1
|
Takezawa Y, Shionoya M. Enzymatic synthesis of ligand-bearing oligonucleotides for the development of metal-responsive DNA materials. Org Biomol Chem 2024. [PMID: 38967487 DOI: 10.1039/d4ob00947a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Metal-mediated artificial base pairs are some of the most promising building blocks for constructing DNA-based supramolecules and functional materials. These base pairs are formed by coordination bonds between ligand-type nucleobases and a bridging metal ion and have been exploited to develop metal-responsive DNA materials and DNA-templated metal arrays. In this review, we provide an overview of methods for the enzymatic synthesis of DNA strands containing ligand-type artificial nucleotides that form metal-mediated base pairs. Conventionally, ligand-bearing DNA oligomers have been synthesized via solid-phase synthesis using a DNA synthesizer. In recent years, there has been growing interest in enzymatic methods as an alternative approach to synthesize ligand-bearing DNA oligomers, because enzymatic reactions proceed under mild conditions and do not require protecting groups. DNA polymerases are used to incorporate ligand-bearing unnatural nucleotides into DNA, and DNA ligases are used to connect artificial DNA oligomers to natural DNA fragments. Template-independent polymerases are also utilized to post-synthetically append ligand-bearing nucleotides to DNA oligomers. In addition, enzymatic replication of DNA duplexes containing metal-mediated base pairs has been intensively studied. Enzymatic methods facilitate the synthesis of DNA strands containing ligand-bearing nucleotides at both internal and terminal positions. Enzymatically synthesized ligand-bearing DNAs have been applied to metal-dependent self-assembly of DNA structures and the allosteric control of DNAzyme activity through metal-mediated base pairing. Therefore, the enzymatic synthesis of ligand-bearing oligonucleotides holds great potential in advancing the development of various metal-responsive DNA materials, such as molecular sensors and machines, providing a versatile tool for DNA supramolecular chemistry and nanotechnology.
Collapse
Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan.
| |
Collapse
|
2
|
Lu B, Ohayon YP, Woloszyn K, Yang CF, Yoder JB, Rothschild LJ, Wind SJ, Hendrickson WA, Mao C, Seeman NC, Canary JW, Sha R, Vecchioni S. Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals. J Am Chem Soc 2023; 145:17945-17953. [PMID: 37530628 DOI: 10.1021/jacs.3c05478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Metal-mediated DNA (mmDNA) presents a pathway toward engineering bioinorganic and electronic behavior into DNA devices. Many chemical and biophysical forces drive the programmable chelation of metals between pyrimidine base pairs. Here, we developed a crystallographic method using the three-dimensional (3D) DNA tensegrity triangle motif to capture single- and multi-metal binding modes across granular changes to environmental pH using anomalous scattering. Leveraging this programmable crystal, we determined 28 biomolecular structures to capture mmDNA reactions. We found that silver(I) binds with increasing occupancy in T-T and U-U pairs at elevated pH levels, and we exploited this to capture silver(I) and mercury(II) within the same base pair and to isolate the titration points for homo- and heterometal base pair modes. We additionally determined the structure of a C-C pair with both silver(I) and mercury(II). Finally, we extend our paradigm to capture cadmium(II) in T-T pairs together with mercury(II) at high pH. The precision self-assembly of heterobimetallic DNA chemistry at the sub-nanometer scale will enable atomistic design frameworks for more elaborate mmDNA-based nanodevices and nanotechnologies.
Collapse
Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, Illinois 60439, United States
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, California 94035, United States
| | - Shalom J Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - James W Canary
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
| |
Collapse
|
3
|
Vecchioni S, Lu B, Livernois W, Ohayon YP, Yoder JB, Yang CF, Woloszyn K, Bernfeld W, Anantram MP, Canary JW, Hendrickson WA, Rothschild LJ, Mao C, Wind SJ, Seeman NC, Sha R. Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210938. [PMID: 37268326 DOI: 10.1002/adma.202210938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/06/2023] [Indexed: 06/04/2023]
Abstract
DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.
