151
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Fu X, Peng F, Lee J, Yang Q, Zhang F, Xiong M, Kong G, Meng HM, Ke G, Zhang XB. Aptamer-Functionalized DNA Nanostructures for Biological Applications. Top Curr Chem (Cham) 2020; 378:21. [PMID: 32030541 DOI: 10.1007/s41061-020-0283-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/17/2020] [Indexed: 12/31/2022]
Abstract
DNA nanostructures hold great promise for various applications due to their remarkable properties, including programmable assembly, nanometric positional precision, and dynamic structural control. The past few decades have seen the development of various kinds of DNA nanostructures that can be employed as useful tools in fields such as chemistry, materials, biology, and medicine. Aptamers are short single-stranded nucleic acids that bind to specific targets with excellent selectivity and high affinity and play critical roles in molecular recognition. Recently, many attempts have been made to integrate aptamers with DNA nanostructures for a range of biological applications. This review starts with an introduction to the features of aptamer-functionalized DNA nanostructures. The discussion then focuses on recent progress (particularly during the last five years) in the applications of these nanostructures in areas such as biosensing, bioimaging, cancer therapy, and biophysics. Finally, challenges involved in the practical application of aptamer-functionalized DNA nanostructures are discussed, and perspectives on future directions for research into and applications of aptamer-functionalized DNA nanostructures are provided.
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Affiliation(s)
- Xiaoyi Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Mengyi Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Gezhi Kong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Hong-Min Meng
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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152
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153
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Jiang Y, Miao P. DNA Dumbbell and Chameleon Silver Nanoclusters for miRNA Logic Operations. RESEARCH (WASHINGTON, D.C.) 2020; 2020:1091605. [PMID: 32342044 PMCID: PMC7071348 DOI: 10.34133/2020/1091605] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 02/17/2020] [Indexed: 04/26/2023]
Abstract
Multiplex miRNA analysis is a fundamental issue for exploring a complex biological system and early diagnosis of miRNA-related diseases. Herein, we have developed a series of novel logic gates for miRNA analysis coupling DNA nanostructures and chameleon silver nanoclusters (AgNCs). DNA dumbbell structures are firstly designed with two independent nucleation sequences for AgNCs at the 5' and 3' ends, respectively. By introducing different miRNA inputs, separations of two AgNCs are controlled and the fluorescence property of AgNCs changes. By studying the ratiometric fluorescence responses, sensitive and selective analysis of multiple miRNAs can be achieved. The present work provides powerful tools for miRNA diagnostics and may also guide future DNA nanostructure-based logic gates.
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Affiliation(s)
- Yiting Jiang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of
Sciences, Suzhou 215163, China
- University of Science and Technology of China, Hefei 230026, China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of
Sciences, Suzhou 215163, China
- University of Science and Technology of China, Hefei 230026, China
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154
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155
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Sun L, Su Y, Wang JG, Xia F, Xu Y, Li D. DNA nanotweezers for stabilizing and dynamically lighting up a lipid raft on living cell membranes and the activation of T cells. Chem Sci 2020; 11:1581-1586. [PMID: 34084389 PMCID: PMC8148038 DOI: 10.1039/c9sc06203c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Lipid rafts are generally considered as nanodomains on cell membranes and play important roles in signaling, viral infection, and membrane trafficking. However, the raft hypothesis is still debated with many inconsistencies because the nanoscale and transient heterogeneous raft structure creates difficulties in its location and functional analysis. In the present study, we report a DNA nanotweezer composed of a cholesterol-functionalized DNA duplex that stabilizes transient lipid rafts, which facilitate the further analysis of the raft component and its functions via other spectroscopy tools. The proposed DNA nanotweezer can induce clustering of raft-associated components (saturated lipids, membrane protein and possibly endogenous cholesterol), leading to the T cell proliferation through clustering of a T-cell antigen receptor (TCR). The flexibility of random sequence noncoding DNA provides versatile possibilities of manipulating lipid rafts and activating T cells, and thus opens new ways in a future T cell therapy. We report a DNA nanotweezer that recruits raft-associated lipids, proteins and possibly endogenous cholesterol on living cell membrane. The DNA nanotweezers could activate T cell proliferation in a nonspecific activation manner.![]()
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Affiliation(s)
- Lele Sun
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
- Institute of Functional Nano & Soft Materials (FUNSOM)
| | - Yingying Su
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Jun-Gang Wang
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Fei Xia
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Ying Xu
- Department of Pathophysiology
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education
- Shanghai Jiao-Tong University School of Medicine
- Shanghai
- China
| | - Di Li
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
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156
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Lin Q, Wang A, Liu S, Li J, Wang J, Quan K, Yang X, Huang J, Wang K. A DNA tetrahedron-based molecular computation device for the logic sensing of dual microRNAs in living cells. Chem Commun (Camb) 2020; 56:5303-5306. [DOI: 10.1039/d0cc01231a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Endogenous miRNA expression patterns are specific to cell type and thus offer high prediction accuracy with regard to different cell identities compared to single miRNA analysis.
