1
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Yadavalli HC, Kim Y, Jung IL, Park S, Kim TH, Shin JY, Nagda R, Thulstrup PW, Bjerrum MJ, Bhang YJ, Lee PH, Yang WH, Shah P, Yang SW. Energy Transfer Between i-Motif DNA Encapsulated Silver Nanoclusters and Fluorescein Amidite Efficiently Visualizes the Redox State of Live Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401629. [PMID: 38824675 DOI: 10.1002/smll.202401629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/21/2024] [Indexed: 06/04/2024]
Abstract
The redox regulation, maintaining a balance between oxidation and reduction in living cells, is vital for cellular homeostasis, intricate signaling networks, and appropriate responses to physiological and environmental cues. Here, a novel redox sensor, based on DNA-encapsulated silver nanoclusters (DNA/AgNCs) and well-defined chemical fluorophores, effectively illustrating cellular redox states in live cells is introduced. Among various i-motif DNAs, the photophysical property of poly-cytosines (C20)-encapsulated AgNCs that sense reactive oxygen species (ROS) is adopted. However, the sensitivity of C20/AgNCs is insufficient for evaluating ROS levels in live cells. To overcome this drawback, the ROS sensing mechanism of C20/AgNCs through gel electrophoresis, mass spectrometry, and small-angle X-ray scattering is primarily defined. Then, by tethering fluorescein amidite (FAM) and Cyanine 5 (Cy5) dyes to each end of the C20/AgNCs sensor, an Energy Transfer (ET) between AgNCs and FAM is achieved, resulting in intensified green fluorescence upon ROS detection. Taken together, the FAM-C20/AgNCs-Cy5 redox sensor enables dynamic visualization of intracellular redox states, yielding insights into oxidative stress-related processes in live cells.
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Affiliation(s)
- Hari Chandana Yadavalli
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Yeolhoe Kim
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Il Lae Jung
- Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, Daejeon, 34057, Republic of Korea
| | - Sooyeon Park
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Tae-Hwan Kim
- Department of Quantum System Engineering, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Jin Young Shin
- Department of Neurology, College of Medicine, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Riddhi Nagda
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Peter Waaben Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, 2100, Denmark
| | - Morten Jannik Bjerrum
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, 2100, Denmark
| | - Yong Joo Bhang
- Xenohelix Research Institute, BT Centre 305, 56 Songdogwahak-ro Yeonsugu, Incheon, 21984, Republic of Korea
| | - Phil Hyu Lee
- Department of Neurology, College of Medicine, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Won Ho Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Pratik Shah
- 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, Republic of Korea
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2
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Hong S, Walker JN, Luong AT, Mathews J, Shields SWJ, Kuo YA, Chen YI, Nguyen TD, He Y, Nguyen AT, Ghimire ML, Kim MJ, Brodbelt JS, Yeh HC. A non-FRET DNA reporter that changes fluorescence colour upon nuclease digestion. NATURE NANOTECHNOLOGY 2024; 19:810-817. [PMID: 38351231 DOI: 10.1038/s41565-024-01612-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/15/2024] [Indexed: 06/21/2024]
Abstract
Fluorescence resonance energy transfer (FRET) reporters are commonly used in the final stages of nucleic acid amplification tests to indicate the presence of nucleic acid targets, where fluorescence is restored by nucleases that cleave the FRET reporters. However, the need for dual labelling and purification during manufacturing contributes to the high cost of FRET reporters. Here we demonstrate a low-cost silver nanocluster reporter that does not rely on FRET as the on/off switching mechanism, but rather on a cluster transformation process that leads to fluorescence color change upon nuclease digestion. Notably, a 90 nm red shift in emission is observed upon reporter cleavage, a result unattainable by a simple donor-quencher FRET reporter. Electrospray ionization-mass spectrometry results suggest that the stoichiometric change of the silver nanoclusters from Ag13 (in the intact DNA host) to Ag10 (in the fragments) is probably responsible for the emission colour change observed after reporter digestion. Our results demonstrate that DNA-templated silver nanocluster probes can be versatile reporters for detecting nuclease activities and provide insights into the interactions between nucleases and metallo-DNA nanomaterials.
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Affiliation(s)
- Soonwoo Hong
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jada N Walker
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Aaron T Luong
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jonathan Mathews
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Samuel W J Shields
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Yu-An Kuo
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Yuan-I Chen
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Trung Duc Nguyen
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Yujie He
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Anh-Thu Nguyen
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Madhav L Ghimire
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | | | - Hsin-Chih Yeh
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Texas Materials Institute, The University of Texas at Austin, Austin, TX, USA.
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3
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Tang X, Lu M, Wang J, Man S, Peng W, Ma L. Recent Advances of DNA-Templated Metal Nanoclusters for Food Safety Detection: From Synthesis, Applications, Challenges, and Beyond. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5542-5554. [PMID: 38377578 DOI: 10.1021/acs.jafc.3c09621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Food safety concerns have become a significant threat to human health and well-being, catching global attention in recent years. As a result, it is imperative to research conceptually novel biosensing and effective techniques for food matrices detection. Currently, DNA-templated metal nanoclusters (DNA-MNCs) are considered as one of the most promising nanomaterials due to their excellent properties in biosensing. While DNA-MNCs have garnered increasing interest, the reviews of design strategies, applications, and futuristic prospects for biosensing have been hardly found especially in food safety. The synthesis of DNA-MNCs and their use as biosensing materials in food contamination detection, including pathogenic bacteria, toxins, heavy metals, residues of pesticides, and others were comprehensively reviewed. In addition, we summarize the properties of DNA-MNCs briefly and discuss the challenges and future trends. The application of DNA-MNCs powered biosensing has been demonstrated and actively studied, which is a promising paradigm for food safety testing that can supplement or even replace current existing methods. Despite the challenges of difficulty regulating accurately, poor stability, low quantum yield, and difficult commercial transformation, the application prospects of DNA-MNCs biosensors are promising. This review aims to provide insights and directions for the future development of DNA-MNCs based food detection technology.
