. As complementary bases, purine-2,6-diamine or 7-deazapurine-2,6-diamine 2'-deoxyribonucleosides were used. 7-Deaza-7-iodo-2'-deoxyxanthosine served as a starting material for Sonogashira cross-coupling and the p-nitrophenylethyl group for base protection. Phosphoramidite building blocks for DNA synthesis were prepared. Oligonucleotides containing single modifications or runs of three purine base pairs embedded in 12-mer Watson-Crick DNA were synthesized and hybridized with complementary strands with purine- or 7-deazapurine-2,6-diamine located opposite to the xanthine derivatives. The stability of base pairs was evaluated in a comparative study on the basis of DNA melting experiments and Tm values. As 7-deazaxanthine and xanthine nucleosides form anionic forms at neutral pH, duplex stability became pK-dependent, and the system with 7-deazapurine displayed a significant higher stability as that containing xanthine. Alkynyl side chains are well accommodated in the purine-purine helix. Click adducts with pyrene showed that short linker arms destabilize duplexes, whereas long linkers increase duplex stability. CD and fluorescence measurements provide further insights into purine-purine base pairing.
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Affiliation(s)
- Somnath Shivaji Chandankar
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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3
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Deng K, Jia W, Ángeles Fernández‐Ibáñez M. Selective Para-C-H Alkynylation of Aniline Derivatives by Pd/S,O-Ligand Catalysis. Chemistry 2022; 28:e202104107. [PMID: 34902180 PMCID: PMC9306564 DOI: 10.1002/chem.202104107] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 11/11/2022]
Abstract
Herein, we report a nondirected para-selective C-H alkynylation of aniline derivatives by a Pd/S,O-ligand-based catalyst. The reaction proceeds under mild conditions and is compatible with a variety of substituted anilines. The scalability and further derivatizations of the alkynylated products have been also demonstrated.
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Affiliation(s)
- Ke‐Zuan Deng
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdam (TheNetherlands
| | - Wen‐Liang Jia
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdam (TheNetherlands
| | - M. Ángeles Fernández‐Ibáñez
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdam (TheNetherlands
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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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Agrahari AK, Bose P, Jaiswal MK, Rajkhowa S, Singh AS, Hotha S, Mishra N, Tiwari VK. Cu(I)-Catalyzed Click Chemistry in Glycoscience and Their Diverse Applications. Chem Rev 2021; 121:7638-7956. [PMID: 34165284 DOI: 10.1021/acs.chemrev.0c00920] [Citation(s) in RCA: 162] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Copper(I)-catalyzed 1,3-dipolar cycloaddition between organic azides and terminal alkynes, commonly known as CuAAC or click chemistry, has been identified as one of the most successful, versatile, reliable, and modular strategies for the rapid and regioselective construction of 1,4-disubstituted 1,2,3-triazoles as diversely functionalized molecules. Carbohydrates, an integral part of living cells, have several fascinating features, including their structural diversity, biocompatibility, bioavailability, hydrophilicity, and superior ADME properties with minimal toxicity, which support increased demand to explore them as versatile scaffolds for easy access to diverse glycohybrids and well-defined glycoconjugates for complete chemical, biochemical, and pharmacological investigations. This review highlights the successful development of CuAAC or click chemistry in emerging areas of glycoscience, including the synthesis of triazole appended carbohydrate-containing molecular architectures (mainly glycohybrids, glycoconjugates, glycopolymers, glycopeptides, glycoproteins, glycolipids, glycoclusters, and glycodendrimers through regioselective triazole forming modular and bio-orthogonal coupling protocols). It discusses the widespread applications of these glycoproducts as enzyme inhibitors in drug discovery and development, sensing, gelation, chelation, glycosylation, and catalysis. This review also covers the impact of click chemistry and provides future perspectives on its role in various emerging disciplines of science and technology.