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Affiliation(s)
- Qing Lin
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Anmin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Shiyuan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Jing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Jiaoli Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Ke Quan
- School of Chemistry and Food Engineering
- Changsha University of Science and Technology
- Changsha
- China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
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157
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Zheng J, Shi H, Wang M, Duan C, Huang Y, Li C, Xiang Y, Li G. Homogenous Electrochemical Method for Ultrasensitive Detection of Tumor Cells Designed by Introduction of Poly(A) Tails onto Cell Membranes. Anal Chem 2019; 92:2194-2200. [PMID: 31850744 DOI: 10.1021/acs.analchem.9b04877] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid and efficient detection of tumor cells is one of the central challenges for modern analytical technology. In this paper, we report a polyadenine (poly(A)) tail-based strategy for ultrasensitive detection of tumor cells in aqueous solution with an electrochemical technique. Specifically, tumor cell-specific EpCAM aptamers without any modification can tightly bind on cell membranes and facilitate the subsequent introduction of multiple poly(A) tails via programmable terminal deoxynucleotidyl transferase (TdT)-mediated elongation. Meanwhile, since tumor cells bearing poly(A) tails can be easily adsorbed onto the surface of gold electrodes through a strong interaction between adenosines and gold, a highly amplified electrochemical signal can be obtained. Thus, by virtue of poly(A) tails, the proposed method allows the detection of as low as 3 cells mL-1. Compared with the previously reported methods for tumor cells detection, this poly(A)-based homogeneous electrochemical method needs just one enzyme and one aptamer without any modification and avoids the complex and time-consuming modification process of the working electrode, which holds great potential application in the future.
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Affiliation(s)
- Ji Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Hai Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Mengjiao Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Yue Huang
- Department of Food Science and Engineering, College of Light Industry and Food Engineering , Nanjing Forestry University , Nanjing 210037 , P. R. China
| | - Chao Li
- School of Food and Biological Engineering , Hefei University of Technology , Hefei , Anhui 230009 , P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
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158
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Geng H, Zhou C, Guo C. DNA-based digital comparator systems constructed by multifunctional nanoswitches. NANOSCALE 2019; 11:21856-21866. [PMID: 31696192 DOI: 10.1039/c9nr08216f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this paper, we propose a strategy involving coupling DNA structural nanoswitches with toehold mediated strand displacement for constructing novel DNA-based digital comparator (DC) logic systems, which are a basic part of traditional electronic computers and can compare whether two or more input numbers are equal. However, when the number of DC inputs is increased to a certain level, the speed and quality of the computing circuit can be affected because of the limitations of conventional electronic computers when it comes to handling large-scale quantities of data. To solve this problem, in this work, we introduce a multi-input to multi-output DNA switch-based platform that can enable complex DC logical comparison. These multifunctional DNA-based switches, each including two hairpin-shaped molecular beacons and a G4/NMM complex, were used as platforms for the step-by-step realization of 2-3 DC, 3-3 DC, and 4-3 DC logic operations. Also, experiments were designed to further verify the excellent selectivity, achieving single-base mismatch operations with the digital comparator. Based on our design, comparators (">", "<" and "=") can be realized. Our prototype can inspire new designs and have intelligent digital comparator and in-field applications.
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Affiliation(s)
- Hongmei Geng
- The Guo China-US Photonics Laboratory, State Key Laboratory for Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyang Zhou
- The Guo China-US Photonics Laboratory, State Key Laboratory for Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, P. R. China.
| | - Chunlei Guo
- The Guo China-US Photonics Laboratory, State Key Laboratory for Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, P. R. China. and The Institute of Optics, University of Rochester, Rochester, New York 14627, USA
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159
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Peng X, Wen ZB, Yang P, Chai YQ, Liang WB, Yuan R. Biomimetic 3D DNA Nanomachine via Free DNA Walker Movement on Lipid Bilayers Supported by Hard SiO 2@CdTe Nanoparticles for Ultrasensitive MicroRNA Detection. Anal Chem 2019; 91:14920-14926. [PMID: 31674756 DOI: 10.1021/acs.analchem.9b03263] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein, a novel three-dimensional (3D) DNA nanomachine with high walking efficiency via free DNA walker movement on biomimetic lipid bilayers supported by hard silica@CdTe quantum dots (SiO2@CdTe) was constructed for ultrasensitive fluorescence detection of microRNA. The synthesized SiO2@CdTe nanoparticles were adopted as the fluorescence indicator and spherical carrier of lipid bilayers, and then the DNA substrates were anchored on lipid bilayers with biomimetic fluidity through the cholesterol-lipid interaction. Once target microRNA-141 interacted with the 3D DNA nanomachine to release cholesterol labeled arm (Chol-arm), the Chol-arm could generate a series of strand displacement reactions by moving freely on the lipid bilayers, resulting in the releasement of numerous quenchers from the SiO2@CdTe nanoparticles and inducing a strong fluorescence signal. Impressively, compared with traditional 3D DNA nanomachine conjugating DNA substrates on hard surfaces (such as gold or silica) with limited reactivity, the proposed biomimetic 3D DNA nanomachine not only immobilized DNA substrates rapidly and effectively but also kept it with a favorable fluidity, which significantly enhanced the walking efficiency. As expected, the biomimetic 3D DNA nanomachine for fluorescence detection of microRNA-141 exhibited an excellent performance with a detection limit of 0.21 pM and presented promising properties in cell lysate detection and intracellular imaging. Thus, the described biomimetic 3D DNA nanomachine provided a novel avenue for sensitive detection of biomolecules, which could be useful for bioanalysis and early clinical diagnoses of disease.
