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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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2
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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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3
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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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4
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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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5
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Ibrahim N, Alami M, Messaoudi S. Recent Advances in Transition-Metal-Catalyzed Functionalization of 1-Thiosugars. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201800449] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nada Ibrahim
- BioCIS, Univ. Paris-Sud; CNRS; University Paris-Saclay; 92290 Châtenay-Malabry France
| | - Mouad Alami
- BioCIS, Univ. Paris-Sud; CNRS; University Paris-Saclay; 92290 Châtenay-Malabry France
| | - Samir Messaoudi
- BioCIS, Univ. Paris-Sud; CNRS; University Paris-Saclay; 92290 Châtenay-Malabry France
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6
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Probing the interaction of copper cofactor and azachalcone substrate with G-quadruplex of DNA based Diels-Alderase by site-specific fluorescence quenching titration. Biochimie 2018; 146:20-27. [DOI: 10.1016/j.biochi.2017.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/02/2017] [Indexed: 01/18/2023]
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7
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Probst N, Lartia R, Théry O, Alami M, Defrancq E, Messaoudi S. Efficient Buchwald-Hartwig-Migita Cross-Coupling for DNA Thioglycoconjugation. Chemistry 2018; 24:1795-1800. [PMID: 29205564 DOI: 10.1002/chem.201705371] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Indexed: 11/11/2022]
Abstract
An efficient method for the thioglycoconjugation of iodinated oligonucleotides by Buchwald-Hartwig-Migita cross-coupling under mild conditions is reported. The method enables divergent synthesis of many different functionalized thioglycosylated ODNs in good yields, without affecting the integrity of the other A, C, and G nucleobases.
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Affiliation(s)
- Nicolas Probst
- BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Rémy Lartia
- University Grenoble-Alpes, DCM, CS 40700, 38058, Grenoble, France
| | - Océane Théry
- University Grenoble-Alpes, DCM, CS 40700, 38058, Grenoble, France
| | - Mouâd Alami
- BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Eric Defrancq
- University Grenoble-Alpes, DCM, CS 40700, 38058, Grenoble, France
| | - Samir Messaoudi
- BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, 92290, Châtenay-Malabry, France
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8
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Flanagan ML, Arguello AE, Colman DE, Kim J, Krejci JN, Liu S, Yao Y, Zhang Y, Gorin DJ. A DNA-conjugated small molecule catalyst enzyme mimic for site-selective ester hydrolysis. Chem Sci 2018; 9:2105-2112. [PMID: 29732115 PMCID: PMC5911826 DOI: 10.1039/c7sc04554a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/10/2018] [Indexed: 12/19/2022] Open
Abstract
The challenge of site-selectivity must be overcome in many chemical research contexts, including selective functionalization in complex natural products and labeling of one biomolecule in a living system. Synthetic catalysts incorporating molecular recognition domains can mimic naturally-occurring enzymes to direct a chemical reaction to a particular instance of a functional group. We propose that DNA-conjugated small molecule catalysts (DCats), prepared by tethering a small molecule catalyst to a DNA aptamer, are a promising class of reagents for site-selective transformations. Specifically, a DNA-imidazole conjugate able to increase the rate of ester hydrolysis in a target ester by >100-fold compared with equimolar untethered imidazole was developed. Other esters are unaffected. Furthermore, DCat-catalyzed hydrolysis follows enzyme-like kinetics and a stimuli-responsive variant of the DCat enables programmable "turn on" of the desired reaction.
