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Han Y, Cao L, Li G, Zhou F, Bai L, Su J. Harnessing Nucleic Acids Nanotechnology for Bone/Cartilage Regeneration. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301996. [PMID: 37116115 DOI: 10.1002/smll.202301996] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/29/2023] [Indexed: 06/19/2023]
Abstract
The effective regeneration of weight-bearing bone defects and critical-sized cartilage defects remains a significant clinical challenge. Traditional treatments such as autologous and allograft bone grafting have not been successful in achieving the desired outcomes, necessitating the need for innovative therapeutic approaches. Nucleic acids have attracted significant attention due to their ability to be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of nucleic acid nanotechnology offer numerous opportunities for in-cell and in vivo applications, and hold great promise for advancing the field of biomaterials. In this review, the current abilities of nucleic acid nanotechnology to be applied in bone and cartilage regeneration are summarized and insights into the challenges and future directions for the development of this technology are provided.
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Affiliation(s)
- Yafei Han
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Liehu Cao
- Department of Orthopedics, Shanghai Luodian Hospital, Shanghai, 201908, China
| | - Guangfeng Li
- Department of Orthopedics, Shanghai Zhongye Hospital, Shanghai, 201941, China
| | - Fengjin Zhou
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiao Tong University, Xi'an, 710000, China
| | - Long Bai
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Jiacan Su
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
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Zhou W, Liao L, Fan X, Yao J, Jiang B. Programmable bidirectional dynamic DNA nano-device for accurate and ultrasensitive fluorescent detection of trace MUC1 biomarker in serums. Anal Chim Acta 2022; 1238:340643. [DOI: 10.1016/j.aca.2022.340643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 11/19/2022]
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Ratiometric fluorescence sensing with logical operation: Theory, design and applications. Biosens Bioelectron 2022; 213:114456. [PMID: 35691083 DOI: 10.1016/j.bios.2022.114456] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/14/2022] [Accepted: 06/04/2022] [Indexed: 11/20/2022]
Abstract
The construction of ratiometric fluorescence sensing logic systems has gradually become a hot topic in fluorescence analysis, due to the multi-target analysis potential of logic operations and the high specificity and selectivity of ratiometric fluorescence sensing. In this paper, the basic principles of various logic functions implemented in ratiometric fluorescence detection are discussed in the context of sensing mechanisms, and the strategies for constructing logic systems in different ratiometric fluorescence sensing application areas are summarized. Although there are limitations such as cumbersome operations and complicated experiments, ratiometric fluorescence sensing logic circuits that combine the visualization of logic operations and the accuracy of ratiometric fluorescence are still worthy of in-depth study. This review may be useful for researchers interested in the construction of logic operations based on ratiometric fluorescence sensing applications.
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Wang J, Ma JY, Wang DX, Liu B, Jing X, Chen DY, Tang AN, Kong DM. Oxidative Cleavage-Based Three-Dimensional DNA Biosensor for Ratiometric Detection of Hypochlorous Acid and Myeloperoxidase. Anal Chem 2021; 93:16231-16239. [PMID: 34818886 DOI: 10.1021/acs.analchem.1c04113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methods to detect and quantify disease biomarkers with high specificity and sensitivity in biological fluids play a key role in enabling clinical diagnosis, including point-of-care testing. Myeloperoxidase (MPO) is an emerging biomarker for the detection of inflammation, neurodegenerative diseases, and cardiovascular disease, where excess MPO can lead to oxidative damage to biomolecules in homeostatic systems. While numerous methods have been developed for MPO analysis, most techniques are challenging in clinical applications due to the lack of amplification methods, high cost, or other practical drawbacks. Enzyme-linked immunosorbent assays are currently used for the quantification of MPO in clinical practice, which is often limited by the availability of antibodies with high affinity and specificity and the significant nonspecific binding of antibodies to the analytical surface. In contrast, nucleic acid-based biosensors are of interest because of their simplicity, fast response time, low cost, high sensitivity, and low background signal, but detection targets are limited to nucleic acids and non-nucleic acid biomarkers are rare. Recent studies reveal that the modification of a genome in the form of phosphorothioate is specifically sensitive to the oxidative effects of the MPO/H2O2/Cl- system. We developed an oxidative cleavage-based three-dimensional DNA biosensor for rapid, ratiometric detection of HOCl and MPO in a "one-pot" method, which is simple, stable, sensitive, specific, and time-saving and does not require a complex reaction process, such as PCR and enzyme involvement. The constructed biosensor has also been successfully used for MPO detection in complex samples. This strategy is therefore of great value in disease diagnosis and biomedical research.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jia-Yi Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bo Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao Jing
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dan-Ye Chen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
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West MES, Yao CY, Melaugh G, Kawamoto K, Uchiyama S, de Silva AP. Fluorescent Molecular Logic Gates Driven by Temperature and by Protons in Solution and on Solid. Chemistry 2021; 27:13268-13274. [PMID: 34233035 DOI: 10.1002/chem.202101892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Indexed: 12/22/2022]
Abstract
Temperature-driven fluorescent NOT logic is demonstrated by exploiting predissociation in a 1,3,5-trisubstituted Δ2 -pyrazoline on its own and when grafted onto silica microparticles. Related Δ2 -pyrazolines become proton-driven YES and NOT logic gates on the basis of fluorescent photoinduced electron transfer (PET) switches. Additional PASS 1 and YES+PASS 1 logic gates on silica are also demonstrated within the same family. Beside these small-molecule systems, a polymeric molecular thermometer based on a benzofurazan-derivatized N-isopropylacrylamide copolymer is attached to silica to produce temperature-driven fluorescent YES logic.