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Affiliation(s)
- Xiaoqin Tang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Minghui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiajing Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Weipan Peng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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4
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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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5
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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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6
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Yang Z, Hu L, Ning K, Wu Y, Liang J. A fluorescence sensor for thiram detection based on DNA-templated silver nanoclusters without metal ion-mediator. Food Chem 2023; 413:135428. [PMID: 36758384 DOI: 10.1016/j.foodchem.2023.135428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
In this work, we firstly found a strong competitive interaction between thiram and silver atoms of DNA-templated silver nanoclusters (DNA-AgNCs), leading to fluorescence quenching of DNA-AgNCs without additional metal ion-mediator. Furthermore, this thiram-induced fluorescence quenching phenomenon was used to develop a sensor for thiram detection. This fluorescence sensor exhibited good linearity with thiram concentration from 0.20 to 2.0 μM and 0.012-0.20 μM under optimized conditions, with a low detection limit of 0.2 μM and 0.01 μM, respectively. Moreover, this sensor showed superior selectivity towards thiram, and its practicability was verified in apples and soil. This study provides a convenient and rapid "mix and detect" approach for thiram detection within 10 min, suggesting its potential for rapid on-site evaluation of thiram in real samples.
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Affiliation(s)
- Ziyan Yang
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Lingling Hu
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Keke Ning
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yuan Wu
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Jiangong Liang
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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7
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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.
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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
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8
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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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9
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Lewis D, Setzler C, Goodwin PM, Thomas K, Branham M, Arrington CA, Petty JT. Interrupted DNA and Slow Silver Cluster Luminescence. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:10574-10584. [PMID: 37313118 PMCID: PMC10258842 DOI: 10.1021/acs.jpcc.3c01050] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/16/2023] [Indexed: 06/15/2023]
Abstract
A DNA-silver cluster conjugate is a hierarchical chromophore with a partly reduced silver core embedded within the DNA nucleobases that are covalently linked by the phosphodiester backbone. Specific sites within a polymeric DNA can be targeted to spectrally tune the silver cluster. Here, the repeated (C2A)6 strand is interrupted with a thymine, and the resulting (C2A)2-T-(C2A)4 forms only Ag106+, a chromophore with both prompt (∼1 ns) green and sustained (∼102 μs) red luminescence. Thymine is an inert placeholder that can be removed, and the two fragments (C2A)2 and (C2A)4 also produce the same Ag106+ adduct. In relation to (C2A)2T(C2A)4, the (C2A)2 + (C2A)4 pair is distinguished because the red Ag106+ luminescence is ∼6× lower, relaxes ∼30% faster, and is quenched ∼2× faster with O2. These differences suggest that a specific break in the phosphodiester backbone can regulate how a contiguous vs broken scaffold wraps and better protects its cluster adduct.
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Affiliation(s)
- David Lewis
- Department
of Chemistry, Furman University, Greenville, South Carolina 29163, United States
| | - Caleb Setzler
- Department
of Chemistry, Furman University, Greenville, South Carolina 29163, United States
| | - Peter M. Goodwin
- Center
for Integrated Nanotechnologies, Mail Stop K771, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Kirsten Thomas
- Department
of Chemistry, Furman University, Greenville, South Carolina 29163, United States
| | - Makayla Branham
- Department
of Chemistry, Furman University, Greenville, South Carolina 29163, United States
| | - Caleb A. Arrington
- Department
of Chemistry, Wofford College, Spartanburg, South Carolina 29303, United States
| | - Jeffrey T. Petty
- Department
of Chemistry, Furman University, Greenville, South Carolina 29163, United States
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10
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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: 12] [Impact Index Per Article: 12.0] [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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11
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Danai L, Rolband LA, Perdomo VA, Skelly E, Kim T, Afonin KA. Optical, structural and antibacterial properties of silver nanoparticles and DNA-templated silver nanoclusters. Nanomedicine (Lond) 2023; 18:769-782. [PMID: 37345552 PMCID: PMC10308257 DOI: 10.2217/nnm-2023-0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023] Open
Abstract
Silver nanoparticles (AgNPs) are increasingly considered for biomedical applications as drug-delivery carriers, imaging probes and antibacterial agents. Silver nanoclusters (AgNCs) represent another subclass of nanoscale silver. AgNCs are a promising tool for nanomedicine due to their small size, structural homogeneity, antibacterial activity and fluorescence, which arises from their molecule-like electron configurations. The template-assisted synthesis of AgNCs relies on organic molecules that act as polydentate ligands. In particular, single-stranded nucleic acids reproducibly scaffold AgNCs to provide fluorescent, biocompatible materials that are incorporable in other formulations. This mini review outlines the design and characterization of AgNPs and DNA-templated AgNCs, discusses factors that affect their physicochemical and biological properties, and highlights applications of these materials as antibacterial agents and biosensors.
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Affiliation(s)
- Leyla Danai
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Lewis A Rolband
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Elizabeth Skelly
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Taejin Kim
- Physical Sciences Department, West Virginia University Institute of Technology, Beckley, WV 25801, USA
| | - Kirill A Afonin
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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12
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David F, Setzler C, Sorescu A, Lieberman RL, Meilleur F, Petty JT. Mapping H + in the Nanoscale (A 2C 4) 2-Ag 8 Fluorophore. J Phys Chem Lett 2022; 13:11317-11322. [PMID: 36453924 DOI: 10.1021/acs.jpclett.2c03161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
When strands of DNA encapsulate silver clusters, supramolecular optical chromophores develop. However, how a particular structure endows a specific spectrum remains poorly understood. Here, we used neutron diffraction to map protonation in (A2C4)2-Ag8, a green-emitting fluorophore with a "Big Dipper" arrangement of silvers. The DNA host has two substructures with distinct protonation patterns. Three cytosines from each strand collectively chelate handle-like array of three silvers, and calorimetry studies suggest Ag+ cross-links. The twisted cytosines are further joined by hydrogen bonds from fully protonated amines. The adenines and their neighboring cytosine from each strand anchor a dipper-like group of five silvers via their deprotonated endo- and exocyclic nitrogens. Typically, exocyclic amines are strongly basic, so their acidification and deprotonation in (A2C4)2-Ag8 suggest that silvers perturb the electron distribution in the aromatic nucleobases. The different protonation states in (A2C4)2-Ag8 suggest that atomic level structures can pinpoint how to control and tune the electronic spectra of these nanoscale chromophores.