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Affiliation(s)
- Moira L Flanagan
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - A Emilia Arguello
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Drew E Colman
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Jiyeon Kim
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Jesse N Krejci
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Shimu Liu
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Yueyu Yao
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Yu Zhang
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - David J Gorin
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
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9
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Lech CJ, Phan AT. Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification. Nucleic Acids Res 2017; 45:6265-6274. [PMID: 28499037 PMCID: PMC5499775 DOI: 10.1093/nar/gkx243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/10/2017] [Indexed: 12/13/2022] Open
Abstract
Functionalized nanoparticles have seen valuable applications, particularly in the delivery of therapeutic and diagnostic agents in biological systems. However, the manufacturing of such nano-scale systems with the consistency required for biological application can be challenging, as variation in size and shape have large influences in nanoparticle behavior in vivo. We report on the development of a versatile nano-scaffold based on the modular functionalization of a DNA G-quadruplex. DNA sequences are functionalized in a modular fashion using well-established phosphoramidite chemical synthesis with nucleotides containing modification of the amino (N2) position of the guanine base. In physiological conditions, these sequences fold into well-defined G-quadruplex structures. The resulting DNA nano-scaffolds are thermally stable, consistent in size, and functionalized in a manner that allows for control over the density and relative orientation of functional chemistries on the nano-scaffold surface. Various chemistries including small modifications (N2-methyl-guanine), bulky aromatic modifications (N2-benzyl-guanine), and long chain-like modifications (N2-6-amino-hexyl-guanine) are tested and are found to be generally compatible with G-quadruplex formation. Furthermore, these modifications stabilize the G-quadruplex scaffold by 2.0–13.3 °C per modification in the melting temperature, with concurrent modifications producing extremely stable nano-scaffolds. We demonstrate the potential of this approach by functionalizing nano-scaffolds for use within the biotin–avidin conjugation approach.
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Affiliation(s)
- Christopher Jacques Lech
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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10
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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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11
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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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12
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Distinct differences in metal ion specificity of RNA and DNA G-quadruplexes. J Biol Inorg Chem 2016; 21:975-986. [PMID: 27704222 DOI: 10.1007/s00775-016-1393-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/02/2016] [Indexed: 01/21/2023]
Abstract
RNA G-quadruplexes, as their well-studied DNA analogs, require the presence of cations to fold and remain stable. This is the first comprehensive study on the interaction of RNA quadruplexes with metal ions. We investigated the formation and stability of two highly conserved and biologically relevant RNA quadruplex-forming sequences (24nt-TERRA and 18nt-NRAS) in the presence of several monovalent and divalent metal ions, namely Li+, Na+, K+, Rb+, Cs+, NH4+, Mg2+, Ca2+, Sr2+, and Ba2+. Circular dichroism was used to probe the influence of these metal ions on the folded fraction of the parallel G-quadruplexes, and UV thermal melting experiments allowed to assess the relative stability of the structures in each cationic condition. Our results show that the RNA quadruplexes are more stable than their DNA counterparts under the same buffer conditions. We have observed that the addition of mainly Na+, K+, Rb+, NH4+, as well as Sr2+ and Ba2+ in water, shifts the equilibrium to the folded quadruplex form, whereby the NRAS sequence responds stronger than TERRA. However, only K+ and Sr2+ lead to a significant increase in the stability of the folded structures, which is consistent with their coordination to the O6 atoms from the G-quartet guanosines. Compared to the respective DNA motives, dNRAS and htelo, the RNA sequences are not stabilized by Na+ ions. Finally, the difference in response between NRAS and TERRA, as well as to the corresponding DNA sequences with respect to different metal ions, could potentially be exploited for selective targeting purposes.
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13
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Dey S, Jäschke A. Tuning the stereoselectivity of a DNA-catalyzed michael addition through covalent modification. Angew Chem Int Ed Engl 2015. [PMID: 26224256 DOI: 10.1002/anie.201503838] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Complexes of G-quadruplex DNA and Cu(II) ions have previously been applied as catalysts in asymmetric reactions, but the largely unspecific and noncovalent nature of the interaction has impeded understanding of the structural basis of catalysis. To better control the formation of a catalytically competent species, DNA quadruplexes were derivatized with linker-bpy-Cu(II) complexes in a site-specific manner and applied in asymmetric aqueous Michael additions. These modified quadruplexes exhibited high rate acceleration and stereoselectivity. Different factors were found to be important for the catalytic performance of the modified G-quadruplexes, among them, the position of modification, the topology of the quadruplex, the nature of the ligand, and the length of the linker between the ligand and DNA. Moving the same ligand by just two nucleotides inverted the stereochemical outcome: quadruplexes modified at position 10 formed the (-)-enantiomer with up to 92 % ee, while DNA derivatized at position 12 formed the (+)-enantiomer with up to 75 % ee. This stereopreference was maintained when applied to structurally different Michael acceptors. This work demonstrates a new and simple way to tune the stereoselectivity in DNA-based asymmetric catalysis.
