1
|
Peng S, Chang Y, Zeng X, Lai R, Yang M, Wang D, Zhou X, Shao Y. Selectivity of natural isoquinoline alkaloid assembler in programming poly(dA) into parallel duplex by polyvalent synergy. Anal Chim Acta 2023; 1241:340777. [PMID: 36657870 DOI: 10.1016/j.aca.2022.340777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/04/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Ligand-induced assembly of disordered DNAs attracts much attention due to its potential action in transcription regulation and molecular switches-based sensors. Among natural isoquinoline alkaloids (NIAs), we screened out nitidine (NIT) as polyvalent-binding assembler to program poly(dA) into a parallel duplex assembly at neutral pH. The molecule planarity of NIAs was believed to be a determinant factor in programming the parallel poly(dA) assembly. Poly(dA) with more than six adenines can initiate the synergistic binding of NIT to generate the parallel assembly. It is expected that one A-A pair in duplex can bind one NIT molecule provided that poly(dA) is long enough, suggesting the pivotal role of the polyvalent synergy of NIT in programming the parallel poly(dA) assembly. A gold nanoparticles-based colorimetric method was also developed to screen NIT out of NIAs having the potential to construct the poly(dA) assembly. Our work will inspire more interest in developing polyadenine-based switches and sensors by concentrating NIT within the polyadenine parallel assembly.
Collapse
Affiliation(s)
- Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yun Chang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xingli Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Rong Lai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Mujing Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China.
| |
Collapse
|
2
|
de Frémont P, Adet N, Parmentier J, Xu X, Jacques B, Dagorne S. Cationic organometallic complexes of group 12 metals: A decade of progress toward the quest of novel Lewis acidic catalysts. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
3
|
Wang J, Wicher B, Méndez-Ardoy A, Li X, Pecastaings G, Buffeteau T, Bassani DM, Maurizot V, Huc I. Loading Linear Arrays of Cu II Inside Aromatic Amide Helices. Angew Chem Int Ed Engl 2021; 60:18461-18466. [PMID: 34014599 PMCID: PMC8456862 DOI: 10.1002/anie.202104734] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/12/2021] [Indexed: 12/25/2022]
Abstract
The very stable helices of 8-amino-2-quinolinecarboxylic acid oligoamides are shown to uptake CuII ions in their cavity through deprotonation of their amide functions with minimal alteration of their shape, unlike most metallo-organic structures which generally differ from their organic precursors. The outcome is the formation of intramolecular linear arrays of a defined number of CuII centers (up to sixteen in this study) at a 3 Å distance, forming a molecular mimic of a metal wire completely surrounded by an organic sheath. The helices pack in the solid state so that the arrays of CuII extend intermolecularly. Conductive-AFM and cyclic voltammetry suggest that electrons are transported throughout the metal-loaded helices in contrast with hole transport observed for analogous foldamers devoid of metal ions.
Collapse
Affiliation(s)
- Jinhua Wang
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Barbara Wicher
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780, Poznan, Poland
| | - Alejandro Méndez-Ardoy
- ISM (UMR 5255), Univ. Bordeaux, CNRS, 351, Cours de la Libération, 33405, Talence, France
| | - Xuesong Li
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Gilles Pecastaings
- LCPO (UMR 5629), Bordeaux INP, CNRS, 16, Av. Pey-Berland, 33600, Pessac, France
- CRPP (UMR 5031), Univ. Bordeaux, CNRS, 115 Avenue du Dr Albert Schweitzer, 33600, Pessac, France
| | - Thierry Buffeteau
- ISM (UMR 5255), Univ. Bordeaux, CNRS, 351, Cours de la Libération, 33405, Talence, France
| | - Dario M Bassani
- ISM (UMR 5255), Univ. Bordeaux, CNRS, 351, Cours de la Libération, 33405, Talence, France
| | - Victor Maurizot
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Ivan Huc
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600, Pessac, France
- Department of Pharmacy, Ludwig-Maximilians-Universität, Butenandstraße 5-13, 81377, Munich, Germany
- Cluster of Excellence e-conversion, 85748, Garching, Germany
| |
Collapse
|
4
|
Wang J, Wicher B, Méndez‐Ardoy A, Li X, Pecastaings G, Buffeteau T, Bassani DM, Maurizot V, Huc I. Loading Linear Arrays of Cu
II
Inside Aromatic Amide Helices. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jinhua Wang
- CBMN (UMR 5248) Univ. Bordeaux CNRS Bordeaux INP 2 rue Robert Escarpit 33600 Pessac France
| | - Barbara Wicher
- Department of Chemical Technology of Drugs Poznan University of Medical Sciences Grunwaldzka 6 60-780 Poznan Poland
| | | | - Xuesong Li
- CBMN (UMR 5248) Univ. Bordeaux CNRS Bordeaux INP 2 rue Robert Escarpit 33600 Pessac France
| | - Gilles Pecastaings
- LCPO (UMR 5629) Bordeaux INP CNRS 16, Av. Pey-Berland 33600 Pessac France
- CRPP (UMR 5031) Univ. Bordeaux CNRS 115 Avenue du Dr Albert Schweitzer 33600 Pessac France
| | - Thierry Buffeteau
- ISM (UMR 5255) Univ. Bordeaux CNRS 351, Cours de la Libération 33405 Talence France
| | - Dario M. Bassani
- ISM (UMR 5255) Univ. Bordeaux CNRS 351, Cours de la Libération 33405 Talence France
| | - Victor Maurizot
- CBMN (UMR 5248) Univ. Bordeaux CNRS Bordeaux INP 2 rue Robert Escarpit 33600 Pessac France
| | - Ivan Huc
- CBMN (UMR 5248) Univ. Bordeaux CNRS Bordeaux INP 2 rue Robert Escarpit 33600 Pessac France
- Department of Pharmacy Ludwig-Maximilians-Universität Butenandstraße 5–13 81377 Munich Germany
- Cluster of Excellence e-conversion 85748 Garching Germany
| |
Collapse
|
5
|
