1
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Gonzàlez-Rosell A, Copp SM. An Atom-Precise Understanding of DNA-Stabilized Silver Nanoclusters. Acc Chem Res 2024; 57:2117-2129. [PMID: 38995323 PMCID: PMC11308368 DOI: 10.1021/acs.accounts.4c00256] [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] [Received: 04/30/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
ConspectusDNA-stabilized silver nanoclusters (AgN-DNAs) are sequence-encoded fluorophores. Like other noble metal nanoclusters, the optical properties of AgN-DNAs are dictated by their atomically precise sizes and shapes. What makes AgN-DNAs unique is that nanocluster size and shape are controlled by nucleobase sequence of the templating DNA oligomer. By choice of DNA sequence, it is possible to synthesize a wide range of AgN-DNAs with diverse emission colors and other intriguing photophysical properties. AgN-DNAs hold significant potential as "programmable" emitters for biological imaging due to their combination of small molecular-like sizes, bright and sequence-tuned fluorescence, low toxicities, and cost-effective synthesis. In particular, the potential to extend AgN-DNAs into the second near-infrared region (NIR-II) is promising for deep tissue imaging, which is a major area of interest for advancing biomedical imaging. Achieving this goal requires a deep understanding of the structure-property relationships that govern AgN-DNAs in order to design AgN-DNA emitters with sizes and geometries that support NIR-II emission.In recent years, major advances have been made in understanding the structure and composition of AgN-DNAs, enabling new insights into the correlation of nanocluster structure and photophysical properties. These advances have hinged on combined innovations in mass characterization and crystallography of compositionally pure AgN-DNAs, together with combinatorial experiments and machine learning-guided design. A combined approach is essential due to the major challenge of growing suitable AgN-DNA crystals for diffraction and to the labor-intensive nature of preparing and solving the molecular formulas of atomically precise AgN-DNAs by mass spectrometry. These approaches alone are not feasibly scaled to explore the large sequence space of DNA oligomer templates for AgN-DNAs.This account describes recent fundamental advances in AgN-DNA science that have been enabled by high throughput synthesis and fluorimetry together with detailed analytical studies of purified AgN-DNAs. First, short introductions to nanocluster chemistry and AgN-DNA basics are presented. Then, we review recent large-scale studies that have screened thousands of DNA templates for AgN-DNAs, leading to discovery of distinct classes of these emitters with unique cluster core compositions and ligand chemistries. In particular, the discovery of a new class of chloride-stabilized AgN-DNAs enabled the first ab initio calculations of AgN-DNA electronic structure and present new approaches to stabilize these emitters in biologically relevant conditions. Near-infrared (NIR) emissive AgN-DNAs are also found to exhibit diverse structures and properties. Finally, we conclude by highlighting recent proof-of-principle demonstrations of NIR AgN-DNAs for targeted fluorescence imaging. Continued efforts may future push AgN-DNAs into the tissue transparency window for fluorescence imaging in the NIR-II tissue transparency window.
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Affiliation(s)
- Anna Gonzàlez-Rosell
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Stacy M. Copp
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
- Department
of Physics and Astronomy, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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2
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Liasi Z, Jensen L, Mikkelsen KV. A Combined Quantum Mechanics and Molecular Mechanics Approach for Simulating the Optical Properties of DNA-Stabilized Silver Nanoclusters. J Chem Theory Comput 2024; 20:937-945. [PMID: 38164716 DOI: 10.1021/acs.jctc.3c01022] [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
DNA-stabilized silver nanoclusters have emerged as an intriguing type of nanomaterial due to their unique optical and electronic properties, with potential applications in areas such as biosensing and imaging. The development of efficient methods for modeling these properties is paramount for furthering the understanding and utilization of these clusters. In this study, a hybrid quantum mechanical and molecular mechanical approach for modeling the optical properties of a DNA-templated silver nanocluster is evaluated. The influence of different parameters, including ligand fragmentation, damping, embedding potential, basis set, and density functional, is investigated. The results demonstrate that the most important parameter is the type of atomic properties used to represent the ligands, with isotropic dipole-dipole polarizabilities outperforming the rest. This underscores the importance of an appropriate representation of the ligands, particularly through the selection of the properties used to represent them. Moreover, the results are compared to experimental data, showing that the applied methodology is reliable and effective for the modeling of DNA-stabilized silver nanoclusters. These findings offer valuable insights that may guide future computational efforts to explore and harness the potential of these novel systems.
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Affiliation(s)
- Zacharias Liasi
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø 2100, Denmark
| | - Lasse Jensen
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø 2100, Denmark
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3
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Guha R, Gonzàlez-Rosell A, Rafik M, Arevalos N, Katz BB, Copp SM. Electron count and ligand composition influence the optical and chiroptical signatures of far-red and NIR-emissive DNA-stabilized silver nanoclusters. Chem Sci 2023; 14:11340-11350. [PMID: 37886084 PMCID: PMC10599602 DOI: 10.1039/d3sc02931j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/09/2023] [Indexed: 10/28/2023] Open
Abstract
Near-infrared (NIR) emissive DNA-stabilized silver nanoclusters (AgN-DNAs) are promising fluorophores in the biological tissue transparency windows. Hundreds of NIR-emissive AgN-DNAs have recently been discovered, but their structure-property relationships remain poorly understood. Here, we investigate 19 different far-red and NIR emissive AgN-DNA species stabilized by 10-base DNA templates, including well-studied emitters whose compositions and chiroptical properties have never been reported before. The molecular formula of each purified species is determined by high-resolution mass spectrometry and correlated to its optical absorbance, emission, and circular dichroism (CD) spectra. We find that there are four distinct compositions for AgN-DNAs emissive at the far red/NIR spectral border. These emitters are either 8-electron clusters stabilized by two DNA oligomer copies or 6-electron clusters with one of three different ligand compositions: two oligomer copies, three oligomer copies, or two oligomer copies with additional chlorido ligands. Distinct optical and chiroptical signatures of 6-electron AgN-DNAs correlate with each ligand composition. AgN-DNAs with three oligomer ligands exhibit shorter Stokes shifts than AgN-DNAs with two oligomers, and AgN-DNAs with chlorido ligands have increased Stokes shifts and significantly suppressed visible CD transitions. Nanocluster electron count also significantly influences electronic structure and optical properties, with 6-electron and 8-electron AgN-DNAs exhibiting distinct absorbance and CD spectral features. This study shows that the optical and chiroptical properties of NIR-emissive AgN-DNAs are highly sensitive to nanocluster composition and illustrates the diversity of structure-property relationships for NIR-emissive AgN-DNAs, which could be harnessed to precisely tune these emitters for bioimaging applications.
