1
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Dong X, Qiu Z, Wang Z, Li J, Qin W, Dang J, Zhou W, Jia G, Chen Y, Wang C. Efficient Silver(I)-Containing I-Motif DNA Hybrid Catalyst for Enantioselective Diels-Alder Reactions. Angew Chem Int Ed Engl 2024; 63:e202407838. [PMID: 38860437 DOI: 10.1002/anie.202407838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/12/2024]
Abstract
The inherent chiral structures of DNA serve as attractive scaffolds to construct DNA hybrid catalysts for valuable enantioselective transformations. Duplex and G-quadruplex DNA-based enantioselective catalysis has made great progress, yet novel design strategies of DNA hybrid catalysts are highly demanding and atomistic analysis of active centers is still challenging. DNA i-motif structures could be finely tuned by different cytosine-cytosine base pairs, providing a new platform to design DNA catalysts. Herein, we found that a human telomeric i-motif DNA containing cytosine-silver(I)-cytosine (C-Ag+-C) base pairs interacting with Cu(II) ions (i-motif DNA(Ag+)/Cu2+) could catalyze Diels-Alder reactions with full conversions and up to 95 % enantiomeric excess. As characterized by various physicochemical techniques, the presence of Ag+ is proved to replace the protons in hemiprotonated cytosine-cytosine (C : C+) base pairs and stabilize the DNA i-motif to allow the acceptance of Cu(II) ions. The i-motif DNA(Ag+)/Cu2+ catalyst shows about 8-fold rate acceleration compared with DNA and Cu2+. Based on DNA mutation experiments, thermodynamic studies and density function theory calculations, the catalytic center of Cu(II) ion is proposed to be located in a specific loop region via binding to one nitrogen-7 atom of an unpaired adenine and two phosphate-oxygen atoms from nearby deoxythymidine monophosphate and deoxyadenosine monophosphate, respectively.
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Affiliation(s)
- Xingchen Dong
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Ziyang Qiu
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Zixiao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jiaqi Li
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Weijun Qin
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jingshuang Dang
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Wenqin Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yashao Chen
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Changhao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
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2
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Zhao L, Ahmed F, Zeng Y, Xu W, Xiong H. Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes. ACS Sens 2022; 7:2833-2856. [PMID: 36112358 DOI: 10.1021/acssensors.2c00992] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na+, K+, Ag+, Tl+, Cu+/Cu2+, Hg2+, and Pb2+) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.
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Affiliation(s)
- Long Zhao
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China.,College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Farid Ahmed
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Yating Zeng
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Weiqing Xu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
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3
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Leveson‐Gower RB, Roelfes G. Biocatalytic Friedel-Crafts Reactions. ChemCatChem 2022; 14:e202200636. [PMID: 36606067 PMCID: PMC9804301 DOI: 10.1002/cctc.202200636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Indexed: 01/07/2023]
Abstract
Friedel-Crafts alkylation and acylation reactions are important methodologies in synthetic and industrial chemistry for the construction of aryl-alkyl and aryl-acyl linkages that are ubiquitous in bioactive molecules. Nature also exploits these reactions in many biosynthetic processes. Much work has been done to expand the synthetic application of these enzymes to unnatural substrates through directed evolution. The promise of such biocatalysts is their potential to supersede inefficient and toxic chemical approaches to these reactions, with mild operating conditions - the hallmark of enzymes. Complementary work has created many bio-hybrid Friedel-Crafts catalysts consisting of chemical catalysts anchored into biomolecular scaffolds, which display many of the same desirable characteristics. In this Review, we summarise these efforts, focussing on both mechanistic aspects and synthetic considerations, concluding with an overview of the frontiers of this field and routes towards more efficient and benign Friedel-Crafts reactions for the future of humankind.
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Affiliation(s)
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
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4
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Duchemin N, Aubert S, de Souza JV, Bethge L, Vonhoff S, Bronowska AK, Smietana M, Arseniyadis S. New Benchmark in DNA-Based Asymmetric Catalysis: Prevalence of Modified DNA/RNA Hybrid Systems. JACS AU 2022; 2:1910-1917. [PMID: 36032523 PMCID: PMC9400053 DOI: 10.1021/jacsau.2c00271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/27/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
By harnessing the chirality of the DNA double helix, chemists have been able to obtain new, reliable, selective, and environmentally friendly biohybrid catalytic systems with tailor-made functions. Nonetheless, despite all the advances made throughout the years in the field of DNA-based asymmetric catalysis, many challenges still remain to be faced, in particular when it comes to designing a "universal" catalyst with broad reactivity and unprecedented selectivity. Rational design and rounds of selection have allowed us to approach this goal. We report here the development of a DNA/RNA hybrid catalytic system featuring a covalently attached bipyridine ligand, which exhibits unmatched levels of selectivity throughout the current DNA toolbox and opens new avenues in asymmetric catalysis.