Wang LL, Zhang QL, Wang Y, Liu Y, Lin J, Xie F, Xu L. Controllable DNA strand displacement by independent metal-ligand complexation. Chem Sci 2021; 12:8698-8705. [PMID: 34257868 PMCID: PMC8246113 DOI: 10.1039/d1sc01041g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Introduction of artificial metal-ligand base pairs can enrich the structural diversity and functional controllability of nucleic acids. In this work, we revealed a novel approach by placing a ligand-type nucleoside as an independent toehold to control DNA strand-displacement reactions based on metal-ligand complexation. This metal-mediated artificial base pair could initiate strand invasion similar to the natural toehold DNA, but exhibited flexible controllability to manipulate the dynamics of strand displacement that was only governed by its intrinsic coordination properties. External factors that influence the intrinsic properties of metal-ligand complexation, including metal species, metal concentrations and pH conditions, could be utilized to regulate the strand dynamics. Reversible control of DNA strand-displacement reactions was also achieved through combination of the metal-mediated artificial base pair with the conventional toehold-mediated strand exchange by cyclical treatments of the metal ion and the chelating reagent. Unlike previous studies of embedded metal-mediated base pairs within natural base pairs, this metal-ligand complexation is not integrated into the nucleic acid structure, but functions as an independent toehold to regulate strand displacement, which would open a new door for the development of versatile dynamic DNA nanotechnologies.
Collapse
Affiliation(s)
- Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Jiao Lin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Fan Xie
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| |
Collapse
|
6
|
Escher D, Müller J. Silver(I)‐mediated hetero base pairs of 6‐pyrazolylpurine and its deaza derivatives. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202000481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Daniela Escher
- Westfälische Wilhelms-Universität Münster Institut für Anorganische und Analytische Chemie Corrensstr. 30 48149 Münster Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster Institut für Anorganische und Analytische Chemie Corrensstr. 30 48149 Münster Germany
| |
Collapse
|
7
|
Flamme M, Röthlisberger P, Levi-Acobas F, Chawla M, Oliva R, Cavallo L, Gasser G, Marlière P, Herdewijn P, Hollenstein M. Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate. ACS Chem Biol 2020; 15:2872-2884. [PMID: 33090769 DOI: 10.1021/acschembio.0c00396] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.
Collapse
Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l’École de Médecine, 75006 Paris, France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| |
Collapse
|
8
|
Chai Y, Guo X, Leonard P, Seela F. Heterochiral DNA with Complementary Strands with α-d and β-d Configurations: Hydrogen-Bonded and Silver-Mediated Base Pairs with Impact of 7-Deazapurines Replacing Purines. Chemistry 2020; 26:13973-13989. [PMID: 32667103 PMCID: PMC7702046 DOI: 10.1002/chem.202002765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/14/2020] [Indexed: 02/05/2023]
Abstract
Heterochiral DNA with hydrogen-bonded and silver-mediated base pairs have been constructed using complementary strands with nucleosides with α-d or β-d configuration. Anomeric phosphoramidites were employed to assemble the oligonucleotides. According to the Tm values and thermodynamic data, the duplex stability of the heterochiral duplexes was similar to that of homochiral DNA, but mismatch discrimination was better in heterochiral DNA. Replacement of purines by 7-deazapurines resulted in stable parallel duplexes, thereby confirming Watson-Crick-type base pairing. When cytosine was facing cytosine, thymine or adenine residues, duplex DNA formed silver-mediated base pairs in the presence of silver ions. Although the CD spectra of single strands with α-d configuration display mirror-like shapes to those with the β-d configuration, the CD spectra of the hydrogen-bonded duplexes and those with a limited number of silver pairs show a B-type double helix almost indistinguishable from natural DNA. Nonmelting silver ion-DNA complexes with entirely different CD spectra were generated when the number of silver ions was equal to the number of base pairs.
Collapse
Affiliation(s)
- Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development LaboratoryWest China HospitalSichuan University610041SichuanP. R. China
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
| |
Collapse
|
9
|
Escher D, Müller J. Silver(I) Coordination in Silver(I)-Mediated Homo Base Pairs of 6-Pyrazolylpurine in DNA Duplexes Involves the Watson-Crick Edge. Chemistry 2020; 26:16043-16048. [PMID: 32627879 PMCID: PMC7756626 DOI: 10.1002/chem.202002803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Indexed: 12/18/2022]
Abstract
DNA duplexes comprising 6‐(1H‐pyrazol‐1‐yl)‐9H‐purine (6PP), 1‐deaza‐6PP (1D6PP), 7‐deaza‐6PP (7D6PP) and 1,7‐dideaza‐6PP (1,7D6PP) 2′‐deoxyribonucleosides, respectively, were investigated towards their ability to form metal‐mediated base pairs in the presence of AgI. In 6PP and 7D6PP, the AgI ion can coordinate to the nucleobase via the endocyclic N1 nitrogen atom, that is, via the Watson–Crick edge. In contrast, this nitrogen atom is not available in 1D6PP and 1,7D6PP, so that in 1D6PP an AgI coordination is only possible via the Hoogsteen edge (N7). Reference duplexes with either adenine:adenine mispairs or canonical adenine:thymine base pairs were used to investigate the impact of the pyrazolyl moiety on the AgI‐binding properties. To determine the thermal and structural duplex stabilities in the absence or presence of AgI, all duplexes were examined by UV and circular dichroism spectroscopic studies. These investigations shed light on the question of whether N1‐ or N7‐coordination is preferred in purine‐based metal‐mediated base pairs.