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Affiliation(s)
- Surjendu Dey
- Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg, 69120 Heidelberg (Germany) http://www.jaeschke.uni-hd.de
| | - Andres Jäschke
- Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg, 69120 Heidelberg (Germany) http://www.jaeschke.uni-hd.de.
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14
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Dey S, Jäschke A. Modulation der Stereoselektivität einer DNA-katalysierten Michael-Addition durch kovalente Modifizierung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503838] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Bonnet R, Lavergne T, Gennaro B, Spinelli N, Defrancq E. Construction of anti-parallel G-quadruplexes through sequential templated click. Chem Commun (Camb) 2015; 51:4850-3. [DOI: 10.1039/c4cc09744k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biologically relevant anti-parallel DNA G-quadruplexes were constrained and stabilised onto addressable cyclopeptide scaffolds through sequential oxime and CuAAc reactions.
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Affiliation(s)
- Romaric Bonnet
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Thomas Lavergne
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Béatrice Gennaro
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Nicolas Spinelli
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Eric Defrancq
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
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16
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Wang LX, Xiang JF, Tang YL. Novel DNA Catalysts Based on G-Quadruplex for Organic Synthesis. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400818] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Das RN, Debnath M, Gaurav A, Dash J. Environment-Sensitive Probes Containing a 2,6-Diethynylpyridine Motif for Fluorescence Turn-On Detection and Induction of Nanoarchitectures of Human Telomeric Quadruplex. Chemistry 2014; 20:16688-93. [DOI: 10.1002/chem.201404795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Indexed: 12/24/2022]
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18
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Discovery of a structural-element specific G-quadruplex "light-up" probe. Sci Rep 2014; 4:3776. [PMID: 24441075 PMCID: PMC3895904 DOI: 10.1038/srep03776] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 12/23/2013] [Indexed: 01/26/2023] Open
Abstract
The development of a fluorescent probe capable of detecting and distinguishing the wide diversity of G-quadruplex structures is particularly challenging. Herein, we report a novel BODIPY-based fluorescent sensor (GQR) that shows unprecedented selectivity to parallel-stranded G-quadruplexes with exposed ends and four medium grooves. Mechanistic studies suggest that GQR associates with G-quadruplex grooves close to the end of the tetrad core, which may explain the dye's specificity to only a subset of parallel structures. This specific recognition favours the disaggregation of GQR in aqueous solutions thereby recovering the inherent fluorescence of the dye. Due to its unique features, GQR represents a valuable tool for basic biological research and the rapid discovery of novel, specific ligands that target similar structural features of G-quadruplexes.
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Raynal M, Ballester P, Vidal-Ferran A, van Leeuwen PWNM. Supramolecular catalysis. Part 2: artificial enzyme mimics. Chem Soc Rev 2013; 43:1734-87. [PMID: 24365792 DOI: 10.1039/c3cs60037h] [Citation(s) in RCA: 665] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The design of artificial catalysts able to compete with the catalytic proficiency of enzymes is an intense subject of research. Non-covalent interactions are thought to be involved in several properties of enzymatic catalysis, notably (i) the confinement of the substrates and the active site within a catalytic pocket, (ii) the creation of a hydrophobic pocket in water, (iii) self-replication properties and (iv) allosteric properties. The origins of the enhanced rates and high catalytic selectivities associated with these properties are still a matter of debate. Stabilisation of the transition state and favourable conformations of the active site and the product(s) are probably part of the answer. We present here artificial catalysts and biomacromolecule hybrid catalysts which constitute good models towards the development of truly competitive artificial enzymes.
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Affiliation(s)
- Matthieu Raynal
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain.