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Affiliation(s)
- Xin Peng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P.R. China
| | - Zhi-Bin Wen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P.R. China
| | - Peng Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P.R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P.R. China
| | - Wen-Bin Liang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P.R. China
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160
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Zhou F, Fu T, Huang Q, Kuai H, Mo L, Liu H, Wang Q, Peng Y, Han D, Zhao Z, Fang X, Tan W. Hypoxia-Activated PEGylated Conditional Aptamer/Antibody for Cancer Imaging with Improved Specificity. J Am Chem Soc 2019; 141:18421-18427. [PMID: 31584808 DOI: 10.1021/jacs.9b05063] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Aptamers and antibodies, as molecular recognition probes, play critical roles in cancer diagnosis and therapy. However, their recognition ability is based on target overexpression in disease cells, not target exclusivity, which can cause on-target off-tumor effects. To address the limitation, we herein report a novel strategy to develop a conditional aptamer conjugate which recognizes its cell surface target, but only after selective activation, as determined by characteristics of the disease microenvironment, which, in our model, involve tumor hypoxia. This conditional aptamer is the result of conjugating the aptamer with PEG5000-azobenzene-NHS, which is responsive to hypoxia, here acting as a caging moiety of conditional recognition. More specifically, the caging moiety is unresponsive in the intact conjugate and prevents target recognition. However, in the presence of sodium dithionite or hypoxia (<0.1% O2) or in the tumor microenvironment, the caging moiety responds by allowing conditional recognition of the cell-surface target, thereby reducing the chance of on-target off-tumor effects. It is also confirmed that the strategy can be used for developing a conditional antibody. Therefore, this study demonstrates an efficient strategy by which to develop aptamer/antibody-based diagnostic probes and therapeutic drugs for cancers with a unique hypoxic microenvironment.
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Affiliation(s)
- Fang Zhou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Qin Huang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Liuting Mo
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Honglin Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Qianqian Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Yongbo Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Dongmei Han
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Zilong Zhao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Xiaohong Fang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , P. R. China.,Institute of Cancer and Basic Medicine , Chinese Academy of Sciences (IBMC); Cancer Hospital, University of Chinese Academy of Sciences , Hangzhou , Zhejiang 310022 , China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , P. R. China.,Institute of Molecular Medicine (IMM), State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University Shanghai , Shanghai , P. R. China.,Institute of Cancer and Basic Medicine , Chinese Academy of Sciences (IBMC); Cancer Hospital, University of Chinese Academy of Sciences , Hangzhou , Zhejiang 310022 , China
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161
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Yang Z, Wu H, Yi X, Tang J, Yun W, Han W, Chen X. A universal converting strategy based on target-induced DNA nanoprobe conformational change for lead (II) ion assay. Biosens Bioelectron 2019; 144:111679. [DOI: 10.1016/j.bios.2019.111679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/04/2019] [Accepted: 09/04/2019] [Indexed: 12/19/2022]
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162
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Chen S, Xu Z, Yang W, Lin X, Li J, Li J, Yang H. Logic-Gate-Actuated DNA-Controlled Receptor Assembly for the Programmable Modulation of Cellular Signal Transduction. Angew Chem Int Ed Engl 2019; 58:18186-18190. [PMID: 31595614 DOI: 10.1002/anie.201908971] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/18/2019] [Indexed: 02/01/2023]
Abstract
Programming cells to sense multiple inputs and activate cellular signal transduction cascades is of great interest. Although this goal has been achieved through the engineering of genetic circuits using synthetic biology tools, a nongenetic and generic approach remains highly demanded. Herein, we present an aptamer-controlled logic receptor assembly for modulating cellular signal transduction. Aptamers were engineered as "robotic arms" to capture target receptors (c-Met and CD71) and a DNA logic assembly functioned as a computer processor to handle multiple inputs. As a result, the DNA assembly brings c-Met and CD71 into close proximity, thus interfering with the ligand-receptor interactions of c-Met and inhibiting its functions. Using this principle, a set of logic gates was created that respond to DNA strands or light irradiation, modulating the c-Met/HGF signal pathways. This simple modular design provides a robust chemical tool for modulating cellular signal transduction.
