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Feng X, Wang X, Liu J, Fu A, Wang Y, Wei S, Chen H, She R, Wang Y, Cui X, Hou H, Xu Y, Wu Y, Meng Q, Zhang L, Wang S, Zhao J. Accelerated Screening of Alternative DNA Base-Organic Molecule-Base Architectures via Integrated Theory and Experiment. Angew Chem Int Ed Engl 2024:e202408003. [PMID: 38771290 DOI: 10.1002/anie.202408003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 05/22/2024]
Abstract
Organic molecule-mediated noncanonical DNA self-assembly expands the standard DNA base-pairing alphabets. However, only a very limited number of small molecules have been recognized as mediators because of the tedious and complicated experiments like crystallization and microscopy imaging. Here we present an integrative screening protocol incorporating molecular dynamics (MD) for fast theoretical simulation and native polyacrylamide gel electrophoresis for convenient experimental validation. Melamine, the molecule that was confirmed mediating noncanonical DNA base-pairing, and 38 other candidate molecules were applied to demonstrate the feasibility of this protocol. We successfully identified seven stable noncanonical DNA duplex structures, and another eight novel structures with sub-stability. In addition, we discovered that hairpins at both ends can significantly stabilize the noncanonical DNA structures, providing a guideline to design small organic molecule-incorporated DNA structures. Such an efficient screening protocol will accelerate the design of alternative DNA-molecule architectures beyond Watson-Crick pairs. Considering the wide range of potential mediators, it will also facilitate applications such as noncovalent, highly dense loading of drug molecules in DNA-based delivery system and probe design for sensitive detection of certain molecules.
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Affiliation(s)
- Xinyu Feng
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Xianwen Wang
- School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Jiahe Liu
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Aiting Fu
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Ying Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Shuheng Wei
- Second Clinical Medical College, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Huichao Chen
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Rui She
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yangying Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Xiao Cui
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui, 230032, China
| | - Hui Hou
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yuanyuan Xu
- Department of Pediatric Critical Care Medicine, Children's Medical Center of Anhui Medical University, Hefei, Anhui, 230051, China
| | - Yujing Wu
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Qian Meng
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Song Wang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jiemin Zhao
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
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2
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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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3
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Takezawa Y, Kudo N, Fuse N, Shionoya M. DNA three-way junction structures with amino acid side chains prepared via post-synthetic amide condensation. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-14. [PMID: 38359331 DOI: 10.1080/15257770.2024.2314645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024]
Abstract
DNA three-way junction (3WJ) structures with three amino acid side chains in the core have been synthesized via post-synthetic DNA modification. Amide condensation reactions of oligonucleotides containing 2'-aminouridine with activated esters yielded DNA strands modified with His, Cys and Asp side chains to form modified 3WJs. Even a 3WJ with three negatively charged Asp side chains formed stably at room temperature. Furthermore, DNA hybridization alone placed two (His and Asp) and three (His, Cys, and Asp) side chains within the 3WJs, indicating that the DNA 3WJs are a useful platform for spatial arrangement of amino acid side chains.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naofumi Kudo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuyuki Fuse
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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4
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Bethur E, Guha R, Zhao Z, Katz BB, Ashby PD, Zeng H, Copp SM. Formation and Nanomechanical Properties of Silver-Mediated Guanine DNA Duplexes in Aqueous Solution. ACS NANO 2024; 18:3002-3010. [PMID: 38227309 PMCID: PMC10832345 DOI: 10.1021/acsnano.3c08008] [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: 08/24/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/17/2024]
Abstract
Silver cations can mediate base pairing of guanine (G) DNA oligomers, yielding linear parallel G-Ag+-G duplexes with enhanced stabilities compared to those of canonical DNA duplexes. To enable their use in programmable DNA nanotechnologies, it is critical to understand solution-state formation and the nanomechanical stiffness of G-Ag+-G duplexes. Using temperature-controlled circular dichroism (CD) spectroscopy, we find that heating mixtures of G oligomers and silver salt above 50 °C fully destabilizes G-quadruplex structures and converts oligomers to G-Ag+-G duplexes. Electrospray ionization mass spectrometry supports that G-Ag+-G duplexes form at stoichiometries of 1 Ag+ per base pair, and CD spectroscopy suggests that as the Ag+/base stoichiometry increases further, G-Ag+-G duplexes undergo additional morphological changes. Using liquid-phase atomic force microscopy, we find that this excess Ag+ enables assembly of long fiberlike structures with ∼2.5 nm heights equivalent to a single DNA duplex but with lengths that far exceed a single duplex. Finally, using the conditions established to form single G-Ag+-G duplexes, we use a surface forces apparatus (SFA) to compare the solution-phase stiffness of single G-Ag+-G duplexes with dG-dC Watson-Crick-Franklin duplexes. SFA shows that G-Ag+-G duplexes are 1.3 times stiffer than dG-dC duplexes, confirming gas-phase ion mobility spectrometry measurements and computational predictions. These findings may guide the development of structural DNA nanotechnologies that rely on silver-mediated base pairing.
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Affiliation(s)
- Eshana Bethur
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Rweetuparna Guha
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Ziqian Zhao
- Department
of Chemical and Materials Engineering, University
of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Benjamin B. Katz
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Paul D. Ashby
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hongbo Zeng
- Department
of Chemical and Materials Engineering, University
of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Stacy M. Copp
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
- Department
of Physics and Astronomy, University of
California, Irvine, California 92697, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
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5
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Kim T, Lee C, Lee JY, Kim DN. Controlling Chiroptical Responses via Chemo-Mechanical Deformation of DNA Origami Structures. ACS NANO 2024; 18:3414-3423. [PMID: 38236130 DOI: 10.1021/acsnano.3c10386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
DNA origami-based templates have been widely used to fabricate chiral plasmonic metamaterials due to their precise control of the placement of nanoparticles (NPs) in a desired configuration. However, achieving various chiroptical responses inevitably requires a change in the structure of DNA origami-based templates or binding sites on them, leading to the use of significantly different sets of DNA strands. Here, we propose an approach to controlling various chiroptical responses with a single DNA origami design using its chemo-mechanical deformation induced by DNA intercalators. The chiroptical response could be finely tuned by altering the concentration of intercalators only. The silver (Ag) enhancement was used to amplify the chiroptical signal by enlarging NPs and to maintain it by stiffening the template DNA structure. Furthermore, the sensitivity in the chiroptical signal change to the concentration of intercalators could be modulated by the type of intercalator, the mixture of two intercalators, and the stiffness of DNA origami structures. This approach would be useful in a variety of optical applications that require programmed spatial modification of chiroptical responses.