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21
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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22
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Roembke BT, Wang J, Nakayama S, Zhou J, Sintim HO. Octameric G8 c-di-GMP is an efficient peroxidase and this suggests that an open G-tetrad site can effectively enhance hemin peroxidation reactions. RSC Adv 2013. [DOI: 10.1039/c3ra23308a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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23
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Wang C, Jia G, Li Y, Zhang S, Li C. Na+/K+ switch of enantioselectivity in G-quadruplex DNA-based catalysis. Chem Commun (Camb) 2013; 49:11161-3. [DOI: 10.1039/c3cc45396k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Abstract
Interlock is a structural element in DNA G-quadruplexes that can be compared with the commonly used complementary binding of ‘sticky ends’ in DNA duplexes. G-quadruplex interlocking can be a basis for the assembly of higher-order structures. In this study, we formulated a rule to engineer (3 + 1) interlocked dimeric G-quadruplexes and established the folding topology of the designed DNA sequences by nuclear magnetic resonance spectroscopy. These interlocked G-quadruplexes are very stable and can serve as compact robust scaffolds for various applications. Different structural elements can be engineered in these robust scaffolds. We demonstrated the anti-HIV inhibition activity of the newly designed DNA sequences.
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Affiliation(s)
- Anh Tuân Phan
- School of Physical and Mathematical Sciences and School of Biological Sciences, Nanyang Technological University, Singapore.
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Sancho Oltra N, Browne WR, Roelfes G. Hierarchical Self-Assembly of a Biomimetic Light-Harvesting Antenna Based on DNA G-Quadruplexes. Chemistry 2012; 19:2457-61. [DOI: 10.1002/chem.201202550] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 11/09/2012] [Indexed: 01/20/2023]
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26
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DNA template-assisted modulation of horseradish peroxidase activity. Int J Biol Macromol 2012; 50:552-7. [DOI: 10.1016/j.ijbiomac.2012.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 01/14/2012] [Accepted: 01/17/2012] [Indexed: 11/20/2022]
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27
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Wang C, Li Y, Jia G, Liu Y, Lu S, Li C. Enantioselective Friedel–Crafts reactions in water catalyzed by a human telomeric G-quadruplex DNA metalloenzyme. Chem Commun (Camb) 2012; 48:6232-4. [DOI: 10.1039/c2cc31320k] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Li H, LaBean TH, Leong KW. Nucleic acid-based nanoengineering: novel structures for biomedical applications. Interface Focus 2011; 1:702-24. [PMID: 23050076 PMCID: PMC3262286 DOI: 10.1098/rsfs.2011.0040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/01/2011] [Indexed: 01/21/2023] Open
Abstract
Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson-Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.
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Affiliation(s)
| | | | - Kam W. Leong
- Department of Biomedical Engineering, Duke University, 136 Hudson Hall, PO Box 90281, Durham, NC 27708, USA
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29
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Deuss PJ, den Heeten R, Laan W, Kamer PCJ. Bioinspired Catalyst Design and Artificial Metalloenzymes. Chemistry 2011; 17:4680-98. [DOI: 10.1002/chem.201003646] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Silverman SK. DNA as a versatile chemical component for catalysis, encoding, and stereocontrol. Angew Chem Int Ed Engl 2011; 49:7180-201. [PMID: 20669202 DOI: 10.1002/anie.200906345] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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31
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Silverman SK. DNA - eine vielseitige chemische Verbindung für die Katalyse, zur Kodierung und zur Stereokontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906345] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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32
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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33
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Jia G, Feng Z, Wei C, Zhou J, Wang X, Li C. Dynamic insight into the interaction between porphyrin and G-quadruplex DNAs: time-resolved fluorescence anisotropy study. J Phys Chem B 2010; 113:16237-45. [PMID: 19924868 DOI: 10.1021/jp906060d] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the nature of the interaction between small molecules and G-quadruplex DNA is crucial for the development of novel anticancer drugs. In this paper, we present the first data on time-resolved fluorescence anisotropy study on the interaction between a water-soluble cationic porphyrin H(2)TMPyP4 and four distinct G-quadruplex DNAs, that is, AG(3)(T(2)AG(3))(3), thrombin-binding aptamer (TBA), (G(4)T(4)G(4))2, and (TG(4)T)4. The anisotropy decay curves show the monoexponential for free H(2)TMPyP4 and the biexponential upon binding to the excess amount of G-quadruplex DNAs. The biexponential anisotropy decay can be well interpreted using a wobbling-in-the-cone model. The orientational diffusion of the bound H(2)TMPyP4 is initially restricted to a limited cone angle within the G-quadruplex DNAs, and then an overall orientational relaxation of the G-quadruplex DNA-H(2)TMPyP4 complexes occurs in a longer time scale. It was found that the dynamics of the restricted internal rotation of bound H(2)TMPyP4 strongly depends on the ending structures of the G-quadruplex DNAs. According to the order parameter (Q) calculated from the wobbling-in-the-cone model, we deduce that the degree of restriction around the bound H(2)TMPyP4 follows the order of TBA > (TG(4)T)4 > AG(3)(T(2)AG(3))(3) > (G(4)T(4)G(4))2. Especially, based on the maximum order parameter (Q) of bound H(2)TMPyP4 within TBA, a new sandwich-type binding mode for TBA-H(2)TMPyP4 complex was proposed in which both terminal G-quartet and T*T base pair stack on the porphyrin ring through pi-pi interaction. This study thus provides a new insight into the interaction between G-quadruplex DNAs and H(2)TMPyP4.