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Affiliation(s)
- Rweetuparna Guha
- 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
| | - Malak Rafik
- Department of Materials Science and Engineering, University of California Irvine CA 92697 USA
| | - Nery Arevalos
- Department of Materials Science and Engineering, University of California Irvine CA 92697 USA
| | - Benjamin B Katz
- Department of Chemistry, 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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4
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Mastracco P, Copp SM. Beyond nature's base pairs: machine learning-enabled design of DNA-stabilized silver nanoclusters. Chem Commun (Camb) 2023; 59:10360-10375. [PMID: 37575075 DOI: 10.1039/d3cc02890a] [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: 08/15/2023]
Abstract
Sequence-encoded biomolecules such as DNA and peptides are powerful programmable building blocks for nanomaterials. This paradigm is enabled by decades of prior research into how nucleic acid and amino acid sequences dictate biomolecular interactions. The properties of biomolecular materials can be significantly expanded with non-natural interactions, including metal ion coordination of nucleic acids and amino acids. However, these approaches present design challenges because it is often not well-understood how biomolecular sequence dictates such non-natural interactions. This Feature Article presents a case study in overcoming challenges in biomolecular materials with emerging approaches in data mining and machine learning for chemical design. We review progress in this area for a specific class of DNA-templated metal nanomaterials with complex sequence-to-property relationships: DNA-stabilized silver nanoclusters (AgN-DNAs) with bright, sequence-tuned fluorescence colors and promise for biophotonics applications. A brief overview of machine learning concepts is presented, and high-throughput experimental synthesis and characterization of AgN-DNAs are discussed. Then, recent progress in machine learning-guided design of DNA sequences that select for specific AgN-DNA fluorescence properties is reviewed. We conclude with emerging opportunities in machine learning-guided design and discovery of AgN-DNAs and other sequence-encoded biomolecular nanomaterials.
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Affiliation(s)
- Peter Mastracco
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, USA.
| | - Stacy M Copp
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, USA.
- Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, USA
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5
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Liasi Z, Hillers-Bendtsen AE, Jensen L, Mikkelsen KV. Elucidating the Mystery of DNA-Templating Effects on a Silver Nanocluster. J Phys Chem Lett 2023:5727-5733. [PMID: 37318362 DOI: 10.1021/acs.jpclett.3c00977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This presentation considers the effects that DNA-templating has on the optical properties of a 16-atom silver cluster. To accomplish this, hybrid quantum mechanical and molecular mechanical simulations of a Ag16-DNA complex have been carried out and compared with pure time-dependent density functional theory calculations of two Ag16 clusters in vacuum. The presented results show that the templating DNA polymers both red-shift the one-photon absorption of the silver cluster and increase its intensity. This occurs through a change in cluster shape prompted by the structural constraints of the DNA ligands combined with silver-DNA interactions. The overall charge of the cluster also contributes to the observed optical response, as oxidation of the cluster results in a simultaneous blue-shift of the one-photon absorption and a decrease in intensity. Additionally, the changes in shape and environment also lead to a blue-shift and enhancement of the two-photon absorption.
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Affiliation(s)
- Zacharias Liasi
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | | - Lasse Jensen
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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6
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Gonzàlez-Rosell A, Malola S, Guha R, Arevalos NR, Matus MF, Goulet ME, Haapaniemi E, Katz BB, Vosch T, Kondo J, Häkkinen H, Copp SM. Chloride Ligands on DNA-Stabilized Silver Nanoclusters. J Am Chem Soc 2023; 145:10721-10729. [PMID: 37155337 DOI: 10.1021/jacs.3c01366] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA-stabilized silver nanoclusters (AgN-DNAs) are known to have one or two DNA oligomer ligands per nanocluster. Here, we present the first evidence that AgN-DNA species can possess additional chloride ligands that lead to increased stability in biologically relevant concentrations of chloride. Mass spectrometry of five chromatographically isolated near-infrared (NIR)-emissive AgN-DNA species with previously reported X-ray crystal structures determines their molecular formulas to be (DNA)2[Ag16Cl2]8+. Chloride ligands can be exchanged for bromides, which red-shift the optical spectra of these emitters. Density functional theory (DFT) calculations of the 6-electron nanocluster show that the two newly identified chloride ligands were previously assigned as low-occupancy silvers by X-ray crystallography. DFT also confirms the stability of chloride in the crystallographic structure, yields qualitative agreement between computed and measured UV-vis absorption spectra, and provides interpretation of the 35Cl-nuclear magnetic resonance spectrum of (DNA)2[Ag16Cl2]8+. A reanalysis of the X-ray crystal structure confirms that the two previously assigned low-occupancy silvers are, in fact, chlorides, yielding (DNA)2[Ag16Cl2]8+. Using the unusual stability of (DNA)2[Ag16Cl2]8+ in biologically relevant saline solutions as a possible indicator of other chloride-containing AgN-DNAs, we identified an additional AgN-DNA with a chloride ligand by high-throughput screening. Inclusion of chlorides on AgN-DNAs presents a promising new route to expand the diversity of AgN-DNA structure-property relationships and to imbue these emitters with favorable stability for biophotonics applications.
