1
|
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.
Collapse
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
| |
Collapse
|
2
|
Liisberg MB, Vosch T. Fluorescence Screening of DNA-AgNCs with Pulsed White Light Excitation. NANO LETTERS 2024; 24:7987-7991. [PMID: 38905483 PMCID: PMC11229690 DOI: 10.1021/acs.nanolett.4c01561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
DNA-stabilized silver nanoclusters (DNA-AgNCs) are a class of fluorophores with interesting photophysical properties dominated by the choice of DNA sequence. Screening methods with ultraviolet excitation and steady state well plate readers have previously been used for deepening the understanding between DNA sequence and emission color of the resulting DNA-AgNCs. Here, we present a new method for screening DNA-AgNCs by using pulsed white light excitation (λex ≈ 490-900 nm). By subtraction and time gating we are able to circumvent the dominating scatter of the white excitation light and extract both temporally and spectrally resolved emission of DNA-AgNCs over the visible to near-infrared range. Additionally, we are able to identify weak long-lived emission, which is often buried underneath the intense nanosecond fluorescence. This new approach will be useful for future screening of DNA-AgNCs (or other novel emissive materials) and aid machine-learning models by providing a richer training data set.
Collapse
Affiliation(s)
- Mikkel Baldtzer Liisberg
- 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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Gupta AK, Marshall N, Yourston L, Rolband L, Beasock D, Danai L, Skelly E, Afonin KA, Krasnoslobodtsev AV. Optical, structural, and biological properties of silver nanoclusters formed within the loop of a C-12 hairpin sequence. NANOSCALE ADVANCES 2023; 5:3500-3511. [PMID: 37383066 PMCID: PMC10295035 DOI: 10.1039/d3na00092c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023]
Abstract
Silver nanoclusters (AgNCs) are the next-generation nanomaterials representing supra-atomic structures where silver atoms are organized in a particular geometry. DNA can effectively template and stabilize these novel fluorescent AgNCs. Only a few atoms in size - the properties of nanoclusters can be tuned using only single nucleobase replacement of C-rich templating DNA sequences. A high degree of control over the structure of AgNC could greatly contribute to the ability to fine-tune the properties of silver nanoclusters. In this study, we explore the properties of AgNCs formed on a short DNA sequence with a C12 hairpin loop structure (AgNC@hpC12). We identify three types of cytosines based on their involvement in the stabilization of AgNCs. Computational and experimental results suggest an elongated cluster shape with 10 silver atoms. We found that the properties of the AgNCs depend on the overall structure and relative position of the silver atoms. The emission pattern of the AgNCs depends strongly on the charge distribution, while all silver atoms and some DNA bases are involved in optical transitions based on molecular orbital (MO) visualization. We also characterize the antibacterial properties of silver nanoclusters and propose a possible mechanism of action based on the interactions of AgNCs with molecular oxygen.
Collapse
Affiliation(s)
- Akhilesh Kumar Gupta
- Department of Physics, University of Nebraska at Omaha Omaha NE 68182 USA +1402-554-3723
| | - Nolan Marshall
- Department of Physics, University of Nebraska at Omaha Omaha NE 68182 USA +1402-554-3723
| | - Liam Yourston
- Department of Physics, University of Nebraska at Omaha Omaha NE 68182 USA +1402-554-3723
| | - Lewis Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
| | - Leyla Danai
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
| | - Elizabeth Skelly
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
| | | |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Chen J, Kumar A, Cerretani C, Vosch T, Zigmantas D, Thyrhaug E. Excited-State Dynamics in a DNA-Stabilized Ag 16 Cluster with Near-Infrared Emission. J Phys Chem Lett 2023; 14:4078-4083. [PMID: 37120843 PMCID: PMC10166082 DOI: 10.1021/acs.jpclett.3c00764] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Due to desirable optical properties, such as efficient luminescence and large Stokes shift, DNA-templated silver nanoclusters (DNA-AgNCs) have received significant attention over the past decade. Nevertheless, the excited-state dynamics of these systems are poorly understood, as studies of the processes ultimately leading to a fluorescent state are scarce. Here we investigate the early time relaxation dynamics of a 16-atom silver cluster (DNA-Ag16NC) featuring NIR emission in combination with an unusually large Stokes shift of over 5000 cm-1. We follow the photoinduced dynamics of DNA-Ag16NC on time ranges from tens of femtoseconds to nanoseconds using a combination of ultrafast optical spectroscopies, and extract a kinetic model to clarify the physical picture of the photoinduced dynamics. We expect the obtained model to contribute to guiding research efforts toward elucidating the electronic structure and dynamics of these novel objects and their potential applications in fluorescence-based labeling, imaging, and sensing.
Collapse
Affiliation(s)
- Junsheng Chen
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Ajeet Kumar
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, D-85747 Garching, Germany
| | - Cecilia Cerretani
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Tom Vosch
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Donatas Zigmantas
- Division of Chemical Physics, Lund University, Naturvetarvägen 16, 22362 Lund, Sweden
| | - Erling Thyrhaug
- Department of Chemistry and Catalysis Research Center (CRC), School of Natural Sciences, Technical University of Munich, D-85747 Garching, Germany
| |
Collapse
|
11
|
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.
Collapse
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.:
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|