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Affiliation(s)
- Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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34
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Megens RP, Roelfes G. Organic co-solvents in aqueous DNA-based asymmetric catalysis. Org Biomol Chem 2010; 8:1387-93. [PMID: 20204212 DOI: 10.1039/b921385f] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Water-miscible organic co-solvents can be used in DNA-based catalytic asymmetric reactions at appreciable concentration without a negative effect on enantioselectivity. While the rate of the copper(II) Diels-Alder reaction is affected negatively by the presence of organic co-solvents, the copper(II) catalyzed Michael addition and Friedel-Crafts alkylation reaction are significantly faster. Additionally, the presence of organic co-solvents allows for reaction temperatures <0 degrees C, which results in higher ee's. This is used to perform enantioselective Michael additions and Friedel-Crafts alkylations at gram scale, using catalyst loadings as low as 0.75 mol%. These results are an important step towards application of the DNA-based catalysis concept in organic synthesis.
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Affiliation(s)
- Rik P Megens
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
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35
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Rosati F, Boersma AJ, Klijn JE, Meetsma A, Feringa BL, Roelfes G. A kinetic and structural investigation of DNA-based asymmetric catalysis using first-generation ligands. Chemistry 2010; 15:9596-605. [PMID: 19579236 DOI: 10.1002/chem.200900456] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recently developed concept of DNA-based asymmetric catalysis involves the transfer of chirality from the DNA double helix in reactions using a noncovalently bound catalyst. To date, two generations of DNA-based catalysts have been reported that differ in the design of the ligand for the metal. Herein we present a study of the first generation of DNA-based catalysts, which contain ligands comprising a metal-binding domain linked through a spacer to a 9-aminoacridine moiety. Particular emphasis has been placed on determining the effect of DNA on the structure of the Cu(II) complex and the catalyzed Diels-Alder reaction. The most important findings are that the role of DNA is limited to being a chiral scaffold; no rate acceleration was observed in the presence of DNA. Furthermore, the optimal DNA sequence for obtaining high enantioselectivities proved to contain alternating GC nucleotides. Finally, DNA has been shown to interact with the Cu(II) complex to give a chiral structure. Comparison with the second generation of DNA-based catalysts, which bear bipyridine-type ligands, revealed marked differences, which are believed to be related to the DNA microenvironment in which the catalyst resides and where the reaction takes place.