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Affiliation(s)
- Shan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Zhifei Xu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Wen Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Xiahui Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Jingying Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China
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163
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Chen S, Xu Z, Yang W, Lin X, Li J, Li J, Yang H. Logic‐Gate‐Actuated DNA‐Controlled Receptor Assembly for the Programmable Modulation of Cellular Signal Transduction. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908971] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Shan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
- Institute of Molecular MedicineRenji HospitalShanghai Jiao Tong University School of MedicineShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Zhifei Xu
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
| | - Wen Yang
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
| | - Xiahui Lin
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
| | - Jingying Li
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
- College of Biological Science and EngineeringFuzhou University Fuzhou 350108 P. R. China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
- Institute of Molecular MedicineRenji HospitalShanghai Jiao Tong University School of MedicineShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
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164
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Song T, Shah S, Bui H, Garg S, Eshra A, Fu D, Yang M, Mokhtar R, Reif J. Programming DNA-Based Biomolecular Reaction Networks on Cancer Cell Membranes. J Am Chem Soc 2019; 141:16539-16543. [PMID: 31600065 DOI: 10.1021/jacs.9b05598] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA is a highly programmable biomolecule and has been used to construct biological circuits for different purposes. An important development of DNA circuits is to process the information on receptors on cell membranes. In this Communication, we introduce an architecture to program localized DNA-based biomolecular reaction networks on cancer cell membranes. Based on our architecture, various types of reaction networks have been experimentally demonstrated, from simple linear cascades to reaction networks of complex structures. These localized DNA-based reaction networks can be used for medical applications such as cancer cell detection. Compared to prior work on DNA circuits for evaluating cell membrane receptors, the DNA circuits made by our architecture have several major advantages including simpler design, lower leak, lower cost, and higher signal-to-background ratio.
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Affiliation(s)
- Tianqi Song
- Department of Computer Science , Duke University , Durham , North Carolina 27708 , United States
| | - Shalin Shah
- Department of Electrical and Computer Engineering , Duke University , Durham , North Carolina 27708 , United States
| | - Hieu Bui
- National Research Council , 500 Fifth Street NW, Keck 576 , Washington , D.C. 20001 , United States
| | - Sudhanshu Garg
- Department of Computer Science , Duke University , Durham , North Carolina 27708 , United States
| | - Abeer Eshra
- Department of Computer Science , Duke University , Durham , North Carolina 27708 , United States.,Department of Computer Science and Engineering, Faculty of Electronic Engineering , Menoufia University , Menouf , Menoufia 32831 , Egypt
| | - Daniel Fu
- Department of Computer Science , Duke University , Durham , North Carolina 27708 , United States
| | - Ming Yang
- Department of Computer Science , Duke University , Durham , North Carolina 27708 , United States
| | - Reem Mokhtar
- Department of Computer Science , Duke University , Durham , North Carolina 27708 , United States
| | - John Reif
- Department of Computer Science , Duke University , Durham , North Carolina 27708 , United States.,Department of Electrical and Computer Engineering , Duke University , Durham , North Carolina 27708 , United States
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165
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Huang D, Guo C, Miao J, Zhang Y, Lin X, Chen D, Yang S, Yang Q, Tang Y. Construction of a novel DNA-based comparator and its application in intelligent analysis. NANOSCALE 2019; 11:16241-16244. [PMID: 31454010 DOI: 10.1039/c9nr05270d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, a novel and general comparator was constructed based on cascaded strand displacement reactions and DNA hybridization and its potential in intelligently weighing the quantitative predominance of two targets was explored in a complex biological matrix, which not only enriches the information processing mode of DNA computation but also provides an instructive way to deal with quantitative analyzing tasks in further DNA-based logic sensors.
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Affiliation(s)
- Dan Huang
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Chen Guo
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Jiarong Miao
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Yi Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Xiao Lin
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Die Chen
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Shu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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166
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Wang W, Yu S, Huang S, Bi S, Han H, Zhang JR, Lu Y, Zhu JJ. Bioapplications of DNA nanotechnology at the solid-liquid interface. Chem Soc Rev 2019; 48:4892-4920. [PMID: 31402369 PMCID: PMC6746594 DOI: 10.1039/c8cs00402a] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.
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Affiliation(s)
- Wenjing Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.