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Affiliation(s)
- Anand K Agrahari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Priyanka Bose
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Manoj K Jaiswal
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Sanchayita Rajkhowa
- Department of Chemistry, Jorhat Institute of Science and Technology (JIST), Jorhat, Assam 785010, India
| | - Anoop S Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Srinivas Hotha
- Department of Chemistry, Indian Institute of Science and Engineering Research (IISER), Pune, Maharashtra 411021, India
| | - Nidhi Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Vinod K Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
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6
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Kondhare D, Zhang A, Leonard P, Seela F. Alkynylated and Dendronized 5-Aza-7-deazaguanine Nucleosides: Cross-Coupling with Tripropargylamine and Linear Alkynes, Click Functionalization, and Fluorescence of Pyrene Adducts†. J Org Chem 2020; 85:10525-10538. [PMID: 32700909 DOI: 10.1021/acs.joc.0c00926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The change of the recognition face of 5-aza-7-deazaguanine bridgehead nucleosides with respect to purine nucleosides permits the construction of new purine-purine or purine-pyrimidine base pairs in DNA and RNA. Clickable derivatives of 5-aza-7-deazaguanine were synthesized by introducing ethynyl, 1,7-octadiynyl, and tripropargylamino side chains in the 7-position of the 5-aza-7-deazapurine moiety by Sonogashira cross-coupling. Click reactions were performed with 1-azidomethylpyrene by the copper-catalyzed azide-alkyne cycloaddition. The copper(I)-catalyzed click reaction on the tripropargylamino nucleoside was significantly faster and higher yielding than that for nucleosides carrying linear alkynyl chains. Also, this reaction could be performed with copper(II) as the catalyst. An autocatalyzed cycle was suggested in which the click product acts as a catalyst. Pyrene click adducts of linear alkynylated nucleosides showed pyrene monomer emission, while tripropargylamino adducts showed monomer and excimer fluorescence. The fluorescence intensities of the 5-aza-7-deazaguanine nucleosides were higher than those of their 7-deazaguanine counterparts. The reported clickable nucleosides can be utilized to functionalize or to cross-link monomeric nucleosides or DNA for diagnostic or imaging purposes and other applications in nucleic acid chemistry and biotechnology.
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Affiliation(s)
- Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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7
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Stogniy MY, Erokhina SA, Druzina AA, Sivaev IB, Bregadze VI. Synthesis of novel carboranyl azides and “click” reactions thereof. J Organomet Chem 2019. [DOI: 10.1016/j.jorganchem.2019.121007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Chen X, Hu R, Qi C, Fu X, Wang J, He B, Huang D, Qin A, Tang BZ. Ethynylsulfone-Based Spontaneous Amino-yne Click Polymerization: A Facile Tool toward Regio- and Stereoregular Dynamic Polymers. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00670] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xuemei Chen
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Rong Hu
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Chunxuan Qi
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Xinyao Fu
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Jia Wang
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Benzhao He
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Die Huang
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Anjun Qin
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Ben Zhong Tang
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
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9
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Guo Y, Zhang J, Ding F, Pan G, Li J, Feng J, Zhu X, Zhang C. Stressing the Role of DNA as a Drug Carrier: Synthesis of DNA-Drug Conjugates through Grafting Chemotherapeutics onto Phosphorothioate Oligonucleotides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1807533. [PMID: 30847970 DOI: 10.1002/adma.201807533] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/22/2019] [Indexed: 05/24/2023]
Abstract
To stress the role of deoxyribonucleic acid (DNA) as a drug carrier, an efficient conjugation strategy in which chemotherapeutics can be grafted onto a phosphorothiolated DNA backbone through the reaction between the phosphorothioate group (PS) and a benzyl bromide group is proposed. As a proof of concept, benzyl-bromide-modified paclitaxel (PTX) is employed to graft onto the DNA backbone at the PS modification sites. Due to the easy preparation of phosphorothiolated DNA at any desired position during its solid-phase synthesis, diblock DNA strands containing both normal phosphodiester segment (PO DNA) and phosphorothiolate segment (PS DNA) are directly grafted with a multitude of PTXs without using complicated and exogenous linkers. Then, the resulting amphiphilic PO DNA-blocked-(PS DNA-grafted PTX) conjugates (PO DNA-b-(PS DNA-g-PTX)) assemble into PTX-loaded spherical nucleic acid (SNA)-like micellar nanoparticles (PTX-SNAs) with a high drug loading ratio up to ≈53%. Importantly, the PO DNA segment maintains its molecular recognition property and biological functions, which allows the as-prepared PTX-SNAs to be further functionalized with tumor-targeting aptamers, fluorescent probe strands, or antisense sequences. These multifunctional PTX-SNAs demonstrate active tumor-targeting delivery, efficient inhibition of tumor growth, and the reversal of drug resistance both in vitro and in vivo for comprehensive antitumor therapy.