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Affiliation(s)
- Fiora Rosati
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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36
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Klapper Y, Sinha N, Ng TWS, Lubrich D. A rotational DNA nanomotor driven by an externally controlled electric field. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:44-47. [PMID: 19943245 DOI: 10.1002/smll.200901106] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Yvonne Klapper
- Forschungszentrum Karlsruhe, Institute for Nanotechnology, PO Box 3640, 76021 Karlsruhe, Germany
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37
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Dijk EW, Boersma AJ, Feringa BL, Roelfes G. On the Role of DNA in DNA-based Catalytic Enantioselective Conjugate Addition Reactions. Org Biomol Chem 2010; 8:3868-73. [DOI: 10.1039/c005048b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Roe S, Ritson DJ, Garner T, Searle M, Moses JE. Tuneable DNA-based asymmetric catalysis using a G-quadruplex supramolecular assembly. Chem Commun (Camb) 2010; 46:4309-11. [DOI: 10.1039/c0cc00194e] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Boersma A, Feringa B, Roelfes G. Enantioselective Friedel-Crafts Reactions in Water Using a DNA-Based Catalyst. Angew Chem Int Ed Engl 2009; 48:3346-8. [DOI: 10.1002/anie.200900371] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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40
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Boersma A, Feringa B, Roelfes G. Enantioselective Friedel-Crafts Reactions in Water Using a DNA-Based Catalyst. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900371] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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41
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42
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Dash J, Shirude PS, Hsu STD, Balasubramanian S. Diarylethynyl amides that recognize the parallel conformation of genomic promoter DNA G-quadruplexes. J Am Chem Soc 2008; 130:15950-6. [PMID: 18980309 PMCID: PMC2746964 DOI: 10.1021/ja8046552] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report bis-phenylethynyl amide derivatives as a potent G-quadruplex binding small molecule scaffold. The amide derivatives were efficiently prepared in 3 steps by employing Sonogashira coupling, ester hydrolysis and a chemoselective amide coupling. Ligand-quadruplex recognition has been evaluated using a fluorescence resonance energy transfer (FRET) melting assay, surface plasmon resonance (SPR), circular dichroism (CD) and (1)H nuclear magnetic resonance (NMR) spectroscopy. While most of the G-quadruplex ligands reported so far comprise a planar, aromatic core designed to stack on the terminal tetrads of a G-quadruplex, these compounds are neither polycyclic, nor macrocyclic and have free rotation around the triple bond enabling conformational flexibility. Such molecules show very good binding affinity, excellent quadruplex:duplex selectivity and also promising discrimination between intramolecular promoter quadruplexes. Our results indicate that the recognition of the c-kit2 quadruplex by these ligands is achieved through groove binding, which favors the formation of a parallel conformation.
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Affiliation(s)
- Jyotirmayee Dash
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Pravin S. Shirude
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Shang-Te Danny Hsu
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Shankar Balasubramanian
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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43
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Dash J, Shirude PS, Balasubramanian S. G-quadruplex recognition by bis-indole carboxamides. Chem Commun (Camb) 2008:3055-7. [PMID: 18688346 PMCID: PMC2746961 DOI: 10.1039/b806042h] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Herein we report the de novo design and synthesis of a geometrically flexible bis-indole carboxamide and a constrained derivative, as a novel class of small molecule scaffold that exhibits high stabilization potential for DNA G-quadruplex sequences associated with the promoters of c-kit2 and c-myc.
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Affiliation(s)
- Jyotirmayee Dash
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
| | - Pravin S. Shirude
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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44
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Silverman SK. Catalytic DNA (deoxyribozymes) for synthetic applications-current abilities and future prospects. Chem Commun (Camb) 2008:3467-85. [PMID: 18654692 DOI: 10.1039/b807292m] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The discovery of naturally occurring catalytic RNA (RNA enzymes, or ribozymes) in the 1980s immediately revised the view of RNA as a passive messenger that solely carries information from DNA to proteins. Because DNA and RNA differ only by the absence or presence of a 2'-hydroxyl group on each ribose ring of the polymer, the question of 'catalytic DNA?' arises. Although no natural DNA catalysts have been reported, since 1994 many artificial DNA enzymes, or 'deoxyribozymes', have been described. Deoxyribozymes offer insight into the mechanisms of natural and artificial ribozymes. DNA enzymes are also used as tools for in vitro and in vivo biochemistry, and they are key components of analytical sensors. This review focuses primarily on catalytic DNA for synthetic applications. Broadly defined, deoxyribozymes may have the greatest potential for catalyzing reactions in which the high selectivities of 'enzymes' are advantageous relative to traditional small-molecule catalysts. Although the scope of DNA-catalyzed synthesis is currently limited in most cases to oligonucleotide substrates, recent efforts have began to expand this frontier in promising new directions.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
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