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Affiliation(s)
- Nicolas Duchemin
- Queen
Mary University of London, Department of Chemistry, Mile End Road, London E1 4NS, United
Kingdom
- NOXXON
Pharma AG, Max-Dohrn-Strasse 8-10, Berlin 10589, Germany
| | - Sidonie Aubert
- Queen
Mary University of London, Department of Chemistry, Mile End Road, London E1 4NS, United
Kingdom
| | - João V. de Souza
- Chemistry−School
of Natural and Environmental Sciences, Newcastle
University, Newcastle NE1 7RU, United Kingdom
| | - Lucas Bethge
- NOXXON
Pharma AG, Max-Dohrn-Strasse 8-10, Berlin 10589, Germany
| | - Stefan Vonhoff
- NOXXON
Pharma AG, Max-Dohrn-Strasse 8-10, Berlin 10589, Germany
| | - Agnieszka K. Bronowska
- Chemistry−School
of Natural and Environmental Sciences, Newcastle
University, Newcastle NE1 7RU, United Kingdom
| | - Michael Smietana
- Institut
des Biomolécules Max Mousseron, Université
de Montpellier, CNRS, ENSCM, 1919 Route de Mende, Montpellier 34095, France
| | - Stellios Arseniyadis
- Queen
Mary University of London, Department of Chemistry, Mile End Road, London E1 4NS, United
Kingdom
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5
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Kumar V, Turnbull WB, Kumar A. Review on Recent Developments in Biocatalysts for Friedel–Crafts Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vajinder Kumar
- Department of Chemistry, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Avneesh Kumar
- Department of Botany, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
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6
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Yang T, Peng S, Zeng R, Xu Q, Zheng X, Wang D, Zhou X, Shao Y. Visible light-driven i-motif-based DNAzymes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 270:120845. [PMID: 35016065 DOI: 10.1016/j.saa.2021.120845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/04/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
DNA foldings provide variant possibilities to develop DNAzymes with remarkable catalytic performance. In spite of fruitful reports on G-quadruplex DNAzymes, four-stranded cytosine-rich i-motifs have not been explored as the potential skeletons of DNAzymes. In this work, we developed a visible light-driven DNAzyme based on human telomeric i-motifs using a natural photosensitizer of hypericin (Hyp) as the cofactor and dissolved oxygen as the oxidant source. The i-motif folding in acidic solution caused the distal thymine overhangs at the 3' and 5' ends to approach each other to provide a favorable binding site for Hyp via an interaction of fully complementary hydrogen bonding. However, the i-motifs without the distal overhangs or with the inappropriate overhang length and the base identity exhibited no binding with Hyp. The binding event converted Hyp from the fully dark state to the emissive state under visible light illumination. Subsequently, the excited Hyp had an opportunity to transfer energy to dissolved oxygen. Resultantly, singlet oxygen (1O2) was generated to initiate the substrate oxidation. The catalytic performance of the DNAzyme can be improved using a long-lived mediator. Our developed i-motif-based DNAzyme can be driven by almost the whole range of visible lights, suggesting broad applications in the photocatalytic fields, for example, as an alternative strategy in developing biodevices.
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Affiliation(s)
- Tong Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Ruidi Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiong Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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7
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Yum JH, Sugiyama H, Park S. Harnessing DNA as a Designable Scaffold for Asymmetric Catalysis: Recent Advances and Future Perspectives. CHEM REC 2022; 22:e202100333. [PMID: 35312235 DOI: 10.1002/tcr.202100333] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Since the first report of DNAzyme by in vitro selection in 1994, catalytic DNA has investigated extensively, and their application has expanded continually in virtue of rapid advances in molecular biology and biotechnology. Nowadays, DNA is in the second prime time by way of DNA-based hybrid catalysts and DNA metalloenzymes in which helical chirality of DNA serves to asymmetric catalysis. DNA-based hybrid catalysts are attractive system to respond the demand of the times to pursuit green and sustainable society beyond traditional catalytic systems that value reaction efficiency. Herein, we highlight the recent advances and perspective of DNA-based hybrid catalysts with various aspects of DNA as a versatile scaffold for asymmetric synthesis. We hope that scientists in a variety of fields will be encouraged to join and promote remarkable evolution of this interesting research.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center (iFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan.,Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan
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8
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Guo J, Wang D, Pantatosaki E, Kuang H, Papadopoulos GK, Tsapatsis M, Kokkoli E. A Localized Enantioselective Catalytic Site on Short DNA Sequences and Their Amphiphiles. JACS AU 2022; 2:483-491. [PMID: 35252997 PMCID: PMC8889555 DOI: 10.1021/jacsau.1c00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 06/14/2023]
Abstract
A DNA-based artificial metalloenzyme (ArM) consisting of a copper(II) complex of 4,4'-dimethyl-2,2'-bipyridine (dmbipy-Cu) bound to double-stranded DNA (dsDNA) as short as 8 base pairs with only 2 contiguous central pairs (G for guanine and C for cytosine) catalyzes the highly enantioselective Diels-Alder reaction, Michael addition, and Friedel-Crafts alkylation in water. Molecular simulations indicate that these minimal sequences provide a single site where dmbipy-Cu is groove-bound and able to function as an enantioselective catalyst. Enantioselective preference inverts when d-DNA is replaced with l-DNA. When the DNA is conjugated to a hydrophobic tail, the obtained ArMs exhibit enantioselective performance in a methanol-water mixture superior to that of non-amphiphilic dsDNA, and dsDNA-amphiphiles with more complex G•C-rich sequences.
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Affiliation(s)
- Jun Guo
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Danyu Wang
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Evangelia Pantatosaki
- School
of Chemical Engineering, National Technical
University of Athens, 15780 Athens, Greece
| | - Huihui Kuang
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - George K. Papadopoulos
- School
of Chemical Engineering, National Technical
University of Athens, 15780 Athens, Greece
- Institute
for Medical Engineering and Science, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael Tsapatsis
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Applied
Physics Laboratory, Johns Hopkins University, Laurel, Maryland 20723, United States
| | - Efrosini Kokkoli
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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9
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Milovanović B, Petković M, Etinski M. Alkaline earth cations binding mode tailors excited-state charge transfer properties of guanine quadruplex: A TDDFT study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120584. [PMID: 34794899 DOI: 10.1016/j.saa.2021.120584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/25/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Quadruplexes formed by nucleic acids and their derivates tend to chelate different monovalent and bivalent cations, which simultaneously affect their excited electronic states properties. Cation binding to every and every other cavity of the central ion channel could be exploited for tuning exited-state charge transfer properties. In this work we utilize set of descriptors constructed on the basis of the one-electron transition density matrix obtained using linear-response TDDFT to study excited states properties of four crystallized tetramolecular quadruplexes that chelate alkaline earth cations (Ca2+, Sr2+ and Ba2+). Here, we show that alkaline earth cations situated at adjacent vacancies promote existence of the nucleobase-metal charge separation (CS) states, contrary to the structures with cations that occupy every second available vacancy. We argued that stabilization of these CS states is due to the strong electric field that stabilizes d orbitals of the cations which accept an excited-electron. Moreover, CS content is increased and redshifted below the first bright transition when number of the chelated cations is increased. Hydration effects stabilized CS states and increased their relative content. We also identified electron detachment states in the broad energy range for the Ca2+ containing system. These findings are valuable for understanding and development of the novel nanostructures based on the quadruplex scaffold with adjustable optical properties.