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167
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Dai Y, Abbasi K, Bandyopadhyay S, Liu CC. Dynamic Control of Peptide Strand Displacement Reaction Using Functional Biomolecular Domain for Biosensing. ACS Sens 2019; 4:1980-1985. [PMID: 31309821 DOI: 10.1021/acssensors.9b00831] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nature's great repository provides nucleic acids and amino acids as the fundamental elements of life. Inspired by the programmability of nucleic acids, DNA nanotechnology has been extensively developed based on the strand displacement reaction of nucleic acids. In comparison with nucleic acids, amino acids possess higher programmability and more functionalities owing to the diversity of the amino acid unit. However, the design of the peptide-based bimolecular cascade is still limited. We herein describe a peptide-based strand displacement reaction, which was granted with a specific biological function by addition of a functional domain onto the coiled-coil peptide based displacement substrate. The displacement substrate was specifically designed to response to Tau protein based on a well-established Tau inhibition sequence. We demonstrated that the kinetics of the designed displacement reaction can be dynamically tuned through blocking the toehold region to prevent migration. A nanomolar Tau detection linear range was achieved through the designed displacement reaction within a rapid turnaround time of 30 min. We also presented the capability of the peptide strand displacement based sensing system operating in real human biological samples and its excellent orthogonality on response to irrelevant biological components. We envision that this will be of especially high utility for the development of next-generation biotechnology.
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168
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Fan D, Wang J, Wang E, Dong S. A Janus-inspired amphichromatic system that kills two birds with one stone for operating a "DNA Janus Logic Pair" (DJLP) library. Chem Sci 2019; 10:7290-7298. [PMID: 31588299 PMCID: PMC6686727 DOI: 10.1039/c9sc01865d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/12/2019] [Indexed: 12/27/2022] Open
Abstract
Although DNA computing has exhibited a magical power across diverse areas, current DNA logic gates with different functions are always separately operated and can only produce hard-to-visualize output. The fussy/obligatory gates' redesign/reconstruction and the non-intuitive output cause the wastage of time and costs, low efficiency and practicality. Herein, inspired by the ancient Roman mythical God Janus, for the first time, we propose the concept of "DNA Janus Logic Pair" (DJLP) to classify the DNA logic gates with contrary functions into "Positive + Negative" gates (DJLP = Pos + Neg). Based on the biocatalytic property of G-quadruplex DNAzyme (G4zyme) and the luminescence quenching ability of oxidized 3,3',5,5'-tetramethylbenzidine (OxTMB) towards the upconversion (UC) particles, we fabricated a universal amphichromatic platform that kills two birds with one stone for operating a versatile DJLP library. Different from the previous DNA logic systems, the "Pos + Neg" gates of each DJLP in this study were concomitantly achieved via the same one-time DNA reaction, which avoided the gates' redesign/reoperation and reduced the operating costs/time of the DNA gates by at least half. Besides, both the amphichromatic outputs (Visual-blue and UC luminescent-green) can be visualized under harmless-NIR, thus bringing greatly enhanced practicality to the method. Moreover, we constructed various concatenated logic circuits via logically modulating the G4zyme's biocatalytic property with glutathione, thus enabling the largely improved computing complexity. Furthermore, taking the circuit "YES-INH-1-2 decoder" as the "computing core", we designed an "antioxidant indicator" with ratiometric logical responses that could recognize the presence of antioxidants smartly (output changed from "10" to "01"), which provided a typical prototype for potential intelligent bio-applications.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Juan Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
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169
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Wang L, Liang H, Sun J, Liu Y, Li J, Li J, Li J, Yang H. Bispecific Aptamer Induced Artificial Protein-Pairing: A Strategy for Selective Inhibition of Receptor Function. J Am Chem Soc 2019; 141:12673-12681. [PMID: 31381313 DOI: 10.1021/jacs.9b05123] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cell surface receptors play a critical role in modulating intracellular signal transduction, making them important drug targets. However, it remains challenging to develop a selective and efficient strategy for regulating receptor function. Herein, we develop a strategy, called bispecific aptamer induced artificial protein-pairing, to selectively regulate receptor function. In this strategy, bispecific aptamer probes act as molecular mediators to bind to both a target receptor protein and a paired protein, which brings the two proteins into close proximity on the living cell membrane. Importantly, the paired proteins work not only as a cancer biomarker for enhancing cell selectivity but also as a blocking assistant to inhibit target receptor function via strong steric hindrance effect. Compared with single-aptamer-mediated regulation, the proposed bispecific aptamer probes afford substantial improvement in selective and efficient regulation of receptor function and downstream signaling pathways. This work offers a versatile methodology to design molecular mediators that can modulate receptor function, thereby providing a new way for developing novel therapeutic drugs.