Collapse
Affiliation(s)
- Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Livernois
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, IL, 60439, USA
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Bernfeld
- Department of Chemistry, New York University, New York, NY, 10003, USA
- ASPIRE Program, King School, Stamford, CT, 06905, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, CA, 94035, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Math, Columbia University, New York, NY, 10027, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
| |
Collapse
|
4
|
Nyenhuis M, Schönrath I, Kamzeeva PN, Zatsepin TS, Müller J, Doltsinis N, Aralov AV. Benzothiazole-substituted 1,3-diaza-2-oxophenoxazine as a luminescent nucleobase surrogate for silver(I)-mediated base pairing. Dalton Trans 2022; 51:13386-13395. [PMID: 35989665 DOI: 10.1039/d2dt01762h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A benzothiazole-substituted derivative (X) of 1,3-diaza-2-oxophenoxazine was evaluated with respect to its ability to engage in Ag(I)-mediated homo base pair formation in two different DNA duplexes. The metal binding was determined by a combination of temperature-dependent UV spectroscopy, CD spectroscopy, and fluorescence spectroscopy, indicating the incorporation of two Ag(I) ions to generate a dinuclear X-Ag(I)2-X base pair. Interestingly, a luminescence increase was observed upon metal binding. Theoretical luminescence spectra were calculated using time-dependent density functional theory (TDDFT) for all possible Ag(I)-mediated X : X base pair geometries to identify the species responsible for the increase in luminescence. The study shows that even bulky non-planar artificial nucleobases can be applied to form stabilizing metal-mediated base pairs.
Collapse
Affiliation(s)
- Marvin Nyenhuis
- Westfälische Wilhelms-Universität Münster, Institute for Solid State Theory and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany.
| | - Isabell Schönrath
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany.
| | - Polina N Kamzeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia.
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia.,Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory Str. 1-3, 119992 Moscow, Russia
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany.
| | - Nikos Doltsinis
- Westfälische Wilhelms-Universität Münster, Institute for Solid State Theory and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany.
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia.
| |
Collapse
|
5
|
Atsugi T, Ono A, Tasaka M, Eguchi N, Fujiwara S, Kondo J. A Novel Ag
I
‐DNA Rod Comprising a One‐Dimensional Array of 11 Silver Ions within a Double Helical Structure. Angew Chem Int Ed Engl 2022; 61:e202204798. [DOI: 10.1002/anie.202204798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Takahiro Atsugi
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Akira Ono
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Miho Tasaka
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Natsumi Eguchi
- Department of Materials and Life Sciences Faculty of Science and Technology Sophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
| | - Shoji Fujiwara
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences Faculty of Science and Technology Sophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
| |
Collapse
|
6
|
Atsugi T, Ono A, Tasaka M, Eguchi N, Fujiwara S, Kondo J. A Novel Ag
I
‐DNA Rod Comprising a One‐Dimensional Array of 11 Silver Ions within a Double Helical Structure. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Takahiro Atsugi
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Akira Ono
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Miho Tasaka
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Natsumi Eguchi
- Department of Materials and Life Sciences Faculty of Science and Technology Sophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
| | - Shoji Fujiwara
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences Faculty of Science and Technology Sophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
| |
Collapse
|
7
|
Todkari I, Gupta MK, Ganesh KN. Silver soldering of PNA:DNA duplexes: assembly of a triple duplex from bimodal PNAs with all-C on one face. Chem Commun (Camb) 2022; 58:4083-4086. [PMID: 35266467 DOI: 10.1039/d1cc07297h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA:bm-PNA duplexes endowed with all-C on either the t-amide or triazole face and mixed base sequence on the other face can be welded with silver ions through C:Ag+:C connects to give triple duplexes in one complex. The interplay of WC and Ag+-mediated duplexes leads to synergistic stability effects on both duplexes and the complex.