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Affiliation(s)
- Taehwi Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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6
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Lefringhausen N, Erbacher C, Elinkmann M, Karst U, Müller J. Contiguous Silver(I)-Mediated Base Pairs of Imidazophenanthroline and Canonical Nucleobases in DNA Duplexes: Formation of Classical Duplexes versus Homodimer Formation. Bioconjug Chem 2024; 35:99-106. [PMID: 38157473 DOI: 10.1021/acs.bioconjchem.3c00494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Metal-mediated base pairs represent a topical alternative to canonical hydrogen-bonded base pairs. In this context, the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was introduced as an artificial nucleobase in a glycol nucleic acid-based nucleoside analogue into a DNA oligonucleotide in a way that the oligonucleotide contains a central block of six contiguous P residues. The ability to engage in Ag+-mediated base pairing was evaluated with respect to the four canonical nucleosides in positions complementary to P. Highly stabilizing Ag+-mediated base pairs were formed with cytosine and guanine (i.e., P-Ag+-C and P-Ag+-G base pairs), whereas the analogous base pairs with thymine and adenine were much less stable and hence formed incompletely. Surprisingly, the intermediate formation of a homodimeric duplex of the P-containing oligonucleotide was observed in all cases, albeit to a different extent. The homodimer is composed of P-Ag+-P base pairs and 18 overhanging mismatched canonical nucleobases. It demonstrates the obstacles present when designing metal-mediated base pairs as metal complexation may take place irrespective of the surrounding natural base pairs. Homodimer formation was found to be particularly prominent when the designated metal-mediated base pairs are of low stability, suggesting that homodimers and regular duplexes are formed in a competing manner.
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Affiliation(s)
- Nils Lefringhausen
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 28/30, Münster 48149, Germany
| | - Catharina Erbacher
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 48, Münster 48149, Germany
| | - Matthias Elinkmann
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 48, Münster 48149, Germany
| | - Uwe Karst
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 48, Münster 48149, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 28/30, Münster 48149, Germany
- Cells in Motion Interfaculty Centre (CiMIC) and Center for Soft Nanoscience (SoN), Universität Münster, Corrensstr. 28/30, Münster 48149, Germany
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7
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Tian WD, Si WD, Havenridge S, Zhang C, Wang Z, Aikens CM, Tung CH, Sun D. Biomimetic crystallization for long-pursued -COOH-functionalized gold nanocluster with near-infrared phosphorescence. Sci Bull (Beijing) 2024; 69:40-48. [PMID: 37985311 DOI: 10.1016/j.scib.2023.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023]
Abstract
As an interdisciplinary product, water-soluble gold nanoclusters (AuNCs) stabilized by ligands containing carboxyl (-COOH) group have garnered significant attention from synthetic chemists and biologists due to their immense potential for biomedical applications. However, revealing the crystallographic structures of -COOH-functionalized AuNCs remains a bottleneck. Herein, we successfully applied the salting-out method to obtain a series of high-quality single crystals of -COOH-functionalized Au25 nanoclusters and revealed their crystallographic structures. Particularly, K3Au25(2-Hmna)9(mna)6]- (Au25a) protected by 2-mercaptonicotinic acid features an unprecedented tetrameric Au4(SRS)3(SRS,N)2 staple motifs surrounding the icosahedral Au13 kernel, breaking the traditional perception on the structure of Au25(SR)18. Au25a exhibits a distinct near-infrared emission at 970 nm with long lifetime of 8690 ns, which have been studied by transient absorption spectroscopy and time-dependent density functional theory. This work compensates for the research gap in the experimental structure of -COOH-functionalized AuNCs and opens up a new avenue to explore their structure-property correlations.
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Affiliation(s)
- Wei-Dong Tian
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Wei-Dan Si
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Shana Havenridge
- Department of Chemistry, Kansas State University, Manhattan KS 66506, USA
| | - Chengkai Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Zhi Wang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Christine M Aikens
- Department of Chemistry, Kansas State University, Manhattan KS 66506, USA
| | - Chen-Ho Tung
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Di Sun
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
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8
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Escher D, Schäfer T, Hebenbrock M, Müller J. 6-Pyrazolylpurine and its deaza derivatives as nucleobases for silver(I)-mediated base pairing with pyrimidines. J Biol Inorg Chem 2023; 28:791-803. [PMID: 37982840 PMCID: PMC10687122 DOI: 10.1007/s00775-023-02022-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/26/2023] [Indexed: 11/21/2023]
Abstract
The artificial nucleobase 6-pyrazolylpurine (6PP) and its deaza derivatives 1-deaza-6-pyrazolylpurine (1D6PP), 7-deaza-6-pyrazolylpurine (7D6PP), and 1,7-dideaza-6-pyrazolylpurine (1,7D6PP) were investigated with respect to their ability to differentiate between the canonical nucleobases cytosine and thymine by means of silver(I)-mediated base pairing. As shown by temperature-dependent UV spectroscopy and by circular dichroism spectroscopy, 6PP and (to a lesser extent) 7D6PP form stable silver(I)-mediated base pairs with cytosine, but not with thymine. 1D6PP and 1,7D6PP do not engage in the formation of stabilizing silver(I)-mediated base pairs with cytosine or thymine. The different behavior of 1D6PP, 7D6PP, and 1,7D6PP indicates that silver(I) binding occurs via the N1 position of the purine derivative, i.e. via the Watson-Crick face. The data show that 6PP is capable of differentiating between cytosine and thymine, which is potentially relevant in the context of detecting single-nucleotide polymorphisms.
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Affiliation(s)
- Daniela Escher
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 30, 48149, Münster, Germany
| | - Tim Schäfer
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 30, 48149, Münster, Germany
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 30, 48149, Münster, Germany.
- Center for Soft Nanoscience (SoN) and Cells in Motion Interfaculty Centre (CiMIC), Universität Münster, Corrensstr. 30, 48149, Münster, Germany.
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9
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Zhang YW, Li S, Wang SM, Li XQ, Cui MR, Kang B, Chen HY, Xu JJ. An intelligent DNA nanomachine for amplified MicroRNA imaging and MicroRNA-Guided efficient gene silencing. Talanta 2023; 265:124820. [PMID: 37331040 DOI: 10.1016/j.talanta.2023.124820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023]
Abstract
The DNA nanomachines as excellent synthetic biological tools have been widely used for the sensitive detection of intracellular microRNA (miRNA) and DNAzyme-involved gene silencing. However, intelligent DNA nanomachines which have the ability to sense intracellular specific biomolecules and respond to external information in complex environments still remain challenging. Herein, we develop a miRNA-responsive DNAzyme cascaded catalytic (MDCC) nanomachine to perform multilayer cascade reactions, enabling the amplified intracellular miRNA imaging and miRNA-guided efficient gene silencing. The intelligent MDCC nanomachine is designed based on multiple DNAzyme subunit-encoded catalyzed hairpin assembly (CHA) reactants sustained by the pH-responsive Zeolitic imidazolate framework-8 (ZIF-8) nanoparticles. After cellular uptake, the MDCC nanomachine degrades in acidic endosome and releases three hairpin DNA reactants and Zn2+, and the latter can act as an effective cofactor for DNAzyme. In the presence of miRNA-21, a catalytic hairpin assembly (CHA) reaction is triggered, which produces a large number of Y-shaped fluorescent DNA constructs containing three DNAzyme modules for gene silencing. The construction of Y-shaped DNA modified with multisite fluorescence and the circular reaction realizes ultrasensitive miRNA-21 imaging of cancer cells. Moreover, miRNA-guided gene silencing inhibits the cancer cell proliferation through the DNAzyme-specific recognition and cleavage of target EGR-1 (Early Growth Response-1) mRNA, which is one key tumor-involved mRNA. The strategy may provide a promising platform for highly sensitive determination of biomolecules and accurate gene therapy of cancer cells.
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Affiliation(s)
- Yu-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Shan Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Shu-Min Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Mei-Rong Cui
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, PR China.
| | - Bin Kang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China.