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Affiliation(s)
- Fred David
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Caleb Setzler
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Alexandra Sorescu
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, North Carolina 27695, United States
- Neutron Scattering Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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13
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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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14
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Kuo YA, Jung C, Chen YA, Kuo HC, Zhao OS, Nguyen TD, Rybarski JR, Hong S, Chen YI, Wylie DC, Hawkins JA, Walker JN, Shields SWJ, Brodbelt JS, Petty JT, Finkelstein IJ, Yeh HC. Massively Parallel Selection of NanoCluster Beacons. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204957. [PMID: 35945159 PMCID: PMC9588665 DOI: 10.1002/adma.202204957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/18/2022] [Indexed: 06/15/2023]
Abstract
NanoCluster Beacons (NCBs) are multicolor silver nanocluster probes whose fluorescence can be activated or tuned by a proximal DNA strand called the activator. While a single-nucleotide difference in a pair of activators can lead to drastically different activation outcomes, termed polar opposite twins (POTs), it is difficult to discover new POT-NCBs using the conventional low-throughput characterization approaches. Here, a high-throughput selection method is reported that takes advantage of repurposed next-generation-sequencing chips to screen the activation fluorescence of ≈40 000 activator sequences. It is found that the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs and positions 4-6 and 2-4 are hotspots to generate yellow-orange and red POTs, respectively. Based on these findings, a "zipper-bag" model is proposed that can explain how these hotspots facilitate the formation of distinct silver cluster chromophores and alter their chemical yields. Combining high-throughput screening with machine-learning algorithms, a pipeline is established to design bright and multicolor NCBs in silico.
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Affiliation(s)
- Yu-An Kuo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Yu-An Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Oliver S Zhao
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Trung D Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - James R Rybarski
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Soonwoo Hong
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Dennis C Wylie
- Computational Biology and Bioinformatics, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX, 78712, USA
| | - John A Hawkins
- European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Samuel W J Shields
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, SC, 29617, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Texas Materials Institute, University of Texas at Austin, Austin, TX, 78712, USA
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15
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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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16
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A colorimetric biosensor based on peroxidase-like activity of CuO nanoparticles for simultaneous detection of microRNAs. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02417-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Petty JT, Lewis D, Carnahan S, Kim D, Couch C. Tug-of-War between DNA Chelation and Silver Agglomeration in DNA-Silver Cluster Chromophores. J Phys Chem B 2022; 126:3822-3830. [PMID: 35594191 DOI: 10.1021/acs.jpcb.2c01054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Supramolecular chromophores form when a DNA traps silvers that then coalesce into clusters with discrete, molecular electronic states. However, DNA strands are polymeric ligands that disperse silvers and thus curb agglomeration. We study this competition using two chromophores that share three common components: a dimeric DNA scaffold, Ag+-nucleobase base pairs, and Ag0 chromophores. The DNA host C4-A2-iC4T mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "i") directions. The backbone directions must alternate to form the two silver clusters, and this interdependence supports a silver-linked structure. This template creates two chromophores with distinct sizes, charges, and hence spectra: (C4-A2-iC4T)2/Ag117+ with λabs/λem = 430/520 nm and (C4-A2-iC4T)2/Ag148+ with λabs/λem = 510/630 nm. The Ag+ and Ag0 constituents in these partially oxidized clusters are linked with structural elements in C4-A2-iC4T. Ag+ alone binds sparsely but strongly to form C4-A2-iC4T/3-4 Ag+ and (C4-A2-iC4T)2/7-8 Ag+ complexes, and these stoichiometries suggest that Ag+ cross-links pairs of cytosines to form a hairpin with a metallo-C4/iC4 duplex and an adenine loop. The Ag0 are chemically orthogonal because they can be oxidatively etched without disrupting the underlying Ag+-DNA matrix, and their reactivity is attributed to their valence electrons and weaker chelation by the adenines. These studies suggest that Ag+ disperses with the cytosines to create an adenine binding pocket for the Ag0 cluster chromophores.
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - David Lewis
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Savannah Carnahan
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Dahye Kim
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Caroline Couch
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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18
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Li T, Hu Z, Yu S, Liu Z, Zhou X, Liu R, Liu S, Deng Y, Li S, Chen H, Chen Z. DNA Templated Silver Nanoclusters for Bioanalytical Applications: A Review. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Due to their unique programmability, biocompatibility, photostability and high fluorescent quantum yield, DNA templated silver nanoclusters (DNA Ag NCs) have attracted increasing attention for bioanalytical application. This review summarizes the recent developments in fluorescence
properties of DNA templated Ag NCs, as well as their applications in bioanalysis. Finally, we herein discuss some current challenges in bioanalytical applications, to promote developments of DNA Ag NCs in biochemical analysis.
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Affiliation(s)
- Taotao Li
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Zhiyuan Hu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Songlin Yu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Zhanjun Liu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Xiaohong Zhou
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Rong Liu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Shiquan Liu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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19
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Yang CL, Zhang YQ, He JY, Li MD, Yuan R, Xu WJ. Target Deoxyribonucleic Acid-Recycled Lighting-Up Amplifiable Ratiometric Fluorescence Biosensing of Bicolor Silver Nanoclusters Hosted in a Switchable Deoxyribonucleic Acid Construct. Anal Chem 2022; 94:6703-6710. [PMID: 35476420 DOI: 10.1021/acs.analchem.1c05445] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ratiometric assays of label-free dual-signaling reporters with enzyme-free amplification are intriguing yet challenging. Herein, yellow- and red-silver nanocluster (yH-AgNC and rH-AgNC) acting as bicolor ratiometric emitters are guided to site-specifically cluster in two template signaling hairpins (yH and rH), respectively, and originally, both of them are almost non-fluorescent. The predesigned complement tethered in yH is recognizable to a DNA trigger (TOC) related to SARS-CoV-2. With the help of an enhancer strand (G15E) tethering G-rich bases (G15) and a linker strand (LS), a switchable DNA construct is assembled via their complementary hybridizing with yH and rH, in which the harbored yH-AgNC close to G15 is lighted-up. Upon introducing TOC, its affinity ligating with yH is further implemented to unfold rH and induce the DNA construct switching into closed conformation, causing TOC-repeatable recycling amplification through competitive strand displacement. Consequently, the harbored rH-AgNC is also placed adjacent to G15 for turning on its red fluorescence, while the yH-AgNC is retainable. As demonstrated, the intensity ratio dependent on varying TOC is reliable with high sensitivity down to 0.27 pM. By lighting-up dual-cluster emitters using one G15 enhancer, it would be promising to exploit a simpler ratiometric biosensing format for bioassays or clinical theranostics.