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Affiliation(s)
- Anna Gonzàlez-Rosell
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
| | - Sami Malola
- Departments of Chemistry and Physics, Nanoscience Center, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Rweetuparna Guha
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
| | - Nery R Arevalos
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
| | - María Francisca Matus
- Departments of Chemistry and Physics, Nanoscience Center, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Meghen E Goulet
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Esa Haapaniemi
- Department of Chemistry, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Benjamin B Katz
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Tom Vosch
- Nanoscience Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark
| | - 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
| | - Hannu Häkkinen
- Departments of Chemistry and Physics, Nanoscience Center, University of Jyväskylä, Jyväskylä 40014, Finland
| | - 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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7
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Mastracco P, Gonzàlez-Rosell A, Evans J, Bogdanov P, Copp SM. Chemistry-Informed Machine Learning Enables Discovery of DNA-Stabilized Silver Nanoclusters with Near-Infrared Fluorescence. ACS NANO 2022; 16:16322-16331. [PMID: 36124941 PMCID: PMC9620400 DOI: 10.1021/acsnano.2c05390] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
DNA can stabilize silver nanoclusters (AgN-DNAs) whose atomic sizes and diverse fluorescence colors are selected by nucleobase sequence. These programmable nanoclusters hold promise for sensing, bioimaging, and nanophononics. However, DNA's vast sequence space challenges the design and discovery of AgN-DNAs with tailored properties. In particular, AgN-DNAs with bright near-infrared luminescence above 800 nm remain rare, placing limits on their applications for bioimaging in the tissue transparency windows. Here, we present a design method for near-infrared emissive AgN-DNAs. By combining high-throughput experimentation and machine learning with fundamental information from AgN-DNA crystal structures, we distill the salient DNA sequence features that determine AgN-DNA color, for the entire known spectral range of these nanoclusters. A succinct set of nucleobase staple features are predictive of AgN-DNA color. By representing DNA sequences in terms of these motifs, our machine learning models increase the design success for near-infrared emissive AgN-DNAs by 12.3 times as compared to training data, nearly doubling the number of known AgN-DNAs with bright near-infrared luminescence above 800 nm. These results demonstrate how incorporating known structure-property relationships into machine learning models can enhance materials study and design, even for sparse and imbalanced training data.
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Affiliation(s)
- Peter Mastracco
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Anna Gonzàlez-Rosell
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Joshua Evans
- Chaffey
Community College, Rancho
Cucamonga, California 91737, United States
| | - Petko Bogdanov
- Department
of Computer Science, University at Albany-SUNY, Albany, New York 12222, United States
| | - 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
- Email
for S.M.C.:
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8
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Gonzàlez-Rosell A, Guha R, Cerretani C, Rück V, Liisberg MB, Katz BB, Vosch T, Copp SM. DNA Stabilizes Eight-Electron Superatom Silver Nanoclusters with Broadband Downconversion and Microsecond-Lived Luminescence. J Phys Chem Lett 2022; 13:8305-8311. [PMID: 36037464 PMCID: PMC9465679 DOI: 10.1021/acs.jpclett.2c02207] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/26/2022] [Indexed: 05/25/2023]
Abstract
DNA oligomers are known to serve as stabilizing ligands for silver nanoclusters (AgN-DNAs) with rod-like nanocluster geometries and nanosecond-lived fluorescence. Here, we report two AgN-DNAs that possess distinctly different structural properties and are the first to exhibit only microsecond-lived luminescence. These emitters are characterized by significant broadband downconversion from the ultraviolet/visible to the near-infrared region. Circular dichroism spectroscopy shows that the structures of these two AgN-DNAs differ significantly from previously reported AgN-DNAs. We find that these nanoclusters contain eight valence electrons, making them the first reported DNA-stabilized luminescent quasi-spherical superatoms. This work demonstrates the important role that nanocluster composition and geometry play in dictating luminescence properties of AgN-DNAs and significantly expands the space of structure-property relations that can be achieved for AgN-DNAs.
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Affiliation(s)
- Anna Gonzàlez-Rosell
- 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
| | - Cecilia Cerretani
- Nanoscience
Center and Department of Chemistry, University
of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Vanessa Rück
- Nanoscience
Center and Department of Chemistry, University
of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Mikkel B. Liisberg
- Nanoscience
Center and Department of Chemistry, University
of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Benjamin B. Katz
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Tom Vosch
- Nanoscience
Center and Department of Chemistry, University
of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - 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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9
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Nagda R, Park S, Jung IL, Nam K, Yadavalli HC, Kim YM, Yang K, Kang J, Thulstrup PW, Bjerrum MJ, Cho M, Kim TH, Roh YH, Shah P, Yang SW. Silver Nanoclusters Serve as Fluorescent Rivets Linking Hoogsteen Triplex DNA and Hairpin-Loop DNA Structures. ACS NANO 2022; 16:13211-13222. [PMID: 35952305 DOI: 10.1021/acsnano.2c06631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Greater understanding of the mutual influence between DNA and the associated nanomaterial on the properties of each other can provide alternative strategies for designing and developing DNA nanomachines. DNA secondary structures are essential for encapsulating highly emissive silver nanoclusters (DNA/AgNCs). Likewise, AgNCs stabilize secondary DNA structures, such as hairpin DNA, duplex DNA, and parallel-motif DNA triplex. In this study, we found that the fluorescence of AgNCs encapsulated within a Hoogsteen triplex DNA structure can be turned on and off in response to pH changes. We also show that AgNCs can act as nanoscale rivets, linking two functionally distinctive DNA nanostructures. For instance, we found that a Hoogsteen triplex DNA structure with a seven-cytosine loop encapsulates red fluorescent AgNCs. The red fluorescence faded under alkaline conditions, whereas the fluorescence was restored in a near-neutral environment. Hairpin DNA and random DNA structures did not exhibit this pH-dependent AgNCs fluorescence. A fluorescence lifetime measurement and a small-angle X-ray scattering analysis showed that the triplex DNA-encapsulated AgNCs were photophysically convertible between bright and dark states. An in-gel electrophoresis analysis indicated that bright and dark convertibility depended on the AgNCs-riveted dimerization of the triplex DNAs. Moreover, we found that AgNCs rivet the triplex DNA and hairpin DNA to form a heterodimer, emitting orange fluorescence. Our findings suggest that AgNCs between two cytosine-rich loops can be used as nanorivets in designing noncanonical DNA origami beyond Watson-Crick base pairing.