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10
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Kulke M, Olson DM, Huang J, Kramer DM, Vermaas JV. Long-Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2304013. [PMID: 37653599 DOI: 10.1002/smll.202304013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/18/2023] [Indexed: 09/02/2023]
Abstract
The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) can transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism, making them promising materials for nanowires. However, fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. Classical molecular dynamics simulations of these fluctuations at the nano- and mesoscopic scales allowed us to develop a graph network representation to estimate maximum electron flow that can be driven through STC wires. In longer nanowires, transient structural fluctuations at protein-protein interfaces tended to obstruct efficient electron transfer, but these blockages are ameliorated in thicker crystals where alternative electron transfer pathways become more efficient. The model implies that more flexible proteinprotein interfaces limit the required minimum diameter to carry currents commensurate with conventional electronics.
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Affiliation(s)
- Martin Kulke
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
| | - Dayna M Olson
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
| | - Jingcheng Huang
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
| | - David M Kramer
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
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11
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Torigoe H, Arakawa F. Importance of isothermal titration calorimetry for the detection of the direct binding of metal ions to mismatched base pairs in duplex DNA. Dalton Trans 2023; 52:13089-13096. [PMID: 37661915 DOI: 10.1039/d2dt02097a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Metal ion-nucleic acid interactions contribute substantially to the structure and biological activity of nucleic acids and have a wide range of potential applications in nanotechnology. In this study, we examined the interactions between metal ions and mismatched base pairs in duplex DNA to reveal the underlying molecular mechanism. UV melting analyses showed that the melting temperature (Tm) of a 21-base pair duplex DNA with each of the C-A, C-C and C-T mismatched base pairs increased upon the addition of Ag+. However, isothermal titration calorimetry (ITC) demonstrated that Ag+ only bound to the C-C mismatched base pair of the duplex DNA to form C-Ag-C bonds, without binding to the C-A and C-T mismatches. These results showed that Tm increased even when metal ions did not bind to the mismatched base pairs of the duplex DNA. Although the increase in Tm upon the addition of the metal ions is often used to detect metal ion binding to mismatched base pairs of duplex DNA, these results indicated that UV melting analyses are unable to detect the direct binding of metal ions to the mismatched base pairs. Because ITC analyses directly detect the heat derived from metal ion binding to mismatched base pairs of duplex DNA, we concluded that this may be an effective detection approach.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Fumihiro Arakawa
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
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12
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Yang ZY, Jiang WY, Ran SY. Reductant-dependent DNA-templated silver nanoparticle formation kinetics. Phys Chem Chem Phys 2023; 25:23197-23206. [PMID: 37605826 DOI: 10.1039/d3cp02623j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
DNA molecules have been demonstrated to be good templates for producing silver nanoparticles (AgNPs), with the advantages of well-controlled sizes, shapes, and properties. Revealing the formation kinetics of DNA-templated AgNPs is crucial for their efficient synthesis. Herein, using magnetic tweezers, we studied the reduction kinetics of the Ag+-DNA structure and the subsequent nucleation kinetics by adding NaBH4, L-ascorbic acid, and sodium citrate solutions. At [Ag+] = 0.01 mM, the addition of NaBH4 solution with the same concentration resulted in the restoration of DNA. In contrast, by increasing the [NaBH4]/[Ag+] ratio (r) to 10 and 100, the DNA extension initially decreased rapidly and then increased, indicating nucleation-dissolution kinetics. With AgNO3 solutions of higher concentrations (0.1 mM and 1 mM), direct particle nucleation and growth kinetics were observed by adding a tenfold (r = 10) or a hundredfold (r = 100) amount of NaBH4, which were evidenced by a significant reduction in DNA extension. The reductant dependence of the kinetics was further investigated. Addition of L-ascorbic acid to the DNA-Ag+ solution yielded an increase-decrease kinetics that was different from that caused by NaBH4, suggesting that nucleation was not initially favored due to the lack of sufficient Ag atoms; while sodium citrate showed a weak nucleation-promoting ability to form AgNPs. We discussed the findings within the framework of classical nucleation theory, in which the supersaturation of the Ag atom is strongly influenced by multiple factors (including the reducing ability of the reductant), resulting in different kinetics.
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Affiliation(s)
- Zi-Yang Yang
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | - Wen-Yan Jiang
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | - Shi-Yong Ran
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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13
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Guha R, Rafik M, Gonzàlez-Rosell A, Copp SM. Heat, pH, and salt: synthesis strategies to favor formation of near-infrared emissive DNA-stabilized silver nanoclusters. Chem Commun (Camb) 2023; 59:10488-10491. [PMID: 37551832 DOI: 10.1039/d3cc02896h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
We present chemical synthesis strategies for DNA-stabilized silver nanoclusters (AgN-DNAs) with near-infrared (NIR) emission in the biological tissue transparency windows. Elevated temperatures can significantly increase chemical yield of near-infrared nanoclusters. In most cases, basic pH favors near-infrared nanoclusters while micromolar amounts of NaCl inhibit their formation.
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Affiliation(s)
- Rweetuparna Guha
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697, USA.
| | - Malak Rafik
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697, USA.
| | - Anna Gonzàlez-Rosell
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697, USA.
| | - Stacy M Copp
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697, USA.
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA
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14
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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.
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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
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15
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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.
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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
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16
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Pan L, Ye S, Xv X, Lin P, Huang R, Wang D. Zeolite-Encaged Luminescent Silver Nanoclusters. MATERIALS (BASEL, SWITZERLAND) 2023; 16:ma16103736. [PMID: 37241363 DOI: 10.3390/ma16103736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
Silver nanoclusters (Ag NCs) are nanoscale aggregates that possess molecular-like discrete energy levels, resulting in electronic configuration-dependent tunable luminescence spanning the entire visible range. Benefiting from the efficient ion exchange capacity, nanometer dimensional cages, and high thermal and chemical stabilities, zeolites have been employed as desirable inorganic matrices to disperse and stabilize Ag NCs. This paper reviewed the recent research progresses on the luminescence properties, spectral manipulation, as well as the theoretical modelling of electronic structure and optical transition of Ag NCs confined inside various zeolites with different topology structures. Furthermore, potential applications of the zeolite-encaged luminescent Ag NCs in lighting, gas monitoring and sensing were presented. This review concludes with a brief comment on the possible future directions in the study of zeolite-encaged luminescent Ag NCs.
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Affiliation(s)
- Ling Pan
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Song Ye
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Xinling Xv
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Peixuan Lin
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Ruihao Huang
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Deping Wang
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
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17
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Danai L, Rolband LA, Perdomo VA, Skelly E, Kim T, Afonin KA. Optical, structural and antibacterial properties of silver nanoparticles and DNA-templated silver nanoclusters. Nanomedicine (Lond) 2023; 18:769-782. [PMID: 37345552 PMCID: PMC10308257 DOI: 10.2217/nnm-2023-0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023] Open
Abstract
Silver nanoparticles (AgNPs) are increasingly considered for biomedical applications as drug-delivery carriers, imaging probes and antibacterial agents. Silver nanoclusters (AgNCs) represent another subclass of nanoscale silver. AgNCs are a promising tool for nanomedicine due to their small size, structural homogeneity, antibacterial activity and fluorescence, which arises from their molecule-like electron configurations. The template-assisted synthesis of AgNCs relies on organic molecules that act as polydentate ligands. In particular, single-stranded nucleic acids reproducibly scaffold AgNCs to provide fluorescent, biocompatible materials that are incorporable in other formulations. This mini review outlines the design and characterization of AgNPs and DNA-templated AgNCs, discusses factors that affect their physicochemical and biological properties, and highlights applications of these materials as antibacterial agents and biosensors.
