1
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Zhang X, Liu X, Zhang X, Cui S, Yao Y, Wang B, Zhang Q. Arbitrary Digital DNA Computing: A Programmable Molecular Perceptron Driven by Lambda Exonuclease for Lighting up Concatenated Circuits. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38688864 DOI: 10.1021/acsami.4c03486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
DNA circuits, as a type of biochemical system, have the capability to synchronize the perception of molecular information with a chemical reaction response and directly process the molecular characteristic information in biological activities, making them a crucial area in molecular digital computing and smart bioanalytical applications. Instead of cascading logic gates, the traditional research approach achieves multiple logic operations which limits the scalability of DNA circuits and increases the development costs. Based on the interface reaction mechanism of Lambda exonuclease, the molecular perceptron proposed in this study, with the need for only adjusting weight and bias parameters to alter the corresponding logic expressions, enhances the versatility of the molecular circuits. We also establish a mathematical model and an improved heuristic algorithm for solving weights and bias parameters for arbitrary logic operations. The simulation and FRET experiment results of a series of logic operations demonstrate the universality of molecular perceptron. We hope the proposed molecular perceptron can introduce a new design paradigm for molecular circuits, fostering innovation and development in biomedical research related to biosensing, targeted therapy, and nanomachines.
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Affiliation(s)
- Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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2
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Mattath MN, Zhang H, Ghosh D, Govindaraju T, Shi S. Nanoclusters with specific DNA overhangs: modifying configurability, engineering contrary logic pairs and the parity generator/checker for error detection. NANOSCALE 2023; 15:17386-17397. [PMID: 37847391 DOI: 10.1039/d3nr04167k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The most promising alternative for next-generation molecular computers is biocomputing, which uses DNAs as its primary building blocks to perform a Boolean operation. DNA nanoclusters (NCs) have emerged as promising candidates for biosensing applications due to their unique self-assembly properties and programmability. It has been demonstrated that adding DNA overhangs to DNA NCs improves their adaptability in identifying specific biomolecular interactions. A recent proposal in DNA computing is the concept of "contrary logic pairs (CLPs)" executed by employing a DNA hybrid architecture as a universal platform. We have designed thymine overhang-modified DNA-templated NCs (T-Au/Ag NCs). These NCs serve as a chemosensing ensemble platform, where the presence of HgII ions mediates the formation of M-Au/Ag NCs. The resulting NCs exhibit the capability to drive elementary CLPs (YES, NOT, OR, NOR, INH and IMP) as well as complex logic operations (XOR and XNOR). Additionally, they can be utilized for advanced non-arithmetic DNA logic devices like a parity generator (pG) and a parity checker (pC) for "error detection". Bit errors are an unavoidable and common occurrence during any computing. A cascade of XOR operations was used to evaluate these errors by introducing the pG and pC at the transmitting (TX) and receiving (RX) ends in binary transmission, respectively, which has devastating implications for reliable logic circuits, especially in advanced logic computation. Moreover, an even/odd natural number from 0 to 9 distinguishable pC was designed based on a dual-source responsive computing platform. This work offers inspiring avenues for a cost-effective strategy to construct highly-intelligent DNA computing devices by enhancing the multi-input responsive single DNA platform concept.
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Affiliation(s)
- Mohamed Nabeel Mattath
- School of Chemical Science and Engineering, Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, 1239 Siping Rd, Shanghai, 200092, PR China.
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India.
| | - Haibin Zhang
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, Tongji University, School of Medicine, Shanghai, 200092, PR China
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India.
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India.
| | - Shuo Shi
- School of Chemical Science and Engineering, Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, 1239 Siping Rd, Shanghai, 200092, PR China.
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3
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Gao R, Wei XS, Chen Z, Xie A, Dong W. Leveraging DNA-Based Nanostructures for Advanced Error Detection and Correction in Data Communication. ACS NANO 2023; 17:18055-18061. [PMID: 37498772 DOI: 10.1021/acsnano.3c04777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
This study demonstrates the implementation of the Hamming code using DNA-based nanostructures for error detection and correction in communication systems. The designed DNA nanostructures conduct logical operations to compute check codes and identify and correct erroneous data based on fluorescence signals. The execution of intricate DNA logic operations requires individuals with specialized training. By interpretation of the fluorescence signals generated by the DNA nanostructures, binary language can be extracted, effectively protecting data security. The findings highlight the potential of DNA as a versatile platform for reliable data transmission.