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Affiliation(s)
- Liping Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350108 , People's Republic of China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
| | - Hong Liang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350108 , People's Republic of China.,Institute of Oceanography , Minjiang University , Fuzhou , Fujian 350108 , People's Republic of China
| | - Jin Sun
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China.,College of Biological Science and Engineering , Fuzhou University , Fuzhou 350108 , People's Republic of China
| | - Yichang Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350108 , People's Republic of China
| | - Jinyu Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350108 , People's Republic of China
| | - Jingying Li
- College of Biological Science and Engineering , Fuzhou University , Fuzhou 350108 , People's Republic of China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350108 , People's Republic of China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350108 , People's Republic of China
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170
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Rong G, Tuttle EE, Neal Reilly A, Clark HA. Recent Developments in Nanosensors for Imaging Applications in Biological Systems. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:109-128. [PMID: 30857408 PMCID: PMC6958676 DOI: 10.1146/annurev-anchem-061417-125747] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Sensors are key tools for monitoring the dynamic changes of biomolecules and biofunctions that encode valuable information that helps us understand underlying biological processes of fundamental importance. Because of their distinctive size-dependent physicochemical properties, materials with nanometer scales have recently emerged as promising candidates for biological sensing applications by offering unique insights into real-time changes of key physiological parameters. This review focuses on recent advances in imaging-based nanosensor developments and applications categorized by their signal transduction mechanisms, namely, fluorescence, plasmonics, MRI, and photoacoustics. We further discuss the synergy created by multimodal nanosensors in which sensor components work based on two or more signal transduction mechanisms.
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Affiliation(s)
- Guoxin Rong
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA;
| | - Erin E Tuttle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Ashlyn Neal Reilly
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA;
| | - Heather A Clark
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA;
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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171
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Seo J, Kim S, Park HH, Nam JM. Biocomputing with Nanostructures on Lipid Bilayers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900998. [PMID: 31026121 DOI: 10.1002/smll.201900998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Biocomputation is the algorithmic manipulation of biomolecules. Nanostructures, most notably DNA nanostructures and nanoparticles, become active substrates for biocomputation when modified with stimuli-responsive, programmable biomolecular ligands. This approach-biocomputing with nanostructures ("nano-bio computing")-allows autonomous control of matter and information at the nanoscale; their dynamic assemblies and beneficial properties can be directed without human intervention. Recently, lipid bilayers interfaced with nanostructures have emerged as a new biocomputing platform. This new nano-bio interface, which exploits lipid bilayers as a chemical circuit board for information processing, offers a unique reaction space for realizing nanostructure-based computation at a previously unexplored dimension. In this Concept, recent advances in nano-bio computing are briefly reviewed and the newly emerging concept of biocomputing with nanostructures on lipid bilayers is introduced.
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Affiliation(s)
- Jinyoung Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Sungi Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Ha H Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
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172
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Du Y, Peng P, Li T. DNA Logic Operations in Living Cells Utilizing Lysosome-Recognizing Framework Nucleic Acid Nanodevices for Subcellular Imaging. ACS NANO 2019; 13:5778-5784. [PMID: 30978283 DOI: 10.1021/acsnano.9b01324] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA logic nanodevices that in situ operate within living cells have attracted increasing interest and shown great promise for gene regulation and target recognition. A challenge remains how to control their activation inside specific cellular compartments. Toward this goal, here we report a lysosome-recognizing framework nucleic acid (FNA) nanodevice using an i-motif and an ATP-binding aptamer (ABA) incorporated into a DNA triangular prism (DTP) as the logic-controlling units. Once entering the lysosomal compartments, the FNA device responds to lysosomal pH and ATP via the folding of i-motif and ABA, which triggers a structural change of FNA and the release of a reporter structure for subcellular imaging. With endogenous proton and ATP as two inputs, an AND logic gate is built and in situ operated within living lysosomes by pH and ATP modulation with external drug stimuli. Given the abnormal levels of pH and ATP within some cancer cells or dysfunctional lysosomal cells, in this context our designed FNA logic device may find extended applications in controllable drug release and disease treatment.
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Affiliation(s)
- Yi Du
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Pai Peng
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Tao Li
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
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173
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Yu Y, Jin B, Li Y, Deng Z. Stimuli-Responsive DNA Self-Assembly: From Principles to Applications. Chemistry 2019; 25:9785-9798. [PMID: 30931536 DOI: 10.1002/chem.201900491] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Indexed: 01/01/2023]
Abstract
Stimuli-responsive DNA self-assembly shares the advantages of both designed stimuli-responsiveness and the molecular programmability of DNA structures, offering great opportunities for basic and applied research in dynamic DNA nanotechnology. In this minireview, we summarize the most recent progress in this rapidly developing field. The trigger mechanisms of the responsive DNA systems are first divided into six categories, which are then explained with illustrative examples following this classification. Subsequently, proof-of-concept applications in terms of biosensing, in vivo pH-mapping, drug delivery, and therapy are discussed. Finally, we provide some remarks on the challenges and opportunities of this highly promising research direction in DNA nanotechnology.