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Affiliation(s)
- Branislav Milovanović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Milena Petković
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia.
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10
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Chen Z, Zhou P, Guo Y, Anna, Bai J, Qiao R, Li C. Guanosine Borate Hydrogel and Self-Assembled Nanostructures Capable of Enantioselective Aldol Reaction in Water. J Org Chem 2022; 87:2624-2631. [PMID: 35104141 DOI: 10.1021/acs.joc.1c02573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A guanosine-based hydrogel formed by the self-assembly of guanosine and 4-((l-prolinamide)methyl)phenylboronic acid was constructed. The G quartets were selectively stabilized by K+ ions to form a self-supporting transparent hydrogel. These guanosine-derived assemblies were used to catalyze the aldol reaction in water without any additives, affording desirable conversion and enantioselectivity of the product. The controlled assays of small-molecule components indicated that the stable assemblies were the definite species that achieved high enantioselective catalysis. The current catalytic system can be readily recovered by simple extraction and still acquired good performance of the reaction after four cycles.
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Affiliation(s)
- Zhaohang Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Pengcheng Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yuanxia Guo
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Anna
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jiakun Bai
- Key Laboratory of Magnetic Molecules and Magnetic Information Material, Ministry of Education, College of Chemistry and Material, Shanxi Normal University, Linfen 041004, P. R. China
| | - Renzhong Qiao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Chao Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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11
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Festa C, Esposito V, Benigno D, De Marino S, Zampella A, Virgilio A, Galeone A. Discovering New G-Quadruplex DNA Catalysts in Enantioselective Sulfoxidation Reaction. Int J Mol Sci 2022; 23:ijms23031092. [PMID: 35163018 PMCID: PMC8835054 DOI: 10.3390/ijms23031092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 02/05/2023] Open
Abstract
The natural human telomeric G-quadruplex (G4) sequence d(GGGTTAGGGTTAGGGTTAGGG) HT21 was extensively utilized as a G4 DNA-based catalytic system for enantioselective reactions. Nine oligonucleotides (ODNs) based on this sequence and containing 8-bromo-2′-deoxyadenosine (ABr), 8-oxo-2′-deoxyadenosine (Aoxo) or β-L-2′-deoxyadenosine (AL) at different single loop positions were investigated to evaluate their performances as DNA catalysts in an enantioselective sulfoxidation reaction of thioanisole. The substitution of an adenosine in the loops of HT21 with these modified residues had a negligible impact on the G4 DNA structural features, thermal stability, and catalytic activity, since almost all investigated ODNs were able to form G-quadruplexes strictly resembling that of HT21 and catalyze a full conversion of the thioanisole substrate. More marked effects were obtained in chiral selectivity of G4 DNA metalloenzymes, considering that in most cases the DNA-modified catalysts induced lower enantioselectivities compared to the natural one. However, the HT21 derivative containing an AL residue in the first loop sequence significantly proved to be capable of producing about 84% enantiomeric excess, the highest enantioselectivity for DNA-based oxidation reaction to date.
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12
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Fu W, Jing H, Xu X, Xu S, Wang T, Hu W, Li H, Zhang N. Two coexisting pseudo-mirror heteromolecular telomeric G-quadruplexes in opposite loop progressions differentially recognized by a low equivalent of Thioflavin T. Nucleic Acids Res 2021; 49:10717-10734. [PMID: 34500466 PMCID: PMC8501994 DOI: 10.1093/nar/gkab755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/24/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
The final 3′-terminal residue of the telomeric DNA G-overhang is inherently less precise. Here, we describe how alteration of the last 3′-terminal base affects the mutual recognition between two different G-rich oligomers of human telomeric DNA in the formation of heteromolecular G-quadruplexes (hetero-GQs). Associations between three- and single-repeat fragments of human telomeric DNA, target d(GGGTTAGGGTTAGGG) and probe d(TAGGGT), in Na+ solution yield two coexisting forms of (3 + 1) hybrid hetero-GQs: the kinetically favourable LLP-form (left loop progression) and the thermodynamically controlled RLP-form (right loop progression). However, only the adoption of a single LLP-form has been previously reported between the same probe d(TAGGGT) and a target variant d(GGGTTAGGGTTAGGGT) having one extra 3′-end thymine. Moreover, the flanking base alterations of short G-rich probe variants also significantly affect the loop progressions of hetero-GQs. Although seemingly two pseudo-mirror counter partners, the RLP-form exhibits a preference over the LLP-form to be recognized by a low equivalent of fluorescence dye thioflavin T (ThT). To a greater extent, ThT preferentially binds to RLP hetero-GQ than with the corresponding telomeric DNA duplex context or several other representative unimolecular GQs.
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Affiliation(s)
- Wenqiang Fu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Xiaojuan Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Suping Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Tao Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Wenxuan Hu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Huihui Li
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China.,High Magnetic Field Laboratory of Anhui Province, Hefei 230031, China
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13
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Yang H, Peng Y, Xu M, Xu S, Zhou Y. Development of DNA Biosensors Based on DNAzymes and Nucleases. Crit Rev Anal Chem 2021; 53:161-176. [PMID: 34225516 DOI: 10.1080/10408347.2021.1944046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.