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Affiliation(s)
- Leyla Danai
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Lewis A Rolband
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Elizabeth Skelly
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Taejin Kim
- Physical Sciences Department, West Virginia University Institute of Technology, Beckley, WV 25801, USA
| | - Kirill A Afonin
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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18
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Torigoe H, Kondo J, Arakawa F. Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J Inorg Biochem 2023; 241:112125. [PMID: 36716510 DOI: 10.1016/j.jinorgbio.2023.112125] [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: 08/28/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023]
Abstract
Metal ion-nucleic acid interactions contribute significantly to nucleic acid structure and biological activity and have potential applications in nanotechnology. Hg2+ specifically binds to the natural T-T mismatched base pair in duplex DNA to form a T-Hg-T base pair. Metal ions may enhance DNA damage induced by DNA-damaging agents, such as oxidative agents. The interactions between metal ions and damaged DNAs, such as mismatched oxidized bases, have not been well characterized. Here, we examined the possibility of Hg2+ binding to an asymmetric mismatched base pair involving thymine and 5-hydroxyuracil (OHdU), an oxidized base produced by the oxidative deamination of cytosine. UV melting analyses showed that only the melting temperature of the single T-OHdU mismatched duplex DNA increased upon Hg2+ addition. CD spectra indicated no significant change in the higher-order structure of the single T-OHdU mismatched duplex DNA upon Hg2+ addition. X-ray crystallographic structure with two consecutive T-OHdU mismatched base pairs and isothermal titration calorimetric analyses with the single T-OHdU mismatched base pair showed that Hg2+ specifically binds to the N3 positions of both T and OHdU in T-OHdU at 1:1 molar ratio, with a 5×105 M-1 binding constant of to form the T-Hg-OHdU base pair. The Hg2+-bound structure and the Hg2+-binding affinity for T-OHdU was similar to those for T-T. This study on T-Hg-OHdU metal-mediated base pair could aid in studying the molecular mechanism of metal ion-mediated DNA damage and their potential applications in nanotechnology.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Jiro Kondo
- Department of Materials and Life Sciences, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Fumihiro Arakawa
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
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19
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Zhang J, Liu Y, Yan Z, Wang Y, Guo P. A Novel Minidumbbell DNA-Based Sensor for Silver Ion Detection. BIOSENSORS 2023; 13:358. [PMID: 36979570 PMCID: PMC10046540 DOI: 10.3390/bios13030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Silver ion (Ag+) is one of the most common heavy metal ions that cause environmental pollution and affect human health, and therefore, its detection is of great importance in the field of analytical chemistry. Here, we report an 8-nucleotide (nt) minidumbbell DNA-based sensor (M-DNA) for Ag+ detection. The minidumbbell contained a unique reverse wobble C·C mispair in the minor groove, which served as the binding site for Ag+. The M-DNA sensor could achieve a detection limit of 2.1 nM and sense Ag+ in real environmental samples with high accuracy. More importantly, the M-DNA sensor exhibited advantages of fast kinetics and easy operation owing to the usage of an ultrashort oligonucleotide. The minidumbbell represents a new and minimal non-B DNA structural motif for Ag+ sensing, allowing for the further development of on-site environmental Ag+ detection devices.
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Affiliation(s)
- Jiacheng Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Yuan Liu
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Zhenzhen Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Yue Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
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20
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Skiba J, Kowalczyk A, Gorski A, Dutkiewicz N, Gapińska M, Stróżek J, Woźniak K, Trzybiński D, Kowalski K. Replacement of the phosphodiester backbone between canonical nucleosides with a dirhenium carbonyl "click" linker-a new class of luminescent organometallic dinucleoside phosphate mimics. Dalton Trans 2023; 52:1551-1567. [PMID: 36655722 DOI: 10.1039/d2dt03995h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The first-in-class luminescent dinucleoside phosphate analogs with a [Re2(μ-Cl)2(CO)6(μ-pyridazine)] "click" linker as a replacement for the natural phosphate group are reported together with the synthesis of luminescent adenosine and thymidine derivatives having the [Re2(μ-Cl)2(CO)6(μ-pyridazine)] entity attached to positions 5' and 3', respectively. These compounds were synthesized by applying inverse-electron-demand Diels-Alder and copper(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition reactions in three or four steps. The obtained compounds exhibited orange emission (λPL ≈ 600 nm, ΦPL ≈ 0.10, and τ = 0.33-0.61 μs) and no toxicity (except for one nucleoside) to human HeLa cervical epithelioid and Ishikawa endometrial adenocarcinoma cancer cells in vitro. Furthermore, the compounds' ability to inhibit the growth of Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli bacterial strains was moderate and only observed at a high concentration of 100 μM. Confocal microscopy imaging revealed that the "dirhenium carbonyl" dinucleosides and nucleosides localized mainly in the membranous structures of HeLa cells and uniformly inside S. aureus and E. coli bacterial cells. An interesting finding was that some of the tested compounds were also found in the nuclei of HeLa cells.
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Affiliation(s)
- Joanna Skiba
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland.
| | - Aleksandra Kowalczyk
- Department of Molecular Microbiology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - Aleksander Gorski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, Poland
| | - Natalia Dutkiewicz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, Poland
| | - Magdalena Gapińska
- Faculty of Biology and Environmental Protection, Laboratory of Microscopic Imaging and Specialized Biological Techniques, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - Józef Stróżek
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland.
| | - Krzysztof Woźniak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Damian Trzybiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Konrad Kowalski
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland.
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21
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Mori K, Takezawa Y, Shionoya M. Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner. Chem Sci 2023; 14:1082-1088. [PMID: 36756334 PMCID: PMC9891364 DOI: 10.1039/d2sc06534g] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023] Open
Abstract
Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and functional transformation of DNA assemblies. In this study, N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleoside with an iminodiacetic acid (IDA) ligand at the 5-position of the uracil base has been developed as a bifacial nucleoside that can form both hydrogen-bonded and metal-mediated base pairs. Metal complexation study of dcaU nucleosides revealed their ability to form a 2:1 complex with a GdIII ion at the monomeric level. The characteristics of base pairing of dcaU nucleosides were then examined inside DNA duplexes. The results revealed that the formation of the metal-mediated dcaU-GdIII-dcaU pair significantly stabilized the DNA duplex containing one dcaU-dcaU mismatch (ΔT m = +16.1 °C). In contrast, a duplex containing a hydrogen-bonded dcaU-A pair was destabilized in the presence of GdIII (ΔT m = -3.5 °C). The GdIII-dependent base pairing of dcaU bases was applied to control the hybridization preference of DNA in response to metal ions. The hybridization partner of a dcaU-containing strand was reversibly exchanged by the addition and removal of GdIII ions. Since the incorporation of a single dcaU base can switch the hybridization behavior of DNA, the bifacial dcaU base would be a versatile building block for imparting metal responsiveness to DNA assemblies, allowing the rational design of dynamic DNA systems.