Collapse
Affiliation(s)
- Iranna Todkari
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India.
| | - Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India. .,Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road Road, Tirupati, 517507, Andhra Pradesh, India
| | - Krishna N Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India. .,Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road Road, Tirupati, 517507, Andhra Pradesh, India
| |
Collapse
|
8
|
Lippert B. “Metal-modified base pairs” vs. “metal-mediated pairs of bases”: not just a semantic issue! J Biol Inorg Chem 2022; 27:215-219. [PMID: 35091756 PMCID: PMC8907086 DOI: 10.1007/s00775-022-01926-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/14/2022] [Indexed: 11/25/2022]
Abstract
A “nucleobase pair” is not identical with a “pair of basic ligands”, as only in the first case, the existence of inter-base hydrogen bonds is implied. The cross-linking of two nucleobases or two basic ligands by a metal ion of suitable geometry produces either “metal-modified” or “metal-mediated” species, but in the author’s opinion, this difference is not always properly made. This commentary is an attempt to provide a clearer distinction between the two scenarios.
Collapse
Affiliation(s)
- Bernhard Lippert
- Fakultät Für Chemie Und Chemische Biologie (CCB), Technische Universität Dortmund, 44221, Dortmund, Germany.
| |
Collapse
|
9
|
Bhai S, Ganguly B. Role of pH in the stability of cytosine-cytosine mismatch and canonical AT and GC base pairs mediated with silver ion: a DFT study. Struct Chem 2021. [DOI: 10.1007/s11224-021-01814-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
10
|
Flamme M, Figazzolo C, Gasser G, Hollenstein M. Enzymatic construction of metal-mediated nucleic acid base pairs. Metallomics 2021; 13:6206861. [PMID: 33791776 DOI: 10.1093/mtomcs/mfab016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/14/2022]
Abstract
Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural base pairs, and low cost of production. These interesting properties combined with ease of chemical and enzymatic synthesis have prompted their use in several practical applications, including the construction of nanomolecular devices, ions sensors, and metal nanowires. Chemical synthesis of metal base pairs is highly efficient and enables the rapid screening of novel metal base pair candidates. However, chemical synthesis is limited to rather short oligonucleotides and requires rather important synthetic efforts. Herein, we discuss recent progress made for the enzymatic construction of metal base pairs that can alleviate some of these limitations. First, we highlight the possibility of generating metal base pairs using canonical nucleotides and then describe how modified nucleotides can be used in this context. We also provide a description of the main analytical techniques used for the analysis of the nature and the formation of metal base pairs together with relevant examples of their applications.
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 de Paris, 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
| | - Chiara Figazzolo
- 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 de Paris, 12 rue de l'École de Médecine, 75006 Paris, France.,Centre de Recherches Interdisciplinaires CRI, 8 rue Charles V, 75004 Paris, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - 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
|
11
|
Pramanik S, Khamari L, Mukherjee S. Differentiating a Least-Stable Single Nucleotide Mismatch in DNA Via Metal Ion-Mediated Base Pairing and Using Thioflavin T as an Extrinsic Fluorophore. J Phys Chem Lett 2021; 12:2547-2554. [PMID: 33683888 DOI: 10.1021/acs.jpclett.1c00146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Monitoring the DNA dynamics in solution has great potential to develop new nucleic acid-based sensors and devices. With spectroscopic approaches, both at the ensemble average and single-molecule resolution, this study is directed to differentiate a single nucleotide mismatch (SNM) via a metal ion-stabilized mismatched base-pairing (C-Ag+-C/C-Cu2+-T) (C = cytosine, T = thymine) and site-selective extrinsic fluorophore, specifically, Thioflavin T (ThT). This is the first approach of its kind where dynamic quantities like molecular diffusion coefficients and diffusion times have been utilized to distinguish the least-stable SNM (CC & CT) formed by the most discriminating nucleobase, specifically, cytosine in a 20-mer duplex DNA. Additionally, this work also quantifies metal ions (Ag+ and Cu2+) at lower concentrations using fluorescence correlation spectroscopy. Our results can provide greater molecular-level insights into the mismatch-dependent metal-DNA interactions and also illuminate ThT as a new fluorophore to monitor the dynamics involved in DNA-metal composites.
Collapse
Affiliation(s)
- Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Laxmikanta Khamari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| |
Collapse
|
12
|
Nakagawa O, Aoyama H, Fujii A, Kishimoto Y, Obika S. Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids. Chemistry 2021; 27:3842-3848. [PMID: 33274789 DOI: 10.1002/chem.202004819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Indexed: 11/08/2022]
Abstract
Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of AgI ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of AgI -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing AgI -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of AgI -mediated base pairs in the central region. The bent duplex structure induced by the addition of AgI ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.