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Affiliation(s)
- Riddhi Nagda
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sooyeon Park
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Il Lae Jung
- Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, Daejeon 34057, Korea
| | - Keonwook Nam
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hari Chandana Yadavalli
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Young Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Kyungjik Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jooyoun Kang
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea
| | | | | | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Tae-Hwan Kim
- Department of Quantum System Engineering, Jeonbuk National University, Jeonju 54896, Korea
| | - Young Hoon Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Pratik Shah
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
- Department of Science and Environment, Roskilde University, Roskilde 4000, Denmark
| | - Seong Wook Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
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10
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Wu Q, Liu C, Cui C, Li L, Yang L, Liu Y, Safari Yazd H, Xu S, Li X, Chen Z, Tan W. Plasmon Coupling in DNA-Assembled Silver Nanoclusters. J Am Chem Soc 2021; 143:14573-14580. [PMID: 34464111 DOI: 10.1021/jacs.1c04949] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quantum-size metal clusters with multiple delocalized electrons could support collective plasmon excitation, and thus, theoretically, coupling of plasmons in the few-atom limit might exist between assembled metal clusters, while currently few experimental observations about this phenomenon have been reported. Here we examined the optical absorption of DNA-templated Ag nanoclusters (DNA-AgNCs) assembled through DNA hybridization and found their absorption peaks were sensitive to the assembled distances, which share common characteristics with classical plasmon coupling. Dipolar charge distribution, multiple transition contributed optical absorption, and strongly enhanced electric field simulated by time-dependent density functional theory (TDDFT) indicated the origin of the absorption of individual DNA-AgNCs is a plasmon. The consistency of the peak-shifting trend between experimental and simulation results for assembled DNA-AgNCs suggested the possible presence of plasmon coupling. Our data imply the possibility for quantum-size structures to support plasmon coupling and also show that DNA-AgNCs possess the potential to be promising materials for construction of plasmon-coupling devices with ultrasmall size, site-specific and stoichiometric binding abilities, and biocompatibility.
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Affiliation(s)
- Qiong Wu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Chengcheng Liu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Cheng Cui
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Long Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Lu Yang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yuan Liu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Hoda Safari Yazd
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Shujuan Xu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Xiang Li
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Zhuo Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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11
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Rück V, Cerretani C, Neacşu VA, Liisberg MB, Vosch T. Observation of microsecond luminescence while studying two DNA-stabilized silver nanoclusters emitting in the 800-900 nm range. Phys Chem Chem Phys 2021; 23:13483-13489. [PMID: 34109959 DOI: 10.1039/d1cp01731d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We investigated two DNA-stabilized silver nanoclusters (DNA-AgNCs) that show multiple absorption features in the visible region, and emit around 811 nm (DNA811-AgNC) and 841 nm (DNA841-AgNC). Both DNA-AgNCs have large Stokes shifts and can be efficiently excited with red light. A comparison with the commercially available Atto740 yielded fluorescence quantum yields in the same order of magnitude, but a higher photon output above 800 nm since both DNA-AgNCs are more red-shifted. The study of both DNA-AgNCs also revealed previously unobserved photophysical behavior for this class of emitters. The fluorescence quantum yield and decay time of DNA841-AgNC can be increased upon consecutive heating/cooling cycles. DNA811-AgNC has an additional absorption band around 470 nm, which is parallel in orientation to the lowest energy transition at 640 nm. Furthermore, we observed for the first time a DNA-AgNC population (as part of the DNA811-AgNC sample) with green and near-infrared emissive states with nanosecond and microsecond decay times, respectively. A similar dual emissive DNA-AgNC stabilized by a different 10-base DNA strand is also reported in the manuscript. These two examples highlight the need to investigate the presence of red-shifted microsecond emission for this class of emitters.
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Affiliation(s)
- Vanessa Rück
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Cecilia Cerretani
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Vlad A Neacşu
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Mikkel B Liisberg
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Tom Vosch
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
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12
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Gonzàlez-Rosell A, Cerretani C, Mastracco P, Vosch T, Copp SM. Structure and luminescence of DNA-templated silver clusters. NANOSCALE ADVANCES 2021; 3:1230-1260. [PMID: 36132866 PMCID: PMC9417461 DOI: 10.1039/d0na01005g] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/21/2021] [Indexed: 05/05/2023]
Abstract
DNA serves as a versatile template for few-atom silver clusters and their organized self-assembly. These clusters possess unique structural and photophysical properties that are programmed into the DNA template sequence, resulting in a rich palette of fluorophores which hold promise as chemical and biomolecular sensors, biolabels, and nanophotonic elements. Here, we review recent advances in the fundamental understanding of DNA-templated silver clusters (Ag N -DNAs), including the role played by the silver-mediated DNA complexes which are synthetic precursors to Ag N -DNAs, structure-property relations of Ag N -DNAs, and the excited state dynamics leading to fluorescence in these clusters. We also summarize the current understanding of how DNA sequence selects the properties of Ag N -DNAs and how sequence can be harnessed for informed design and for ordered multi-cluster assembly. To catalyze future research, we end with a discussion of several opportunities and challenges, both fundamental and applied, for the Ag N -DNA research community. A comprehensive fundamental understanding of this class of metal cluster fluorophores can provide the basis for rational design and for advancement of their applications in fluorescence-based sensing, biosciences, nanophotonics, and catalysis.
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Affiliation(s)
- Anna Gonzàlez-Rosell
- Department of Materials Science and Engineering, University of California Irvine California 92697-2585 USA
| | - Cecilia Cerretani
- Nanoscience Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5 2100 Copenhagen Denmark
| | - Peter Mastracco
- Department of Materials Science and Engineering, University of California Irvine California 92697-2585 USA
| | - Tom Vosch
- Nanoscience Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5 2100 Copenhagen Denmark
| | - Stacy M Copp
- Department of Materials Science and Engineering, University of California Irvine California 92697-2585 USA
- Department of Physics and Astronomy, University of California Irvine California 92697-4575 USA
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13
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Copp SM, Gonzàlez-Rosell A. Large-scale investigation of the effects of nucleobase sequence on fluorescence excitation and Stokes shifts of DNA-stabilized silver clusters. NANOSCALE 2021; 13:4602-4613. [PMID: 33605954 PMCID: PMC8043073 DOI: 10.1039/d0nr08300c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
DNA-stabilized silver clusters (AgN-DNAs) exhibit diverse sequence-programmed fluorescence, making these tunable nanoclusters promising sensors and bioimaging probes. Recent advances in the understanding of AgN-DNA structures and optical properties have largely relied on detailed characterization of single species isolated by chromatography. Because most AgN-DNAs are unstable under chromatography, such studies do not fully capture the diversity of these clusters. As an alternative method, we use high-throughput synthesis and spectroscopy to measure steady state Stokes shifts of hundreds of AgN-DNAs. Steady state Stokes shift is of interest because its magnitude is determined by energy relaxation processes which may be sensitive to specific cluster geometry, attachment to the DNA template, and structural engagement of solvent molecules. We identify 305 AgN-DNA samples with single-peaked emission and excitation spectra, a characteristic of pure solutions and single emitters, which thus likely contain a dominant emissive AgN-DNA species. Steady state Stokes shifts of these samples vary widely, are in agreement with values reported for purified clusters, and are several times larger than for typical organic dyes. We then examine how DNA sequence selects AgN-DNA excitation energies and Stokes shifts, comment on possible mechanisms for energy relaxation processes in AgN-DNAs, and discuss how differences in AgN-DNA structure and DNA conformation may result in the wide distribution of optical properties observed here. These results may aid computational studies seeking to understand the fluorescence process in AgN-DNAs and the relations of this process to AgN-DNA structure.