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Affiliation(s)
- Matthew E S West
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, BT9 5AG, UK
| | - Chao-Yi Yao
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, BT9 5AG, UK
| | - Gavin Melaugh
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, BT9 5AG, UK
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Kyoko Kawamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Seiichi Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan
| | - A Prasanna de Silva
- School of Chemistry and Chemical Engineering, Queen's University, Belfast, BT9 5AG, UK
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Wang DX, Wang J, Wang YX, Du YC, Huang Y, Tang AN, Cui YX, Kong DM. DNA nanostructure-based nucleic acid probes: construction and biological applications. Chem Sci 2021; 12:7602-7622. [PMID: 34168817 PMCID: PMC8188511 DOI: 10.1039/d1sc00587a] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022] Open
Abstract
In recent years, DNA has been widely noted as a kind of material that can be used to construct building blocks for biosensing, in vivo imaging, drug development, and disease therapy because of its advantages of good biocompatibility and programmable properties. However, traditional DNA-based sensing processes are mostly achieved by random diffusion of free DNA probes, which were restricted by limited dynamics and relatively low efficiency. Moreover, in the application of biosystems, single-stranded DNA probes face challenges such as being difficult to internalize into cells and being easily decomposed in the cellular microenvironment. To overcome the above limitations, DNA nanostructure-based probes have attracted intense attention. This kind of probe showed a series of advantages compared to the conventional ones, including increased biostability, enhanced cell internalization efficiency, accelerated reaction rate, and amplified signal output, and thus improved in vitro and in vivo applications. Therefore, reviewing and summarizing the important roles of DNA nanostructures in improving biosensor design is very necessary for the development of DNA nanotechnology and its applications in biology and pharmacology. In this perspective, DNA nanostructure-based probes are reviewed and summarized from several aspects: probe classification according to the dimensions of DNA nanostructures (one, two, and three-dimensional nanostructures), the common connection modes between nucleic acid probes and DNA nanostructures, and the most important advantages of DNA self-assembled nanostructures in the applications of biosensing, imaging analysis, cell assembly, cell capture, and theranostics. Finally, the challenges and prospects for the future development of DNA nanostructure-based nucleic acid probes are also discussed.
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Affiliation(s)
- Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Jing Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Ya-Xin Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yan Huang
- College of Life Sciences, Nankai University Tianjin 300071 P. R. China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- College of Life Sciences, Nankai University Tianjin 300071 P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
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Wang YX, Wang DX, Ma JY, Wang J, Du YC, Kong DM. DNA nanolantern-based split aptamer probes for in situ ATP imaging in living cells and lighting up mitochondria. Analyst 2021; 146:2600-2608. [PMID: 33721010 DOI: 10.1039/d1an00275a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate and specific analysis of adenosine triphosphate (ATP) expression levels in living cells can provide valuable information for understanding cell metabolism, physiological activities and pathologic mechanisms. Herein, DNA nanolantern-based split aptamer nanoprobes are prepared and demonstrated to work well for in situ analysis of ATP expression in living cells. The nanoprobes, which carry multiple split aptamer units on the surface, are easily and inexpensively prepared by a "one-pot" assembly reaction of four short oligonucleotide strands. A series of characterization experiments verify that the nanoprobes have good monodispersity, strong biostability, high cell internalization efficiency, and fluorescence resonance energy transfer (FRET)-based ratiometric response to ATP in the concentration range covering the entire intracellular ATP expression level. By changing the intracellular ATP level via different treatments, the nanoprobes are demonstrated to show excellent performance in intracellular ATP expression analysis, giving a highly ATP concentration-dependent ratiometric fluorescence signal output. ATP-induced formation of large-sized DNA aggregates not only amplifies the FRET signal output, but also makes in situ ATP-imaging analysis in living cells possible. In situ responsive crosslinking of nanoprobes also makes them capable of lighting up the mitochondria of living cells. By simply changing the split aptamer sequence, the proposed DNA nanolantern-based split aptamer strategy might be easily extended to other targets.
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Affiliation(s)
- Ya-Xin Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - Jia-Yi Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - Jing Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
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8
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Xing C, Chen Z, Lin Y, Wang M, Xu X, Dai J, Wang J, Lu C. Accelerated DNA tetrahedron-based molecular beacon for efficient microRNA imaging in living cells. Chem Commun (Camb) 2021; 57:3251-3254. [PMID: 33647084 DOI: 10.1039/d0cc08172h] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Herein, we develop an accelerated DNA tetrahedron based molecular beacon for efficient detection and imaging of miRNA in living cells. Our study provides an improved strategy for fluorescence amplified RNA imaging in early clinical diagnosis.
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Affiliation(s)
- Chao Xing
- Fujian Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, Minjiang University, Fuzhou 350108, P. R. China.
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