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Affiliation(s)
- Hualin Yang
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Peng
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Mingming Xu
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Shuxia Xu
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China.,College of Ecology and Environment, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Zhou
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science, Yangtze University, Jingzhou, Hubei, China
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14
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Chen K, He Z, Xiong W, Wang CJ, Zhou X. Enantioselective Diels–Alder reactions with left-handed G-quadruplex DNA-based catalysts. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.12.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Punt PM, Langenberg MD, Altan O, Clever GH. Modular Design of G-Quadruplex MetalloDNAzymes for Catalytic C-C Bond Formations with Switchable Enantioselectivity. J Am Chem Soc 2021; 143:3555-3561. [PMID: 33630569 DOI: 10.1021/jacs.0c13251] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal-binding DNA structures with catalytic function are receiving increasing interest. Although a number of metalloDNAzymes have been reported to be highly efficient, the exact coordination/position of their catalytic metal center is often unknown. Here, we present a new approach to rationally develop metalloDNAzymes for Lewis acid-catalyzed reactions such as enantioselective Michael additions. Our strategy relies on the predictable folding patterns of unimolecular DNA G-quadruplexes, combined with the concept of metal-mediated base-pairing. Transition-metal coordination environments were created in G-quadruplex loop regions, accessible by substrates. Therefore, protein-inspired imidazole ligandoside L was covalently incorporated into a series of G-rich DNA strands by solid-phase synthesis. Iterative rounds of DNA sequence design and catalytic assays allowed us to select tailored metalloDNAzymes giving high conversions and excellent enantioselectivities (≥99%). Based on their primary sequence, folding pattern, and metal coordination mode, valuable information on structure-activity relationships could be extracted. Variation of the number and position of ligand L within the sequence allowed us to control the formation of (S) and (R) enantiomeric reaction products, respectively.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Marie D Langenberg
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Okan Altan
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
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16
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Ma Y, Xu M, Wang Y, Liu Z, Ye B. A highly sensitive and adjustable colorimetric assay of hydrogen sulfide by signal amplification based on G-quadruplex-Cu 2+ peroxidase mimetics. Analyst 2021; 145:2995-3001. [PMID: 32129377 DOI: 10.1039/d0an00093k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This work reports the first example of a colorimetric H2S sensor constructed through G-quadruplex-Cu2+ (G4-Cu2+) peroxidase mimetics employing Cu2+ ions and G-rich DNA with signal amplification. In the hydrogen peroxide (H2O2)-mediated oxidation of 3,3',5,5'-tetramethylbenzidine (TMB), the catalytic capacity of Cu2+ can be greatly improved in the presence of 22AG DNA, where 22AG DNA acts as a signal amplifier. However, G4-Cu2+ peroxidase mimetics lose their catalytic abilities after reacting with H2S. This is employed to develop a colorimetric assay of H2S without complex synthesis and instrumentation, with a linear range from 0.01 μM to 150 μM and a detection limit of 7.5 nM. The sensitivity of the sensor can also be adjusted by changing the concentration of Cu2+. Moreover, the developed sensor is successfully applied for the quantitative determination of H2S in human serum samples.
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Affiliation(s)
- Yu Ma
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Maotian Xu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, School of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, China. and Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongxiang Wang
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, School of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, China.
| | - Zi Liu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Baoxian Ye
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
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17
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18
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Yu Y, Zhang Q, Gao H, Yan C, Zheng X, Yang T, Zhou X, Shao Y. Metalloenzyme-mimic innate G-quadruplex DNAzymes using directly coordinated metal ions as active centers. Dalton Trans 2020; 49:13160-13166. [PMID: 32936164 DOI: 10.1039/d0dt02871a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
G-quadruplex DNAs (G4s) have been reported to exhibit the DNAzyme activities by binding with some metal complexes and functional organic ligands. However, there is a challenge to develop metalloenzyme-mimic G4-based innate DNAzymes using the complexed metal ions directly serving as the active centers. This will diversify DNAzymes for developing novel devices since G4 structures are more polymorphic than the other DNA foldings. In this work, we found that the lanthanide trivalent cerium ion of Ce3+ can bind to the human telomere G4 (htG4) according to a 1 : 2 binding mode favorable for creating metalloenzymes-mimic G4 DNAzymes. This Ce3+-G4 entity exhibits a peroxidase activity towards the oxidation of the substrate of 3,3,5,5-tetramethylbenzidine (TMB) by hydrogen peroxide. The 5' G4 tetrads with the orderly arranged carbonyl oxygen atoms are believed to be the coordination sites for Ce3+ and favor the conversion between Ce3+ and Ce4+. Our work provides an alternative feasibility in developing the G4-based innate DNAzymes for variant applications.
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Affiliation(s)
- Yali Yu
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Qingqing Zhang
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Heng Gao
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Chenxiao Yan
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Xiong Zheng
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Tong Yang
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Xiaoshun Zhou
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Yong Shao
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
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19
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Wang C, Qi Q, Li W, Dang J, Hao M, Lv S, Dong X, Gu Y, Wu P, Zhang W, Chen Y, Hartig JS. A Cu(II)-ATP complex efficiently catalyses enantioselective Diels-Alder reactions. Nat Commun 2020; 11:4792. [PMID: 32963238 PMCID: PMC7508818 DOI: 10.1038/s41467-020-18554-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/26/2020] [Indexed: 11/09/2022] Open
Abstract
Natural biomolecules have been used extensively as chiral scaffolds that bind/surround metal complexes to achieve stereoselectivity in catalytic reactions. ATP is ubiquitously found in nature as an energy-storing molecule and can complex diverse metal cations. However, in biotic reactions ATP-metal complexes are thought to function mostly as co-substrates undergoing phosphoanhydride bond cleavage reactions rather than participating in catalytic mechanisms. Here, we report that a specific Cu(II)-ATP complex (Cu2+·ATP) efficiently catalyses Diels-Alder reactions with high reactivity and enantioselectivity. We investigate the substrates and stereoselectivity of the reaction, characterise the catalyst by a range of physicochemical experiments and propose the reaction mechanism based on density functional theory (DFT) calculations. It is found that three key residues (N7, β-phosphate and γ-phosphate) in ATP are important for the efficient catalytic activity and stereocontrol via complexation of the Cu(II) ion. In addition to the potential technological uses, these findings could have general implications for the chemical selection of complex mixtures in prebiotic scenarios.