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Affiliation(s)
- Stacy M Copp
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697-2585, USA. and Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA and Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-2580, USA
| | - Anna Gonzàlez-Rosell
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697-2585, USA.
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14
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Jabed MA, Dandu N, Tretiak S, Kilina S. Passivating Nucleobases Bring Charge Transfer Character to Optically Active Transitions in Small Silver Nanoclusters. J Phys Chem A 2020; 124:8931-8942. [PMID: 33079551 DOI: 10.1021/acs.jpca.0c06974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-wrapped silver nanoclusters (DNA-AgNCs) are known for their efficient luminescence. However, their emission is highly sensitive to the DNA sequence, the cluster size, and its charge state. To get better insights into photophysics of these hybrid systems, simulations based on density functional theory (DFT) are performed. Our calculations elucidate the effect of the structural conformations, charges, solvent polarity, and passivating bases on optical spectra of DNA-AgNCs containing five and six Ag atoms. It is found that inclusion of water in calculations as a polar solvent media results in stabilization of nonplanar conformations of base-passivated clusters, while their planar conformations are more stable in vacuum, similar to the bare Ag5 and Ag6 clusters. Cytosines and guanines interact with the cluster twice stronger than thymines, due to their larger dipole moments. In addition to the base-cluster interactions, hydrogen bonds between bases notably contribute to the structure stabilization. While the relative intensity, line width, and the energy of absorption peaks are slightly changing depending on the cluster charge, conformations, and base types, the overall spectral shape with five well-resolved bands at 2.5-5.5 eV is consistent for all structures. Independent of the passivating bases and the cluster size and charge, the low energy optical transitions at 2.5-3.5 eV exhibit a metal to ligand charge transfer (MLCT) character with the main contribution emerging from Ag-core to the bases. Cytosines facilitate the MLCT character to a larger degree comparing to the other bases. However, the doublet transitions in clusters with the open shell electronic structure (Ag5 and Ag6+) result in appearance of additional red-shifted (<2.5 eV) and optically weak band with negligible MLCT character. The passivated clusters with the closed shell electronic structure (Ag5+ and Ag6) exhibit higher optical intensity of their lowest transitions with much higher MLCT contribution, thus having better potential for emission, than their open shell counterparts.
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Affiliation(s)
- Mohammed A Jabed
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Naveen Dandu
- Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Sergei Tretiak
- Center for Nonlinear Studies, Center for Integrated Nanotechnologies, and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Svetlana Kilina
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
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15
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Yourston LE, Krasnoslobodtsev AV. Micro RNA Sensing with Green Emitting Silver Nanoclusters. Molecules 2020; 25:E3026. [PMID: 32630693 PMCID: PMC7411700 DOI: 10.3390/molecules25133026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022] Open
Abstract
Micro RNA (miR) are regulatory non-coding RNA molecules, which contain a small number of nucleotides ~18-28 nt. There are many various miR sequences found in plants and animals that perform important functions in developmental, metabolic, and disease processes. miRs can bind to complementary sequences within mRNA molecules thus silencing mRNA. Other functions include cardiovascular and neural development, stem cell differentiation, apoptosis, and tumors. In tumors, some miRs can function as oncogenes, others as tumor suppressors. Levels of certain miR molecules reflect cellular events, both normal and pathological. Therefore, miR molecules can be used as biomarkers for disease diagnosis and prognosis. One of these promising molecules is miR-21, which can serve as a biomarker with high potential for early diagnosis of various types of cancer. Here, we present a novel design of miR detection and demonstrate its efficacy on miR-21. The design employs emissive properties of DNA-silver nanoclusters (DNA/AgNC). The detection probe is designed as a hairpin DNA structure with one side of the stem complimentary to miR molecule. The binding of target miR-21 opens the hairpin structure, dramatically modulating emissive properties of AgNC hosted by the C12 loop of the hairpin. "Red" fluorescence of the DNA/AgNC probe is diminished in the presence of the target miR. At the same time, "green" fluorescence is activated and its intensity increases several-fold. The increase in intensity of "green" fluorescence is strong enough to detect the presence of miR-21. The intensity change follows the concentration dependence of the target miR present in a sample, which provides the basis of developing a new, simple probe for miR detection. The detection strategy is specific, as demonstrated using the response of the DNA/AgNC probe towards the scrambled miR-21 sequence and miR-25 molecule. Additionally, the design reported here is very sensitive with an estimated detection limit at ~1 picomole of miR-21.
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16
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Xu S, Jiang L, Wang J, Gao Y, Luo X. Ratiometric Multicolor Analysis of Intracellular MicroRNA Using a Chain Hybrid Substitution-Triggered Self-Assembly of Silver Nanocluster-Based Label-Free Sensing Platform. ACS APPLIED MATERIALS & INTERFACES 2020; 12:373-379. [PMID: 31840494 DOI: 10.1021/acsami.9b19709] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A simple and label-free sensing platform with low background based on the chain-displacement triggered self-assembly of Ag NCs was developed for ratiometric visual analysis of intracellular miRNA-21. Based on this sensitively ratiometric sensing approach, a picomole limit detection for miRNA-21 can be obtained. Most importantly, compared with the traditional single base mismatch detection method, our proposed method can realize single base mismatch detection according to the remarkable fluorescence color conversion, rather than simple fluorescence intensity change, which can obviously improve the accuracy and reliability. In addition, successful multicolor real-time monitoring of intracellular miRNA-21 makes the probe a potential candidate for miRNA-21 inhibiting drug screening. Furthermore, MCF-7, HeLa, and normal L02 cells can also be visually differentiated according to the fluorescence color by using the label-free sensing platform, showing its potential prospect in target visual analysis.