Collapse
Affiliation(s)
- Daniela Escher
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
| |
Collapse
|
10
|
Kliuev PN, Sokolov PA, Ramazanov RR. QM/MM-MD dissociation of Ag+ and H+ mediated cytosine pairs: Monomers and dimers. J Organomet Chem 2020. [DOI: 10.1016/j.jorganchem.2020.121333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
11
|
Funai T, Tagawa C, Nakagawa O, Wada SI, Ono A, Urata H. Enzymatic formation of consecutive thymine–HgII–thymine base pairs by DNA polymerases. Chem Commun (Camb) 2020; 56:12025-12028. [DOI: 10.1039/d0cc04423g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ten consecutive T–HgII–T base pairs were successfully formed by DNA polymerase-catalyzed primer extension reactions.
Collapse
Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Chizuko Tagawa
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Osamu Nakagawa
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Shun-ichi Wada
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Akira Ono
- Department of Material & Life Chemistry
- Faculty of Engineering, Kanagawa University
- 3-27-1 Rokkakubashi
- Kanagawa-ku
- Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| |
Collapse
|
12
|
Funai T, Aotani M, Kiriu R, Nakamura J, Miyazaki Y, Nakagawa O, Wada S, Torigoe H, Ono A, Urata H. Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases. Chembiochem 2019; 21:517-522. [DOI: 10.1002/cbic.201900450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Megumi Aotani
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Risa Kiriu
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Junko Nakamura
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Yuki Miyazaki
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Osamu Nakagawa
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
- Present address: Graduate School of Pharmaceutical SciencesOsaka University 1–6 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Shun‐ichi Wada
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Hidetaka Torigoe
- Department of Applied ChemistryFaculty of ScienceTokyo University of Science 1-3 Kagurazaka, Shinjuku-ku Tokyo 162-8601 Japan
| | - Akira Ono
- Department of Material and Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Japan
| | - Hidehito Urata
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| |
Collapse
|
13
|
Levi-Acobas F, Röthlisberger P, Sarac I, Marlière P, Herdewijn P, Hollenstein M. On the Enzymatic Formation of Metal Base Pairs with Thiolated and pK a -Perturbed Nucleotides. Chembiochem 2019; 20:3032-3040. [PMID: 31216100 DOI: 10.1002/cbic.201900399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Indexed: 12/15/2022]
Abstract
The formation of artificial metal base pairs is an alluring and versatile method for the functionalization of nucleic acids. Access to DNA functionalized with metal base pairs is granted mainly by solid-phase synthesis. An alternative, yet underexplored method, envisions the installation of metal base pairs through the polymerization of modified nucleoside triphosphates. Herein, we have explored the possibility of using thiolated and pKa -perturbed nucleotides for the enzymatic construction of artificial metal base pairs. The thiolated nucleotides S2C, S6G, and S4T as well as the fluorinated analogue 5FU are readily incorporated opposite a templating S4T nucleotide through the guidance of metal cations. Multiple incorporation of the modified nucleotides along with polymerase bypass of the unnatural base pairs are also possible under certain conditions. The thiolated nucleotides S4T, S4T, S2C, and S6G were also shown to be compatible with the synthesis of modified, high molecular weight single-stranded (ss)DNA products through TdT-mediated tailing reactions. Thus, sulfur-substitution and pKa perturbation represent alternative strategies for the design of modified nucleotides compatible with the enzymatic construction of metal base pairs.
Collapse
Affiliation(s)
- Fabienne Levi-Acobas
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Pascal Röthlisberger
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Ivo Sarac
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbruères, 91030, Evry, France
| | - Piet Herdewijn
- Department of Medicinal Chemistry, Institute for Medical Research, KU Leuven, Herestraat, 49, Leuven, 3000, Belgium
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| |
Collapse
|
14
|
Chen P, Huang K, Zhang P, Sawyer E, Wu Z, Wei X, Ying B, Geng J. Exonuclease III-assisted strand displacement reaction-driven cyclic generation of G-quadruplex strategy for homogeneous fluorescent detection of melamine. Talanta 2019; 203:255-260. [DOI: 10.1016/j.talanta.2019.05.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/01/2019] [Accepted: 05/02/2019] [Indexed: 02/06/2023]
|
15
|
Naskar S, Guha R, Müller J. Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads. Angew Chem Int Ed Engl 2019; 59:1397-1406. [PMID: 31259475 DOI: 10.1002/anie.201905913] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 01/02/2023]
Abstract
The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of AgI -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.