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Affiliation(s)
- Changhao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China.
| | - Qianqian Qi
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Wenying Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Jingshuang Dang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Min Hao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Shuting Lv
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Xingchen Dong
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Youkun Gu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Peizhe Wu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Wenyue Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Yashao Chen
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
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20
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Zhong H, Lo W, Man T, Williams BP, Li D, Chen S, Pei H, Li L, Tsung C. Stabilizing DNAzymes through Encapsulation in a Metal–Organic Framework. Chemistry 2020; 26:12931-12935. [DOI: 10.1002/chem.202002178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Huiye Zhong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Wei‐Shang Lo
- Department of Chemistry Merkert Chemistry Center Boston College 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Benjamin P. Williams
- Department of Chemistry Merkert Chemistry Center Boston College 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Dan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Sheng‐Yu Chen
- School of Physical Science and Technology ShanghaiTech University 393 Middle Huaxia Road Pudong, Shanghai 201210 P.R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Chia‐Kuang Tsung
- Department of Chemistry Merkert Chemistry Center Boston College 2609 Beacon Street Chestnut Hill MA 02467 USA
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21
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Qi Q, Lv S, Hao M, Dong X, Gu Y, Wu P, Zhang W, Chen Y, Wang C. An Efficient Cyclic Di-AMP Based Artificial Metalloribozyme for Enantioselective Diels-Alder Reactions. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Qianqian Qi
- Key Laboratory of Applied Surface and Colloid Chemistry; Ministry of Education; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 West Chang'an Avenue 710119 Xi'an China
| | - Shuting Lv
- Key Laboratory of Applied Surface and Colloid Chemistry; Ministry of Education; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 West Chang'an Avenue 710119 Xi'an China
| | - Min Hao
- Key Laboratory of Applied Surface and Colloid Chemistry; Ministry of Education; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 West Chang'an Avenue 710119 Xi'an China
| | - Xingchen Dong
- Key Laboratory of Applied Surface and Colloid Chemistry; Ministry of Education; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 West Chang'an Avenue 710119 Xi'an China
| | - Youkun Gu
- Key Laboratory of Applied Surface and Colloid Chemistry; Ministry of Education; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 West Chang'an Avenue 710119 Xi'an China
| | - Peizhe Wu
- Key Laboratory of Applied Surface and Colloid Chemistry; Ministry of Education; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 West Chang'an Avenue 710119 Xi'an China
| | - Wenyue Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry; Ministry of Education; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 West Chang'an Avenue 710119 Xi'an China
| | - Yashao Chen
- Key Laboratory of Applied Surface and Colloid Chemistry; Ministry of Education; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 West Chang'an Avenue 710119 Xi'an China
| | - Changhao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry; Ministry of Education; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 West Chang'an Avenue 710119 Xi'an China
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22
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Dey S, Jäschke A. Covalently Functionalized DNA Duplexes and Quadruplexes as Hybrid Catalysts in an Enantioselective Friedel-Crafts Reaction. Molecules 2020; 25:E3121. [PMID: 32650544 PMCID: PMC7397069 DOI: 10.3390/molecules25143121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 12/01/2022] Open
Abstract
The precise site-specific positioning of metal-ligand complexes on various DNA structures through covalent linkages has gained importance in the development of hybrid catalysts for aqueous-phase homogeneous catalysis. Covalently modified double-stranded and G-quadruplex DNA-based hybrid catalysts have been investigated separately. To understand the role of different DNA secondary structures in enantioselective Friedel-Crafts alkylation, a well-known G-quadruplex-forming sequence was covalently modified at different positions. The catalytic performance of this modified DNA strand was studied in the presence and absence of a complementary DNA sequence, resulting in the formation of two different secondary structures, namely duplex and G-quadruplex. Indeed, the secondary structures had a tremendous effect on both the yield and stereoselectivity of the catalyzed reaction. In addition, the position of the modification, the topology of the DNA, the nature of the ligand, and the length of the linker between ligand and DNA were found to modulate the catalytic performance of the hybrid catalysts. Using the optimal linker length, the quadruplexes formed the (-)-enantiomer with up to 65% ee, while the duplex yielded the (+)-enantiomer with up to 62% ee. This study unveils a new and simple way to control the stereochemical outcome of a Friedel-Crafts reaction.
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Affiliation(s)
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany;
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23
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24
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Zou BQ, Huang XL, Qin QP, Wang ZF, Wu XY, Tan MX, Liang H. Transition metal complexes with 6,7-dichloro-5,8-quinolinedione as mitochondria-targeted anticancer agents. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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25
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Wang C, Hao M, Qi Q, Dang J, Dong X, Lv S, Xiong L, Gao H, Jia G, Chen Y, Hartig JS, Li C. Highly Efficient Cyclic Dinucleotide Based Artificial Metalloribozymes for Enantioselective Friedel–Crafts Reactions in Water. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Changhao Wang
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - Min Hao
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - Qianqian Qi
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - Jingshuang Dang
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - Xingchen Dong
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - Shuting Lv
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - Ling Xiong
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - Huanhuan Gao
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - Guoqing Jia
- State Key Laboratory of CatalysisDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yashao Chen
- Key Laboratory of Applied Surface and Colloid ChemistryMinistry of EducationSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - Jörg S. Hartig
- Department of ChemistryKonstanz Research School Chemical Biology (KoRS-CB)University of Konstanz 78457 Konstanz Germany
| | - Can Li
- State Key Laboratory of CatalysisDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
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26
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Bai J, Sun X, Wang H, Li C, Qiao R. Guanosine-Based Self-Assembly as an Enantioselective Catalyst Scaffold. J Org Chem 2020; 85:2010-2018. [PMID: 31935325 DOI: 10.1021/acs.joc.9b02718] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A self-assembled G-quadruplex formed by guanosine and borate as the chiral scaffold was used to catalyze the asymmetric Friedel-Crafts reaction in water. Catalysis, depending on the self-assembly of guanosine and borate into a fibrillar structure in the presence of Cu2+ ions, can be modulated by the assembly concentration, temperature, and amount of Cu2+ ions. Detailed spectral experiments proved that the guanosine-based assembly in solution was responsible for the enantioselective catalysis, rather than small-molecule species. Some of the similar G-quartet assemblies were unable to promote the asymmetric reaction, implying unique properties of the current system, including excellent lifetime stability and supramolecular chiral structures. This work provided the first example of the self-assembled G-quadruplex achieving enantioselective catalysis and some perspective to better understand the design of nucleoside-based self-assemblies for an enantioselective reaction. In view of guanosine as a building block, these findings may be applied to discuss the prebiotic chiral catalyst preceded ribozymes.