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Affiliation(s)
- Shenghao Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
| | - Liping Jiang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
| | - Jun Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
| | - Yuhuan Gao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
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17
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Blevins MS, Kim D, Crittenden CM, Hong S, Yeh HC, Petty JT, Brodbelt JS. Footprints of Nanoscale DNA-Silver Cluster Chromophores via Activated-Electron Photodetachment Mass Spectrometry. ACS NANO 2019; 13:14070-14079. [PMID: 31755695 PMCID: PMC7047740 DOI: 10.1021/acsnano.9b06470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
DNA-templated silver clusters (AgC) are fluorescent probes and biosensors whose electronic spectra can be tuned by their DNA hosts. However, the underlying rules that relate DNA sequence and structure to DNA-AgC fluorescence and photophysics are largely empirical. Here, we employ 193 nm activated electron photodetachment (a-EPD) mass spectrometry as a hybrid MS3 approach to gain structural insight into these nanoscale chromophores. Two DNA-AgC systems are investigated with a 20 nt single-stranded DNA (ssDNA) and a 28 nt hybrid hairpin/single-stranded DNA (hpDNA). Both oligonucleotides template Ag10 clusters, but the two complexes are distinct chromophores: the former has a violet absorption at 400 nm with no observable emission, while the latter has a blue-green absorption at 490 nm with strong green emission at 550 nm. Via identification of both apo and holo (AgC-containing) sequence ions generated upon a-EPD and mapping areas of sequence dropout, specific DNA regions that encapsulate the AgC are assigned and attributed to the coordination with the DNA nucleobases. These a-EPD footprints are distinct for the two complexes. The ssDNA contacts the cluster via four nucleobases (CCTT) in the central region of the strand, whereas the hpDNA coordinates the cluster via 13 nucleobases (TTCCCGCCTTTTG) in the double-stranded region of the hairpin. This difference is consistent with prior X-ray scattering spectra and suggests that the clusters can adapt to different DNA hosts. More importantly, the a-EPD footprints directly identify the nucleobases that are in direct contact with the AgC. As these contacting nucleobases can tune the electronic structures of the Ag core and protect the AgC from collisional quenching in solution, understanding the DNA-silver contacts within these complexes will facilitate future biosensor designs.
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Affiliation(s)
- Molly S. Blevins
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dahye Kim
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | | | - Soonwoo Hong
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
- Texas Materials Institute, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jeffrey T. Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Corresponding Author:.
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18
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DNA-Silver Nanocluster Binary Probes for Ratiometric Fluorescent Detection of HPV-related DNA. Chem Res Chin Univ 2019. [DOI: 10.1007/s40242-019-9085-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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19
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Cerretani C, Vosch T. Switchable Dual-Emissive DNA-Stabilized Silver Nanoclusters. ACS OMEGA 2019; 4:7895-7902. [PMID: 31459877 PMCID: PMC6693819 DOI: 10.1021/acsomega.9b00614] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/19/2019] [Indexed: 05/10/2023]
Abstract
We investigated an ss-DNA sequence that can stabilize a red- and a green-emissive silver nanocluster (DNA-AgNC). These two emitters can convert between each other in a reversible way. The change from red- to green-emitting DNA-AgNCs can be triggered by the addition of H2O2, while the opposite conversion can be achieved by the addition of NaBH4. Besides demonstrating the switching between red- and green-emissive DNA-AgNCs and determining the recoverability, we fully characterized the photophysical properties, such as steady-state emission, quantum yield, fluorescence lifetime, and anisotropy of the two emissive species. Understanding the mechanism behind the remarkable conversion between the two emitters could lead to the development of a new range of DNA-AgNC-based ratiometric sensors.
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20
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Mistry L, El-Zubir O, Dura G, Clegg W, Waddell PG, Pope T, Hofer WA, Wright NG, Horrocks BR, Houlton A. Addressing the properties of "Metallo-DNA" with a Ag(i)-mediated supramolecular duplex. Chem Sci 2019; 10:3186-3195. [PMID: 30996900 PMCID: PMC6429620 DOI: 10.1039/c8sc05103h] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/08/2019] [Indexed: 01/04/2023] Open
Abstract
The silver-nucleoside complex [Ag(i)-(N3-cytidine)2]+, 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA.
The silver-nucleoside complex [Ag(i)-(N3-cytidine)2], 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA. A combination of complementary hydrogen-bonding, hydrophobic and argentophilic interactions drive the formation of a double-helix with a continuous silver core. Electrical measurements on 1 show that despite having Ag···Ag distances within <5% of the metallic radii, the material is electrically insulating. This is due to the electronic structure which features a filled valence band, an empty conduction band dominated by the ligand, and a band gap of 2.5 eV. Hence, as-prepared, such Ag(i)-DNA systems should not be considered molecular nanowires but, at best, proto-wires. The structural features seen in 1 are essentially retained in the corresponding organogel which exhibits thixotropic self-healing that can be attributed to the reversible nature of the intermolecular interactions. Photo-reduced samples of the gel exhibit luminescence confirming that these poly-cytidine sequences appropriately pre-configure silver ions for the formation of quantum-confined metal clusters in line with contemporary views on DNA-templated clusters. Microscopy data reveals the resulting metal cluster/particles are approximately spherical and crystalline with lattice spacing (111) similar to bulk Ag.