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Affiliation(s)
- Yuanyuan Guo
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jiao Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Fei Ding
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Gaifang Pan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jing Li
- Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, 6600 Nanfeng Road, Shanghai, 201400, China
| | - Jing Feng
- Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, 6600 Nanfeng Road, Shanghai, 201400, China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
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10
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Huang D, Liu Y, Qin A, Tang BZ. Structure–Property Relationship of Regioregular Polytriazoles Produced by Ligand-Controlled Regiodivergent Ru(II)-Catalyzed Azide–Alkyne Click Polymerization. Macromolecules 2019. [DOI: 10.1021/acs.macromol.8b02671] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Die Huang
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Yong Liu
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong, China
| | - Anjun Qin
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
| | - Ben Zhong Tang
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou 510640, China
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong, China
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11
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Osman EA, Gadzikwa T, Gibbs JM. Quick Click: The DNA-Templated Ligation of 3'-O-Propargyl- and 5'-Azide-Modified Strands Is as Rapid as and More Selective than Ligase. Chembiochem 2018; 19:2081-2087. [PMID: 30059599 DOI: 10.1002/cbic.201800305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 12/24/2022]
Abstract
The copper(I)-mediated azide-alkyne cycloaddition (CuAAC) of 3'-propargyl ether and 5'-azide oligonucleotides is a particularly promising ligation system because it results in triazole linkages that effectively mimic the phosphate-sugar backbone of DNA, leading to unprecedented tolerance of the ligated strands by polymerases. However, for a chemical ligation strategy to be a viable alternative to enzymatic systems, it must be equally as rapid, as discriminating, and as easy to use. We found that the DNA-templated reaction with these modifications was rapid under aerobic conditions, with nearly quantitative conversion in 5 min, resulting in a kobs value of 1.1 min-1 , comparable with that measured in an enzymatic ligation system by using the highest commercially available concentration of T4 DNA ligase. Moreover, the CuAAC reaction also exhibited greater selectivity in discriminating C:A or C:T mismatches from the C:G match than that of T4 DNA ligase at 29 °C; a temperature slightly below the perfect nicked duplex dissociation temperature, but above that of the mismatched duplexes. These results suggest that the CuAAC reaction of 3'-propargyl ether and 5'-azide-terminated oligonucleotides represents a complementary alternative to T4 DNA ligase, with similar reaction rates, ease of setup and even enhanced selectivity for certain mismatches.
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Affiliation(s)
- Eiman A Osman
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Tendai Gadzikwa
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
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12
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Favalli N, Biendl S, Hartmann M, Piazzi J, Sladojevich F, Gräslund S, Brown PJ, Näreoja K, Schüler H, Scheuermann J, Franzini R, Neri D. A DNA-Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition. ChemMedChem 2018; 13:1303-1307. [PMID: 29856130 PMCID: PMC6126618 DOI: 10.1002/cmdc.201800193] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Indexed: 11/06/2022]
Abstract
A DNA-encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5-bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a Kd value of 6 nm, while compounds with the same substituents on an equidistant but flexible l-lysine scaffold showed 140-fold lower affinity. A 18 nm tankyrase-1 binder featured l-lysine as linking moiety, while molecules based on d-Lysine or (2S,4S)-amino-l-proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries.
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Affiliation(s)
- Nicholas Favalli
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Stefan Biendl
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Marco Hartmann
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | | | - Filippo Sladojevich
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La, Roche Ltd., Grenzacherstrasse 124, 4070 Basel (Switzerland)
| | - Susanne Gräslund
- Structural Genomics Consortium (SGC), University of Toronto, Toronto, M5G 1L7 (Canada)
- Department Structural Biology, Dept. of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Scheeles väg 2, S-17177 Stockholm
| | - Peter J. Brown
- Structural Genomics Consortium (SGC), University of Toronto, Toronto, M5G 1L7 (Canada)
| | - Katja Näreoja
- Department Structural Biology, Dept. of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Scheeles väg 2, S-17177 Stockholm
| | - Herwig Schüler
- Department Structural Biology, Dept. of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Scheeles väg 2, S-17177 Stockholm
| | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Raphael Franzini
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
- University of Utah, College of Pharmacy, 30 South 2000 East, Salt Lake City, UT 84112 (801) 581-6731
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
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13
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Gładysz M, Nowak-Karnowska J, Pasternak A, Milecki J. Synthesis and hybridization properties of oligonucleotide analogues with novel acyclic triazole internucleotide linkages. Bioorg Chem 2017; 72:161-167. [PMID: 28460358 DOI: 10.1016/j.bioorg.2017.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 03/13/2017] [Accepted: 04/08/2017] [Indexed: 12/11/2022]
Abstract
Herein, we describe synthesis of novel acyclic dinucleotide analogues connected via triazole linkage in CuAAC reaction. Synthesis pathway starting from previously obtained building blocks containing alkyne or azide functional group is described. Further functionalization and application of dinucleotide analogues in DNA phosphoramidite solid-phase synthesis is also explained. Additionally, we have examined the influence of novel modifications on DNA duplex thermodynamic stability.