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Affiliation(s)
- Chun-Li Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yu-Qing Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jia-Yang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Meng-Die Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wen-Ju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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20
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Wu Q, Liu C, Liu Y, Cui C, Ge J, Tan W. Multibranched Linear DNA-Controlled Assembly of Silver Nanoclusters and Their Applications in Aptamer-Based Cell Recognition. ACS APPLIED MATERIALS & INTERFACES 2022; 14:14953-14960. [PMID: 35344322 DOI: 10.1021/acsami.1c24547] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNA-templated silver nanoclusters (DNA-AgNCs) are promising fluorescent materials and have been used in cancer diagnosis. Although many different DNA-AgNC applications have been realized, most of them rely on individual DNA-AgNCs or assembled DNA-AgNCs with limited recognition abilities, resulting in low detection sensitivity or off-target effects, in turn, hindering the performance of DNA-AgNCs in cancer cell recognition. As a solution, we assembled DNA-AgNCs by a multibranched linear (MBL) DNA structure formed through a trigger-initiated hybridization chain reaction (HCR) regarding the natural compatibility of DNA-AgNCs with DNA programmability and the advantages of DNA assembly in incorporating repetitive and functional moieties into one structure. By the specific modification of the trigger, MBL-AgNCs tethered with the targeting aptamer and partially hybridized duplex, which works as a component of DNA logic platform relying on the combination of cascade strand displacement reaction and specific recognition ability of aptamers, were obtained, respectively. DNA-AgNCs assembled by the aptamer-tethered MBL structure exhibited about 20-fold enhanced detection sensitivity in recognizing cancer cells compared to individual aptamer-tethered DNA-AgNCs. DNA-AgNCs assembled by the duplex-attached MBL exhibited logic performance in analyzing dual cell surface receptors with the assistance of "AND" logic platform, thus identifying cancer cells with high sensitivity and resolution. The facile conjugation of the MBL structure with different functional DNA structures makes it an ideal platform to assemble DNA-AgNCs used for aptamer-based cell recognition, thus broadening the potential applications of DNA-AgNCs.
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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
| | - Yuan 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
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Cheng Cui
- 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 410082, China
| | - Jia Ge
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Weihong Tan
- 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 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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21
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Ma H, Wang J, Zhang XD. Near-infrared II emissive metal clusters: From atom physics to biomedicine. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214184] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Bao W, Ai J, Ga L. Controllable synthesis of fluorescent silver nanoparticles with different length oligonucleotides. IET Nanobiotechnol 2021; 15:512-518. [PMID: 34694757 PMCID: PMC8675809 DOI: 10.1049/nbt2.12049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/04/2020] [Accepted: 11/30/2020] [Indexed: 11/24/2022] Open
Abstract
Silver nanomaterials have become important research topics in recent years. As a new type of fluorescent material, silver nanomaterials have been applied to fluorescent sensors, bioimaging and materials targeting cancer cells. Here, an approach to the oligonucleotide‐templated controllable formation of fluorescent Ag nanomaterials is reported. In this experiment, silver nanoparticles (NPs) were synthesised from oligonucleotides chains, sodium borohydride (NaBH4) and silver nitrate (AgNO3) by changing the molar ratio of DNA to sodium borohydride (NaBH4) and silver nitrate (AgNO3). Fluorescent assay and transmission electron microscopy were used to characterise the silver NPs. The optimal selection of DNA chains with different lengths as templates for the synthesis of silver NPs was found. This work successfully develops the capping oligonucleotides scaffolds of silver nanoclusters.
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Affiliation(s)
- Wenhui Bao
- College of Chemistry and Environmental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, Hohhot, China
| | - Jun Ai
- College of Chemistry and Environmental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, Hohhot, China
| | - Lu Ga
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
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23
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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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24
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Zhang Y, He C, de La Harpe K, Goodwin PM, Petty JT, Kohler B. A single nucleobase tunes nonradiative decay in a DNA-bound silver cluster. J Chem Phys 2021; 155:094305. [PMID: 34496579 DOI: 10.1063/5.0056836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
DNA strands are polymeric ligands that both protect and tune molecular-sized silver cluster chromophores. We studied single-stranded DNA C4AC4TC3XT4 with X = guanosine and inosine that form a green fluorescent Ag10 6+ cluster, but these two hosts are distinguished by their binding sites and the brightness of their Ag10 6+ adducts. The nucleobase subunits in these oligomers collectively coordinate this cluster, and fs time-resolved infrared spectra previously identified one point of contact between the C2-NH2 of the X = guanosine, an interaction that is precluded for inosine. Furthermore, this single nucleobase controls the cluster fluorescence as the X = guanosine complex is ∼2.5× dimmer. We discuss the electronic relaxation in these two complexes using transient absorption spectroscopy in the time window 200 fs-400 µs. Three prominent features emerged: a ground state bleach, an excited state absorption, and a stimulated emission. Stimulated emission at the earliest delay time (200 fs) suggests that the emissive state is populated promptly following photoexcitation. Concurrently, the excited state decays and the ground state recovers, and these changes are ∼2× faster for the X = guanosine compared to the X = inosine cluster, paralleling their brightness difference. In contrast to similar radiative decay rates, the nonradiative decay rate is 7× higher with the X = guanosine vs inosine strand. A minor decay channel via a dark state is discussed. The possible correlation between the nonradiative decay and selective coordination with the X = guanosine/inosine suggests that specific nucleobase subunits within a DNA strand can modulate cluster-ligand interactions and, in turn, cluster brightness.
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Affiliation(s)
- Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | - Chen He
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
| | - Kimberly de La Harpe
- Department of Physics, United States Air Force Academy, U.S. Air Force Academy, Colorado 80840, USA
| | - Peter M Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop K771, Los Alamos, New Mexico 87545, USA
| | - Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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25
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Petty JT, Carnahan S, Kim D, Lewis D. Long-lived Ag 10 6+ luminescence and a split DNA scaffold. J Chem Phys 2021; 154:244302. [PMID: 34241360 DOI: 10.1063/5.0056214] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular silver clusters emit across the visible to near-infrared, and specific chromophores can be formed using DNA strands. We study C4AC4TC3G that selectively coordinates and encapsulates Ag10 6+, and this chromophore has two distinct electronic transitions. The green emission is strong and prompt with ϕ = 18% and τ = 1.25 ns, and the near-infrared luminescence is weaker, slower with τ = 50 µs, and is partly quenched by oxygen, suggesting phosphorescence. This lifetime can be modulated by the DNA host, and we consider two derivatives of C4AC4TC3G with similar sequences but distinct structures. In one variant, thymine was excised to create an abasic gap in an otherwise intact strand. In the other, the covalent phosphate linkage was removed to split the DNA scaffold into two fragments. In relation to the contiguous strands, the broken template speeds the luminescence decay by twofold, and this difference may be due to greater DNA flexibility. These modifications suggest that a DNA can be structurally tuned to modulate metastable electronic states in its silver cluster adducts.