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Affiliation(s)
- Jiakun Bai
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , No. 15, Beisanhuan East Road , Beijing 100029 , China
| | - Xiaolin Sun
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , No. 15, Beisanhuan East Road , Beijing 100029 , China
| | - Haisheng Wang
- Harbin Pharmaceutical Group Holding Co., Ltd. , Harbin 150018 , China
| | - Chao Li
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , No. 15, Beisanhuan East Road , Beijing 100029 , China
| | - Renzhong Qiao
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , No. 15, Beisanhuan East Road , Beijing 100029 , China
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27
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Wang C, Hao M, Qi Q, Dang J, Dong X, Lv S, Xiong L, Gao H, Jia G, Chen Y, Hartig JS, Li C. Highly Efficient Cyclic Dinucleotide Based Artificial Metalloribozymes for Enantioselective Friedel-Crafts Reactions in Water. Angew Chem Int Ed Engl 2020; 59:3444-3449. [PMID: 31825550 DOI: 10.1002/anie.201912962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/25/2019] [Indexed: 01/01/2023]
Abstract
The diverse secondary structures of nucleic acids are emerging as attractive chiral scaffolds to construct artificial metalloenzymes (ArMs) for enantioselective catalysis. DNA-based ArMs containing duplex and G-quadruplex scaffolds have been widely investigated, yet RNA-based ArMs are scarce. Here we report that a cyclic dinucleotide of c-di-AMP and Cu2+ ions assemble into an artificial metalloribozyme (c-di-AMP⋅Cu2+ ) that enables catalysis of enantioselective Friedel-Crafts reactions in aqueous media with high reactivity and excellent enantioselectivity of up to 97 % ee. The assembly of c-di-AMP⋅Cu2+ gives rise to a 20-fold rate acceleration compared to Cu2+ ions. Based on various biophysical techniques and density function theory (DFT) calculations, a fine coordination structure of c-di-AMP⋅Cu2+ metalloribozyme is suggested in which two c-di-AMP form a dimer scaffold and the Cu2+ ion is located in the center of an adenine-adenine plane through binding to two N7 nitrogen atoms and one phosphate oxygen atom.
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Affiliation(s)
- Changhao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Min Hao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Qianqian Qi
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jingshuang Dang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Xingchen Dong
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Shuting Lv
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Ling Xiong
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Huanhuan Gao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yashao Chen
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jörg S Hartig
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457, Konstanz, Germany
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Kitamura Y, Azuma Y, Katsuda Y, Ihara T. Catalytic formation of luminescent lanthanide complexes using an entropy-driven DNA circuit. Chem Commun (Camb) 2020; 56:3863-3866. [DOI: 10.1039/d0cc00602e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Luminescent lanthanide complexes were catalytically formed through an entropy-driven DNA circuit triggered by a target nucleic acid.
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Affiliation(s)
- Yusuke Kitamura
- Division of Materials Science and Chemistry
- Faculty of Advanced Science and Technology
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Yukina Azuma
- Division of Materials Science and Chemistry
- Faculty of Advanced Science and Technology
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Yousuke Katsuda
- Division of Materials Science and Chemistry
- Faculty of Advanced Science and Technology
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry
- Faculty of Advanced Science and Technology
- Kumamoto University
- Kumamoto 860-8555
- Japan
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29
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Ye T, Gao H, Zhang Q, Yan C, Yu Y, Fei Y, Gao L, Zhou X, Shao Y. Polarity inversion sensitized G-quadruplex metal sensors with K + tolerance. Biosens Bioelectron 2019; 145:111703. [PMID: 31546203 DOI: 10.1016/j.bios.2019.111703] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022]
Abstract
Due to the high abundance of K+ in environments and K+-induced high stability of G-quadruplex (G4), developing a selective G4-based fluorescent sensor for other metal ions with K+ tolerance is a great challenge. Herein, we found that even in the presence of 15000-fold excess of K+, Ba2+ exhibits a highly specific binding with a human telomeric G4 (htG4) in comparison with other G4-binding metal ions such as Pb2+ and Sr2+. This specific binding event can be recognized by a natural fluorophore of hypericin with a lighting-up fluorescence response. Interestingly, inverting the polarity of the most 3' G in htG4 can sensitize the Ba2+ response with the retaining Ba2+ specificity and K+ tolerance. This polarity inversion of htG4 causes a G4 conformation change in K+ and the polarity-inverted htG4 tends to favorably dimerize in response to the Ba2+ specific binding. To our knowledge, this is the first report that polarity inversion of G4 can be applied to construct a selective metal sensor with K+ tolerance. Our findings will open a new way to conveniently regulate the G4 conformation and stability by polarity inversion towards developing high-performance sensors.
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Affiliation(s)
- Ting Ye
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yali Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yifan Fei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Longlong Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China.