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Affiliation(s)
- Michał Gładysz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
| | - Joanna Nowak-Karnowska
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89 b, 61-614 Poznań, Poland
| | - Anna Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jan Milecki
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89 b, 61-614 Poznań, Poland
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14
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Hu J, Sun P, Jiang X, Zhu W, Zhang K. Tadpole-shaped polymers based on UV-induced strain promoted azide-alkyne cycloaddition reaction. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0126-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Ponomarenko AI, Brylev VA, Sapozhnikova KA, Ustinov AV, Prokhorenko IA, Zatsepin TS, Korshun VA. Tetrahedral DNA conjugates from pentaerythritol-based polyazides. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.03.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Zhang Z, Zhou Q, Ye F, Xia Y, Wu G, Hossain ML, Zhang Y, Wang J. Copper(I)-Catalyzed Three-Component Coupling ofN-Tosylhydrazones, Alkynes and Azides: Synthesis of Trisubstituted 1,2,3-Triazoles. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500377] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Ryazantsev DY, Kvach MV, Tsybulsky DA, Prokhorenko IA, Stepanova IA, Martynenko YV, Gontarev SV, Shmanai VV, Zavriev SK, Korshun VA. Design of molecular beacons: 3' couple quenchers improve fluorogenic properties of a probe in real-time PCR assay. Analyst 2015; 139:2867-72. [PMID: 24736939 DOI: 10.1039/c4an00081a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Convenient preparation of fluorogenic hairpin DNA probes (molecular beacons) carrying a pair of FAM fluorophores (located close to 5'-terminus of the probe) or a pair of BHQ1 quenchers on 3'-terminus (with (BHQ1)2 or BHQ1-BHQ1 composition) is reported. These probes were used for the first time in a real-time PCR assay and showed considerable improvements in fluorogenic properties (the total fluorescence increase or signal-to-background ratio) in assay conditions vs. conventional one-FAM-one-BHQ1 molecular beacon probes as well as vs. hydrolyzable one-FAM-one-BHQ1 TaqMan probes. At the same time, such multiple modifications of the probe do not influence its Cq (a fractional PCR cycle used for quantification). The probe MB14 containing a BHQ1-BHQ1 pair showed a PCR fluorescence/background value of 9.6 which is more than two times higher than that of a regular probe MB2 (4.6). This study demonstrates prospects for the design of highly fluorogenic molecular beacon probes suitable for quantitative real-time PCR and for other potential applications (e.g. intracellular RNA detection and SNP/mutation analysis).
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Affiliation(s)
- Dmitry Y Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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Polydopamine-mediated immobilization of phenylboronic acid on magnetic microspheres for selective enrichment of glycoproteins and glycopeptides. Sci China Chem 2015. [DOI: 10.1007/s11426-014-5286-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Luo YL, Baathulaa K, Kannekanti VK, Zhou CH, Cai GX. Novel benzimidazole derived naphthalimide triazoles: synthesis, antimicrobial activity and interactions with calf thymus DNA. Sci China Chem 2015. [DOI: 10.1007/s11426-014-5296-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Thiol-ene coupling: An efficient tool for the synthesis of new biobased aliphatic amines for epoxy curing. POLYMER 2014. [DOI: 10.1016/j.polymer.2014.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Fomich MA, Kvach MV, Navakouski MJ, Weise C, Baranovsky AV, Korshun VA, Shmanai VV. Azide phosphoramidite in direct synthesis of azide-modified oligonucleotides. Org Lett 2014; 16:4590-3. [PMID: 25156193 DOI: 10.1021/ol502155g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Azide and phosphoramidite functions were found to be compatible within one molecule and stable for months in solution kept frozen at -20 °C. An azide-carrying phosphoramidite was used for direct introduction of multiple azide modifications into synthetic oligonucleotides. A series of azide-containing oligonucleotides were modified further using click reactions with alkynes.
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Affiliation(s)
- Maksim A Fomich
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, 220072 Minsk, Belarus
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