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Affiliation(s)
- Ruru Gao
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Xiu-Shen Wei
- School of Computer Science and Engineering, Southeast University, Nanjing, 210096, China
- Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications (Southeast University), Ministry of Education, Nanjing, 210096, China
| | - Zelin Chen
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Aming Xie
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Wei Dong
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
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4
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Yan C, Mu L, Mei M, Wang Y, She G, Shi W. Fluorescence Enhancement Method for Aptamer-Templated Silver Nanoclusters and Its Application in the Construction of a β-Amyloid Oligomer Sensor. Anal Chem 2023; 95:6915-6922. [PMID: 37079771 DOI: 10.1021/acs.analchem.3c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
DNA-templated silver nanoclusters (DNA-AgNCs) have attracted significant attention due to their unique fluorescence properties. However, so far, the relatively low quantum yields of the DNA-AgNCs and the complex design of DNA-AgNC-based sensors have limited their application in biosensing or bioimaging. Herein, we report a novel fluorescence enhancement method. The β-Amyloid Oligomer (AβO) aptamer (AptAβO) with A10/T10 at its 3' end can be directly used as the template to fabricate the AgNCs. When the AgNCs were hybridized with the complementary strand that has 12 bases suspended at its 3' terminal, being the same or complementary to the A/T at the 3' end of the AptAβO, and two-base mismatches in the complementary region of the aptamer excluded A10/T10, a dramatic fluorescence enhancement (maximum: ∼500-fold; maximum quantum yield: 31.5%) can be realized. The fluorescence enhancement should result from the aggregation-induced emission of the AgNCs, which can be attributed to forming the reticular structure of the hybridized product. To some extent, the method developed in this work is extendable. The fluorescence enhancement was also realized from the thrombin aptamer-templated AgNCs through designing the aptamer and the corresponding complementary strand according to the method. Based on the fluorescence enhancement of the AptAβO-templated AgNCs, an "on-off" fluorescence sensor was constructed for the sensitive and selective detection of AβO. This work provides a rational strategy to realize fluorescence enhancement for the aptamer-templated AgNCs and design an aptamer-based fluorescence sensor.
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Affiliation(s)
- Chenyuan Yan
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixuan Mu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Mingliang Mei
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangwei She
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Wensheng Shi
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Liu QY, Wu Y, Bu ZQ, Quan MX, Lu JY, Huang WT. Sequential-Dependent Synthesis of Bimetallic Silver-Chromium Nanoparticles for Multichannel Sensing, Logic Computing, and 3 in 1 Information Protection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2207436. [PMID: 37026417 DOI: 10.1002/smll.202207436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/12/2023] [Indexed: 06/19/2023]
Abstract
Bimetallic nanomaterials (BNMs) have been used in sensing, biomedicine, and environmental remediation, but their multipurpose and comprehensive applications in molecular logic computing and information security protection have received little attention. Herein, This synthesis method is achieved by sequentially adding reactants under ice bath conditions. Interestingly, Ag-Cr NPs can dynamically selectively sense anions and reductants in multiple channels. Especially, ClO- can be quantitatively detected by oxidizing Ag-Cr NPs with detection limits of 98.37 nM (at 270 nm) and 31.83 nM (at 394 nm). Based on sequential-dependent synthesis process of Ag-Cr NPs, Boolean logic gates and customizable molecular keypad locks are constructed by setting the reactants as the inputs, the states of the resulting solutions as the outputs. Furthermore, dynamically selective response patterns of the Ag-Cr NPs can be converted into binary strings to exploit molecular crypto-steganography to encode, store, and hide information. By integrating the three dimensions of authorization, encryption, and steganography, 3 in 1 advanced information protection based on Ag-Cr nanosensing system can be achieved, which can enhance the anti-cracking ability of information. This research will promote the development and application of nanocomposites in the field of information security and deepen the connection between molecular sensing and the information world.
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Affiliation(s)
- Qing Yu Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
| | - Ying Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
| | - Zhen Qi Bu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
| | - Min Xia Quan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
| | - Jiao Yang Lu
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Academician Workstation, Changsha Medical University, Changsha, 410219, P. R. China
| | - Wei Tao Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, P. R. China
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6
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He MQ, Ai Y, Hu W, Jia X, Wu L, Ding M, Liang Q. Dual-Functional Capping Agent-Mediated Transformation of Silver Nanotriangles to Silver Nanoclusters for Dual-Mode Biosensing. Anal Chem 2023; 95:6130-6137. [PMID: 37002208 DOI: 10.1021/acs.analchem.3c00426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
The localized surface plasmon resonance (LSPR) property, depending on the structure (morphology and assembly) of nanoparticles, is very sensitive to the environmental fluctuation. Retaining the colorimetric effect derived from the LSPR property while introducing new optical properties (such as fluorescence) that provide supplementary information is an effective means to improve the controllability in structures and reproducibility in optical properties. DNA as a green and low-cost etching agent has been demonstrated to effectively control the morphology and optical properties (the blue shift of the LSPR peak) of the plasmonic nanoparticles. Herein, taking silver nanotriangles (AgNTs) as a proof of concept, we report a novel strategy to induce precisely tunable LSPR and fluorescence-composited dual-mode signals by using mono-DNA first as an etching agent for etching the morphology of AgNTs and later as a template for synthesizing fluorescent silver nanoclusters (AgNCs). In addition, common templates for synthesizing AgNCs, such as l-glutathione and bovine serum albumin, were demonstrated to have the capability to serve as etching agents. More importantly, these biomolecules as dual-functional capping agents (etching agents and templates) follow the size-dependent rule: as the size of the thiolated biomolecule increases, the blue shift of the LSPR peak increases; at the same time, the fluorescence intensity increases. The enzyme that can change the molecular weight (size) of the biomolecular substrates (DNA, peptides, and proteins) through an enzymatic cleavage reaction was explored to regulate the LSPR and fluorescent properties of the resulting nanoparticles (by etching of AgNTs and synthesis of AgNCs), achieving excellent performance in detection of cancer-related proteases. This study can be expanded to other biopolymers to impact both fundamental nanoscience and applications and provide powerful new tools for bioanalytical biosensors and nanomedicine.