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Mansot J, Vasseur J, Arseniyadis S, Smietana M. α,β‐Unsaturated 2‐Acyl‐Imidazoles in Asymmetric Biohybrid Catalysis. ChemCatChem 2019. [DOI: 10.1002/cctc.201900743] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Justine Mansot
- Institut des Biomolécules Max MousseronUMR 5247 CNRS Université de Montpellier, ENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Jean‐Jacques Vasseur
- Institut des Biomolécules Max MousseronUMR 5247 CNRS Université de Montpellier, ENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Stellios Arseniyadis
- Queen Mary University of LondonSchool of Biological and Chemical Sciences Mile End Road E1 4NS London UK
| | - Michael Smietana
- Institut des Biomolécules Max MousseronUMR 5247 CNRS Université de Montpellier, ENSCM Place Eugène Bataillon 34095 Montpellier France
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31
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Kitamura Y, Nozaki A, Ozaki R, Katsuda Y, Ihara T. Catalytic Formation of Luminescent Complex Clusters Based on Autonomous Strand Exchange Reaction of DNA. ACS APPLIED BIO MATERIALS 2019; 2:2988-2993. [DOI: 10.1021/acsabm.9b00326] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Akihiro Nozaki
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Rie Ozaki
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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Han XY, Fan QX, Chen ZH, Deng LX, Fang ZQ, Shi G, Zhang M. Coordination polymers of Tb 3+/Nucleotide as smart chemical nose/tongue toward pattern-recognition-based and time-resolved fluorescence sensing. Biosens Bioelectron 2019; 139:111335. [PMID: 31128478 DOI: 10.1016/j.bios.2019.111335] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 02/06/2023]
Abstract
The abundant functional groups on guanosine monophosphate (GMP) make it possible to interact with various metal ions. The subtle difference in the structure of GMP and deoxy-guanosine monophosphate (dGMP) coupled with Tb3+ can be readily exploited to form two coordination polymers, which have been unveiled as two time-resolved fluorescence (TRF) sensing reporters (Tb-GMP and Tb-dGMP) in our study. Based on this finding, herein, we have proposed a novel TRF orthogonal sensing array (Tb-GMP/dGMP) for pattern-recognition-based sensing of various metal ions. In addition, upon integration of some thiol-affinity metal ions, Tb-GMP/dGMP can be further extended to construct two metal ion-involved pattern-recognition-based sensor arrays (Tb-GMP/dGMP-Cu, Tb-GMP/dGMP-Ag) for the TRF sensing different levels of disease-relevant biothiols in biofluids, illustrating the powerful and multifunctional capabilities of the Tb-GMP/dGMP system and would inspire simpler and more widespread designs of chemical nose/tongue-based applications.
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Affiliation(s)
- Xin-Yue Han
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Qian-Xi Fan
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Zi-Han Chen
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Ling-Xue Deng
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Zheng-Qi Fang
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Guoyue Shi
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Min Zhang
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
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Yum JH, Park S, Hiraga R, Okamura I, Notsu S, Sugiyama H. Modular DNA-based hybrid catalysts as a toolbox for enantioselective hydration of α,β-unsaturated ketones. Org Biomol Chem 2019; 17:2548-2553. [PMID: 30762058 DOI: 10.1039/c9ob00196d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The direct addition of water to a carbon-carbon double bond remains a challenge, but such a reaction is essential for the development of efficient catalysts that enable direct access to chiral alcohols. We now report on the enantioselective hydration of α,β-unsaturated ketones, catalyzed by modular DNA-based hybrid catalysts, affording β-hydroxy ketones with up to 87% enantiomeric excess. Oligonucleotides containing an intrastrand bipyridine ligand were readily synthesized by a straightforward process using an automated solid-phase synthesis. A library of DNA-based hybrid catalysts could be systematically generated based on the composition of nucleobases, and the incorporation of a binding ligand and a nonbinding steric moiety. This study demonstrates the potential of modular DNA-based hybrid catalysts as a toolbox to accomplish the challenging enantioselective hydration reaction.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
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Yum JH, Park S, Sugiyama H. G-quadruplexes as versatile scaffolds for catalysis. Org Biomol Chem 2019; 17:9547-9561. [DOI: 10.1039/c9ob01876j] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review summarizes the beginning, progress, and prospects of non-canonical DNA-based hybrid catalysts focusing on G-quadruplexes as versatile scaffolds for catalysis.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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35
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Heravi MM, Zadsirjan V, Masoumi B, Heydari M. Organometal-catalyzed asymmetric Friedel-Crafts reactions. J Organomet Chem 2019. [DOI: 10.1016/j.jorganchem.2018.10.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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36
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Insight into Stereo-Induction by Minor Modification in the Ligand in DNA-Based Hybrid Catalysis. Catal Letters 2018. [DOI: 10.1007/s10562-018-2549-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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37
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Wang ZG, Wang H, Liu Q, Duan F, Shi X, Ding B. Designed Self-Assembly of Peptides with G-Quadruplex/Hemin DNAzyme into Nanofibrils Possessing Enzyme-Mimicking Active Sites and Catalytic Functions. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00896] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Fangyuan Duan
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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38
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39
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40
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Electrochemical strategy for pyrophosphatase detection Based on the peroxidase-like activity of G-quadruplex-Cu2+ DNAzyme. Talanta 2018; 178:491-497. [DOI: 10.1016/j.talanta.2017.09.069] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/23/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022]
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41
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Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications. J Nucleic Acids 2018; 2018:5307106. [PMID: 29666699 PMCID: PMC5831849 DOI: 10.1155/2018/5307106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/25/2017] [Accepted: 11/05/2017] [Indexed: 02/06/2023] Open
Abstract
Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity. This review discusses the recent advances on the electrochemical characterization, design, and applications of G-quadruplex electrochemical biosensors in the evaluation of metal ions, G-quadruplex ligands, and other small organic molecules, proteins, and cells. The electrochemical and atomic force microscopy characterization of G-quadruplexes is presented. The incubation time and cations concentration dependence in controlling the G-quadruplex folding, stability, and nanostructures formation at carbon electrodes are discussed. Different G-quadruplex electrochemical biosensors design strategies, based on the DNA folding into a G-quadruplex, the use of G-quadruplex aptamers, or the use of hemin/G-quadruplex DNAzymes, are revisited.