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Affiliation(s)
- Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - 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
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22
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Lefringhausen N, Seiffert V, Erbacher C, Karst U, Müller J. Chiral-at-Metal Silver-Mediated Base Pairs: Metal-Centred Chirality versus DNA Helical Chirality. Chemistry 2023; 29:e202202630. [PMID: 36219466 PMCID: PMC10098492 DOI: 10.1002/chem.202202630] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 11/23/2022]
Abstract
When covalently incorporating ligands capable of forming chiral metal complexes into a DNA oligonucleotide duplex, an enantiospecific formation of metal-mediated base pairs is possible. We have been investigating the chirality of the silver-mediated base pair P-AgI -P (P, 1H-imidazo[4,5-f][1,10]phenanthroline) depending on the number of consecutive P : P pairs within a series of duplexes. Towards this end, both enantiomers of the nucleoside analogue 3-(1H-imidazo[4,5-f][1,10]phenanthrolin-1-yl)propane-1,2-diol comprising an acyclic backbone were introduced into DNA duplexes, resulting in diastereomeric metal-mediated base pairs. The same chiral-at-metal complex is formed inside the duplex for up to five neighbouring P-AgI -P pairs, irrespective of whether (S)-P or (R)-P is used. With six silver-mediated base pairs, the chirality of the metal complex is inverted for (S)-P but not for (R)-P. This indicates an intricate balance of what determines the configuration of the metal complex, the intrinsically preferred metal-centred chirality or the DNA helical chirality.
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Affiliation(s)
- Nils Lefringhausen
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149, Münster, Germany
| | - Victoria Seiffert
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149, Münster, Germany
| | - Catharina Erbacher
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 48, 48149, Münster, Germany
| | - Uwe Karst
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 48, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Center for Soft Nanoscience (SoN) and Cells in Motion Interfaculty Centre (CiMIC), Corrensstr. 28/30, 48149, Münster, Germany
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23
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Zhang D, Hermann T. Metalated Nucleic Acid Nanostructures. Methods Mol Biol 2023; 2709:97-103. [PMID: 37572274 DOI: 10.1007/978-1-0716-3417-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Nucleic acid nanotechnology takes advantage of the self-assembling property of nucleic acids to form a variety of shapes and structures. The incorporation of metal ions into these structures introduces functionality for sensor and molecular electronic applications. Here, we describe a protocol for the incorporation of silver ions into polygonal nanoshapes that self-assemble from RNA and DNA modules.
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Affiliation(s)
- Douglas Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA.
- Center for Drug Discovery Innovation, University of California, San Diego, CA, USA.
- Program in Materials Science and Engineering, University of California, San Diego, CA, USA.
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24
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Li H, Wang P, Zhu C, Zhang W, Zhou M, Zhang S, Zhang C, Yun Y, Kang X, Pei Y, Zhu M. Triple-Helical Self-Assembly of Atomically Precise Nanoclusters. J Am Chem Soc 2022; 144:23205-23213. [DOI: 10.1021/jacs.2c11341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hao Li
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
| | - Pu Wang
- Department of Chemistry, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105, Hunan, P. R. China
| | - Chen Zhu
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
| | - Wei Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Meng Zhou
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - San Zhang
- National Laboratory of Solid State Microstructures, School of Physics, and Collaborative Innovation Center for Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Chunfeng Zhang
- National Laboratory of Solid State Microstructures, School of Physics, and Collaborative Innovation Center for Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yapei Yun
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
| | - Xi Kang
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
| | - Yong Pei
- Department of Chemistry, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Xiangtan University, Xiangtan 411105, Hunan, P. R. China
| | - Manzhou Zhu
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, Anhui, China
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25
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David F, Setzler C, Sorescu A, Lieberman RL, Meilleur F, Petty JT. Mapping H + in the Nanoscale (A 2C 4) 2-Ag 8 Fluorophore. J Phys Chem Lett 2022; 13:11317-11322. [PMID: 36453924 DOI: 10.1021/acs.jpclett.2c03161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
When strands of DNA encapsulate silver clusters, supramolecular optical chromophores develop. However, how a particular structure endows a specific spectrum remains poorly understood. Here, we used neutron diffraction to map protonation in (A2C4)2-Ag8, a green-emitting fluorophore with a "Big Dipper" arrangement of silvers. The DNA host has two substructures with distinct protonation patterns. Three cytosines from each strand collectively chelate handle-like array of three silvers, and calorimetry studies suggest Ag+ cross-links. The twisted cytosines are further joined by hydrogen bonds from fully protonated amines. The adenines and their neighboring cytosine from each strand anchor a dipper-like group of five silvers via their deprotonated endo- and exocyclic nitrogens. Typically, exocyclic amines are strongly basic, so their acidification and deprotonation in (A2C4)2-Ag8 suggest that silvers perturb the electron distribution in the aromatic nucleobases. The different protonation states in (A2C4)2-Ag8 suggest that atomic level structures can pinpoint how to control and tune the electronic spectra of these nanoscale chromophores.
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Affiliation(s)
- Fred David
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Caleb Setzler
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Alexandra Sorescu
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, North Carolina 27695, United States
- Neutron Scattering Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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26
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Qin C, Lu YX, Borch T, Yang LL, Li YW, Zhao HM, Hu X, Gao Y, Xiang L, Mo CH, Li QX. Interactions between Extracellular DNA and Perfluoroalkyl Acids (PFAAs) Decrease the Bioavailability of PFAAs in Pakchoi ( Brassica chinensis L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14622-14632. [PMID: 36375011 DOI: 10.1021/acs.jafc.2c04597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Perfluoroalkyl acids (PFAAs) are emerging ionic organic pollutants worldwide. Great amounts of extracellular DNA (∼mg/kg) coexist with PFAAs in the environment. However, PFAA-DNA interactions and effects of such interactions have not been well studied. Herein, we used isothermal titration calorimetry (ITC), spectroscopy, and computational simulations to investigate the PFAA-DNA interactions. ITC assays showed that specific binding affinities of PFHxA-DNA, PFOA-DNA, PFNA-DNA, and PFOS-DNA were 5.14 × 105, 3.29 × 105, 1.99 × 105, and 2.18 × 104 L/mol, respectively, which were about 1-2 orders of magnitude stronger than those of PFAAs with human serum albumin. Spectral analysis suggested interactions of PFAAs with adenine (A), cytosine (C), guanine (G), and thymine (T), among which grooves associated with thymine were the major binding sites. Molecular dynamics simulations and quantum chemical calculations suggested that hydrogen bonds and van der Waals forces were the main interaction forces. Such a PFAA-DNA binding decreased the bioavailability of PFAAs in plant seedlings. The findings will help to improve the current understanding of the interaction between PFAAs and biomacromolecules, as well as how such interactions affect the bioavailability of PFAAs.
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Affiliation(s)
- Chao Qin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Ying-Xin Lu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Thomas Borch
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, Colorado80523, United States
- Department of Soil and Crop Sciences, Colorado State University, 1170 Campus Delivery, Fort Collins, Colorado80523, United States
| | - Ling-Ling Yang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii96822, United States
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27
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Hao J, Cao D, Zhao Q, Zhang D, Wang H. Intramolecular Folding of PolyT Oligonucleotides Induced by Cooperative Binding of Silver(I) Ions. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227842. [PMID: 36431941 PMCID: PMC9694225 DOI: 10.3390/molecules27227842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Ag+-bridged T-Ag+-T was recently discovered in a Ag+-DNA nanowire crystal, but it was reported that Ag+ had little to no affinity to T nucleobases and T-rich oligonucleotides in solution. Therefore, the binding mode for the formation of this type of novel metallo base pair in solution is elusive. Herein, we demonstrate that Ag+ can interact with polyT oligonucleotides once the concentration of Ag+ in solution exceeds a threshold value. The threshold value is independent of the concentration of the polyT oligonucleotide but is inversely proportional to the length of the polyT oligonucleotide. The polyT oligonucleotides are intramolecularly folded due to their positively cooperative formation and the stack of T-Ag+-T base pairs, resulting in the 5'- and 3'-ends being in close proximity to each other. The intramolecular Ag+-folded polyT oligonucleotide has a higher thermal stability than the duplex and can be reversibly modulated by cysteine.