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Affiliation(s)
- Meng-Qi He
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Laboratory of Flexible Electronics Technology, Center for Synthetic and Systems Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Yongjian Ai
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Laboratory of Flexible Electronics Technology, Center for Synthetic and Systems Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Wanting Hu
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Laboratory of Flexible Electronics Technology, Center for Synthetic and Systems Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Xiaomeng Jia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Laboratory of Flexible Electronics Technology, Center for Synthetic and Systems Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Lei Wu
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Laboratory of Flexible Electronics Technology, Center for Synthetic and Systems Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Mingyu Ding
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Laboratory of Flexible Electronics Technology, Center for Synthetic and Systems Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Qionglin Liang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Laboratory of Flexible Electronics Technology, Center for Synthetic and Systems Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
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7
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Meng F, Yu W, Niu M, Tian X, Miao Y, Li X, Zhou Y, Ma L, Zhang X, Qian K, Yu Y, Wang J, Huang L. Ratiometric electrochemical OR gate assay for NSCLC-derived exosomes. J Nanobiotechnology 2023; 21:104. [PMID: 36964516 PMCID: PMC10037838 DOI: 10.1186/s12951-023-01833-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/26/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common pathological type of LC and ranks as the leading cause of cancer deaths. Circulating exosomes have emerged as a valuable biomarker for the diagnosis of NSCLC, while the performance of current electrochemical assays for exosome detection is constrained by unsatisfactory sensitivity and specificity. Here we integrated a ratiometric biosensor with an OR logic gate to form an assay for surface protein profiling of exosomes from clinical serum samples. By using the specific aptamers for recognition of clinically validated biomarkers (EpCAM and CEA), the assay enabled ultrasensitive detection of trace levels of NSCLC-derived exosomes in complex serum samples (15.1 particles μL-1 within a linear range of 102-108 particles μL-1). The assay outperformed the analysis of six serum biomarkers for the accurate diagnosis, staging, and prognosis of NSCLC, displaying a diagnostic sensitivity of 93.3% even at an early stage (Stage I). The assay provides an advanced tool for exosome quantification and facilitates exosome-based liquid biopsies for cancer management in clinics.
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Affiliation(s)
- Fanyu Meng
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Wenjun Yu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Minjia Niu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xiaoting Tian
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yayou Miao
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xvelian Li
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yan Zhou
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yongchun Yu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
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8
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Cascaded molecular logic gates using antibiotics as inputs based on exonuclease III and DNAzyme. Talanta 2023; 252:123832. [DOI: 10.1016/j.talanta.2022.123832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/07/2022] [Indexed: 11/18/2022]
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9
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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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10
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Mattath MN, Ghosh D, Dong C, Govindaraju T, Shi S. Mercury mediated DNA-Au/Ag nanocluster ensembles to generate a gray code encoder for biocomputing. MATERIALS HORIZONS 2022; 9:2109-2114. [PMID: 35792070 DOI: 10.1039/d2mh00598k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Boolean operations utilizing DNA as a platform for biocomputing have become a promising tool for next-generation bio-molecular computers. In the whole process of any binary data transmission, bit errors are unavoidable and commonly occur. Cascades of exclusive-OR (XOR) operations show the great potential to evaluate these errors by introducing a parity generator (pG) and a parity checker (pC). Herein, we constructed a DNA hybrid architecture platform employing a chemosensing ensemble of mercury-mediated DNA-Au/Ag nanoclusters (M-Au/Ag NCs) to operate unconventional pG/pC for "error detection". Taking advantage of pG/pC, the transmitted and received data is converted to secure information using a binary to gray code encoder. To the best of our knowledge, this is the first molecular gray code encoder for biocomputing, which discovers an exciting avenue to protect information security through sophisticated logic circuits.