Collapse
Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| |
Collapse
|
16
|
Naskar S, Guha R, Müller J. Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| |
Collapse
|
17
|
Chen P, Sawyer E, Sun K, Zhang X, Chen C, Ying B, Wei X, Wu Z, Geng J. A general strategy for label-free homogeneous bioassays based on selective recognition and silver ion-mediated conformational switch. Talanta 2019; 201:9-15. [DOI: 10.1016/j.talanta.2019.03.088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/11/2019] [Accepted: 03/24/2019] [Indexed: 12/26/2022]
|
18
|
Fujii A, Nakagawa O, Kishimoto Y, Okuda T, Nakatsuji Y, Nozaki N, Kasahara Y, Obika S. 1,3,9-Triaza-2-oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self-Base Pairs with Three Ag I Ions in a Duplex. Chemistry 2019; 25:7443-7448. [PMID: 30843298 DOI: 10.1002/chem.201900373] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Indexed: 12/23/2022]
Abstract
Metal-mediated base pairs (MMBPs) formed by natural or artificial nucleobases have recently been developed. The metal ions can be aligned linearly in a duplex by MMBP formation. The development of a three- or more-metal-coordinated MMBPs has the potential to improve the conductivity and enable the design of metal ion architectures in a duplex. This study aimed to develop artificial self-bases coordinated by three linearly aligned AgI ions within an MMBP. Thus, artificial nucleic acids with a 1,3,9-triaza-2-oxophenoxazine (9-TAP) nucleobase were designed and synthesized. In a DNA/DNA duplex, self-base pairs of 9-TAP could form highly stable MMBPs with three AgI ions. Nine equivalents of AgI led to the formation of three consecutive 9-TAP self-base pairs with extremely high stability. The complex structures of 9-TAP MMBPs were determined by using electrospray ionization mass spectrometry and UV titration experiments. Highly stable self-9-TAP MMBPs with three AgI ions are expected to be applicable to new DNA nanotechnologies.
Collapse
Affiliation(s)
- Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| |
Collapse
|
19
|
Dinuclear Metal-Mediated Guanine–Uracil Base Pairs: Theoretical Studies of GUM22+ (M = Cu, Ag, and Au) Ions. J CLUST SCI 2019. [DOI: 10.1007/s10876-019-01503-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
20
|
Röthlisberger P, Levi-Acobas F, Sarac I, Marlière P, Herdewijn P, Hollenstein M. Towards the enzymatic formation of artificial metal base pairs with a carboxy-imidazole-modified nucleotide. J Inorg Biochem 2018; 191:154-163. [PMID: 30529723 DOI: 10.1016/j.jinorgbio.2018.11.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/08/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023]
Abstract
The identification of synthetic nucleotides that sustain the formation of orthogonal, unnatural base pairs is an important goal in synthetic biology. Such artificial synthons have been used for the generation of semi-synthetic organisms as well as functional nucleic acids with enhanced binding properties. The enzymatic formation of artificial metal-base pairs is a vastly underexplored and alluring alternative to existing systems. Here, we report the synthesis and biochemical characterization of 1‑(2-deoxy‑β‑d‑ribofuranosyl) imidazole‑4‑carboxylate nucleoside triphosphate (dImCTP) which is equipped with a carboxylic acid moiety on the imidazole moiety in order to increase the coordination environment to [2 + 2] and [2 + 1]. A clear metal dependence was observed for the single incorporation of the modified nucleotide into DNA by the DNA polymerase from Thermus aquaticus (Taq). The presence of AgI in primer extension reactions conducted with combinations of 1‑(2‑deoxy‑β‑d‑ribofuranosyl) imidazole nucleoside triphosphate (dImTP) and dImCTP supported the unusual [2 + 1] coordination pattern. The efficiency of the tailing reactions mediated by the terminal deoxynucleotidyl transferase (TdT) was markedly improved when using dImCTP instead of dImTP. Even though products with multiple modified nucleotides were not observed, the appendage of additional metal binding ligands on the imidazole nucleobase appears to be a valid approach to improve the biochemical properties of modified triphosphates in the context of an expansion of the genetic alphabet with metal base pairs.
Collapse
Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| |
Collapse
|
21
|
Nakagawa O, Fujii A, Kishimoto Y, Nakatsuji Y, Nozaki N, Obika S. 2'-O,4'-C-Methylene-Bridged Nucleic Acids Stabilize Metal-Mediated Base Pairing in a DNA Duplex. Chembiochem 2018; 19:2372-2379. [PMID: 30168891 DOI: 10.1002/cbic.201800448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Indexed: 11/08/2022]
Abstract
The 2'-O,4'-C-methylene-bridged or locked nucleic acid (2',4'-BNA/LNA), with an N-type sugar conformation, effectively improves duplex-forming ability. 2',4'-BNA/LNA is widely used to improve gene knockdown in nucleic acid based therapies and is used in gene diagnosis. Metal-mediated base pairs (MMBPs), such as thymine (T)-HgII -T and cytosine (C)-AgI -C have been developed and used as attractive tools in DNA nanotechnology studies. This study aimed to investigate the application of 2',4'-BNA/LNA in the field of MMBPs. 2',4'-BNA/LNA with 5-methylcytosine stabilized the MMBP of C with AgI ions. Moreover, the 2',4'-BNA/LNA sugar significantly improved the duplex-forming ability of the DNA/DNA complex, relative to that by the unmodified sugar. These results suggest that the sugar conformation is important for improving the stability of duplex-containing MMBPs. The results indicate that 2',4'-BNA/LNA can be applied not only to nucleic acid based therapies, but also to MMBP technologies.