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Affiliation(s)
- Liam Mistry
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
| | - Osama El-Zubir
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
| | - Gema Dura
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
| | - William Clegg
- Chemistry , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Paul G Waddell
- Chemistry , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Thomas Pope
- Chemistry , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Werner A Hofer
- Chemistry , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Nick G Wright
- School of Engineering , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Benjamin R Horrocks
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
| | - Andrew Houlton
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
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21
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DNA-templated gold nanocluster as a novel fluorometric sensor for glutathione determination. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2018.10.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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22
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Gafner SL, Bashkova DA, Gafner YY. Temperature-induced structure evolution of Ag nanoparticles. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1757-899x/447/1/012056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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23
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Kang H, Buchman JT, Rodriguez RS, Ring HL, He J, Bantz KC, Haynes CL. Stabilization of Silver and Gold Nanoparticles: Preservation and Improvement of Plasmonic Functionalities. Chem Rev 2018; 119:664-699. [DOI: 10.1021/acs.chemrev.8b00341] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Hyunho Kang
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Joseph T. Buchman
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Rebeca S. Rodriguez
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Hattie L. Ring
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Jiayi He
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Kyle C. Bantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Christy L. Haynes
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
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24
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Chen X, Makkonen E, Golze D, Lopez-Acevedo O. Silver-Stabilized Guanine Duplex: Structural and Optical Properties. J Phys Chem Lett 2018; 9:4789-4794. [PMID: 30079734 DOI: 10.1021/acs.jpclett.8b01908] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Recent experimental duplexes of DNA stabilized by Ag cations, pairing homostrands of guanine-guanine, cytosine-cytosine, adenine-thymine, and thymine-thymine, display much higher stability than the Watson-Crick paired DNA duplexes; these broaden the range of applications for DNA nanotechnology. Here we focus on silver-stabilized guanine duplexes in water. Using hybrid quantum mechanics/molecular mechanics simulations, we propose an atomic structure for the Ag+-mediated guanine duplex with two nucleobases per strand, G2-Ag2+-G2. We then compare experimental and time-dependent density functional theory-simulated electronic circular dichroism (ECD) spectra to validate our results. Both experimental and simulated ECD share two negative peaks around 220 and 280 nm, with no positive signal in the measured wavelength range. We found that the left- or right-handed disposition of bases in the structure has a decisive effect on the signs of the ECD. We conclude that G2-Ag2+-G2 is left-hand-oriented, and extrapolation of this orientation to longer strands gives rise to a left-hand-oriented parallel helix stabilized by interplanar H bonds.
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Affiliation(s)
- Xi Chen
- Department of Applied Physics , Aalto University , Otakaari 1 , FI-02150 Espoo , Finland
| | - Esko Makkonen
- Department of Applied Physics , Aalto University , Otakaari 1 , FI-02150 Espoo , Finland
| | - Dorothea Golze
- Department of Applied Physics , Aalto University , Otakaari 1 , FI-02150 Espoo , Finland
- Department of Electrical Engineering and Automation , Aalto University , P.O. Box 13500, 00076 Aalto , Finland
| | - Olga Lopez-Acevedo
- Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales , Universidad de Antioquia UdeA ; Calle 70 No. 52-21 , 050010 Medellín , Colombia
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25
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Bogh SA, Carro-Temboury MR, Cerretani C, Swasey SM, Copp SM, Gwinn EG, Vosch T. Unusually large Stokes shift for a near-infrared emitting DNA-stabilized silver nanocluster. Methods Appl Fluoresc 2018; 6:024004. [DOI: 10.1088/2050-6120/aaa8bc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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26
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Taccone MI, Berdakin M, Pino GA, Sánchez CG. Optical properties and charge distribution in rod-shape DNA–silver cluster emitters. Phys Chem Chem Phys 2018; 20:22510-22516. [DOI: 10.1039/c8cp03895c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our results show that the experimental optical properties of DNA–Agn are theoretically reproduced by considering the zigzag rod-shape structure of the metal cluster.
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Affiliation(s)
- Martín I. Taccone
- Departamento de Fisicoquímica
- Fac. de Ciencias Químicas
- Universidad Nacional de Córdoba
- Ciudad Universitaria
- X5000HUA Córdoba
| | - Matías Berdakin
- Departamento de Física
- Facultad de Ciencias Físicas y Matemáticas
- Universidad de Chile
- Santiago
- Chile
| | - Gustavo A. Pino
- Departamento de Fisicoquímica
- Fac. de Ciencias Químicas
- Universidad Nacional de Córdoba
- Ciudad Universitaria
- X5000HUA Córdoba
| | - Cristián G. Sánchez
- INFIQC (CONICET)
- Ciudad Universitaria
- 5000 Córdoba
- Argentina
- Departamento de Química Teórica y Computacional
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27
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Zhang X, Qian Y, Ma X, Xia M, Li S, Zhang Y. Thiolated DNA-templated silver nanoclusters with strong fluorescence emission and a long shelf-life. NANOSCALE 2017; 10:76-81. [PMID: 29210418 DOI: 10.1039/c7nr06358j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thiolated DNA (DNA-SH) was employed as a template in the synthesis and stabilization of AgNCs (DNA-SH-AgNCs). Resulting from the synergistic protective effect of specific Ag+-DNA interactions and Ag-S bonding, DNA-SH-AgNCs exhibited high quantum yields and resistance to oxidation.
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Affiliation(s)
- Xiaohong Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China.
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28
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Bogh S, Cerretani C, Kacenauskaite L, Carro-Temboury MR, Vosch T. Excited-State Relaxation and Förster Resonance Energy Transfer in an Organic Fluorophore/Silver Nanocluster Dyad. ACS OMEGA 2017; 2:4657-4664. [PMID: 31457751 PMCID: PMC6641894 DOI: 10.1021/acsomega.7b00582] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/03/2017] [Indexed: 05/21/2023]
Abstract
A single-stranded DNA-based (ssDNA) dyad was constructed comprising 15 silver atoms stabilized by a ssDNA scaffold (DNA-AgNC) and an Alexa 546 fluorophore bound to the 5' end. The Alexa 546 was chosen to function as a Förster resonance energy transfer (FRET) donor for the AgNC. Time-correlated single photon counting (TCSPC) experiments allowed unraveling the excited-state relaxation processes of the purified DNA-AgNC-only system. The TCSPC results revealed slow relaxation dynamics and a red shift of the emission spectrum during the excited-state lifetime. The results from the model systems were needed to understand the more complicated decay pathways present in the collected high-performance liquid chromatography fraction, which contained the dyad (37% of the emissive population). In the dyad system, the FRET efficiency between donor and acceptor was determined to be 94% using TCSPC, yielding a center-to-center distance of 4.6 nm. To date, only limited structural information on DNA-AgNCs is available and the use of TCSPC and FRET can provide information on the center-to-center distance between chromophores and provide positional information in nanostructures composed of AgNCs.