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Affiliation(s)
- Mohamed Nabeel Mattath
- School of Chemical Science and Engineering, Department of Oncology, Shanghai East Hospital, Tongji University, 1239 Siping Rd, Shanghai, 200092, P. R. China.
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India.
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India.
| | - Chunyan Dong
- School of Chemical Science and Engineering, Department of Oncology, Shanghai East Hospital, Tongji University, 1239 Siping Rd, Shanghai, 200092, P. R. China.
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India.
| | - Shuo Shi
- School of Chemical Science and Engineering, Department of Oncology, Shanghai East Hospital, Tongji University, 1239 Siping Rd, Shanghai, 200092, P. R. China.
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11
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Luo T, Li J, He Y, Liu H, Deng Z, Long X, Wan Q, Ding J, Gong Z, Yang Y, Zhong S. Designing a CRISPR/Cas12a- and Au-Nanobeacon-Based Diagnostic Biosensor Enabling Direct, Rapid, and Sensitive miRNA Detection. Anal Chem 2022; 94:6566-6573. [PMID: 35451838 DOI: 10.1021/acs.analchem.2c00401] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Direct, rapid, sensitive, and selective detection of nucleic acids in complex biological fluids is crucial for medical early diagnosis. We herein combine the trans-cleavage ability of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a with Au-nanobeacon to establish a CRISPR-based biosensor, providing rapid miRNA detection with high speed and attomolar sensitivity. In this strategy, we first report that the trans-cleavage activity of CRISPR/cas12a, which was previously reported to be triggered only by target ssDNA or dsDNA, can be activated by the target miRNA directly. Therefore, this method is direct, i.e., does not need the conversion of miRNA into its complementary DNA (cDNA). Meanwhile, as compared to the traditional ssDNA reporters and molecular beacon (MB) reporters, the Au-nanobeacon reporters exhibit improved reaction kinetics and sensitivity. In this assay, the miRNA-21 could be detected with very high sensitivity in only 5 min. Finally, the proposed strategy enables rapid, sensitive, and selective miRNA determination in complex biological samples, providing a potential tool for medical early diagnosis.
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Affiliation(s)
- Tong Luo
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jiacheng Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Yao He
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Hui Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zhiwei Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Xi Long
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Qingqing Wan
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jiacheng Ding
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zan Gong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Yanjing Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Shian Zhong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
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12
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Liu X, Zhang Q, Zhang X, Liu Y, Yao Y, Kasabov N. Construction of Multiple Logic Circuits Based on Allosteric DNAzymes. Biomolecules 2022; 12:biom12040495. [PMID: 35454084 PMCID: PMC9032175 DOI: 10.3390/biom12040495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
In DNA computing, the implementation of complex and stable logic operations in a universal system is a critical challenge. It is necessary to develop a system with complex logic functions based on a simple mechanism. Here, the strategy to control the secondary structure of assembled DNAzymes’ conserved domain is adopted to regulate the activity of DNAzymes and avoid the generation of four-way junctions, and makes it possible to implement basic logic gates and their cascade circuits in the same system. In addition, the purpose of threshold control achieved by the allosteric secondary structure implements a three-input DNA voter with one-vote veto function. The scalability of the system can be remarkably improved by adjusting the threshold to implement a DNA voter with 2n + 1 inputs. The proposed strategy provides a feasible idea for constructing more complex DNA circuits and a highly integrated computing system.
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Affiliation(s)
- Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
- Correspondence: ; Tel.: +86-0411-84708470
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; (X.L.); (X.Z.); (Y.L.); (Y.Y.)