Collapse
Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Hiroshi Aoyama
- 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
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| |
Collapse
|
13
|
Ukale DU, Tähtinen P, Lönnberg T. 1,8-Dimercuri-6-Phenyl-1H-Carbazole as a Monofacial Dinuclear Organometallic Nucleobase. Chemistry 2020; 26:2164-2168. [PMID: 31913530 DOI: 10.1002/chem.201905434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/25/2019] [Indexed: 12/19/2022]
Abstract
A C-nucleoside with 6-phenyl-1H-carbazole as the base moiety has been synthesized and incorporated in the middle of an oligonucleotide. Mercuration of this modified residue at positions 1 and 8 gave the first example of an oligonucleotide featuring a monofacial dinuclear organometallic nucleobase. The dimercurated oligonucleotide formed stable duplexes with unmodified oligonucleotides placing either cytosine, guanine, or thymine opposite to the organometallic nucleobase. A highly stabilizing (ΔTm =7.3 °C) HgII -mediated base pair was formed with thymine. According to DFT calculations performed at the PBE0DH level of theory, this base pair is most likely dinuclear, with the two HgII ions coordinated to O2 and O4 of the thymine base.
Collapse
Affiliation(s)
| | - Petri Tähtinen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| |
Collapse
|
14
|
Naskar S, Müller J. Light-Induced Formation of Thymine-Containing Mercury(II)-Mediated Base Pairs. Chemistry 2019; 25:16214-16218. [PMID: 31682036 PMCID: PMC6972992 DOI: 10.1002/chem.201903789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/14/2019] [Indexed: 12/16/2022]
Abstract
By applying caged thymidine residues, DNA duplexes were created in which HgII‐mediated base pair formation can be triggered by irradiation with light. When a bidentate ligand was used as the complementary nucleobase, an unprecedented stepwise formation of different metal‐mediated base pairs was achieved.
Collapse
Affiliation(s)
- Shuvankar Naskar
- 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
|
15
|
Ono A, Kanazawa H, Ito H, Goto M, Nakamura K, Saneyoshi H, Kondo J. A Novel DNA Helical Wire Containing Hg
II
‐Mediated T:T and T:G Pairs. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Akira Ono
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Hiroki Kanazawa
- Department of Materials and Life SciencesFaculty of Science and TechnologySophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
- Present address: IBMC-CNRSUniversité de Strasbourg 2 allée Konrad Roentgen 67084 Strasbourg France
| | - Hikari Ito
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Misato Goto
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Koudai Nakamura
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Hisao Saneyoshi
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Jiro Kondo
- Department of Materials and Life SciencesFaculty of Science and TechnologySophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
| |
Collapse
|
16
|
Ono A, Kanazawa H, Ito H, Goto M, Nakamura K, Saneyoshi H, Kondo J. A Novel DNA Helical Wire Containing Hg II -Mediated T:T and T:G Pairs. Angew Chem Int Ed Engl 2019; 58:16835-16838. [PMID: 31507027 DOI: 10.1002/anie.201910029] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/09/2019] [Indexed: 12/22/2022]
Abstract
Numerous applications of metal-mediated base pairs (metallo-base-pairs) to nucleic acid based nanodevices and genetic code expansion have been extensively studied. Many of these metallo-base-pairs are formed in DNA and RNA duplexes containing Watson-Crick base pairs. Recently, a crystal structure of a metal-DNA nanowire with an uninterrupted one-dimensional silver array was reported. We now report the crystal structure of a novel DNA helical wire containing HgII -mediated T:T and T:G base pairs and water-mediated C:C base pairs. The Hg-DNA wire does not contain any Watson-Crick base pairs. Crystals of the Hg-DNA wire, which is the first DNA wire structure driven by HgII ions, were obtained by mixing the short oligonucleotide d(TTTGC) and HgII ions. This study demonstrates the potential of metallo-DNA to form various structural components that can be used for functional nanodevices.