Collapse
Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| |
Collapse
|
22
|
Cao GJ. A dinuclear Cu(i)-mediated complex: Theoretical studies of the G 2Cu 2 4+ cluster ion. J Chem Phys 2018; 149:144308. [PMID: 30316268 DOI: 10.1063/1.5038366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recently, the T-Hg(ii)2-A base pair containing two equivalents of Hg(ii) has been prepared and characterized experimentally, which implies that there might exist considerable stable metal-mediated base pairs holding two neighbouring metal centers. Here we report a quantum chemical study on geometries, electronic structures, and bonding of various G2Cu2 4+ (G = guanine) isomers including one di-copper(i) unit. Different density functional methods [Becke 3-parameter-Lee-Yang-Parr, Perdew-Becke-Ernzerhof, Becke-Perdew, Density Functional Theory with Dispersion Corrections (DFT-D)] assign ambiguous relative energies to these isomers with the singlet and triplet states. High-level ab initio [domain-based local pair natural orbital (DLPNO) coupled-cluster with single and double excitations and DLPNO-coupled-cluster with single, double, and perturbative triple excitations] calculations confirm that the lowest-lying isomer of the G2Cu2 4+ ion has C 2h symmetry with the singlet state and is comparable to the singly and doubly charged homologues (G2Cu2 + and G2Cu2 2+). The extended transition state (ETS)-natural orbitals for the chemical valence (ETS-NOCV) calculations point out that it has larger instantaneous interaction energy and bond dissociation energy than the corresponding singly and doubly charged complexes due to its relatively stronger attractive energies and weaker Pauli repulsion. The orbital interactions in the quadruply charged cluster chiefly come from Cu2 4+ ← G⋯G π donations. The results may help the understanding of the bonding properties of other potential metal-base pair complexes with the electron transfer.
Collapse
Affiliation(s)
- Guo-Jin Cao
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| |
Collapse
|
23
|
Léon JC, González-Abradelo D, Strassert CA, Müller J. Fluorescent DNA-Templated Silver Nanoclusters from Silver(I)-Mediated Base Pairs. Chemistry 2018; 24:8320-8324. [DOI: 10.1002/chem.201801858] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Indexed: 12/19/2022]
Affiliation(s)
- J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Darío González-Abradelo
- CeNTech and Physikalisches Institut; Westfälische Wilhelms-Universität Münster; Heisenbergstrasse 11 48149 Münster Germany
| | - Cristian A. Strassert
- CeNTech and Physikalisches Institut; Westfälische Wilhelms-Universität Münster; Heisenbergstrasse 11 48149 Münster Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| |
Collapse
|
24
|
Mandal S, Hebenbrock M, Müller J. A dinuclear silver(I)-mediated base pair in DNA formed from 1, N 6 -ethenoadenine and thymine. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.05.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
25
|
Méndez‐Arriaga JM, Maldonado CR, Dobado JA, Galindo MA. Silver(I)‐Mediated Base Pairs in DNA Sequences Containing 7‐Deazaguanine/Cytosine: towards DNA with Entirely Metallated Watson–Crick Base Pairs. Chemistry 2018; 24:4583-4589. [DOI: 10.1002/chem.201705131] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Indexed: 12/13/2022]
Affiliation(s)
- José M. Méndez‐Arriaga
- Departamento de Química InorgánicaUniversidad de Granada Avd Fuentenueva s/n 18071 Spain
| | - Carmen R. Maldonado
- Departamento de Química InorgánicaUniversidad de Granada Avd Fuentenueva s/n 18071 Spain
| | - José A. Dobado
- Grupo de Modelización y Diseño Molecular, Departamento de Química OrgánicaUniversidad de Granada Avd Fuentenueva s/n 18071 Spain
| | - Miguel A. Galindo
- Departamento de Química InorgánicaUniversidad de Granada Avd Fuentenueva s/n 18071 Spain
| |
Collapse
|
26
|
Müller J. Metal-mediated base pairs in parallel-stranded DNA. Beilstein J Org Chem 2017; 13:2671-2681. [PMID: 29564004 PMCID: PMC5753045 DOI: 10.3762/bjoc.13.265] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 01/03/2023] Open
Abstract
In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine-Ag(I)-cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.
Collapse
Affiliation(s)
- Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany
| |
Collapse
|
27
|
Guo X, Leonard P, Ingale SA, Seela F. Gemcitabine, Pyrrologemcitabine, and 2'-Fluoro-2'-Deoxycytidines: Synthesis, Physical Properties, and Impact of Sugar Fluorination on Silver Ion Mediated Base Pairing. Chemistry 2017; 23:17740-17754. [PMID: 28906062 DOI: 10.1002/chem.201703427] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/05/2017] [Indexed: 01/06/2023]
Abstract
The stability of silver-mediated "dC-dC" base pairs relies not only on the structure of the nucleobase, but is also sensitive to structural modification of the sugar moiety. 2'-Fluorinated 2'-deoxycytidines with fluorine atoms in the arabino (up) and ribo (down) configuration as well as with geminal fluorine substitution (anticancer drug gemcitabine) and the novel fluorescent phenylpyrrolo-gemcitabine (ph PyrGem) have been synthesized. All the nucleosides display the recognition face of naturally occurring 2'-deoxycytidine. The nucleosides were converted into phosphoramidites and incorporated into 12-mer oligonucleotides by solid-phase synthesis. The addition of silver ions to DNA duplexes with a fluorine-modified "dC-dC" pair near the central position led to significant duplex stabilization. The increase in stability was higher for duplexes with fluorinated sugar residues than for those with an unchanged 2'-deoxyribose moiety. Similar observations were made for "dC-dT" pairs and to a minor extent for "dC-dA" pairs. The increase in silver ion mediated base-pair stability was reversed by annulation of a pyrrole ring to the cytosine moiety, as shown for 2'-fluorinated ph PyrGem in comparison with phenylpyrrolo-dC (ph PyrdC). This phenomenon results from stereoelectronic effects induced by fluoro substitution, which are transmitted from the sugar moiety to the silver ion mediated base pairs. The extent of the effect depends on the number of fluorine substituents, their configuration, and the structure of the nucleobase.