| | - Nikola Kasabov
- Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, Auckland 1010, New Zealand;
- Intelligent Systems Research Center, Ulster University, Londonderry BT52 1SA, UK
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13
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Li M, Yao B, Jing C, Chen H, Zhang Y, Zhou N. Engineering a G-quadruplex-based logic gate platform for sensitive assay of dual biomarkers of ovarian cancer. Anal Chim Acta 2022; 1198:339559. [DOI: 10.1016/j.aca.2022.339559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/06/2022] [Accepted: 01/26/2022] [Indexed: 11/24/2022]
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14
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Pan J, Deng F, Liu Z, Shi G, Chen J. Toehold-Mediated Cascade Catalytic Assembly for Mycotoxin Detection and Its Logic Applications. Anal Chem 2022; 94:3693-3700. [PMID: 35176850 DOI: 10.1021/acs.analchem.1c05485] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this work, an enzyme-free biosensor is reported for mycotoxin detection based on a toehold-mediated catalytic hairpin assembly (CHA) and a DNAzyme-cascaded hydrolysis reaction. In the presence of a mycotoxin, the recognition between an aptamer and the mycotoxin releases the trigger DNA. The trigger DNA initiates the toehold-mediated CHA, generating large amounts of partial duplex B/C with four toeholds, which can be used to assemble the DNAzyme-cascaded hydrolysis reaction. Furthermore, through a collaborative autoassembly reaction among the B/C duplex, DNA1, and DNA2, supramolecular nanostructures corresponding to Mg2+-dependent DNAzymes can be formed. With the incubation of Mg2+, the dual-modified (TAMRA/BHQ2) substrate strand DNA2 will be cleaved into two fragments, yielding a high TAMRA fluorescence signal for mycotoxin testing. Under optimal conditions, the sensing system was ultrasensitive and showed low detection limits of 0.2 pM for ochratoxin A (OTA), 0.13 pM for aflatoxin B1 (AFB1), and 0.17 pM for zearalenone (ZEN). The mycotoxin aptasensor also exhibited high selectivity and was successfully applied for the quantitative analysis of OTA, AFB1, and ZEN in wine samples. Due to the advantages of flexibility and versatility, this mycotoxin platform was used to fabricate several concatenated logic gates including "AND-INHIBIT", "INHIBIT-OR", "OR-AND", and "OR-INHIBIT" logic biocomputings. Such multiple functions of the logic system provided a universal sensing strategy for the intelligent detection of multiplex mycotoxins, demonstrating considerable potential in food safety and environmental monitoring.
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Affiliation(s)
- Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fang Deng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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15
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Zhu L, Yu L, Meng T, Peng Y, Yang X. Contrary Logic Pair Library, Parity Generator/Checker and Various Concatenated Logic Circuits Engineered by a Label-Free and Immobilization-Free Electrochemiluminescence Resonance Energy Transfer System. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102881. [PMID: 34792279 DOI: 10.1002/smll.202102881] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/24/2021] [Indexed: 06/13/2023]
Abstract
Herein, a label-free and immobilization-free electrochemiluminescence resonance energy transfer (ECL-RET) system based on graphitic carbon nitride nanosheets (GCNNs)/Ru(phen)32+ donor/acceptor pair is developed, in which the ECL-RET is regulated by regulating the diffusivity of Ru(phen)32+ molecules toward the negatively charged GCNNs through logically programmed DNA hybridization reactions. The two optical signals of GCNNs (445 nm) and Ru(phen)32+ (593 nm) show completely opposite changes through the same one-time DNA hybridization reaction. Based on this ECL-RET system, a contrary logic pair (CLP) library, a parity generator/checker system for differentiating the erroneous bits during data transmission, the parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits including a six-input logic gate capable of implementing of 64 input combinations for meeting the needs of computational complexity are developed. The ECL-RET-based molecular logic system avoids the time-consuming, costly and inefficient labeling procedures and the laborious processes of immobilization, presenting great potential for building more complicated and advanced logic gates, and providing a refreshing inspiration for the construction of combinatorial logic circuits based on ECL method.
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Affiliation(s)
- Liping Zhu
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Linying Yu
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Tian Meng
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Yao Peng
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xiurong Yang
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
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16
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Zhu L, Yu L, Yang X. Electrochemical-Based DNA Logic Devices Regulated by the Diffusion and Intercalation of Electroactive Dyes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:42250-42257. [PMID: 34452580 DOI: 10.1021/acsami.1c12650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Electrochemical-based logic gates are simple to operate, sensitive, controllable, and easy to integrate with silicon-based semiconductor logic devices, showing great application prospects and remaining largely unexplored. Herein, an immobilization-free dual-output electrochemical molecular logic system based on the different diffusivity of electroactive dyes ferrocene (Fc) and methylene blue (MB) toward an indium tin oxide (ITO) electrode under different DNA hybridization reactions was developed. In this system, the hybridization of the catalytic strand IN1 with Fc-modified hairpin DNA H1 triggered an exonuclease III (Exo III) cleavage cycle to obtain free Fc and produce a large number of long double-stranded DNAs via the hybridization chain reaction for intercalating MB, which was previously in the free state. Such a hybridization reaction caused a significant change in the diffusion capacity of MB and Fc toward the ITO electrode, resulting in two electrochemical signals with opposite changes. On this basis, a contrary logic pair library, a parity generator/checker system for differentiating the erroneous bits during data transmission, a parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits for meeting the needs of computational complexity were developed. The proposed electrochemical-based molecular logic system greatly expanded the application of the electrochemical method in the construction of logic circuits and provided a conceptual prototype for the development of more advanced and complicated logic devices.