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Affiliation(s)
- Jinghua Hao
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Cao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qiang Zhao
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dapeng Zhang
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-10-62849611; Fax: +86-10-62849600
| | - Hailin Wang
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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28
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Kuo YA, Jung C, Chen YA, Kuo HC, Zhao OS, Nguyen TD, Rybarski JR, Hong S, Chen YI, Wylie DC, Hawkins JA, Walker JN, Shields SWJ, Brodbelt JS, Petty JT, Finkelstein IJ, Yeh HC. Massively Parallel Selection of NanoCluster Beacons. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204957. [PMID: 35945159 PMCID: PMC9588665 DOI: 10.1002/adma.202204957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/18/2022] [Indexed: 06/15/2023]
Abstract
NanoCluster Beacons (NCBs) are multicolor silver nanocluster probes whose fluorescence can be activated or tuned by a proximal DNA strand called the activator. While a single-nucleotide difference in a pair of activators can lead to drastically different activation outcomes, termed polar opposite twins (POTs), it is difficult to discover new POT-NCBs using the conventional low-throughput characterization approaches. Here, a high-throughput selection method is reported that takes advantage of repurposed next-generation-sequencing chips to screen the activation fluorescence of ≈40 000 activator sequences. It is found that the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs and positions 4-6 and 2-4 are hotspots to generate yellow-orange and red POTs, respectively. Based on these findings, a "zipper-bag" model is proposed that can explain how these hotspots facilitate the formation of distinct silver cluster chromophores and alter their chemical yields. Combining high-throughput screening with machine-learning algorithms, a pipeline is established to design bright and multicolor NCBs in silico.
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Affiliation(s)
- Yu-An Kuo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Yu-An Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Oliver S Zhao
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Trung D Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - James R Rybarski
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Soonwoo Hong
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Dennis C Wylie
- Computational Biology and Bioinformatics, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX, 78712, USA
| | - John A Hawkins
- European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Samuel W J Shields
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, SC, 29617, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Texas Materials Institute, University of Texas at Austin, Austin, TX, 78712, USA
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29
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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.
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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.
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30
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Zhang L, Liu J, Gao M, Han L, Liu X, Xing X. Fluorescent Determination of Mercury(II) and Glutathione with Binding to Thymine–Guanine Base Pairs. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2109044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Liyuan Zhang
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Jinxiao Liu
- College of Materials Science and Engineering, Zhengzhou University, Zhengzhou, China
| | - Mengying Gao
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Li Han
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Department of Biology and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Xueguo Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Department of Biology and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Xiaojing Xing
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
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31
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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
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32
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Imani M, Mohajeri N, Rastegar M, Zarghami N. Synthesis and Characterization of N-rich Fluorescent Bio-dots as a Reporter in the Design of Dual-labeled FRET Probe for TaqMan PCR: a Feasibility Study. Biotechnol Appl Biochem 2022; 70:645-658. [PMID: 35900086 DOI: 10.1002/bab.2387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/12/2022] [Indexed: 11/07/2022]
Abstract
DNA-based analytical techniques have provided an advantageous sensing assay in the realm of biotechnology. Bio-inspired fluorescent nanodots are a novel type of biological staining agent with excellent optical properties widely used for cellular imaging and diagnostics. In the present research, we successfully synthesized bio-dots with excellent optical properties and high-quantum yield from DNA sodium salt through the hydrothermal method. We conjugated the bio-dots with 3' Eclipse® Dark Quencher (Eclipse) labeled single strand oligodeoxyribonucleotide according to carbodiimide chemistry, to design a fluorescence resonance energy transfer (FRET) probe. The results confirmed the prosperous synthesis and surface functionalization of the bio-dot. Analysis of size, zeta potential, and FTIR spectroscopy verified successful bioconjugation of the bio-dots with probes. UV-Visibility analysis and fluorescence intensity profile of the bio-dot and bio-dot@probes represented a concentration-dependent quenching of fluorescent signal of bio-dot by Eclipse after probe conjugation. The results demonstrated that TaqMan PCR was not feasible using the designed bio-dot@probes. Our results indicated that bio-dot can be used as an efficient fluorescent tag in the design of fluorescently labeled oligonucleotides with high biocompatibility and optical features. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mahsa Imani
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasrin Mohajeri
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Nosratollah Zarghami
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Aydin University, Istanbul, Turkey
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33
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Mesoscopic model confirms strong base pair metal mediated bonding for T-Hg 2+-T and weaker for C-Ag +-C. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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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
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35
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Heddinga MH, Müller J. Modulating aptamer function by copper(II)-mediated base pair formation. Org Biomol Chem 2022; 20:4787-4793. [PMID: 35640171 DOI: 10.1039/d2ob00788f] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two aptamers, one for ATP and one for arginine, were modified using an artificial 2'-dexoyribonucleoside based on the nucleobase surrogate imidazole-4-carboxylate. This synthetic nucleoside substitute does not engage in hydrogen bonding but is capable of forming Cu(II)-mediated base pairs instead. Hence, the addition of Cu(II) can be used to influence the ability of the aptamer derivatives to adopt the correct fold necessary for binding their respective target molecule. As a result, aptamer function can be modulated via the addition of Cu(II). The extent of modulation ability depends on the identity of the aptamer and on the exact location of the artificial nucleosides within the oligonucleotide sequence.
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Affiliation(s)
- Marius H Heddinga
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany.
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany. .,Westfälische Wilhelms-Universität Münster, Center for Soft Nanoscience (SoN) and Cells in Motion Interfaculty Centre (CiMIC), Corrensstraße 28/30, 48149 Münster, Germany
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36
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Petty JT, Lewis D, Carnahan S, Kim D, Couch C. Tug-of-War between DNA Chelation and Silver Agglomeration in DNA-Silver Cluster Chromophores. J Phys Chem B 2022; 126:3822-3830. [PMID: 35594191 DOI: 10.1021/acs.jpcb.2c01054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Supramolecular chromophores form when a DNA traps silvers that then coalesce into clusters with discrete, molecular electronic states. However, DNA strands are polymeric ligands that disperse silvers and thus curb agglomeration. We study this competition using two chromophores that share three common components: a dimeric DNA scaffold, Ag+-nucleobase base pairs, and Ag0 chromophores. The DNA host C4-A2-iC4T mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "i") directions. The backbone directions must alternate to form the two silver clusters, and this interdependence supports a silver-linked structure. This template creates two chromophores with distinct sizes, charges, and hence spectra: (C4-A2-iC4T)2/Ag117+ with λabs/λem = 430/520 nm and (C4-A2-iC4T)2/Ag148+ with λabs/λem = 510/630 nm. The Ag+ and Ag0 constituents in these partially oxidized clusters are linked with structural elements in C4-A2-iC4T. Ag+ alone binds sparsely but strongly to form C4-A2-iC4T/3-4 Ag+ and (C4-A2-iC4T)2/7-8 Ag+ complexes, and these stoichiometries suggest that Ag+ cross-links pairs of cytosines to form a hairpin with a metallo-C4/iC4 duplex and an adenine loop. The Ag0 are chemically orthogonal because they can be oxidatively etched without disrupting the underlying Ag+-DNA matrix, and their reactivity is attributed to their valence electrons and weaker chelation by the adenines. These studies suggest that Ag+ disperses with the cytosines to create an adenine binding pocket for the Ag0 cluster chromophores.