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
| | - Savannah Carnahan
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
| | - Dahye Kim
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
| | - David Lewis
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
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26
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Tiwari N, Mishra RK, Gupta S, Srivastava R, Aggarwal S, Bandyopadhyay P, Munde M. Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9385-9395. [PMID: 34313447 DOI: 10.1021/acs.langmuir.1c00949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The real motivation in the present work is to tune the synthesis variables that can result in a highly fluorescent and stable DNA copper nanocluster (CuNC) and also to understand the intricate mechanism behind this process. Here, carefully optimized concentrations of various reactants enabled the creation of a DNA-encapsulated CuNC for AT-DNA, displaying a size of <1.0 nm as confirmed by transmission electron microscopy and dynamic light scattering. The extremely small size of the AT-DNACuNC supports the discrete electronic transitions, also characterized by an exceptionally strong negative circular dichroism (CD) band around 350 nm, whose intensity is well correlated with the observed strong fluorescence emission intensity. This remarkably strong CD can open new applications in the detection and quantification of a specific DNACuNC. Further, time-dependent fluorescence analysis suggested stronger photostabilization of these DNACuNCs. The simulation study, based on Cu ion distribution, explained how AT-DNA is a better candidate for NC formation than GC-DNA. In conclusion, the better-tuned synthesis procedure has resulted in a highly compact, well-defined three-dimensional conformation that promotes a more favorable microenvironment to sequester a DNA-based CuNC with high brightness and outstanding photostability.
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Affiliation(s)
- Neha Tiwari
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sakshi Gupta
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rakesh Srivastava
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Soumya Aggarwal
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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27
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Fluorescent functional nucleic acid: Principles, properties and applications in bioanalyzing. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116292] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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28
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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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29
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Gambucci M, Zampini G, Quaglia G, Vosch T, Latterini L. Probing the Fluorescence Behavior of DNA‐Stabilized Silver Nanoclusters in the Presence of Biomolecules. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202000262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marta Gambucci
- Department of Chemistry, Biology and Biotechnology University of Perugia Via Elce di Sotto, 8 06123 Perugia Italy
| | - Giulia Zampini
- Department of Chemistry, Biology and Biotechnology University of Perugia Via Elce di Sotto, 8 06123 Perugia Italy
| | - Giulia Quaglia
- Department of Chemistry, Biology and Biotechnology University of Perugia Via Elce di Sotto, 8 06123 Perugia Italy
| | - Tom Vosch
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Loredana Latterini
- Department of Chemistry, Biology and Biotechnology University of Perugia Via Elce di Sotto, 8 06123 Perugia Italy
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30
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Li D, Chen H, Gao X, Mei X, Yang L. Development of General Methods for Detection of Virus by Engineering Fluorescent Silver Nanoclusters. ACS Sens 2021; 6:613-627. [PMID: 33660987 DOI: 10.1021/acssensors.0c02322] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Viruses have caused significant damage to the world. Effective detection is required to relieve the impact of viral infections. A biomolecule can be used as a template such as deoxyribonucleic acid (DNA), peptide, or protein, for the growth of silver nanoclusters (AgNCs) and for recognizing a virus. Both the AgNCs and the recognition elements are tunable, which is promising for the analysis of new viruses. Considering that a new virus such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently requires a facile sensing strategy, various virus detection strategies based on AgNCs including fluorescence enhancement, color change, quenching, and recovery are summarized. Particular emphasis is placed on the molecular analysis of viruses using DNA stabilized AgNCs (DNA-AgNCs), which detect the virus's genetic material. The more widespread applications of AgNCs for general virus detection are also discussed. Further development of these technologies may address the challenge for facile detection of SARS-CoV-2.
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Affiliation(s)
- Dan Li
- Department of Basic Science, Jinzhou Medical University, Jinzhou 121001, China
- Department of Orthopedics, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, China
| | - Hui Chen
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xianhui Gao
- Department of Basic Science, Jinzhou Medical University, Jinzhou 121001, China
- Department of Orthopedics, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, China
| | - Xifan Mei
- Department of Basic Science, Jinzhou Medical University, Jinzhou 121001, China
- Department of Orthopedics, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, China
| | - Liqun Yang
- NHC Key Laboratory of Reproductive Health and Medical Genetics (Liaoning Research Institute of Family Planning), China Medical University, Shenyang 110122, China
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31
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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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32
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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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33
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de la Hoz A, Navarro A, Aviñó A, Eritja R, Gargallo R. Studies on the interactions of Ag(i) with DNA and their implication on the DNA-templated synthesis of silver nanoclusters and on the interaction with complementary DNA and RNA sequences. RSC Adv 2021; 11:9029-9042. [PMID: 35423401 PMCID: PMC8695332 DOI: 10.1039/d1ra00194a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 02/15/2021] [Indexed: 12/22/2022] Open
Abstract
Silver nanoclusters (AgNCs) prepared by the reduction of silver ions in the presence of DNA oligonucleotides have attracted great interest as potential diagnostic tools for their tunable and high fluorescent properties. In this work, three DNA sequences that consist of a 12-nucleotide long probe sequence at the 5′-end linked to the complementary sequence to three miRNAs are studied. First, the interaction of these sequences with Ag(i) was characterized by means of circular dichroism spectroscopy. By applying multivariate methods to the analysis of spectroscopic data, two complexes with different Ag(i) : DNA ratios were resolved. Secondly, the impact of several experimental variables, such as temperature, borohydride concentration and reaction time, on the formation of AgNCs templated by these three sequences was studied. Finally, the fluorescence properties of the duplexes formed by DNA probes with complementary DNA or miRNA sequences were studied. The results presented here highlight the role of the secondary structure adopted by the DNA probe on the fluorescence properties of DNA-stabilized AgNCs which, in turn, affect the development of methods for miRNA detection. Variables affecting the fluorescent properties of DNA-stabilized silver nanoclusters are studied. The secondary structure of the AgNC-stabilizing DNA sequence dramatically affects the analytical signal behind the hybridization reaction.![]()
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Affiliation(s)
- Alejandra de la Hoz
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona Marti i Franquès 1 E-08028 Barcelona Spain
| | - Alba Navarro
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona Marti i Franquès 1 E-08028 Barcelona Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN Jordi Girona 18-26 E-08034 Barcelona Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN Jordi Girona 18-26 E-08034 Barcelona Spain
| | - Raimundo Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona Marti i Franquès 1 E-08028 Barcelona Spain
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34
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Li F, Li G, Cao S, Liu B, Ren X, Kang N, Qiu F. Target-triggered entropy-driven amplification system-templated silver nanoclusters for multiplexed microRNA analysis. Biosens Bioelectron 2021; 172:112757. [PMID: 33129074 DOI: 10.1016/j.bios.2020.112757] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/09/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
MicroRNAs (miRNAs) are important biomarkers for the diagnosis, prognosis, and treatment of human diseases. Sensitive and selective detection of multiple miRNAs simultaneously will greatly facilitate the early and accurate diagnosis of cancers. Herein, a novel entropy-driven amplification system-templated silver nanoclusters sensing platform was developed for the multiplexed analysis of tumor-associated miRNAs. The sensing platform was constructed by coupling target-triggered entropy-driven catalysis with luminescence adjustable DNA-templated silver nanoclusters (Ag NCs). In the presence of target miRNA, the sensing platform initiates the branch migration and strand displacement of the complex, which has a six-base cytosine loop for stabilizing the luminous Ag NCs. The target is cyclically generated for new catalysis while turning off the fluorescence of Ag NCs; this is accompanied by a significantly amplified optical readout. In this study, two different complex-stabilized Ag NCs systems were proposed, the yellow-emitting Ag NCs and red-emitting Ag NCs biosensors enabled the analysis of miRNA-141 and miRNA-155 with detection limits of 6.1 pM and 8.7 pM, respectively. Impressively, owing to the excellent selectivity, flexibility, and narrow-band excitation of the platform, the multiplexed synchronous detection of miRNA-141 and miRNA-155 were achieved in buffer, biological cell lysates and human serum samples with satisfactory results. The simple, flexible, and convenient strategy provides a powerful tool for multiple biomarkers analysis and related clinical applications.