Collapse
Affiliation(s)
- Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| |
Collapse
|
28
|
Chen X, Karpenko A, Lopez-Acevedo O. Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block. ACS OMEGA 2017; 2:7343-7348. [PMID: 30023548 PMCID: PMC6045379 DOI: 10.1021/acsomega.7b01089] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/19/2017] [Indexed: 05/10/2023]
Abstract
The DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag+-base bonding rather than by Watson-Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies.
Collapse
Affiliation(s)
- Xi Chen
- Department
of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
| | - Alexander Karpenko
- Department
of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
| | - Olga Lopez-Acevedo
- Department
of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
- Facultad
de Ciencias Básicas, Universidad
de Medellín, Carrera
87 No. 30-65, Medellín 050026, Colombia
- E-mail:
| |
Collapse
|
29
|
Jash B, Müller J. Metal-Mediated Base Pairs: From Characterization to Application. Chemistry 2017; 23:17166-17178. [PMID: 28833684 DOI: 10.1002/chem.201703518] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/11/2022]
Abstract
The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.
Collapse
Affiliation(s)
- Biswarup Jash
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry, Corrensstr. 28/30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry, Corrensstr. 28/30, 48149, Münster, Germany
| |
Collapse
|
30
|
Al-Mahamad LLG, El-Zubir O, Smith DG, Horrocks BR, Houlton A. A coordination polymer for the site-specific integration of semiconducting sequences into DNA-based materials. Nat Commun 2017; 8:720. [PMID: 28959026 PMCID: PMC5620084 DOI: 10.1038/s41467-017-00852-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/31/2017] [Indexed: 11/09/2022] Open
Abstract
Advances in bottom-up material design have been significantly progressed through DNA-based approaches. However, the routine integration of semiconducting properties, particularly long-range electrical conduction, into the basic topological motif of DNA remains challenging. Here, we demonstrate this with a coordination polymer derived from 6-thioguanosine (6-TG-H), a sulfur-containing analog of a natural nucleoside. The complexation reaction with Au(I) ions spontaneously assembles luminescent one-dimensional helical chains, characterized as {AuI(μ-6-TG)} n , extending many μm in length that are structurally analogous to natural DNA. Uniquely, for such a material, this gold-thiolate can be transformed into a wire-like conducting form by oxidative doping. We also show that this self-assembly reaction is compatible with a 6-TG-modified DNA duplex and provides a straightforward method by which to integrate semiconducting sequences, site-specifically, into the framework of DNA materials, transforming their properties in a fundamental and technologically useful manner.Integration of semiconducting properties into the basic topological motif of DNA remains challenging. Here, the authors show a coordination polymer derived from 6-thioguanosine that complexes with Au(I) ions to form a wire-like material that can also integrate semiconducting sequences into the framework of DNA materials.
Collapse
Affiliation(s)
- Lamia L G Al-Mahamad
- Chemical Nanoscience Labs, School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,Department of Chemistry, College of Science, Al-Mustansiriya University, Baghdad, Iraq
| | - Osama El-Zubir
- Chemical Nanoscience Labs, School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - David G Smith
- Chemical Nanoscience Labs, School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,School of Chemistry, University of Sydney, Sydney, NSW, 2006, Australia
| | - Benjamin R Horrocks
- Chemical Nanoscience Labs, School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Andrew Houlton
- Chemical Nanoscience Labs, School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
| |
Collapse
|
31
|
Ye MY, Zhu RT, Li X, Zhou XS, Yin ZZ, Li Q, Shao Y. Adaptively Recognizing Parallel-Stranded Duplex Structure for Fluorescent DNA Polarity Analysis. Anal Chem 2017; 89:8604-8608. [DOI: 10.1021/acs.analchem.7b02467] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mei-Yun Ye
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Rui-Tao Zhu
- Department
of Chemistry, Taiyuan Normal University, Taiyuan 030031, China
| | - Xiang Li
- Langzhong People’s Hospital, Langzhong 637400, Sichuan, China
| | - Xiao-Shun Zhou
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Zheng-Zhi Yin
- College
of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, Zhejiang, China
| | - Qian Li
- Institute
of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yong Shao
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| |
Collapse
|
32
|
Jash B, Müller J. Application of a Metal-Mediated Base Pair to the Detection of Medicinally Relevant Single Nucleotide Polymorphisms. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700665] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstr. 28/30 48149 Münster Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstr. 28/30 48149 Münster Germany
| |
Collapse
|
33
|
Takezawa Y, Müller J, Shionoya M. Artificial DNA Base Pairing Mediated by Diverse Metal Ions. CHEM LETT 2017. [DOI: 10.1246/cl.160985] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
| |
Collapse
|
34
|
Léon JC, She Z, Kamal A, Shamsi MH, Müller J, Kraatz HB. DNA Films Containing the Artificial Nucleobase Imidazole Mediate Charge Transfer in a Silver(I)-Responsive Way. Angew Chem Int Ed Engl 2017; 56:6098-6102. [DOI: 10.1002/anie.201700248] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/03/2017] [Indexed: 12/22/2022]
Affiliation(s)
- J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Zhe She
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Ajar Kamal
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Mohtashim Hassan Shamsi
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
- Current address: Department of Chemistry and Biochemistry; Southern Illinois University Carbondale; Carbondale USA
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| |
Collapse
|
35
|
Léon JC, She Z, Kamal A, Shamsi MH, Müller J, Kraatz HB. DNA-Filme mit der künstlichen Nucleobase Imidazol vermitteln Ladungstransfer in einer Silber(I)-abhängigen Weise. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700248] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Zhe She