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Affiliation(s)
- Liping Zhu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Linying Yu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Xiurong Yang
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
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17
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Chai Q, Wan Y, Zou Y, Zhu T, Li N, Chen J, Lai G. Ultrasensitive and turn-on homogeneous Hg 2+ sensing based on a target-triggered isothermal cycling reaction and dsDNA-templated copper nanoparticles. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3521-3526. [PMID: 34278388 DOI: 10.1039/d1ay00880c] [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
In this work, an ultrasensitive and turn-on sensor for homogeneous Hg2+ detection has been constructed based on a target-triggered isothermal cycling reaction and rapid label-free signal output with dsDNA-templated copper nanoparticles (CuNPs). As the key component of the sensor, a hairpin DNA without any labels was designed to contain different functional sequence segments and to resist digestion by exonuclease due to the protruding 3'-terminus. In the presence of Hg2+, the formation of a T-Hg2+-T structure turned the protruding 3'-terminus of the hairpin DNA to a blunt end that could be efficiently digested by Exo III, accompanied by Hg2+ release, followed by another digestion cycle. Hence, the Hg2+-triggered isothermal cycling reaction accumulated numerous dsDNA templates that facilitated fluorescent CuNP generation and finally output an amplified signal used to identify the target. This protocol is capable of Hg2+ sensing in a concentration range of 5 orders of magnitude with a detection limit down to 3.9 pM. The as-constructed sensor also revealed high selectivity, as well as satisfactory results in recovery experiments of Hg2+ detection in real water samples.
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Affiliation(s)
- Qingli Chai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
| | - Yuqi Wan
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
| | - Yanyun Zou
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
| | - Ting Zhu
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
| | - Ningxing Li
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Jinyang Chen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
| | - Guosong Lai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
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18
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Wu H, Wang H, Wu J, Han G, Liu Y, Zou P. A novel fluorescent aptasensor based on exonuclease-assisted triple recycling amplification for sensitive and label-free detection of aflatoxin B1. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125584. [PMID: 33743380 DOI: 10.1016/j.jhazmat.2021.125584] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Aflatoxins are the most toxic type of mycotoxins, which may cause serious carcinogenesis, teratogenesis, and mutagenesis to humans and animals. In this work, we demonstrate a novel label-free fluorescent aptasensor based on exonuclease-assisted triple recycling amplification for the sensitive detection of aflatoxin B1 (AFB1). With the close cooperation of T7 exonuclease and three elaborately designed hairpin probes, the target AFB1 can perform three consecutive cycles of amplification reactions. In this process, each hairpin probe is fully utilized, and the target AFB1, the secondary target and the tertiary target are recycled, thereby achieving a high amplification. Interestingly and importantly, the secondary and tertiary targets generated by amplification are also excellent DNA template sequences for silver nanoclusters (AgNCs). In the presence of NaBH4 and AgNO3, a great number of DNA-AgNCs are synthesized, thereby producing a strong fluorescent signal. Under optimal conditions, the developed aptasensor exhibited high sensitivity to AFB1 with a low detection limit of 0.19 pg mL-1 and a wide dynamic range of 1 × 10-6-1 μg mL-1. In addition, the aptasensor also performed well in the determination of AFB1 in real samples.
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Affiliation(s)
- Hao Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| | - Hongyong Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Jun Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Guoqing Han
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Yaling Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| | - Pei Zou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China; Jiangsu Kanion Pharmaceutical CO. LTD, Lianyungang 222001, China; State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Lianyungang 222001, China.
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19
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Tao Y, Aparicio T, Li M, Leong KW, Zha S, Gautier J. Inhibition of DNA replication initiation by silver nanoclusters. Nucleic Acids Res 2021; 49:5074-5083. [PMID: 33905520 PMCID: PMC8136792 DOI: 10.1093/nar/gkab271] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 03/10/2021] [Accepted: 04/07/2021] [Indexed: 01/19/2023] Open
Abstract
Silver nanoclusters (AgNCs) have outstanding physicochemical characteristics, including the ability to interact with proteins and DNA. Given the growing number of diagnostic and therapeutic applications of AgNCs, we evaluated the impact of AgNCs on DNA replication and DNA damage response in cell-free extracts prepared from unfertilized Xenopus laevis eggs. We find that, among a number of silver nanomaterials, AgNCs uniquely inhibited genomic DNA replication and abrogated the DNA replication checkpoint in cell-free extracts. AgNCs did not affect nuclear membrane or nucleosome assembly. AgNCs-supplemented extracts showed a strong defect in the loading of the mini chromosome maintenance (MCM) protein complex, the helicase that unwinds DNA ahead of replication forks. FLAG-AgNCs immunoprecipitation and mass spectrometry analysis of AgNCs associated proteins demonstrated direct interaction between MCM and AgNCs. Our studies indicate that AgNCs directly prevent the loading of MCM, blocking pre-replication complex (pre-RC) assembly and subsequent DNA replication initiation. Collectively, our findings broaden the scope of silver nanomaterials experimental applications, establishing AgNCs as a novel tool to study chromosomal DNA replication.