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - David Lewis
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Savannah Carnahan
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Dahye Kim
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Caroline Couch
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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Hu L, Takezawa Y, Shionoya M. Metal-mediated DNA base pairing of easily prepared 2-oxo-imidazole-4-carboxylate nucleotides. Chem Sci 2022; 13:3977-3983. [PMID: 35440985 PMCID: PMC8985573 DOI: 10.1039/d2sc00926a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022] Open
Abstract
Metal-mediated DNA base pairs, which consist of two ligand-type artificial nucleobases and a bridging metal ion, have attracted increasing attention in recent years as a different base pairing mode from natural base pairing. Metal-mediated base pairing has been extensively studied, not only for metal-dependent thermal stabilisation of duplexes, but also for metal assembly by DNA templates and construction of functional DNAs that can be controlled by metals. Here, we report the metal-mediated base paring properties of a novel 2-oxo-imidazole-4-carboxylate (ImOC) nucleobase and a previously reported 2-oxo-imidazole-4-carboxamide (ImOA) nucleobase, both of which can be easily derived from a commercially available uridine analogue. The ImOC nucleobases were found to form stable ImOC–CuII–ImOC and ImOC–HgII–ImOC base pairs in the presence of the corresponding metal ions, leading to an increase in the duplex melting temperature by +20 °C and +11 °C, respectively. The ImOC bases did not react with other divalent metal ions and showed superior metal selectivity compared to similar nucleobase design reported so far. The ImOC–CuII–ImOC base pair was much more stable than mismatch pairs with other natural nucleobases, confirming the base pair specificity in the presence of CuII. Furthermore, we demonstrated the quantitative assembly of three CuII ions inside a DNA duplex with three consecutive ImOC–ImOC pairs, showing great potential of DNA-template based CuII nanoarray construction. The study of easily-prepared ImOC base pairs will provide a new design strategy for metal-responsive DNA materials. A novel 2-oxo-imidazole-4-carboxylate (ImOC) nucleobase, which can be easily derived from a commercially available uridine analogue, was found to form stable CuII- and HgII-mediated base pairs in DNA duplexes.![]()
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Affiliation(s)
- Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - 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
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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.
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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
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39
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Samanta D, Zhou W, Ebrahimi SB, Petrosko SH, Mirkin CA. Programmable Matter: The Nanoparticle Atom and DNA Bond. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107875. [PMID: 34870875 DOI: 10.1002/adma.202107875] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/22/2021] [Indexed: 05/21/2023]
Abstract
Colloidal crystal engineering with DNA has led to significant advances in bottom-up materials synthesis and a new way of thinking about fundamental concepts in chemistry. Here, programmable atom equivalents (PAEs), comprised of nanoparticles (the "atoms") functionalized with DNA (the "bonding elements"), are assembled through DNA hybridization into crystalline lattices. Unlike atomic systems, the "atom" (e.g., the nanoparticle shape, size, and composition) and the "bond" (e.g., the DNA length and sequence) can be tuned independently, yielding designer materials with unique catalytic, optical, and biological properties. In this review, nearly three decades of work that have contributed to the evolution of this class of programmable matter is chronicled, starting from the earliest examples based on gold-core PAEs, and then delineating how advances in synthetic capabilities, DNA design, and fundamental understanding of PAE-PAE interactions have led to new classes of functional materials that, in several cases, have no natural equivalent.
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Affiliation(s)
- Devleena Samanta
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Wenjie Zhou
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sasha B Ebrahimi
- Department of Chemical Engineering and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sarah Hurst Petrosko
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
- Department of Chemical Engineering and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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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.
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Affiliation(s)
- Bernhard Lippert
- Fakultät Für Chemie Und Chemische Biologie (CCB), Technische Universität Dortmund, 44221, Dortmund, Germany.
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41
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Levi-Acobas F, McKenzie LK, Hollenstein M. Towards polymerase-mediated synthesis of artificial RNA–DNA metal base pairs. NEW J CHEM 2022. [DOI: 10.1039/d2nj00427e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Polymerase-mediated synthesis of RNA-DNA metal base pairs.
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Affiliation(s)
- Fabienne Levi-Acobas
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Luke K. McKenzie
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- 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, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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42
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Fardian-Melamed N, Katrivas L, Rotem D, Kotlyar A, Porath D. Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules. NANO LETTERS 2021; 21:8987-8992. [PMID: 34694812 DOI: 10.1021/acs.nanolett.1c02269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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43
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Schönrath I, Aukam H, Jasper-Peter B, Müller J. Silver(I)-mediated base pairing involving an S-glycosidic GNA nucleoside analogue. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2021; 41:23-35. [PMID: 34686119 DOI: 10.1080/15257770.2021.1994146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
The 4S-Ag(I)-C base pair (4S, 3-((2-(methylthio)pyrimidin-4-yl)thio)propane-1,2-diol; C, deoxycytidine) represents the first metal-mediated base pair comprising an S-glycosidic nucleoside analogue. We report here the synthesis of the phosphoramidite suitable for the automated solid-phase synthesis of DNA oligonucleotides containing 4S and its silver(I)-binding ability. The DNA duplexes comprising a 4S:C mispair exhibit a large thermal stabilization upon the addition of one equivalent of silver ions, giving rise to the formation of the above-mentioned silver(I)-mediated base pair. By formally replacing the sulfur atom in the glycosidic bond by an oxygen atom, i.e., by applying 3-((2-(methylthio)pyrimidin-4-yl)oxy)propane-1,2-diol (4 O) as the artificial nucleoside analogue, the participation of this atom as a donor atom in silver(I)-mediated base pairing is shown to be neglectable.Supplemental data for this article is available online at.