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Kitanosono T, Masuda K, Xu P, Kobayashi S. Catalytic Organic Reactions in Water toward Sustainable Society. Chem Rev 2017; 118:679-746. [PMID: 29218984 DOI: 10.1021/acs.chemrev.7b00417] [Citation(s) in RCA: 382] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Traditional organic synthesis relies heavily on organic solvents for a multitude of tasks, including dissolving the components and facilitating chemical reactions, because many reagents and reactive species are incompatible or immiscible with water. Given that they are used in vast quantities as compared to reactants, solvents have been the focus of environmental concerns. Along with reducing the environmental impact of organic synthesis, the use of water as a reaction medium also benefits chemical processes by simplifying operations, allowing mild reaction conditions, and sometimes delivering unforeseen reactivities and selectivities. After the "watershed" in organic synthesis revealed the importance of water, the development of water-compatible catalysts has flourished, triggering a quantum leap in water-centered organic synthesis. Given that organic compounds are typically practically insoluble in water, simple extractive workup can readily separate a water-soluble homogeneous catalyst as an aqueous solution from a product that is soluble in organic solvents. In contrast, the use of heterogeneous catalysts facilitates catalyst recycling by allowing simple centrifugation and filtration methods to be used. This Review addresses advances over the past decade in catalytic reactions using water as a reaction medium.
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Affiliation(s)
- Taku Kitanosono
- Department of Chemistry, School of Science, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Koichiro Masuda
- Department of Chemistry, School of Science, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Pengyu Xu
- Department of Chemistry, School of Science, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shu Kobayashi
- Department of Chemistry, School of Science, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Sakashita S, Park S, Sugiyama H. Copper-containing DNA–Silica Mineral Complexes for the Asymmetric Diels–Alder Reaction. CHEM LETT 2017. [DOI: 10.1246/cl.170411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sohei Sakashita
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501
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45
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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46
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Dey S, Rühl CL, Jäschke A. Catalysis of Michael Additions by Covalently Modified G-Quadruplex DNA. Chemistry 2017; 23:12162-12170. [DOI: 10.1002/chem.201700632] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Surjendu Dey
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; 69120 Heidelberg Germany
| | - Carmen L. Rühl
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; 69120 Heidelberg Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; 69120 Heidelberg Germany
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47
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Relations between the loop transposition of DNA G-quadruplex and the catalytic function of DNAzyme. Biochim Biophys Acta Gen Subj 2017; 1861:1913-1920. [PMID: 28533132 DOI: 10.1016/j.bbagen.2017.05.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/26/2017] [Accepted: 05/18/2017] [Indexed: 01/11/2023]
Abstract
The structures of DNA G-quadruplexes are essential for their functions in vivo and in vitro. Our present study revealed that sequential order of the three G-quadruplex loops, that is, loop transposition, could be a critical factor to determinate the G-quadruplex conformation and consequently improved the catalytic function of G-quadruplex based DNAzyme. In the presence of 100mM K+, loop transposition induced one of the G-quadruplex isomers which shared identical loops but differed in the sequential order of loops into a hybrid topology while the others into predominately parallel topologies. 1D NMR spectroscopy and mutation analysis suggested that the hydrogen bonding from loops residues with nucleotides in flanking sequences may be responsible for the stabilization of the different conformations. A well-known DNAzyme consisting of G-quadruplex and hemin (Ferriprotoporphyrin IX chloride) was chosen to test the catalytic function. We found that the loop transposition could enhance the reaction rate obviously by increasing the hemin binding affinity to G-quadruplex. These findings disclose the relations between the loop transposition, G-quadruplex conformation and catalytic function of DNAzyme.
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48
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Zhou H, Chen D, Bai JK, Sun XL, Li C, Qiao RZ. Effect of ligand sequence-specific modification on DNA hybrid catalysis. Org Biomol Chem 2017; 15:6738-6745. [DOI: 10.1039/c7ob01249g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a sequence-specific catalytic ligand as a chemical modification strategy to achieve DNA-based asymmetric reactions with sequence-dependent enantioselectivity.
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Affiliation(s)
- H. Zhou
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - D. Chen
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - J. K. Bai
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - X. L. Sun
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - C. Li
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - R. Z. Qiao
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences
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49
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Duchemin N, Heath-Apostolopoulos I, Smietana M, Arseniyadis S. A decade of DNA-hybrid catalysis: from innovation to comprehension. Org Biomol Chem 2017; 15:7072-7087. [DOI: 10.1039/c7ob00176b] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Since the pioneering work of Roelfes and Feringa in the field of DNA-based asymmetric catalysis, the unique chirality of oligonucleotides has allowed the development of a variety of asymmetric synthetic transformations. This review offers a complete overview of the field.
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Affiliation(s)
- Nicolas Duchemin
- Queen Mary University of London
- School of Biological and Chemical Sciences
- London
- UK
| | | | - Michael Smietana
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
| | - Stellios Arseniyadis
- Queen Mary University of London
- School of Biological and Chemical Sciences
- London
- UK
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50
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Qin QP, Qin JL, Meng T, Lin WH, Zhang CH, Wei ZZ, Chen JN, Liu YC, Liang H, Chen ZF. High in vivo antitumor activity of cobalt oxoisoaporphine complexes by targeting G-quadruplex DNA, telomerase and disrupting mitochondrial functions. Eur J Med Chem 2016; 124:380-392. [DOI: 10.1016/j.ejmech.2016.08.063] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 12/27/2022]
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