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Affiliation(s)
- Yu Tao
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Tomas Aparicio
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Mingqiang Li
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Shan Zha
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Departments of Pediatrics, Pathology and Cell Biology, Immunology and Microbiology, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
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20
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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: 25] [Impact Index Per Article: 8.3] [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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21
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Guo Y, Wang M, Shen F, Hu Z, Ding H, Yao W, Qian H. Sensitive detection of RNA based on concatenated self-fuelled strand displacement amplification and hairpin-AgNCs. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:447-452. [PMID: 33355546 DOI: 10.1039/d0ay01762k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Herein, a self-fuelled amplification strategy (SFAS) is proposed, in which two strand displacement amplification (SDA) processes were concatenated for the proliferation of ssDNA. The ssDNA then initiated a polymerase action and caused the destruction of hairpin-templated silver nanoclusters (AgNCs), resulting in decreased fluorescence for sensing miRNA-21. This SFAS-based sensor is less complicated in design and facile in operation, because of the easy concatenation of SDA and mutual enzymes used in the signal output process. The sensitivity of this SFAS-based miRNA sensor was 1.78 × 10-11 M with a linear relationship in the range 0.02-1.0 × 10-9 M, and the recoveries of this method ranged from 82.07% to 106.58% with an average RSD of 10.96%.
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Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China.
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22
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Guo Y, Lv M, Ren J, Wang E. Regulating Catalytic Activity of DNA-Templated Silver Nanoclusters Based on their Differential Interactions with DNA Structures and Stimuli-Responsive Structural Transition. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006553. [PMID: 33350148 DOI: 10.1002/smll.202006553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/05/2020] [Indexed: 05/21/2023]
Abstract
This work reports exquisite engineering of catalytic activity of DNA-templated silver nanoclusters (DNA-AgNCs) based on unique adsorption phenomena of DNAs on DNA-AgNCs and reversible transition between double and triple-stranded DNAs. Four DNA homopolymers exhibit different inhibition effects on the catalytic activity of DNA-AgNCs, poly adenine (polyA) > poly guanine (polyG) > poly cytosine (polyC) > poly thymine (polyT), demonstrating that polyA strands have the strongest adsorption affinity on DNA-AgNCs. Through the formation of T-A•T triplex DNAs, catalytic activity of DNA-AgNCs is restored from the deactivated state by double or single-stranded DNAs, indicating the participation of N7 groups of adenine bases in binding to DNA-AgNCs and blocking active sites. Accordingly, reversibly regulating catalytic activity of DNA-AgNCs can be realized based on DNA input-stimulated transition between duplex and triplex structures. In the end, two low-cost and facile biosensing methods are presented, which are derived from the activity-switchable platform. It is worthy to anticipate that the DNA-AgNCs with controlled catalytic activity will inspire researchers to devise more functionalized nanocatalysts and contribute to the exploration of intelligent biomedicine in the future.
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Affiliation(s)
- Yuchun Guo
- College of Chemistry, Jilin University, Changchun, Jilin, 130012, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Mengmeng Lv
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Erkang Wang
- College of Chemistry, Jilin University, Changchun, Jilin, 130012, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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23
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Ma J, Niu H, Gu S. The spatial organization of trace silver atoms on a DNA template. RSC Adv 2020; 11:1153-1163. [PMID: 35423706 PMCID: PMC8693506 DOI: 10.1039/d0ra08066g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
DNA with programmable information can be used to encode the spatial organization of silver atoms. Based on the primary structures of a DNA template containing a controllable base arrangement and number, the surrounding environment and cluster together can induce the folding of the DNA template into an appropriate secondary structure for forming AgNCs with different fluorescence emissions, such as i-motif, G-quadruplex, dimeric template, triplex, monomeric or dimeric C-loop, emitter pair, and G-enhancer/template conjugate. Stimuli can induce the dynamic structural transformation of the DNA template with a recognition site for favourably or unfavourably forming AgNCs, along with varied fluorescence intensities and colours. The array of several or more of the same and different clusters can be performed on simple and complex nanostructures, while maintaining their original properties. By sorting out this review, we systematically conclude the link between the performance of AgNCs and the secondary structure of the DNA template, and summarize the precise arrangement of nanoclusters on DNA nanotechnology. This clear review on the origin and controllability of AgNCs based on the secondary structure of the DNA template is beneficial for exploring the new probe and optical devices.