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| | - Ajar Kamal
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| | - Mohtashim Hassan Shamsi
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
- Department of Chemistry and Biochemistry; Southern Illinois University Carbondale; Carbondale USA
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| |
Collapse
|
36
|
Zhao H, Leonard P, Guo X, Yang H, Seela F. Silver-Mediated Base Pairs in DNA Incorporating Purines, 7-Deazapurines, and 8-Aza-7-deazapurines: Impact of Reduced Nucleobase Binding Sites and an Altered Glycosylation Position. Chemistry 2017; 23:5529-5540. [PMID: 28195414 DOI: 10.1002/chem.201605982] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Indexed: 02/05/2023]
Abstract
Formation of silver-mediated DNA was studied with oligonucleotides incorporating 8-aza-7-deazapurine, 7-deazapurine, and purine nucleosides. The investigation was performed on non-self-complementary duplexes with one or two modifications and self-complementary duplexes with an alternating dA-dT motif. Homo base pairs as well as base pair mismatches of dA analogues with dC and Watson-Crick pairs with dT were studied by stoichiometric silver ion titration and Tm measurements. N8 -Glycosylated 8-aza-7-deazaadenine forms silver-ion-mediated base pairs capturing two silver ions (low silver content) whereas regularly glycosylated 8-aza-7-deazapurine, 7-deazapurine (c7 Ad ), and dA do not form comparable structures. Stable silver-mediated "dA-dC" base pair mismatches were detected for all nucleosides. Two silver ions per base pair are bound by 8-aza-7-deazapurine whereas c7 Ad binds only one silver ion. The situation is different when the equivalents of silver ions were increased to the number of total base pairs. Surprisingly, in 12-mer duplexes as well as in related 25-mer duplexes every base pair consumed one silver ion.
Collapse
Affiliation(s)
- Hang Zhao
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| |
Collapse
|
37
|
Mandal S, Müller J. Metal-mediated DNA assembly with ligand-based nucleosides. Curr Opin Chem Biol 2017; 37:71-79. [PMID: 28214670 DOI: 10.1016/j.cbpa.2017.01.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/22/2017] [Accepted: 01/24/2017] [Indexed: 01/12/2023]
Abstract
Nucleic acids such as DNA are increasingly being applied in nanotechnology, as a result of their capability to self-assemble reversibly. The formal replacement of canonical base pairs by metal-mediated ones enables a site-specific introduction of metal-based functionality into these biomolecules, leading to the formation of predesigned metal arrays. This article offers an overview of structural aspects of metal-mediated base pairs, reviews recent advances in the field of metal-mediated base pairing and presents potential applications of the resulting metal-modified nucleic acids. It particularly focuses on recently developed metal-mediated base pairs with purine-derived nucleosides, gives an overview of metal-responsive systems relying on metal-mediated base pairs and summarizes various applications beyond metal-ion sensors.
Collapse
Affiliation(s)
- Soham Mandal
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany(*)
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany(*).
| |
Collapse
|
38
|
Jash B, Scharf P, Sandmann N, Fonseca Guerra C, Megger DA, Müller J. A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases. Chem Sci 2017; 8:1337-1343. [PMID: 28451274 PMCID: PMC5360170 DOI: 10.1039/c6sc03482a] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/12/2016] [Indexed: 12/17/2022] Open
Abstract
A nucleoside analogue comprising the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was applied to develop a molecular beacon capable of discriminating the canonical nucleobases cytosine and thymine. The beacon is based on the formation of a stable Ag+-mediated base pair between P and cytosine, whereas the presence of Ag+ strongly destabilizes nucleic acids comprising an artificial base pair between P and thymine. Metal-mediated base pair formation was investigated by temperature-dependent UV spectroscopy and CD spectroscopy and complemented by extensive DFT calculations. The molecular beacon significantly extends the application spectrum of nucleic acids with metal-mediated base pairs. It is of potential use in the detection of single-nucleotide polymorphisms.
Collapse
Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
- NRW Graduate School of Chemistry , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany
| | - Philipp Scharf
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
| | - Nikolas Sandmann
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry , Amsterdam Center for Multiscale Modeling (ACMM) , VU Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands .
| | - Dominik A Megger
- Medizinisches Proteom-Center , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
- NRW Graduate School of Chemistry , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany
| |
Collapse
|
39
|
Mandal S, Hebenbrock M, Müller J. Ein zweikerniges Quecksilber(II)-vermitteltes Basenpaar in DNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608354] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Soham Mandal
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
- NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
- NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| |
Collapse
|
40
|
Mandal S, Hebenbrock M, Müller J. A Dinuclear Mercury(II)-Mediated Base Pair in DNA. Angew Chem Int Ed Engl 2016; 55:15520-15523. [PMID: 27862734 DOI: 10.1002/anie.201608354] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/30/2016] [Indexed: 11/08/2022]
Abstract
The first dinuclear metal-mediated base pair containing divalent metal ions has been prepared. A combination of the neutral bis(monodentate) purine derivative 1,N6 -ethenoadenine (ϵA), which preferentially binds two metal ions with a parallel alignment of the N-M bonds, and the canonical nucleobase thymine (T), which readily deprotonates in the presence of HgII and thereby partially compensates the charge accumulation due to the two closely spaced divalent metal ions, yields the dinuclear T-HgII2 -ϵA base pair. This metal-mediated base pair stabilizes the DNA oligonucleotide duplex as shown by an increase of 8 °C in its melting temperature. Formation of the base pair was demonstrated by temperature-dependent UV spectroscopy as well as by titration experiments monitored by UV and CD spectroscopy.