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Affiliation(s)
- Fengyun Li
- School of Chinese Materia Medica, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Gen Li
- School of Chinese Materia Medica, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Shijie Cao
- Tianjin Key Laboratory of TCM Chemistry and Analysis, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Boshi Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Xiaoliang Ren
- School of Chinese Materia Medica, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Ning Kang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Feng Qiu
- School of Chinese Materia Medica, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China.
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35
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Yang M, Chen X, Su Y, Liu H, Zhang H, Li X, Xu W. The Fluorescent Palette of DNA-Templated Silver Nanoclusters for Biological Applications. Front Chem 2020; 8:601621. [PMID: 33262973 PMCID: PMC7686567 DOI: 10.3389/fchem.2020.601621] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/20/2020] [Indexed: 12/29/2022] Open
Abstract
Recently years have witnessed a surge in application of DNA-AgNCs in optics, catalysis, sensing, and biomedicine. DNA-templated silver nanoclusters (DNA-AgNCs), as emerging fluorophores, display superior optical performance since their size is close to the Fermi wavelength. DNA-AgNCs possess unique features, including high fluorescence quantum yields and stability, biocompatibility, facile synthesis, and low toxicity, which are requisite for fluorescent probes. The fluorescent emission of DNA-AgNCs can cover the violet to near-infrared (NIR) region by varying the DNA sequences, lengths, and structures or by modifying the environmental factors (such as buffer, pH, metal ions, macromolecular polymers, and small molecules). In view of the above excellent properties, we overview the DNA-AgNCs from the viewpoints of synthesis and fluorescence properties, and summarized its biological applications of fluorescence sensing and imaging.
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Affiliation(s)
- Min Yang
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Xu Chen
- Institute of Nutrition and Health, China Agricultural University, Beijing, China
| | - Yuan Su
- Institute of Nutrition and Health, China Agricultural University, Beijing, China
| | - Haiyan Liu
- Faculty of Public Health, North China University of Technology, Tangshan, China
| | - Hongxing Zhang
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Xiangyang Li
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Wentao Xu
- Institute of Nutrition and Health, China Agricultural University, Beijing, China
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Zhang Y, He C, Petty JT, Kohler B. Time-Resolved Vibrational Fingerprints for Two Silver Cluster-DNA Fluorophores. J Phys Chem Lett 2020; 11:8958-8963. [PMID: 33030904 DOI: 10.1021/acs.jpclett.0c02486] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA-templated silver clusters are chromophores in which the nucleobases encode the cluster spectra and brightness. We describe the coordination environments of two nearly identical Ag106+ clusters that form with 18-nucleotide strands CCCCA CCCCT CCCX TTTT, with X = guanosine and inosine. For the first time, femtosecond time-resolved infrared (TRIR) spectroscopy with visible excitation and mid-infrared probing is used to correlate the response of nucleobase vibrational modes to electronic excitation of the metal cluster. A rich pattern of transient TRIR peaks in the 1400-1720 cm-1 range decays synchronously with the visible emission. Specific infrared signatures associated with the single guanosine/inosine along with a subset of cytidines, but not the thymidines, are observed. These fingerprints suggest that the network of bonds between a silver cluster adduct and its polydentate DNA ligands can be deciphered to rationally tune the coordination and thus spectra of molecular silver chromophores.
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Affiliation(s)
- Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Chen He
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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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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Li C, Chen Z, Zhang Y, He J, Yuan R, Xu W. Guanine-Lighting-Up Fluorescence Biosensing of Silver Nanoclusters Populated in Functional DNA Constructs by a pH-Triggered Switch. Anal Chem 2020; 92:13369-13377. [PMID: 32900187 DOI: 10.1021/acs.analchem.0c02744] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Dark or weak-emissive DNA-harbored silver nanoclusters (AgNCs) can be remarkably lighted up when approaching to guanine bases. The resultant bright AgNCs acting as a fluorescent reporter are fascinating in biosensing. To explore the applicable guanine-enhanced emission of AgNCs for biosensing microRNA-155 (miR-155) as a model, here we designed a unique stem-loop hairpin beacon (HB) encoding with an miR-155-recognizable sequence and a AgNCs-nucleable template, as well as a hairpin helper tethering a partially locked guanine-rich (15-nt) tail (G15H), while two identical cytosine-rich segments were inserted in HB and G15H to merge for folding/unfolding of i-motif at changed pHs. Initially, the intact clusters populated in HB (HB/AgNCs) were almost nonfluorescent in a buffer (pH 7.0). Then, miR-155 was introduced to trigger a repeated hairpin assembly of HB and G15H by competitive strand displacement reactions at decreased pH 5.0 within 10 min, consequently generating numerous duplex DNA constructs (DDCs). With the resultant template of pH-responsive i-motifs incorporated in DDCs, their folding at pH 5.0 brought the proximity of unlocked G15 overhang to the clusters in a crowded environment, remarkably lighting up the red-emitting fluorescence of HB/AgNCs (λem = 628 ± 5 nm) for amplified signal readout. About 3.5-fold enhancement of quantum yield was achievable using different variants of i-motif length and G15 position. Simply by adding OH-, the configuration fluctuation of i-motifs was implemented for switchable fluorescence biosensing to variable miR-155. Based on a one-step amplification and signaling scheme, this subtle strategy was rapid, low-cost, and specific for miR-155 with high sensitivity down to 67 pM.