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Affiliation(s)
- Isabell Schönrath
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Hanne Aukam
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Beate Jasper-Peter
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
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44
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Suea-Ngam A, Howes PD, deMello AJ. An amplification-free ultra-sensitive electrochemical CRISPR/Cas biosensor for drug-resistant bacteria detection. Chem Sci 2021; 12:12733-12743. [PMID: 34703560 PMCID: PMC8494034 DOI: 10.1039/d1sc02197d] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/13/2021] [Indexed: 12/23/2022] Open
Abstract
Continued development of high-performance and cost-effective in vitro diagnostic tools is vital for improving infectious disease treatment and transmission control. For nucleic acid diagnostics, moving beyond enzyme-mediated amplification assays will be critical in reducing the time and complexity of diagnostic technologies. Further, an emerging area of threat, in which in vitro diagnostics will play an increasingly important role, is antimicrobial resistance (AMR) in bacterial infections. Herein, we present an amplification-free electrochemical CRISPR/Cas biosensor utilizing silver metallization (termed E-Si-CRISPR) to detect methicillin-resistant Staphylococcus aureus (MRSA). Using a custom-designed guide RNA (gRNA) targeting the mecA gene of MRSA, the Cas12a enzyme allows highly sensitive and specific detection when employed with silver metallization and square wave voltammetry (SWV). Our biosensor exhibits excellent analytical performance, with detection and quantitation limits of 3.5 and 10 fM, respectively, and linearity over five orders of magnitude (from 10 fM to 0.1 nM). Importantly, we observe no degradation in performance when moving from buffer to human serum samples, and achieve excellent selectivity for MRSA in human serum in the presence of other common bacteria. The E-Si-CRISPR method shows significant promise as an ultrasensitive field-deployable device for nucleic acid-based diagnostics, without requiring nucleic acid amplification. Finally, adjustment to a different disease target can be achieved by simple modification of the gRNA protospacer. An amplification-free electrochemical CRISPR/Cas biosensor utilizing silver metallization (termed E-Si-CRISPR) allows detection of methicillin-resistant Staphylococcus aureus (MRSA) with excellent sensitivity and specificity.![]()
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Affiliation(s)
- Akkapol Suea-Ngam
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg1 8093 Zürich Switzerland
| | - Philip D Howes
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg1 8093 Zürich Switzerland .,Division of Mechanical Engineering and Design, School of Engineering, London South Bank University 103 Borough Road London SE1 0AA UK
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg1 8093 Zürich Switzerland
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45
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46
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A dissipative pathway for the structural evolution of DNA fibres. Nat Chem 2021; 13:843-849. [PMID: 34373598 DOI: 10.1038/s41557-021-00751-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
Biochemical networks interconnect, grow and evolve to express new properties as different chemical pathways are selected during a continuous cycle of energy consumption and transformation. In contrast, synthetic systems that push away from equilibrium usually return to the same self-assembled state, often generating waste that limits system recyclability and prevents the formation of adaptable networks. Here we show that annealing by slow proton dissipation selects for otherwise inaccessible morphologies of fibres built from DNA and cyanuric acid. Using single-molecule fluorescence microscopy, we observe that proton dissipation influences the growth mechanism of supramolecular polymerization, healing gaps within fibres and converting highly branched, interwoven networks into nanocable superstructures. Just as the growth kinetics of natural fibres determine their structural attributes to modulate function, our system of photoacid-enabled depolymerization and repolymerization selects for healed materials to yield organized, robust fibres. Our method provides a chemical route for error-checking, distinct from thermal annealing, that improves the morphologies and properties of supramolecular materials using out-of-equilibrium systems.
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47
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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.
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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
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Dairaku T, Kawai R, Kanaba T, Ono T, Yoshida K, Sato H, Nozawa-Kumada K, Kondo Y, Kondo J, Ono A, Tanaka Y, Kashiwagi Y. Effect of cytosine-Ag +-cytosine base pairing on the redox potential of the Ag +/Ag couple and the chemical reduction of Ag + to Ag by tetrathiafulvalene. Dalton Trans 2021; 50:7633-7639. [PMID: 33973617 DOI: 10.1039/d1dt00975c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The redox properties of metallo-base pairs remain to be elucidated. Herein, we report the detailed 1H/13C/109Ag NMR spectroscopic and cyclic voltammetric characterisation of the [Ag(cytidine)2]+ complex as isolated cytosine-Ag+-cytosine (C-Ag+-C) base pairs. We also performed comparative studies between cytidine/Ag+ and other nucleoside/Ag+ systems by using cyclic voltammetry measurements. In addition, to evaluate the effect of [Ag(cytidine)2]+ formation on the chemical reduction of Ag+ to Ag, we utilised the redox reaction between Ag+ and tetrathiafulvalene (TTF). We found that Ag+-mediated base pairing lowers the redox potential of the Ag+/Ag couple. In addition, C-Ag+-C base pairing makes it more difficult to reduce captured Ag+ ions than in other nucleoside/Ag+ systems. Remarkably, the cytidine/Ag+ system can be utilised to control the redox potential of the Ag+/Ag couple in DMSO. This feature of the cytidine/Ag+ system may be exploited for Ag nanoparticle synthesis by using the redox reaction between Ag+ and TTF.
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Affiliation(s)
- Takenori Dairaku
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Rika Kawai
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Teppei Kanaba
- Application, Bruker Japan K.K., 3-9 Moriya-cho, Kanagawa-ku, Yokohama, Kanagawa 221-0022, Japan
| | - Tetsuya Ono
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Kentaro Yoshida
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
| | - Hajime Sato
- Application, Bruker Japan K.K., 3-9 Moriya-cho, Kanagawa-ku, Yokohama, Kanagawa 221-0022, Japan
| | - Kanako Nozawa-Kumada
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yoshinori Kondo
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Akira Ono
- Department of Material & Life Chemistry, Faculty of Engineering, Kangawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686, Japan
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Yoshitomo Kashiwagi
- School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan.
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49
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Kohl FR, Zhang Y, Charnay AP, Martínez-Fernández L, Kohler B. Ultrafast excited state dynamics of silver ion-mediated cytosine-cytosine base pairs in metallo-DNA. J Chem Phys 2021; 153:105104. [PMID: 32933288 DOI: 10.1063/5.0020463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To better understand the nexus between structure and photophysics in metallo-DNA assemblies, the parallel-stranded duplex formed by the all-cytosine oligonucleotide, dC20, and silver nitrate was studied by circular dichroism (CD), femtosecond transient absorption spectroscopy, and time-dependent-density functional theory calculations. Silver(I) ions mediate Cytosine-Cytosine (CC) base pairs by coordinating to the N3 atoms of two cytosines. Although these silver(I) mediated CC base pairs resemble the proton-mediated CC base pairs found in i-motif DNA at first glance, a comparison of experimental and calculated CD spectra reveals that silver ion-mediated i-motif structures do not form. Instead, the parallel-stranded duplex formed between dC20 and silver ions is proposed to contain consecutive silver-mediated base pairs with high propeller twist-like ones seen in a recent crystal structure of an emissive, DNA-templated silver cluster. Femtosecond transient absorption measurements with broadband probing from the near UV to the near IR reveal an unusually long-lived (>10 ns) excited state in the dC20 silver ion complex that is not seen in dC20 in single-stranded or i-motif forms. This state is also absent in a concentrated solution of cytosine-silver ion complexes that are thought to assemble into planar ribbons or sheets that lack stacked silver(I) mediated CC base pairs. The large propeller twist angle present in metal-mediated base pairs may promote the formation of long-lived charged separated or triplet states in this metallo-DNA.
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Affiliation(s)
- Forrest R Kohl
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Aaron P Charnay
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Bern Kohler
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
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Pérez‐Romero A, Domínguez‐Martín A, Galli S, Santamaría‐Díaz N, Palacios O, Dobado JA, Nyman M, Galindo MA. Single‐Stranded DNA as Supramolecular Template for One‐Dimensional Palladium(II) Arrays. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Antonio Pérez‐Romero
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - Alicia Domínguez‐Martín
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - Simona Galli
- 2 Dipartimento di Scienza e Alta Tecnologia Università dell'Insubria Via Valleggio 11 22100 Como Italy
| | - Noelia Santamaría‐Díaz
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - Oscar Palacios
- Departament de Química Facultat de Ciències Universitat Autònoma de Barcelona Campus Bellaterra s/n 08193 Cerdanyola del Vallès, Barcelona Spain
| | - José A. Dobado
- Grupo de Modelización y Diseño Molecular Departamento de Química Orgánica Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - May Nyman
- Department of Chemistry Oregon State University Corvallis OR 97331-4003 USA
| | - Miguel A. Galindo
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
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