Collapse
Affiliation(s)
- Akira Ono
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Hiroki Kanazawa
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554, Tokyo, Japan.,Present address: IBMC-CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, 67084, Strasbourg, France
| | - Hikari Ito
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Misato Goto
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Koudai Nakamura
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Hisao Saneyoshi
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554, Tokyo, Japan
| |
Collapse
|
17
|
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
|
18
|
|
19
|
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
|
20
|
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]
|
21
|
Ono A, Atsugi T, Goto M, Saneyoshi H, Tomori T, Seio K, Dairaku T, Kondo J. Crystal structure of a DNA duplex cross-linked by 6-thioguanine–6-thioguanine disulfides: reversible formation and cleavage catalyzed by Cu( ii) ions and glutathione. RSC Adv 2019; 9:22859-22862. [PMID: 35514505 PMCID: PMC9067110 DOI: 10.1039/c9ra03515j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/04/2019] [Indexed: 11/21/2022] Open
Abstract
Herein, we determined the crystal structure of a DNA duplex containing consecutive 6-thioguanine–6-thioguanine disulfides. The disulfide bonds were reversibly formed and cleaved in the presence of Cu(ii) ions and glutathione. To our knowledge, this is the first reaction in which metal ions efficiently accelerated disulfide bond formation between thio-bases in duplexes. The crystal structure of a DNA duplex cross-linked by 6-thioguanine–6-thioguanine disulfides has been solved.![]()
Collapse
Affiliation(s)
- Akira Ono
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Takahiro Atsugi
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Misato Goto
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Hisao Saneyoshi
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Takahito Tomori
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Kohji Seio
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | | | - Jiro Kondo
- Department of Materials and Life Sciences
- Faculty of Science and Technology
- Sophia University
- Tokyo 102-8554
- Japan
| |
Collapse
|
22
|
Sandmann N, Bachmann J, Hepp A, Doltsinis NL, Müller J. Copper(ii)-mediated base pairing involving the artificial nucleobase 3H-imidazo[4,5-f]quinolin-5-ol. Dalton Trans 2019; 48:10505-10515. [DOI: 10.1039/c9dt02043h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A highly stabilizing Cu(ii)-mediated base pair is introduced into DNA using a large artificial nucleobase.
Collapse
Affiliation(s)
- Nikolas Sandmann
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jim Bachmann
- Institut für Festkörpertheorie and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Alexander Hepp
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Nikos L. Doltsinis
- Institut für Festkörpertheorie and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| |
Collapse
|
23
|
Xing X, Feng Y, Yu Z, Hidaka K, Liu F, Ono A, Sugiyama H, Endo M. Direct Observation of the Double-Stranded DNA Formation through Metal Ion-Mediated Base Pairing in the Nanoscale Structure. Chemistry 2018; 25:1446-1450. [DOI: 10.1002/chem.201805394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/26/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Xiwen Xing
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
- Department of Biotechnology; Key Laboratory of Virology of Guangzhou; College of Life Science and Technology; Jinan University; Guangzhou P. R. China
| | - Yihong Feng
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
| | - Zutao Yu
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
| | - Kumi Hidaka
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
| | - Fenyong Liu
- Department of Biotechnology; Key Laboratory of Virology of Guangzhou; College of Life Science and Technology; Jinan University; Guangzhou P. R. China
| | - Akira Ono
- Department of Materials & Life Chemistry; Faculty of Engineering; Kanagawa University; 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
- Institute for Integrated Cell-Material Sciences; Kyoto University
| | - Masayuki Endo
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
- Institute for Integrated Cell-Material Sciences; Kyoto University
| |
Collapse
|
24
|
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
|
25
|
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
|
26
|
Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory. Int J Mol Sci 2018; 19:ijms19082346. [PMID: 30096923 PMCID: PMC6122091 DOI: 10.3390/ijms19082346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/16/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022] Open
Abstract
We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.
Collapse
|
27
|
Jash B, Müller J. Concomitant Site-Specific Incorporation of Silver(I) and Mercury(II) Ions into a DNA Duplex. Chemistry 2018; 24:10636-10640. [DOI: 10.1002/chem.201802470] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| |
Collapse
|
28
|
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
|