Collapse
Affiliation(s)
- Soham Mandal
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
| |
Collapse
|
41
|
Kumar J, Pratibha, Verma S. Crystallographic signatures of silver-purine frameworks with an azide functionality. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
42
|
Structure and properties of a copper-mediated nucleobase pair from density functional theory investigation. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
43
|
The effect of chemical modification of DNA base on binding of HgII and AgI in metal-mediated base pairs. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
44
|
Sinha I, Kösters J, Müller J. Synthesis and structure of a coordination polymer based on 6-furylpurine. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2016. [DOI: 10.1515/znb-2016-0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The synthesis and structure of [Ag(9-methyl-6-furylpurine)(NO3)]
n
are reported. The title compound represents a rare example of a purine derivative metalated at all three endocyclic nitrogen atoms. It forms a two-dimensional coordination polymer comprising 14-membered trinuclear metallacycles. Density functional theory calculations helped to understand the metal-binding behavior of the 6-furylpurine moiety by showing the silver(I)-binding affinities of all three nitrogen donor atoms to be essentially identical under aqueous conditions.
Collapse
Affiliation(s)
- Indranil Sinha
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, 48149 Münster, Germany
| | - Jutta Kösters
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, 48149 Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany
| |
Collapse
|
45
|
Jana SK, Guo X, Mei H, Seela F. Robust silver-mediated imidazolo-dC base pairs in metal DNA: dinuclear silver bridges with exceptional stability in double helices with parallel and antiparallel strand orientation. Chem Commun (Camb) 2016; 51:17301-4. [PMID: 26463426 DOI: 10.1039/c5cc06734k] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new unprecedented metal-mediated base pair was designed that stabilizes reverse Watson-Crick DNA (parallel strand orientation, ps) as well as canonical Watson-Crick DNA (antiparallel strand orientation, aps). This base pair contains two imidazolo-dC units decorated with furan residues. Tm measurements and spectroscopic studies reveal that each silver-mediated furano-imidazolo-dC forms exceptionally stable duplexes with ps and aps chain orientation. This stability increase by a silver-mediated base pair is the highest reported so far for ps and aps DNA helices.
Collapse
Affiliation(s)
- Sunit Kumar Jana
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany and Institute for Nanobiomedical Technology and Membrane Biology, Sichuan University, No. 1 Keyuan 4th Road, Gaopengdadao, Chengdu 610041, P. R. China
| | - Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany and Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany.
| |
Collapse
|
46
|
Schweizer K, Léon JC, Ravoo BJ, Müller J. Thermodynamics of the formation of Ag(I)-mediated azole base pairs in DNA duplexes. J Inorg Biochem 2016; 160:256-63. [DOI: 10.1016/j.jinorgbio.2016.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 02/08/2016] [Accepted: 03/12/2016] [Indexed: 12/26/2022]
|
47
|
Mandal S, Wang C, Prajapati RK, Kösters J, Verma S, Chi L, Müller J. Metal-Mediated Assembly of 1,N6-Ethenoadenine: From Surfaces to DNA Duplexes. Inorg Chem 2016; 55:7041-50. [DOI: 10.1021/acs.inorgchem.6b00927] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Can Wang
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
| | - Rajneesh K. Prajapati
- Department of Chemistry, DST Thematic Unit of Excellence
on Soft Nanofabrication, Indian Institute of Technology−Kanpur, Kanpur, Uttar Pradesh 208016, India
| | | | - Sandeep Verma
- Department of Chemistry, DST Thematic Unit of Excellence
on Soft Nanofabrication, Indian Institute of Technology−Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Lifeng Chi
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
- Institute
of Functional Nano and Soft Materials, Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren’ai
Road, Suzhou, 215123 Jiangsu, People’s Republic of China
| | | |
Collapse
|
48
|
Léon JC, Sinha I, Müller J. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes. Int J Mol Sci 2016; 17:554. [PMID: 27089326 PMCID: PMC4849010 DOI: 10.3390/ijms17040554] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase.
Collapse
Affiliation(s)
- J Christian Léon
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
| | - Indranil Sinha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
- NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
- NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
| |
Collapse
|
49
|
Santamaría-Díaz N, Méndez-Arriaga JM, Salas JM, Galindo MA. Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600924] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Noelia Santamaría-Díaz
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - José M. Méndez-Arriaga
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Juan M. Salas
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Miguel A. Galindo
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| |
Collapse
|
50
|
Santamaría-Díaz N, Méndez-Arriaga JM, Salas JM, Galindo MA. Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs. Angew Chem Int Ed Engl 2016; 55:6170-4. [DOI: 10.1002/anie.201600924] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Noelia Santamaría-Díaz
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - José M. Méndez-Arriaga
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Juan M. Salas
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Miguel A. Galindo
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| |
Collapse
|