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Affiliation(s)
| | | | - Laura Kacenauskaite
- Nanoscience Center and Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Miguel R. Carro-Temboury
- Nanoscience Center and Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Tom Vosch
- Nanoscience Center and Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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29
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Zhou W, Dong S. A new AgNC fluorescence regulation mechanism caused by coiled DNA and its applications in constructing molecular beacons with low background and large signal enhancement. Chem Commun (Camb) 2017; 53:12290-12293. [DOI: 10.1039/c7cc06872g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A AgNC fluorescence interference strategy caused by a coiled DNA sequence (A) and its applications in target DNA detection (B).
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Affiliation(s)
- Weijun Zhou
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
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30
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Cerretani C, Carro-Temboury MR, Krause S, Bogh SA, Vosch T. Temperature dependent excited state relaxation of a red emitting DNA-templated silver nanocluster. Chem Commun (Camb) 2017; 53:12556-12559. [DOI: 10.1039/c7cc06785b] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The average fluorescence decay time of DNA-stabilized silver nanoclusters is temperature dependent and could find applications in nanothermometry.
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Affiliation(s)
- Cecilia Cerretani
- Nanoscience Center and Department of Chemistry
- University of Copenhagen
- Universitetsparken 5
- 2100 Copenhagen
- Denmark
| | - Miguel R. Carro-Temboury
- Nanoscience Center and Department of Chemistry
- University of Copenhagen
- Universitetsparken 5
- 2100 Copenhagen
- Denmark
| | - Stefan Krause
- Nanoscience Center and Department of Chemistry
- University of Copenhagen
- Universitetsparken 5
- 2100 Copenhagen
- Denmark
| | - Sidsel Ammitzbøll Bogh
- Nanoscience Center and Department of Chemistry
- University of Copenhagen
- Universitetsparken 5
- 2100 Copenhagen
- Denmark
| | - Tom Vosch
- Nanoscience Center and Department of Chemistry
- University of Copenhagen
- Universitetsparken 5
- 2100 Copenhagen
- Denmark
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31
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Bossert N, de Bruin D, Götz M, Bouwmeester D, Heinrich D. Fluorescence-tunable Ag-DNA biosensor with tailored cytotoxicity for live-cell applications. Sci Rep 2016; 6:37897. [PMID: 27901090 PMCID: PMC5129012 DOI: 10.1038/srep37897] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/01/2016] [Indexed: 01/08/2023] Open
Abstract
DNA-stabilized silver clusters (Ag-DNA) show excellent promise as a multi-functional nanoagent for molecular investigations in living cells. The unique properties of these fluorescent nanomaterials allow for intracellular optical sensors with tunable cytotoxicity based on simple modifications of the DNA sequences. Three Ag-DNA nanoagent designs are investigated, exhibiting optical responses to the intracellular environments and sensing-capability of ions, functional inside living cells. Their sequence-dependent fluorescence responses inside living cells include (1) a strong splitting of the fluorescence peak for a DNA hairpin construct, (2) an excitation and emission shift of up to 120 nm for a single-stranded DNA construct, and (3) a sequence robust in fluorescence properties. Additionally, the cytotoxicity of these Ag-DNA constructs is tunable, ranging from highly cytotoxic to biocompatible Ag-DNA, independent of their optical sensing capability. Thus, Ag-DNA represents a versatile live-cell nanoagent addressable towards anti-cancer, patient-specific and anti-bacterial applications.
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Affiliation(s)
- Nelli Bossert
- Leiden Institute of Physics, LION, Huygens-Kamerlingh Onnes Laboratory, Leiden University, The Netherlands
| | - Donny de Bruin
- Leiden Institute of Physics, LION, Huygens-Kamerlingh Onnes Laboratory, Leiden University, The Netherlands
| | - Maria Götz
- Fraunhofer-Institut for Silicate Research ISC, Würzburg, Germany
- Fakultaet fuer Chemie und Pharmazie, Julius-Maximilians-Universitaet Würzburg, Germany
| | - Dirk Bouwmeester
- Leiden Institute of Physics, LION, Huygens-Kamerlingh Onnes Laboratory, Leiden University, The Netherlands
- Physics Department and California Nanosystems Institute UCSB, Santa Barbara, USA
| | - Doris Heinrich
- Leiden Institute of Physics, LION, Huygens-Kamerlingh Onnes Laboratory, Leiden University, The Netherlands
- Fraunhofer-Institut for Silicate Research ISC, Würzburg, Germany
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32
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Ramazanov RR, Sych TS, Reveguk ZV, Maksimov DA, Vdovichev AA, Kononov AI. Ag-DNA Emitter: Metal Nanorod or Supramolecular Complex? J Phys Chem Lett 2016; 7:3560-6. [PMID: 27564452 DOI: 10.1021/acs.jpclett.6b01672] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ligand-stabilized luminescent metal clusters, in particular, DNA-based Ag clusters, are now employed in a host of applications such as sensing and bioimaging. Despite their utility, the nature of their excited states as well as detailed structures of the luminescent metal-ligand complexes remain poorly understood. We apply a new joint experimental and theoretical approach based on QM/MM-MD simulations of the fluorescence excitation spectra for three Ag clusters synthesized on a 12-mer DNA. Contrary to a previously proposed "rod-like" model, our results show that (1) three to four Ag atoms suffice to form a partially oxidized nanocluster emitting in visible range; (2) charge transfer from Ag cluster to DNA contributes to the excited states of the complexes; and (3) excitation spectra of the clusters are strongly affected by the bonding of Ag atoms to DNA bases. The presented approach can also provide a practical way to determine the structure and properties of other luminescent metal clusters.
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Affiliation(s)
- Ruslan R Ramazanov
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University , 199034 St. Petersburg, Russia
| | - Tomash S Sych
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University , 199034 St. Petersburg, Russia
| | - Zakhar V Reveguk
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University , 199034 St. Petersburg, Russia
| | - Dmitriy A Maksimov
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University , 199034 St. Petersburg, Russia
| | - Artem A Vdovichev
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University , 199034 St. Petersburg, Russia
| | - Alexei I Kononov
- Department of Molecular Biophysics and Polymer Physics, St. Petersburg State University , 199034 St. Petersburg, Russia
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