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Affiliation(s)
- Yang Yu
- Anhui Province Key Laboratory of Advanced Catalytic Materials, and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Bang Jin
- Anhui Province Key Laboratory of Advanced Catalytic Materials, and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials, and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, China
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174
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Wang X, Hu P, Wang Z, Liu Q, Xu T, Kou M, Huang K, Chen P. A Fluorescence Strategy for Silver Ion Assay via Cation Exchange Reaction and Formation of Poly(thymine)-templated Copper Nanoclusters. ANAL SCI 2019; 35:917-922. [PMID: 31061241 DOI: 10.2116/analsci.19p036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The detection of Ag+ ions in the environment and biological systems is important to both environmental monitoring and modern medicine. Herein, a novel and label-free method was developed for Ag+ detection, which utilizes a florescence strategy combining DNA-templated copper nanoclusters (Cu NCs) with cation exchange reactions. The method is primarily based on the effective detection of an Ag+-triggered cation exchange reaction and the release of free Cu2+ from CuS nanoparticles (CuS NPs), while the probe T30 serves as an effective template for the formation of fluorescence-inducing Cu NCs. Under optimal conditions, this sensing system displays high sensitivity with a 50 nM limit of detection and a range from 0 - 100 μM. In addition, the proposed method exhibits high selectivity and, therefore, was successfully applied to the analysis of real samples. Overall, these results demonstrate that our established method has advantages of design and operation simplicity, as well as cost-effectiveness.
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Affiliation(s)
- Xiu Wang
- College of Chemistry and Material Science, Sichuan Normal University
| | - Pingyue Hu
- College of Chemistry and Material Science, Sichuan Normal University
| | - Zhipeng Wang
- College of Chemistry and Material Science, Sichuan Normal University
| | - Qiuyun Liu
- College of Chemistry and Material Science, Sichuan Normal University
| | - Ting Xu
- College of Chemistry and Material Science, Sichuan Normal University
| | - Mengqian Kou
- College of Chemistry and Material Science, Sichuan Normal University
| | - Ke Huang
- College of Chemistry and Material Science, Sichuan Normal University
| | - Piaopiao Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy
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175
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Liu H, Yang Q, Peng R, Kuai H, Lyu Y, Pan X, Liu Q, Tan W. Artificial Signal Feedback Network Mimicking Cellular Adaptivity. J Am Chem Soc 2019; 141:6458-6461. [DOI: 10.1021/jacs.8b13816] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hui Liu
- 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
| | - Qiuxia Yang
- 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
| | - Ruizi Peng
- 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
| | - Hailan Kuai
- 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
| | - Yifan Lyu
- 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
| | - Xiaoshu Pan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Qiaoling Liu
- 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
- 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
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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176
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Xue J, Chen F, Bai M, Cao X, Huang P, Zhao Y. All-in-One Synchronized DNA Nanodevices Facilitating Multiplexed Cell Imaging. Anal Chem 2019; 91:4696-4701. [PMID: 30859815 DOI: 10.1021/acs.analchem.9b00089] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multifunctional DNA nanodevices perform ever more tasks with applications ranging from in vitro biomarker detection to in situ cell imaging. However, most developed ones consist of a series of split building blocks, which suffer from asynchronous behaviors in complicated cellular microenvironments (endocytosis pathway, diffusion-limited cytoplasm, etc.), causing the loss of stoichiometric information and additional postassembly processes. Herein, we constructed all-in-one DNA nanodevices to achieve synchronous multiplexed imaging. All DNA components, including two sets of probe modules (each containing target-specific walkers, i.e., hairpin tracks with chemically damaged bases), are modified on individual gold nanoparticles. This design not only enables their integrated internalization into cells, circumventing inhomogeneous distribution of different building blocks and increasing the local concentrations of the interacting modules, but also avoids the impact of stochastic diffusion in viscous cytoplasm. A couple of intracellular enzymes in situ actuate the synchronized motion of the modules, all on-particle, after specific recognition of intracellular targets (such as RNAs and proteins), thus facilitating synchronized, multiplexed cell imaging. Finally, the proposed all-in-one nanodevices were successfully applied to monitor intracellular microRNA-21 and telomerase expression levels. The flexible design can be extended to detect other cytoplasmic molecules and monitor related pathways by simply changing the sequences.