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Affiliation(s)
- Chong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Zehui Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yuxuan Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Jiayang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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Buglak AA, Kononov AI. Comparative study of gold and silver interactions with amino acids and nucleobases. RSC Adv 2020; 10:34149-34160. [PMID: 35519047 PMCID: PMC9056802 DOI: 10.1039/d0ra06486f] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/09/2020] [Indexed: 12/13/2022] Open
Abstract
Metal nanoclusters (NCs) have gained much attention in the last decade. In solution, metal nanoclusters can be stabilized by proteins, and, thus, exhibit many advantages in biocatalysis, biosensing, and bioimaging. In spite of much progress in the synthesis of polypeptide-stabilized gold (Au) clusters, their structure, as well as amino acid-cluster and amino acid-Au+ interactions, remain poorly understood. It is not entirely clear which amino acid (AA) residues and sites in the protein are preferred for binding. The understanding of NC-protein interactions and how they evolve in the polypeptide templates is the key to designing Au NCs. In this work, binding of gold ion Au+ and diatomic neutral gold nanocluster Au2 with a full set of α-proteinogenic amino acids is studied using Density Functional Theory (DFT) and the ab initio RI-MP2 method in order to find the preferred sites of gold interaction in proteins. We demonstrated that the interaction of gold cations and clusters with protonated and deprotonated amino acid residues do not differ greatly. The binding affinity of AAs to the Au2 cluster increases in the following order: Cys(-H+) > Asp(-H+) > Tyr(-H+) > Glu(-H+) > Arg > Gln, His, Met ≫ Asn, Pro, Trp > Lys, Tyr, Phe > His(+H+) > Asp > Lys(+H+) > Glu, Leu > Arg(+H+) > Ile, Val, Ala > Thr, Ser > Gly, Cys, which agrees with the available experimental data that gold cluster synthesis occurs in a wide range of pH - amino acid residues with different protonation states are involved in this process. The significant difference in the binding energy of metal atoms with nucleobases and amino acids apparently means that unlike on DNA templates, neutral metal atoms are strongly bound to amino acid residues and can't freely diffuse in a polypeptide globula. This fact allows one to conclude that formation of metal NCs in proteins occurs through the nucleation of reduced Au atoms bound to the neighboring amino acid residues, and the flexibility of the amino acid residue side-chains and protein chain as a whole plays a significant role in this process.
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Affiliation(s)
- Andrey A Buglak
- St. Petersburg State University 199034 Saint-Petersburg Russia
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40
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Yourston L, Rolband L, West C, Lushnikov A, Afonin KA, Krasnoslobodtsev AV. Tuning properties of silver nanoclusters with RNA nanoring assemblies. NANOSCALE 2020; 12:16189-16200. [PMID: 32705105 DOI: 10.1039/d0nr03589k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Combining atomically resolved DNA-templated silver nanoclusters (AgNCs) with nucleic acid nanotechnology opens new exciting possibilities for engineering bioinorganic nanomaterials with uniquely tunable properties. In this unforeseen cooperation, nucleic acids not only drive the formation of AgNCs but also promote their spatial organization in supra-assemblies. In this work, we confirm the feasibility of this approach using programmable RNA rings to control formation and optical properteis of six individual AgNCs. "Red" (λEXC/λEM = 565/623 nm) and "green" (λEXC/λEM = 440/523 nm) emitting AgNCs are templated on cytosine-rich DNA fragments embedded into the RNA rings. Optical properties of the AgNCs formed on the RNA rings are characterized in detail. While all "red" species passively transition to "green" emitters with time, the initial fluorescent properties and relative stabilities of "red" AgNCs can be regulated by altering the relative orientation of AgNCs within the RNA rings. As such, the oxidative stability increases dramatically for AgNC positioned towards the center of the RNA rings rather than facing outward. Overall, our findings expand the existing AgNC fluorescent toolkit while uncovering the complexity of the AgNC electronic structures with the abundance of possibilities for controlling de-excitation processes.
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Affiliation(s)
- Liam Yourston
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA.
| | - Lewis Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Caroline West
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Alexander Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Alexey V Krasnoslobodtsev
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA. and Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA
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41
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Geczy R, Christensen NJ, Rasmussen KK, Kálomista I, Tiwari MK, Shah P, Yang SW, Bjerrum MJ, Thulstrup PW. Formation and Structure of Fluorescent Silver Nanoclusters at Interfacial Binding Sites Facilitating Oligomerization of DNA Hairpins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Reka Geczy
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Niels Johan Christensen
- Department of Chemistry University of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Kim K. Rasmussen
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Ildikó Kálomista
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Manish K. Tiwari
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Pratik Shah
- Department of Systems Biology Institute of Life Science and Biotechnology Yonsei University Seoul 03722 Korea
| | - Seong Wook Yang
- Department of Systems Biology Institute of Life Science and Biotechnology Yonsei University Seoul 03722 Korea
| | - Morten J. Bjerrum
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Peter W. Thulstrup
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
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42
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Geczy R, Christensen NJ, Rasmussen KK, Kálomista I, Tiwari MK, Shah P, Yang SW, Bjerrum MJ, Thulstrup PW. Formation and Structure of Fluorescent Silver Nanoclusters at Interfacial Binding Sites Facilitating Oligomerization of DNA Hairpins. Angew Chem Int Ed Engl 2020; 59:16091-16097. [DOI: 10.1002/anie.202005102] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/18/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Reka Geczy
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Niels Johan Christensen
- Department of Chemistry University of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Kim K. Rasmussen
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Ildikó Kálomista
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Manish K. Tiwari
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Pratik Shah
- Department of Systems Biology Institute of Life Science and Biotechnology Yonsei University Seoul 03722 Korea
| | - Seong Wook Yang
- Department of Systems Biology Institute of Life Science and Biotechnology Yonsei University Seoul 03722 Korea
| | - Morten J. Bjerrum
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Peter W. Thulstrup
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
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43
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Dembska A, Świtalska A, Fedoruk-Wyszomirska A, Juskowiak B. Development of fluorescence oligonucleotide probes based on cytosine- and guanine-rich sequences. Sci Rep 2020; 10:11006. [PMID: 32620895 PMCID: PMC7335195 DOI: 10.1038/s41598-020-67745-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
The properties of cytosine- and guanine-rich oligonucleotides contributed to employing them as sensing elements in various biosensors. In this paper, we report our current development of fluorescence oligonucleotide probes based on i-motif or G-quadruplex forming oligonucleotides for cellular measurements or bioimaging applications. Additionally, we also focus on the spectral properties of the new fluorescent silver nanoclusters based system (ChONC12-AgNCs) that is able to anchor at the Langmuir monolayer interface, which is mimicking the surface of living cells membrane.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614, Poznan, Poland.