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Affiliation(s)
- Jinliang Ma
- College of Food and Bioengineering, Henan University of Science and Technology Luoyang Henan 471023 China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Huawei Niu
- College of Food and Bioengineering, Henan University of Science and Technology Luoyang Henan 471023 China
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology Luoyang Henan 471023 China
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24
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Ma J, Li K, Gu S. Efficient Editing of Silver Nanoclusters by Changing Simply One Cytosine in a DNA Template. Chembiochem 2020; 22:1210-1214. [PMID: 33174392 DOI: 10.1002/cbic.202000640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/09/2020] [Indexed: 11/07/2022]
Abstract
DNA with genetic information was edited to regulate and repair the structure and function of a protein. In DNA nanotechnology, DNA with programmable information can be designed to edit the fluorescence intensity and emissive colors of DNA-stabilized silver nanoclusters (DNA/AgNCs). By introducing and moving one cytosine in the spacer of the emitter domain, we have built up a simple strategy to regulate the excitation and emission wavelengths of AgNCs. When replacing thymine in the spacer of the emitter with one cytosine, the expected excitation and emission change do not occur. However, after moving the introduced cytosine, DNA templates produce AgNCs with extremely different excitation and emission wavelengths from those of the initial template, leading to a template for near-infrared (NIR) emissive species with the highest fluorescence intensity. The formation of AgNCs induces the DNA template into condensed secondary structure based on an altered migration rate in PAGE. The simple strategy of moving one cytosine in a spacer in the emitter domain can enrich the library of templates for synthesizing diverse DNA/AgNCs and has great potential in bioimaging and probe design.
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Affiliation(s)
- Jinliang Ma
- College of Food and Bioengineering, Henan University of Science and Technology, 471023, Luoyang, Henan, P. R. China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, P. R. China
| | - Kexin Li
- College of Food and Bioengineering, Henan University of Science and Technology, 471023, Luoyang, Henan, P. R. China
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology, 471023, Luoyang, Henan, P. R. China
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Lin X, Yang S, Huang D, Guo C, Chen D, Yang Q, Li F. A supramolecular aggregation-based constitutional dynamic network for information processing. Chem Sci 2020; 11:9617-9622. [PMID: 34094228 PMCID: PMC8161677 DOI: 10.1039/d0sc03392h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Concepts and strategies offered by constitutional dynamic chemistry (CDC) hold great promise for designing molecular computing systems adaptive to external environments. Despite demonstrable success in storing and processing chemical information using CDC, further employment of such constitutional dynamic networks (CDNs) for processing more complex digital information has not been realized yet. Herein, we introduced a supramolecular CDN based on the aggregation of cyanine MTC (Agg-CDN), which is composed of four reversibly interconvertible constituents, i.e. monomers, dimers, J-aggregates, and H-aggregates. We demonstrated that the equilibrated Agg-CDN is reconfigurable through constituent exchange in response to well-defined chemical inputs. More importantly, the equilibrated states of the Agg-CDN are spectroscopically distinguishable because of the unique optical properties of MTC. We further tuned the Agg-CDN to at least nine unique states for transforming the chemical inputs into digital outputs, and successfully employed it for encoding and encrypting complex digital information, such as multi-pixel images. We constructed a supramolecular cyanine MTC aggregation-based constitutional dynamic network, which can transform the chemical information into image information reversibly.![]()
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Affiliation(s)
- Xiao Lin
- College of Chemistry, Sichuan University Chengdu 610064 China
| | - Shu Yang
- West China School of Pharmacy, Sichuan University Chengdu 610041 China
| | - Dan Huang
- College of Chemistry, Sichuan University Chengdu 610064 China
| | - Chen Guo
- College of Chemistry, Sichuan University Chengdu 610064 China
| | - Die Chen
- West China School of Pharmacy, Sichuan University Chengdu 610041 China
| | - Qianfan Yang
- College of Chemistry, Sichuan University Chengdu 610064 China
| | - Feng Li
- College of Chemistry, Sichuan University Chengdu 610064 China
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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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Dong J, Wang M, Zhou Y, Zhou C, Wang Q. DNA‐Based Adaptive Plasmonic Logic Gates. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine andi-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Meng Wang
- College of Food Science and Engineering Nanjing University of Finance and Economics Nanjing 210023 P. R. China
| | - Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine andi-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Chao Zhou
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine andi-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine andi-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
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28
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Dong J, Wang M, Zhou Y, Zhou C, Wang Q. DNA‐Based Adaptive Plasmonic Logic Gates. Angew Chem Int Ed Engl 2020; 59:15038-15042. [DOI: 10.1002/anie.202006029] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine andi-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Meng Wang
- College of Food Science and Engineering Nanjing University of Finance and Economics Nanjing 210023 P. R. China
| | - Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine andi-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Chao Zhou
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine andi-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine andi-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
- School of Physical Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
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