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Affiliation(s)
- Jing Xue
- State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , PR China.,The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , PR China
| | - Feng Chen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , PR China
| | - Min Bai
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , PR China
| | - Xiaowen Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , PR China
| | - Ping Huang
- State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , PR China
| | - Yongxi Zhao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , PR China
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177
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Chen F, Xue J, Bai M, Qin J, Zhao Y. Programming in situ accelerated DNA walkers in diffusion-limited microenvironments. Chem Sci 2019; 10:3103-3109. [PMID: 30996893 PMCID: PMC6432271 DOI: 10.1039/c8sc05302b] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/22/2019] [Indexed: 12/29/2022] Open
Abstract
Macromolecule diffusion in cellular microenvironments dictates the kinetics of biochemical processes, yet inevitably limiting the assembly and operation of biomimetic motors. Herein we program in situ accelerated DNA walkers in diffusion-limited microenvironments such as molecularly crowded solutions and cytoplasm. All DNA components, including single-foot walkers, chemically damaged tracks and calibration elements, are anchored on individual gold nanoparticles. Two endogenous enzymes participating in base repair pathways are used to actuate on-particle walking via a base excision/hydrolyzation coupled reaction. The walkers are in situ driven without requiring external drivers and accelerated several times. They also avoid low-efficiency diffusion/assembly procedures and respond to heterogeneous cellular milieus with calibration function. We further regulated the walking kinetics via DNA densities and sets of enzymes, and demonstrated cytoplasmic behaviors of three kinds of walkers. They were utilized to profile DNA repair pathways and monitor enzyme catalysis in living cells.
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Affiliation(s)
- Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Jing Xue
- Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
- State Key Laboratory for Mechanical Behavior of Materials , School of Materials Science and Engineering , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Min Bai
- Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Jing Qin
- Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
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178
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Abstract
The field of nanomedicine has made substantial strides in the areas of therapeutic and diagnostic development. For example, nanoparticle-modified drug compounds and imaging agents have resulted in markedly enhanced treatment outcomes and contrast efficiency. In recent years, investigational nanomedicine platforms have also been taken into the clinic, with regulatory approval for Abraxane® and other products being awarded. As the nanomedicine field has continued to evolve, multifunctional approaches have been explored to simultaneously integrate therapeutic and diagnostic agents onto a single particle, or deliver multiple nanomedicine-functionalized therapies in unison. Similar to the objectives of conventional combination therapy, these strategies may further improve treatment outcomes through targeted, multi-agent delivery that preserves drug synergy. Also, similar to conventional/unmodified combination therapy, nanomedicine-based drug delivery is often explored at fixed doses. A persistent challenge in all forms of drug administration is that drug synergy is time-dependent, dose-dependent and patient-specific at any given point of treatment. To overcome this challenge, the evolution towards nanomedicine-mediated co-delivery of multiple therapies has made the potential of interfacing artificial intelligence (AI) with nanomedicine to sustain optimization in combinatorial nanotherapy a reality. Specifically, optimizing drug and dose parameters in combinatorial nanomedicine administration is a specific area where AI can actionably realize the full potential of nanomedicine. To this end, this review will examine the role that AI can have in substantially improving nanomedicine-based treatment outcomes, particularly in the context of combination nanotherapy for both N-of-1 and population-optimized treatment.
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Affiliation(s)
- Dean Ho
- Department of Biomedical Engineering, NUS Engineering, National University of Singapore, Singapore.
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179
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Xu X, Zhang P, Zhang R, Zhang N, Jiang W. A DNA walker powered by endogenous enzymes for imaging uracil-DNA glycosylase activity in living cells. Chem Commun (Camb) 2019; 55:6026-6029. [DOI: 10.1039/c9cc01912j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A DNA walker powered by endogenous enzymes detects uracil-DNA glycosylase activity in living cells.
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Affiliation(s)
- Xiaowen Xu
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Pingping Zhang
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Ruiyuan Zhang
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Nan Zhang
- Department of Oncology
- Jinan Central Hospital Affiliated to Shandong University
- 250012 Jinan
- P. R. China
| | - Wei Jiang
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
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180
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Wen ZB, Peng X, Yang ZZ, Zhuo Y, Chai YQ, Liang WB, Yuan R. A dynamic 3D DNA nanostructure based on silicon-supported lipid bilayers: a highly efficient DNA nanomachine for rapid and sensitive sensing. Chem Commun (Camb) 2019; 55:13414-13417. [DOI: 10.1039/c9cc07071k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we have developed a dynamic three-dimensional (3D) self-powered DNA nanomachine by anchoring cholesterol-labelled DNA probes to silicon-supported lipid bilayers via cholesterol–lipid interaction.
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Affiliation(s)
- Zhi-Bin Wen
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Xin Peng
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ze-Zhou Yang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ying Zhuo
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ya-Qin Chai
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Wen-Bin Liang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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181
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Chen H, Gu Z, An H, Chen C, Chen J, Cui R, Chen S, Chen W, Chen X, Chen X, Chen Z, Ding B, Dong Q, Fan Q, Fu T, Hou D, Jiang Q, Ke H, Jiang X, Liu G, Li S, Li T, Liu Z, Nie G, Ovais M, Pang D, Qiu N, Shen Y, Tian H, Wang C, Wang H, Wang Z, Xu H, Xu JF, Yang X, Zhu S, Zheng X, Zhang X, Zhao Y, Tan W, Zhang X, Zhao Y. Precise nanomedicine for intelligent therapy of cancer. Sci China Chem 2018. [DOI: 10.1007/s11426-018-9397-5] [Citation(s) in RCA: 279] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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