| | - Angelika Świtalska
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614, Poznan, Poland.
| | | | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614, Poznan, Poland
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44
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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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45
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Mora-Sanz V, Saa L, Briz N, Möller M, Pavlov V. Antibody-Directed Synthesis of Catalytic Nanoclusters for Bioanalytical Assays. ACS APPLIED MATERIALS & INTERFACES 2020; 12:28993-28999. [PMID: 32501677 DOI: 10.1021/acsami.0c05229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Synthesis of atomic nanoclusters (NCs) using proteins as a scaffold has attracted great attention. Usually, the synthetic conditions for the synthesis of NCs stabilized with proteins require extreme pH values or temperature. These harsh reaction conditions cause the denaturation of the proteins and end up in the loss of their biological functions. Until now, there are no examples of the use of antibodies as NC stabilizers. In this work, we present the first method for the synthesis of catalytic NCs that uses antibodies for the stabilization of NCs. Anti-BSA IgG was used as a model to demonstrate that it is possible to use an antibody as a scaffold for the synthesis of semiconductor and metallic NCs with catalytic properties. The synthesis of antibodies modified with NCs is carried out under nondenaturing conditions, which do not affect the antibody structure. The resulting antibodies still maintain the affinity for target antigens and protein G. The catalytic properties of the anti-BSA IgG modified with NCs can be used to the quantification of bovine serum albumin (BSA) in a direct sandwich enzyme-linked immunosorbent assay (ELISA).
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Affiliation(s)
- Verónica Mora-Sanz
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, Donostia San Sebastián 20014, Spain
- Tecnalia, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de San Sebastián, Paseo Mikeletegi 2, Donostia-San Sebastian 20009, Spain
| | - Laura Saa
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, Donostia San Sebastián 20014, Spain
| | - Nerea Briz
- Tecnalia, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de San Sebastián, Paseo Mikeletegi 2, Donostia-San Sebastian 20009, Spain
| | - Marco Möller
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, Donostia San Sebastián 20014, Spain
| | - Valeri Pavlov
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, Donostia San Sebastián 20014, Spain
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46
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Lambert BP, Gillen AJ, Boghossian AA. Synthetic Biology: A Solution for Tackling Nanomaterial Challenges. J Phys Chem Lett 2020; 11:4791-4802. [PMID: 32441940 DOI: 10.1021/acs.jpclett.0c00929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bioengineers have mastered practical techniques for tuning a biomaterial's properties with only limited information on the relationship between the material's structure and function. These techniques have been quintessential to engineering proteins, which are most often riddled with ill-defined structure-function relationships. In this Perspective, we review bioengineering approaches aimed at overcoming the elusive protein structure-function relation. We extend these principles to engineering synthetic nanomaterials, specifically applying the underlying theory to optical sensors based on single-stranded DNA-wrapped single-walled carbon nanotubes (ssDNA-SWCNTs). Bioengineering techniques such as directed evolution, computational design, and noncanonical synthesis are reviewed in the broader context of nanomaterials engineering. We further provide an order-of-magnitude analysis of empirical approaches that rely on random or guided searches for designing new nanomaterials. The underlying concepts presented in these approaches can be further extended to a broad range of engineering fields confronted with empirical design strategies, including catalysis, metal-organic frameworks (MOFs), pharmaceutical dosing, and optimization algorithms.
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Affiliation(s)
- Benjamin P Lambert
- École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Alice J Gillen
- École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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47
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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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Cerretani C, Kanazawa H, Vosch T, Kondo J. Crystal structure of a NIR‐Emitting DNA‐Stabilized Ag
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Nanocluster. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906766] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Cecilia Cerretani
- Department of Chemistry and NanoScience CenterUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Hiroki Kanazawa
- Department of Materials and Life SciencesSophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
- Present address: IBMC-CNRSUniversité de Strasbourg 2 allée Konrad Roentgen 67084 Strasbourg France
| | - Tom Vosch
- Department of Chemistry and NanoScience CenterUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Jiro Kondo
- Department of Materials and Life SciencesSophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
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Target-induced in-situ formation of fluorescent DNA-templated copper nanoparticles by a catalytic hairpin assembly: application to the determination of DNA and thrombin. Mikrochim Acta 2019; 186:760. [PMID: 31712919 DOI: 10.1007/s00604-019-3927-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/12/2019] [Indexed: 12/15/2022]
Abstract
A fluorometric method is described for nucleic acid signal amplification through target-induced catalytic hairpin assembly with DNA-templated copper nanoparticles (Cu NPs). The toehold-mediated self-assembly of three metastable hairpins is triggered in presence of target DNA. This leads to the formation of a three-way junction structure with protruding mononucleotides at the 3' terminus. The target DNA is released from the formed branched structure and triggers another assembly cycle. As a result, plenty of branched DNA becomes available for the synthesis of Cu NPs which have fluorescence excitation/emission maxima at 340/590 nm. At the same time, the branched structure protects the Cu NPs from digestion by exonuclease III. The unreacted hairpins are digested by exonuclease III, and this warrants a lower background signal. The method can detect ssDNA (24 nt) at low concentration (44 pM) and is selective over single-nucleotide polymorphism. On addition of an aptamer, the strategy can also be applied to the quantitation of thrombin at levels as low as 0.9 nM. Graphical abstractSchematic representation of target-induced catalytic hairpin assembly to form branched DNA template for the in situ synthesis of fluorescent Cu nanoparticles.
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Label-free and ultrasensitive electrochemical biosensor for the detection of EBV-related DNA based on AgDNCs@DNA/AgNCs nanocomposites and lambda exonuclease-assisted target recycling. Biosens Bioelectron 2019; 143:111610. [DOI: 10.1016/j.bios.2019.111610] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/07/2019] [Accepted: 08/17/2019] [Indexed: 11/18/2022]
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